"Books such as Noncoding RNAs and epigenetic regulation of gene expression, published by Caister Academic Press, become essential guidelines to help us understand the current status of the very fast paced field of RNA research, which has only just started to uncover the roles of non-coding RNAs (ncRNAs) in the regulation of gene expression. ... Edited by Kevin V. Morris (The Scripps Research Institute, La Jolla, CA), who discovered how ncRNAs could influence splicing by inhibition of transcription initiation, the book presents a comprehensive review of the role that ncRNAs play on the epigenetic regulation of gene expression ... This book brings together more than a decade's worth of research by leaders in the field of ncRNAs and epigenetics. Each chapter is presented in a compressed and well-balanced format that can stand alone as a review article, including the history behind NATs and ncRNAs, the technical advances made, as well as current examples and discussions relevant to the chapter topic. The well-referenced and up to date text is further supported by explanatory, clearly illustrated figures, and is a must-have for any post-graduate student or researcher in the field of epigenetics and RNA." from Marguerite Blignaut (Department of Botany and Zoology; Stellenbosch University; Stellenbosch, South Africa) writing in Epigenetics Volume 7, Issue 6 June 2012 read more ...

Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection Edited by: Kevin V. Morris ISBN: 978-1-904455-94-3 Publisher: Caister Academic Press Publication Date: February 2012 Cover: hardback "a must-have" (Epigenetics)

"This is an excellent resource ... an extremely useful book on non-coding RNAs and their role in disease and therapeutics." from Omer Iqbal (Loyola University, USA) writing in Doodys read more ...

Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection Edited by: Kevin V. Morris ISBN: 978-1-904455-94-3 Publisher: Caister Academic Press Publication Date: February 2012 Cover: hardback "excellent resource" (Doodys)

from Dacia Kwiatkowski and Kirk Deitsch writing in Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection:

Much of what is currently know about complex cellular questions, including regulation of gene expression, RNA production and epigenetic influence, has been derived from experiments performed in well studied model organisms such as yeast, Drosophila, mice or human cell lines. In all of these systems, examples have been described of how non-coding RNAs (ncRNAs), which often act in accordance with epigenetic mechanisms, play a vital role in regulating gene expression. These studies have established a strong precedent for the vital role that these molecules can play in complex cellular functions, which is now being extended to other diverse organisms such as viruses and protozoans of distant evolutionary lineages. The focus of this chapter is the role that long ncRNAs play in gene regulation in the protozoan parasite Plasmodium falciparum, the causative agent of the most severe form of human malaria. In particular, we will consider ncRNAs that influence the expression of the genes encoding the primary virulence factors expressed by these parasites, the epigenetic marks associated with them, and how this process enables the parasites to avoid the immune response of their human hosts.

Further reading: Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection

from Sandra N. Oliver and E. Jean Finnegan writing in Epigenetics: A Reference Manual:

Polycomb-group (PcG) complexes are essential regulators of plant development. These multiprotein complexes repress gene expression by establishing and maintaining trimethylation of lysine 27 at histone H3, a modification that is associated with repressive chromatin. Recent studies have indicated that plant PcG complexes regulate key genes involved in responses to low temperature. Vernalization is a long-term response to low temperatures whereby plants coordinate their seasonal flowering to occur after winter. In contrast, acclimation of plants to low temperatures, a key step in the establishment of frost tolerance, involves rapid activation of cold-acclimation genes. In this chapter, we describe the dynamics of PcG-mediated gene regulation underlying these two important agronomic traits that are triggered by low temperatures.

Further reading: Epigenetics: A Reference Manual

from Benjamin Chanrion, Yurong Xin and Fatemeh Haghighi writing in Epigenetics: A Reference Manual:

DNA methylation plays an essential role in normal human development, where abnormalities in proper establishment and maintenance of DNA methylation patterns result in human disease. Many experimental approaches have been developed for assaying DNA methylation patterns, including enzymatic-based approaches. In this chapter, we highlight some of these approaches and describe their relative advantages and disadvantages. We also describe advances in microarray and sequencing technologies that have improved resolution of enzymatic-based methods, providing expanded coverage of CpG dinucleotides throughout the genome. These approaches are important tools in characterizing the role of DNA methylation in genome organization and function.

Further reading: Epigenetics: A Reference Manual

from Yuk Jing Loke and Jeffrey M. Craig writing in Epigenetics: A Reference Manual:

Epigenetics can appear as an impenetrable subject; not just to those encountering it for the first time, but to those within the field too. However, epigenetics, like any subject can be made easier to understand using a combination of clear language, creative illustrations and even animations and film clips. This chapter aims to point readers of all experiences towards helpful and easy-to-read resources that educate about epigenetics. It is split into two main sections, the first aimed at a lay audience including teachers and high school students and the second, at graduate and postgraduate students and beyond. Each section contains summaries of published articles and web sites. The chapter ends with a short section on epigenetic societies and research networks and a summary table of resources. It is intended to provide a sample of some of the best short to medium length reviews on general topics within the field of epigenetics and while we cover a wide variety of themes, we apologise for any areas not covered. We cite the URLs of freely-available articles wherever possible, but many articles will require library access. We also urge readers to contact authors or publishers if they wish to distribute any of the articles for teaching purposes.

Further reading: Epigenetics: A Reference Manual

from Moshe Szyf writing in Epigenetics: A Reference Manual:

The DNA molecule contains within its chemical structure two layers of information. The DNA sequence that bears the ancestral genetic information and the pattern of distribution of covalently bound methyl groups to cytosines in DNA. While the genetic information is similar in all tissues in the individual, the pattern of distribution of methylation across the genome is cell-type specific. DNA methylation is an important regulator of gene function. Recent data that will be discussed here that supports the hypothesis that DNA methylation is a reversible biological signal. This expands the potential role of DNA methylation beyond embryogenesis to other time-points in life and to post mitotic tissues such as the brain. DNA methylation is proposed to act as a genomic response to both physical and social signals from the environment at different time points in life and to serve as a genomic memory of these exposures at different time scales, stably altering gene expression programming and thus modulating the physical and behavioral phenotypes to respond to these environments. It is hypothesized that DNA methylation provides within the structure of the DNA a dynamic interface between the changing world around us and the relatively fixed and stable genome.

Further reading: Epigenetics: A Reference Manual

from Hengmi Cui, Isabelle Cui and Xi Yang writing in Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection:

Antisense RNA is the first RNA molecule identified to function as a regulator in the cell. With advances in biological science, antisense RNA is now recognized to be involved in not only post-transcriptional regulation, but also the transcriptional regulation of various important genes including tumor suppressor genes (TSGs). Recent studies indicate that the modulation of TSGs by antisense RNA may be through either up- or down- regulation, occurring either transcriptionally, post-transcriptionally or both, dependent on features of sense and antisense. Antisense RNA is the main contributor of TSG epigenetic silencing in tumorigenesis. While a general picture of the pathways involved in antisense RNA mediated gene regulation has emerged, many questions remain unaddressed: Why does some antisense RNAs function as down-regulators but others as up-regulators in different TSGs? Are the molecular mechanisms of antisense RNA regulation highly gene- and species-specific? Are they spatially and temporally restricted? Is there an antisense RNA-induced silencing complex (ARISC)? What factor(s) cause aberrant expression of antisense RNA in tumor cells? There is the potential for using antisense RNA as a biomarker for the early diagnosis of tumors and developing new therapeutic strategies for tumor treatment by targeting and controlling antisense RNA.

Further reading: Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection

from Kevin V. Morris writing in Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection:

A growing body of evidence is beginning to emerge in human cells suggesting that particular species of non-coding RNAs can regulate gene transcription by modulating loci specific epigenetic states. While such observations were in the past relegated to imprinted genes, it is now becoming apparent that several genes in differentiated cells may be under some form of non-coding RNA based transcriptional and epigenetic control. Importantly, this form of regulation may be highly influenced by selective pressures and function in the governance and adaptability of the cell. Many studies have been carried out to date, which have begun to discern the mechanism of action whereby non-coding RNAs modulate gene transcription. Some evidence points to a role of long non-coding RNAs in controlling gene transcription by actively recruiting epigenetic silencing complexes to homology containing loci in the genome. While other studies point to a role for long intergenic non-coding RNAs in scaffold like features that are most likely equally implicit in the regulation of gene expression. The results of these studies will be considered in detail as well as the implications that a vast array of non-coding RNA based regulatory networks may be operative in human cells. Knowledge of this emerging RNA based epigenetic regulatory network has implications in cellular evolution as well as an entirely new area of pharmacopeia, namely RNA mediated epigenetic regulation of gene expression.

Further reading: Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection

from Andre Irsigler and Karen M. McGinnis writing in Epigenetics: A Reference Manual:

Maize has served as an excellent model for the study of epigenetic gene regulation for the past several decades. The pioneering work of maize geneticists like Barbara McClintock, Alexander Brink, Marcus Rhoades, and others led to the observation of many fascinating phenomena that were later demonstrated to be epigenetically regulated events. Since these observations were made, a great deal of progress has been made in determining the underlying causes of the phenomena, and many of these examples of epigenetic gene regulation are currently being used to elucidate the mechanisms of epigenetic heritability in plants. Today, these phenomena and the mutants that impact them serve as resources for studying how DNA methylation, chromatin structure, and small RNAs act to influence paramutation, gene silencing, and parent-of-origin dependent dosage compensation. The key attributes and potential contributions of each resource are discussed in the context of understanding the mechanisms and significance of epigenetic gene regulation in large, complex genomes.

Further reading: Epigenetics: A Reference Manual

from Chihiro Kohama and Hidenori Kiyosawa writing in Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection:

Genomic DNA and full-length cDNA sequencing projects have provided fundamental data that have led us to the novel notion that antisense transcription is a universal phenomenon in many organisms, including mammals and plants. Successive expression analyses utilizing microarrays, genome-tiling arrays, and recent RNA sequencing with next-generation sequencers have supported this concept. We review how these genome-wide, natural antisense transcript analyses have proceeded, and we then introduce representative examples of the known functions and functional implications of antisense transcripts. The variety of modes in which antisense transcripts function in cells reveals that these transcripts do not constitute a uniform group, but perform various types of gene expression regulation.

Further reading: Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection

from Marcel W. Coolen and Susan J. Clark writing in Epigenetics: A Reference Manual:

Over the past decades it has become ever more apparent that understanding the genome did not stop with unravelling the genetic code. Regulatory mechanisms are needed to determine which parts of the genome are active or inactive, and to form a memory system that can be passed on over multiple cell divisions for proper functioning of the cell. These mechanisms underpinning heritable gene regulation are encapsulated by the term "epigenetics" and include histone modifications, miRNA and non-coding RNA expression, and methylation of cytosine residues in DNA. In this review, we compare the various methods that can be used to analyse DNA methylation patterns throughout the genome, and discuss their advantages and disadvantages. In addition, we present a detailed protocol for genome-wide DNA methylation analysis based on the capture of methylated DNA using a methyl-CpG binding domain-based (MBD) protein combined with second generation sequencing.

Further reading: Epigenetics: A Reference Manual

January 17 - 22, 2012 Epigenomics
Keystone Symposium. This meeting will highlight recent advances in the application of genomics techniques to the study of epigenetics.

January 20 - 22, 2012 RNA-UK 2012
RNA-UK is a biannual meeting that focuses on the increasingly important functions of RNA. The meeting will focus on current research on RNA processing, RNA-mediated gene regulation, RNA localisation, RNA stability/decay, RNA function and RNA structure.

February 7 - 12, 2012 Gene Silencing by Small RNAs
Keystone Symposium. The impact of small non-coding RNAs has profoundly touched the fields of development and cell biology, functional genomics, human disease and drug therapy. This mode of gene regulation is not restricted to eukaryotes; bacteria utilize small RNAs, notably those made from CRISPR loci that silence the expression of bacteriophages, transposons and plasmids.

March 25 - 27, 2012 microRNA 2012: International Symposium
Covers various cover themes on microRNA research.

March 27 - 29, 2012 RNAi 2012
The 7th Annual Oxford RNAi Conference, RNAi2012, will address most aspects of biology and application of RNA interference, and welcomes proposals on endogenous and exogenous roles of small RNAs in gene regulation, health and disease.

March 31 - April 5, 2012 Non-Coding RNAs
Keystone Symposium. The goal of the Keystone Symposia meeting on Non-Coding RNAs is to highlight the similarities and differences in various model systems to better understand the role of long ncRNAs in the regulation of genomes.

April 21 - 27, 2012 Analysis of small non-coding RNAs
EMBO Practical Course. Analysis of small non-coding RNAs: From massively parallel sequencing to in-situ hybridization, from discovery to validation.

May 1 - 2, 2012 RNAi, MicroRNAs 2012
International conference at the cutting edge of the life-science industry.

June 11 - 16, 2012 Antiviral RNAi: From Molecular Biology Towards Applications
ESF-EMBO Symposium. RNAi-based strategies have been used to engineer plants that resist a large variety of viruses, and administration of antiviral small RNAs has been demonstrated to be highly efficient in inhibiting viral infections in mammals, and a number of clinical trials are currently ongoing to assess the safety and efficacy of this therapeutic strategy.

July 9 - 10, 2012 Epigenomics 2012
International conference at the cutting edge of the life-science industry.

September 16 - 19, 2012 The reciprocal interactions of signalling pathways and non-coding RNA
EMBO Workshop.

Full details at our conference website Non-coding RNA and Epigenetics Conferences

from Rakesh Kumar Singh, Johanna Paik and Akash Gunjan writing in Epigenetics: A Reference Manual:

In eukaryotes, the genetic material in the form of DNA is wrapped around histone proteins to form nucleoprotein filaments called chromatin. Histones help package the DNA to fit it inside the nucleus of each cell, which in turn regulates access to the genetic information contained within the DNA. Hence, all DNA transactions are likely to be affected by histone metabolism. Eukaryotes carry multiple histones genes that can potentially generate enormous quantities of histone proteins. When present in excess, the positively charged histones can potentially "stick" non-specifically to the negatively charged DNA and adversely affect processes that require access to DNA. Not surprisingly, aberrant histone stoichiometry, chromatin assembly or chromatin structure lead to genomic instability, which is characterized by the increased rate of acquisition of alterations in the genome and is associated with deleterious human conditions such as cancer and aging. Hence, histone synthesis is coupled to ongoing DNA replication and is regulated transcriptionally and posttranscriptionally. To further avoid the deleterious consequences of excess histones, a posttranslational regulatory mechanism was described recently whereby excess histones are targeted for degradation by the ubiquitin-proteasome system. In this chapter, we discuss the causes and consequences of excess histone accumulation, as well as the strategies that cells have evolved to deal with them.

Further reading: Epigenetics: A Reference Manual

from Stéphane Labialle, Patrice Vitali, and Jérôme Cavaillé writing in Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection:

Genomic imprinting is a developmentally controlled form of epigenetic regulation that triggers parent-of-origin specific expression of a few mammalian genes. That is, for a given gene, only one of the two parental alleles is transcriptionnally active. Over the last several years, many imprinted small regulatory non-coding RNAs (ncRNAs, including microRNAs and box C/D small nucleolar RNAs) have been described at four evolutionarily distinct imprinted loci: the Snurf-Snrpn/Prader-Willi Syndrome and Dlk1-Dio3 chromosomal domains, and more recently at the C19MC locus and the Sfmbt2 gene. Remarkably, many imprinted ncRNA loci are clustered within large arrays formed by tandemly-repeated genes of related sequences and processed from long non-coding transcripts extending over hundreds of kilobases. Imprinted gene loci therefore give rise to unique opportunities to address both the impact of small and long non-coding RNA genes on the evolution, expression and function of mammalian genomes. In this chapter, we survey our current understanding of the functions of imprinted ncRNAs, with a particular attention to their suspected involvement in the Prader-Willi disease and higher-brain functions, as well as to their hypothetical contribution in the evolution and/or control of genomic imprinting.

Further reading: Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection

from Sarah A. Kinkel and Hamish S. Scott writing in Epigenetics: A Reference Manual:

DNMT3L (DNA methyltransferase 3 like) is member of the DNA methyltransferase family of enzymes responsible for the methylation of CpG dinucleotides. Biochemical studies have revealed that while DNMT3L lacks DNA methyltransferase activity, it can bind to and stimulate the activity of de novo DNA methyltransferases DNMT3A and DNMT3B. DNMT3L has also been shown to interact directly with chromatin via its plant homeodomain (PHD)-like zinc finger domain. Studies in Dnmt3L-deficient mice have revealed that DNMT3L is essential for establishing correct methylation patterns at RetroTransposable Elements (RTE), unique loci and parentally imprinted genes in germ cells, and mice without DNMT3L are rendered infertile. Female Dnmt3L^-/- mice have apparently normal meiosis but in male Dnmt3L-/- germ cells there is asynapsis of chromosomes, and "meiotic catastrophe". Dnmt3L was among the first mammalian genes shown to have a paternal effect, where the genotype of the father (Dnmt3L^+/-) affects sex chromosome aneuploidy in adult and embryonic offspring. This chapter will discuss the role of DNMT3L in establishing DNA methylation patterns during gametogenesis, as well as the proven and potential consequences of DNMT3L-deficiency to fertility and somatic and germline genetic disease in light of the increasing evidence that epigenetic reprogramming is a dose sensitive and partially stochastic process.

Further reading: Epigenetics: A Reference Manual

from Jessica M. Silva and David I. Smith writing in Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection:

There are numerous non-coding transcripts in addition to those housekeeping transcripts (ribosomal RNAs and transfer RNAs) that participate in the processes of protein production within the cells. These include the large number of small RNAs such as microRNAs, piwiRNAs and snoRNAs. In addition to these relatively small transcripts there are also considerably longer non-coding transcripts that also play important roles within the genome. These long non-coding RNAs (lncRNAs) can be differentiated from each other based upon where they are derived from within the genome. For instance, there are intronic lncRNAs (transcribed between exons of genes), intergenic lncRNAs (transcribed in the space between genes), and lncRNAs that are more complex as they overlap both intron and exon of a coding gene. Each of these lncRNAs may also be in the sense or in the antisense direction. The list of long non-coding RNAs (lncRNAs) that are associated with diseases is rapidly increasing. Some lncRNAs have been found to be aberrantly expressed in various diseases including psoriasis, mental disorders, autism, and also cancer. The list of lncRNAs associated with cancer is increasing. However, relatively little is known about the precise functions of most cancer associated lncRNAs, but of what is known suggest that these long non-coding transcripts function in many different ways within cells and promote cancer development and progression. We will review what is known about the role that some of the lncRNAs play in cancer

Further reading: Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection

from Brian P. Chadwick writing in Epigenetics: A Reference Manual:

The recent completion of several mammalian genome sequences makes obvious that we share a near-identical collection of genes. What defines us as human must therefore be encoded within regions of the genome where we differ, providing an added level of complexity that probably influences the spatial and temporal expression of genes. Most DNA sequence variation occurs within the repetitive DNA, once called 'Junk DNA' that accounts for at least half of the human genome, and evidence is mounting for its important role in genome function. Although some repeat elements are conserved to some extent between mammals, their precise copy number and genomic location typically are not. In addition, some repeats are not conserved, including the large tandem repeats. This chapter focuses on two large tandem arrays in the human genome that can adopt quite different chromatin configurations as a result of epigenetic changes; one as a direct consequence of X chromosome inactivation and the other in the context of disease susceptibility. Both cases highlight how alternate packaging of these unusual DNA sequences probably results in differing functions. In each instance, common denominators are the acquisition of the epigenetic organizer protein CTCF and a distinct change in transcripts originating from the array.

Further reading: Epigenetics: A Reference Manual

from Thomas Mikeska and Alexander Dobrovic writing in Epigenetics: A Reference Manual:

Methylation-sensitive high resolution melting (MS-HRM) is an inexpensive and robust closed tube screening methodology that enables rapid analysis of locus specific DNA methylation for multiple samples. MS-HRM is based on the differential melting behaviour of PCR amplification products derived from methylated and unmethylated templates after bisulfite treatment. The melting profiles of an unknown sample are compared to the melting profiles of standards with known DNA methylation levels. MS-HRM has the advantage of allowing ready distinction between homogenous and heterogeneous DNA methylation. Estimation of DNA methylation to quite low levels in a semi-quantitative manner is possible for homogeneously methylated templates where all the CpG sites are methylated. However for heterogeneous methylation, the formation of multiple heteroduplexes makes quantitation difficult. Digital MS-HRM utilises limiting dilution to amplify single templates enabling DNA methylation analysis at a single allele resolution and enables the quantitative analysis of both homogenous and heterogeneous methylation. The PCR products either generated by MS-HRM or digital MS-HRM can subsequently undergo Sanger DNA sequencing or pyrosequencing to investigate DNA methylation at individual CpG positions.

Further reading: Epigenetics: A Reference Manual

from Brian Spetman, Sarah Lueking, Brooke Roberts and Jonathan H. Dennis writing in Epigenetics: A Reference Manual:

The location and density of nucleosomes in the eukaryotic genome plays a role in regulating nuclear processes including transcription, replication, recombination, and repair. Microarray mapping of nucleosomally protected DNA has emerged as a powerful, cost-effective, high-throughput method to analyze the relationship between nucleosome position and genomic regulation. In this chapter we discuss experimental considerations such as sample preparation and microarray design. In addition, two procedures are detailed: (1) Formaldehyde Crosslink and Harvest Cells, Isolate Nuclei, and MNase cut chromatin, and (2) Isolation of mononucleosomally protected DNA and fluorescent labeling of DNA for microarray hybridization. With the information specified in this chapter, most any laboratory equipped for molecular biology with institutional or commercial access to microarray facilities should be should be able to map nucleosome position and occupancy.

Further reading: Epigenetics: A Reference Manual

from Jennifer E. Cropley and Catherine M. Suter writing in Epigenetics: A Reference Manual:

Epigenetic states are faithfully inherited through mitotic cell division, but are generally cleared and reset on passage through the mammalian germline. But this clearing of epigenetic marks is not always complete, leading to transgenerational inheritance of epigenotype. Transgenerational epigenetic inheritance has been demonstrated in several organisms, including mammals, and has been most comprehensively studied in mouse strains carrying variants of the agouti (A^vy) and axin (Axin^Fu) alleles. The most prominent feature of transgenerational epigenetic inheritance is its non-Mendelian nature: not all offspring that inherit the genetic locus also inherit the parental epigenetic state. Transgenerational epigenetic inheritance is emerging as an important facet of mammalian biology. It may underlie the etiology of human diseases that display complex patterns of inheritance, including diabetes, mental illnesses and autoimmune diseases. As variable epigenetic states can be inherited on an invariant genotype, epigenetic variation may provide a substrate for Darwinian selection that is independent of genetic variation.

Further reading: Epigenetics: A Reference Manual

from Mohammad Ali Faghihi and Claes Wahlestedt writing in Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection:

One prominent and complex class of regulatory RNAs is natural antisense transcripts. Natural antisense transcripts (also known as antisense RNAs or antisense transcripts) are RNA molecules that are transcribed from the opposite DNA strand and are often overlapping in part with mRNA of conventional sense genes. Transcription of antisense RNA, similar to sense RNA, is tissue and cell line specific. Indeed a large fraction of antisense transcripts is expressed in specific regions of the brain, supporting involvement of these regulatory RNAs in sophisticated brain functions as well as in complex neurological disorders. Recent research on natural antisense transcripts, including several large-scale expression-profiling studies, has conclusively established the existence of antisense transcripts in eukaryotic genomes. In fact, the consensus opinion is that natural antisense transcripts, most of which represent non-protein-coding RNAs, transcribed abundantly in the mammalian genome. However, there are many unanswered questions that still exist concerning antisense transcripts biological functions and their heterogeneous mode of actions in various cells. For instance, what fraction of antisense RNAs may have functional significance, and how many different regulatory mechanisms may exist for these RNA molecules? Natural antisense transcripts appear to be utilizing various cellular pathways, but it is still not clear which intrinsic properties of antisense RNA molecules or extrinsic features, such as protein interactions, cellular and developmental context are decisive for the selection of any given pathway. How is the expression of these non-protein-coding RNAs regulated in various cells, and what are the extrinsic factors that affect the transcription of antisense RNAs? Considering tissue- and cell type-specific expression patterns of antisense RNAs and their heterogeneous proposed functions, natural antisense transcripts appear to be a heterogeneous group of regulatory RNAs with a wide variety of biological roles.

Further reading: Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection

from Enrique M. Muro and Miguel A. Andrade writing in Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection:

Pseudogenes are genome loci that look like genes but have sequences apparently prevented to produce any functional product due to genetic defects. However, recent advances in the field of molecular biology urge the revisiting of this definition. In this chapter we will discuss some of those advances. There is experimental and computational evidence of some biological function arising from pseudogene transcription but this evidence is not easy to find. Accordingly, not that many studies have been published on the topic. It seems that if there is pseudogene transcript functionality, it arises in certain tissues, and in certain conditions, with much more specificity than gene expression. Some of this complexity relates to the fact that this function involves non-coding RNAs (ncRNAs), a molecular entity for which novel tools and biological paradigms are still being worked out. A particular type of ncRNAs are Natural Antisense Transcripts (NATs) and these have a special relevance for the study of pseudogene functionality for reasons that we will discuss.

Further reading: Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection

from Salah Mahmoudi, Anna Vilborg and Marianne Farnebo writing in Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection:

The p53 tumor suppressor is arguably the most important player in preventing tumor formation and progression. p53 mutations are found with high frequency (about 50%) in human tumors, however virtually all tumors have inactivated the p53 pathway in some fashion.The p53 protein functions as a transcription factor with a crucial role in orchestrating the cellular stress response. p53 can be activated by a large variety of stress factors, and reacts by triggering an appropriate response, the nature of which will vary with the triggering factor and the cellular background. The most classical outcomes of p53 activation are cell cycle arrest and apoptosis, and it is generally believed that these two, together with senescence, irreversible cell cycle arrest, are the p53 responses with greatest impact on preventing tumor formation2. However, it has lately become evident that p53 is involved in many other processes in addition to these. p53 can promote several forms of DNA repair, thus contributing to maintaining genomic integrity. Further, p53 may promote differentiation of stem and progenitor cells into more specialized cell types, and can also prevent self-renewal of stem cells. Paradoxically, p53 can also induce genes involved in promoting survival. One of these genes is p21, while being a classical cell cycle arrest-inducing p53 target, p21 antagonizes apoptosis. The list of pro-survival p53 targets also includes several antioxidant genes and genes involved in metabolism. The logic behind this surprising p53 function may be that the elimination of every cell ever exposed to any kind of stress is not desirable, while protecting us from getting cancer, it would lead to tissue degeneration. In addition to its crucial role in cancer, p53 has been implicated in several other diseases, generally diseases connected to excessive cell death. These include diabetes, cell death after ischemia, and various neurodegenerative diseases such as Huntington, Parkinson, and Alzheimer. Since p53 is able to eliminate cells through apoptosis and senescence and to induce differentiation, thus reducing stem cell populations, p53 has also been suggested to promote aging. Initial studies in mice expressing constitutively active p53 also seemed to confirm this hypothesis, However, subsequent mice models carrying an extra copy of p53 but under control of its normal regulatory elements demonstrated that properly controlled p53 did not induce aging. Instead it actually promoted longevity, largely by preventing tumorigenesis. Due to its critical function in deciding on life or death for the cell, strict regulation of p53 levels and activity is crucial. p53 protein levels are kept under tight control by multiple mechanisms. Further, p53 mRNA stability and translation is subject to regulation by a number of factors, including long non-coding RNA.

Further reading: Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection

from Alka Saxena and Piero Carninci writing in Epigenetics: A Reference Manual:

In the past decade, we have become acquainted with an entire new world of fine regulatory control within cells governed by non-coding RNAs. Although we have not completely explored this world, we know from a few well studied examples that not only gene dosage but protein function also, is fine tuned by non-coding RNAs. It appears that proper cell function is largely dependent on non-coding RNAs, many of which were invisible to us until the advent of high throughput sequencing and tiling array technology. The realization, that transcripts with no open reading frames are biologically active molecules with multiple functions including regulation of the expression of coding RNA, shifts the power from proteins to non-coding RNAs as key modulators of cellular function. In this review, we discuss the various classes of non coding RNAs and the mechanisms employed by them to achieve this status, with a particular focus on their ability to induce epigenetic modifications.

Further reading: Epigenetics: A Reference Manual

from Fabricio F. Costa writing in Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection:

During the past two decades, new technologies in molecular biology and human genetics have enabled the discovery of different types of non-coding RNAs. Non-coding RNAs are RNA transcripts that have no apparent protein product. These molecules have been grouped in different classes such as microRNAs, small RNAs and long RNAs (lncRNAs) according to their size and function. LncRNAs have been strongly associated to epigenetic mechanisms in different cell types. Conceivably, they have been described as an essential part of the human epigenome. In this chapter, examples of lncRNAs and their function will be presented. A historical perspective on the impact of lncRNAs in epigenetic mechanisms, human disease and evolution will be also discussed.

Further reading: Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection

from Nicholas C. Wong writing in Epigenetics: A Reference Manual:

Biological experiments are rapidly moving into the information age with the explosion of data generated from rapidly evolving technologies. Microarrays can interrogate many thousands to millions of loci within any one sample, while massively parallel sequencing platforms can essentially measure the entire genome. Keeping up with this rapid pace of data accumulation has required the development of online tools for the processing, analysis and annotation of data generated from large numbers of microarrays or next generation sequencing (NGS) experiments. I will cover a selected range of tools available to the biological researcher, from online discussion forums and blogs, to curated databases that store the data and associated annotations. I will then cover viewer tools that enable visualisation the annotations and finally review tools for assay design for follow up validation of NGS and microarray analyses. I will pay particular attention to DNA methylation and provide the reader with an insight into what is available online for the epigenetics researcher aiming to make sense of epigenomic data. As a disclaimer, this chapter is by no means a comprehensive list of available epigenetics resources, which are constantly being updated and expanded through the Internet and just a mouse click through Google away.

Further reading: Epigenetics: A Reference Manual

from Mario A. Arteaga-Vazquez and Ana E. Dorantes-Acosta writing in Epigenetics: A Reference Manual:

Paramutation is a fascinating phenomenon in which epigenetic information can be transmitted through trans-interactions between one allele of a gene to another allele or between homologous DNA sequences that establishes a state of gene expression that is heritable for generations. Paramutation was discovered in maize and similar phenomena have been described in other plants, fungi and animals. In this chapter, we describe several classic plant paramutation systems and discuss recent advances that implicate a role for RNA and a number of components of an RNA-based transcriptional silencing pathway on paramutation.

Further reading: Epigenetics: A Reference Manual

from Andreas Werner writing in Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection:

The complexity of an organism is driven by a positive balance between creative and destructive forces in the process of evolution. Small non-protein-coding RNAs play an instrumental role in both regulating gene expression (creative influence) as well as suppressing selfish genetic elements (defensive role). There are three main groups of small RNAs including microRNAs, endogenous siRNAs and piRNAs. MicroRNAs represent the most important gene regulatory small RNAs and act by tuning the expression level of eukaryotic mRNAs. Interestingly, endogenous siRNAs as well as piRNAs apparently serve both regulatory and defensive purposes. They suppress the expression of repetitive DNA elements but also influence the expression of protein coding genes. For endo-siRNAs, intriguing roles in epigenetic regulation are emerging. The multiple tasks of small RNAs are in line with a role as drivers of organismal complexity.

Further reading: Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection

from Mariano Alló and Alberto R. Kornblihtt writing in Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection:

Since the discovery of splicing in 1977, alternative splicing was seen for more than two decades as an interesting mechanism to generate protein diversity but with limited genome-wide influence because it was thought to affect only 20% of mammalian genes. The sequencing of the human and other mammals‰Ûª genomes in the early 2000's together with more recent high throughput analyses of splicing isoforms generated a renewed interest in alternative splicing. We know now that alternative splicing affects more than 90% of human genes, that normal and pathological cell differentiation not only depends on differential gene transcription but also on alternative splicing patterns, that mutations that either create or abolish alternative splicing regulatory sequences, named splicing enhancers and silencers, are a widespread source of human disease and that alternative splicing factors can be misregulated in cancer. The relationship between splicing and non-coding RNAs has emerged recently in the middle of an avalanche of papers showing how chromatin context could affect splicing choices. The convergence of these previously unrelated areas (non-coding RNAs, chromatin and splicing) has presented a novel and intriguing scenario that will be covered in this chapter, starting with a brief overview of transcription and splicing introducing the understanding of how these processes could be modulated by external factors. Then we will focus on our work using non-coding small RNAs (ncsRNAs) to regulate alternative splicing in human cells. Finally, we will discuss the evidence supporting the potential activity of endogenous non-coding RNAs as modulators of alternative splicing.

Further reading: Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection

from Hongchang Cui writing in Epigenetics: A Reference Manual:

Cell-fate specification and stem-cell renewal are fundamental processes in the development of multicellular organisms. In both animals and plants, a key role for transcription factors in these processes has been established, but an accumulating body of evidence indicates that epigenetic regulation also plays a critical role. Once regarded as stable marks, all epigenetic modifications, including DNA and histone methylation, are now known to be reversible, and a cohort of enzymes that add or erase epigenetic marks has been identified. Throughout the life of an organism, the epigenome is dynamically modified, leading in turn to transcriptional changes and ultimately cell-fate specification. Here, I review the recent literature that has shaped this view. Plants are unique among complex organisms in having the ability to generate a whole new organism from a single differentiated cell. How plant cells retain this amazing capability while maintaining their cell identity is a mystery. I introduce a model system for study of cell-fate specification, stem-cell renewal, and reprogramming.

Further reading: Epigenetics: A Reference Manual

from Marnie E. Blewitt and Linden J. Gearing writing in Epigenetics: A Reference Manual:

X chromosome inactivation is the method of dosage compensation that has evolved to equalise expression of X-linked genes between female (XX) and male (XY) mammals. In somatic cells only one X chromosome is active; the second X in female cells is silenced early during embryonic development, a process that involves the co-ordination of multiple levels of epigenetic regulation to ensure stable chromosome-wide silencing. In this chapter we shall focus on the molecular mechanisms involved in X chromosome inactivation, discuss how the epigenetic marks are believed to elicit stable transcriptional silencing, and why X inactivation represents an excellent model system for studying epigenetic regulation in mammals.

Further reading: Epigenetics: A Reference Manual

from Daniel H. Kim and Jeannie T. Lee writing in Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection:

X-chromosome inactivation provides a model for discovering the still emerging functions of noncoding RNAs, which exhibit diverse roles in regulating the epigenome. Combining recent insights into X-chromosome noncoding RNAs with the advent of next-generation sequencing technologies promises many new discoveries in interrogating the functions of noncoding RNAs at the genomic level. Global RNA-protein interaction information is readily available through utilizing RNA immunoprecipitation followed by high-throughput sequencing (RIP-Seq), which has recently uncovered the diversity of the noncoding Polycomb transcriptome. In this chapter, we discuss noncoding RNAs of the X-inactivation center that have provided unique insights into RNA molecules as molecular switches, guides and tethers to the epigenome, and key participants in diverse regulatory pathways, including RNA interference and Polycomb silencing.

Further reading: Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection

from Danny Rangasamy writing in Epigenetics: A Reference Manual:

The histone variants of the H2A family are highly conserved in mammals, playing critical roles in regulating many nuclear processes by altering chromatin structure. One of the key H2A variants, H2A.X, marks DNA damage, facilitating the recruitment of DNA repair proteins to restore genomic integrity. Another variant, H2A.Z, plays an important role in both gene activation and repression. A high level of H2A.Z expression is ubiquitously detected in many cancers and is significantly associated with cellular proliferation and genomic instability. This review summarizes the current understanding of these variants and their functions, as well as their links to cancer development. Furthermore, the significance of dysfunction of these variants is highlighted with respect to their potential as biomarkers and as new targets for anticancer therapy.

Further reading: Epigenetics: A Reference Manual

from Justin A. Fincher and Jonathan H. Dennis writing in Epigenetics: A Reference Manual:

DNA in eukaryotes is efficiently and compactly organized into chromatin, the fundamental subunit of which is the nucleosome: approximately 150 bp of DNA spooled 1.65 times around a histone octamer. The location and density of nucleosomes play a role in regulating nuclear processes including transcription, replication, recombination, and repair. Mechanisms acting in trans, like ATP-dependent remodelers and cellular memory complexes, as well as in cis features intrinsic to the DNA sequence itself regulate the location and density of nucleosomes. Here, we review the three cis acting DNA sequence features that affect the distribution of nucleosomes: (1) two frameworks defining the relationship between the histone octamer and the underlying DNA sequence (nucleosome occupancy and nucleosome position, then statistical positioning and a nucleosome positioning code), (2) the organization of DNA into the nucleosome core particle, and (3) specific DNA sequence features and DNA templates that promote or inhibit the formation of nucleosomes. We close by describing three computational algorithms trained on DNA sequence that have been used to predict nucleosome position and density. In summary, we hope to draw attention to multiple aspects of DNA sequence that specify organization of sequence into nucleosomes and influence the distribution of nucleosomes in eukaryotic genomes.

Further reading: Epigenetics: A Reference Manual

from Samson Mani and Zdenko Herceg writing in Epigenetics: A Reference Manual:

DNA methylation is an important regulator of gene transcription and a large body of evidence has demonstrated that aberrant DNA methylation is associated with unscheduled gene silencing, and the genes with high levels of 5-methylcytosine in their promoter region are transcriptionally silent. DNA methylation is essential during embryonic development, and in somatic cells, patterns of DNA methylation are generally transmitted to daughter cells with a high fidelity. Aberrant DNA methylation patterns have been associated with a large number of human malignancies and found in two distinct forms: hypermethylation and hypomethylation compared to normal tissue. Hypermethylation is one of the major epigenetic modifications that repress transcription via promoter region of tumour suppressor genes. Hypermethylation typically occurs at CpG islands in the promoter region and is associated with gene inactivation. Global hypomethylation has also been implicated in the development and progression of cancer through different mechanisms. This chapter will focus on DNA methylation as the major epigenetic mechanism involved in normal biological processes and abnormal events leading to cancer development. It will also focus on the interaction between DNA methylation and other epigenetic mechanisms.

Further reading: Epigenetics: A Reference Manual

from Anne K. Voss and Tim Thomas writing in Epigenetics: A Reference Manual:

A histone (H3-H4)₂ tetramer flanked by two H2A-H2B heterodimers form the core protein structure, around which DNA is wrapped. DNA and the histone octamer together form the smallest chromatin particle, the nucleosome. How intimately the DNA associates with the core histones and how tightly the nucleosomes are packed with each other is determined by a key post-translational modification of the histone proteins, namely acetylation. Histone acetylation was first discovered in the early 1960s. After a dearth of progress, due to technical limitations, our knowledge of histone acetylation has exploded in the last fifteen years. Enzymes that catalyse acetylation of histones, the histone acetyltransferases, have been discovered, proteins associated with these have been identified and their preferences for specific histone residues have been determined. Importantly, we are gaining a better understanding of the relevance of histone acetylation in health and disease through the discovery of genetic mutations underlying human diseases in loci encoding histone acetyltransferases (HATs) and through examination of mouse strains deficient in specific histone acetyltransferases. Here we discuss the principles of histone acetyltransferase biology.

Further reading: Epigenetics: A Reference Manual

from Sebastian Lunke and Assam El-Osta writing in Epigenetics: A Reference Manual:

With the advances in traditional genetics failing to provide causal genes for many complex diseases, the focus of research is shifting towards determining the importance of gene-environment interactions, more specifically epigenetic regulation. Paramount to answering this question is the knowledge of which transcription factors bind to what sequence, as well as a detailed understanding of how the transcriptional state of a genetic sequence is epigenetically distinguished. The chromatin immuno-precipitation (ChIP) strategy has proven to be a powerful tool to investigate these mechanisms, but has been limited for a long time to single locus analysis. The recent emergence of next-generation sequencing (NGS) technology however has revolutionized the field of epigenomics and for the first time enabled unbiased genome-wide analysis of ChIPed DNA. Here we provide a detailed discussion and protocol on how to best perform ChIP for NGS analysis.

Further reading: Epigenetics: A Reference Manual

from Emma L. Northrop and Lee H. Wong writing in Epigenetics: A Reference Manual:

In eukaryotes, each chromosome has one centromere and its ends are protected by telomeres. The centromere is a specialized chromosomal locus that directs kinetochore assembly and provides the site for microtubule attachment, allowing accurate chromosome segregation during cell division. Despite the critical role centromeres play, centromeric DNA sequences are highly variable and not conserved between species. Increasing evidence, including the discovery of functional neocentromeres, suggests that centromere identity and function is epigenetically defined through the formation of a specialised chromatin structure. This chapter reviews recent studies addressing the structural and functional characterisation of centromere chromatin, its assembly and propagation during cell division. Telomeres are specialized nucleoprotein complexes that protect the chromosome ends from degradation. In recent years, it has become increasingly clear that heterochromatic marks at telomeres act as negative epigenetic regulators of telomere elongation, repress recombination events at the telomere and are critical for maintaining telomere structural integrity. Recent research reporting telomeres being transcribed by RNA polymerase II to give rise to TERRA RNA, open up an additional level of regulation at the telomere. This chapter will discuss the links between the epigenetic status of telomeres, telomere function and telomere-length regulation, and the implications on cellular reprogramming, aging and cancer.

Further reading: Epigenetics: A Reference Manual

from Miina Ollikainen writing in Epigenetics: A Reference Manual:

A large variety of methods to measure DNA methylation have been developed and used extensively over the last twenty years. These have been based on selective restriction digestion of methylated DNA, the capture of methylated DNA by methyl binding proteins or antibodies, or bisulphite conversion of DNA. However, all restriction enzyme based methods are dependent on available restriction sites for methylation-specific restriction enzymes and therefore cannot be used to analyse every CpG site in the genome. Although immunoprecipitation methods are not sequence specific, they are unable to provide methylation data at a single-base resolution. Therefore, both of these approaches are limited in their applicability. On the other hand, bisulphite conversion based methods allow methylation studies directed to any CpG site in the genome. Sodium bisulphite treatment of DNA converts all unmethylated cytosines into uracil while methylated cytosines remain unchanged, thus transferring an epigenetic difference into a measureable genetic difference. A variety of downstream methods such as Polymerase Chain Reaction (PCR), sequencing, Single Nucleotide Polymorphism (SNP) genotyping and mass spectrometry can be coupled with bisulphite conversion. This chapter provides an overview of some of these methods, concentrating on bisulphite sequencing, methylation-specific PCR, pyrosequencing, MassARRAY EpiTYPER and Infinium HumanMethylation27 BeadChip. Considerations for assay selection and detailed protocols for each method are presented in the end of this chapter.

Further reading: Epigenetics: A Reference Manual

from Mark D. Robinson, Bryan Beresford-Smith, Anthony Kaspi and I. Haviv writing in Epigenetics: A Reference Manual:

Since biological phenotype and differentiation is regulated partially through CpG DNA methylation, and this mark is relatively easy to measure, genome-wide profiling of methylation landscape is a popular tool in epigenetic research. The burden then falls on bioinformatics to provide normalization, quality control, and interpretation, while adopting to the vast number of versatile methods to interrogate methylation profiles. While creating a relational report of the results from either of these methods is critical for data to cross over from lab to lab, and from research to diagnostic and translation purposes, the methods are each introducing their unique bias to the data. Ideally, one would hope all labs would adopt a single method, but since each method offers a unique advantage, such as price, sensitivity, or confidence, one has to overcome the disparity hurdle via bioinformatic tools. Thus identifying the methodological biases of each technique, and the way to compensate for those in the process of generating a universal CpG methylation prediction on a genome region is the ultimate goal we are describing here. Follow up of CpG methylation with other read outs, such as impact on gene expression or coincidence with locations in the genome, where allelic variation is associated with the investigated phenotype, are also key to proper interpretation of the results.

Further reading: Epigenetics: A Reference Manual

from Jeffrey E. Squires and Thomas Preiss writing in Epigenetics: A Reference Manual:

A wealth of nucleobase and ribose modifications have been identified in multiple types of RNA including tRNAs, rRNAs, mRNAs, and small regulatory RNAs. Among them, 5-methylcytosine (m⁵C) has been detected in rRNAs, tRNAs, and early reports have indicated its presence in mRNAs. Well established as an epigenetic mark in DNA, the prevalence and function of m⁵C in RNA is either incompletely explored (tRNA, rRNA) or virtually unknown (mRNA, other noncoding RNA). Two eukaryotic m⁵C RNA methyltransferases have been identified; however, their substrate specificity and biological roles are incompletely understood. With recent advances in bisulfite sequencing of RNA, comprehensive analyses to determine the occurrence and functions of m⁵C in the transcriptome now appear feasible. In this chapter, we summarise the current knowledge in this field, focussing primarily on eukaryotic transcriptomes.

Further reading: Epigenetics: A Reference Manual