RNA meets chromatin

Meiotic silencing and fragmentation of the male germline restricted chromosome in zebra finch

During male meiotic prophase in mammals, X and Y are in a largely unsynapsed configuration, which is thought to trigger meiotic sex chromosome inactivation (MSCI). In avian species, females are ZW, and males ZZ. Although Z and W in chicken oocytes show complete, largely heterologous synapsis, they too undergo MSCI, albeit only transiently. The W chromosome is already inactive in early meiotic prophase, and inactive chromatin marks may spread on to the Z upon synapsis. Mammalian MSCI is considered as a specialised form of the general meiotic silencing mechanism, named meiotic silencing of unsynapsed chromatin (MSUC). Herein, we studied the avian form of MSUC, by analysing the behaviour of the peculiar germline restricted chromosome (GRC) that is present as a single copy in zebra finch spermatocytes. In the female germline, this chromosome is present in two copies, which normally synapse and recombine. In contrast, during male meiosis, the single GRC is always eliminated. We found that the GRC in the male germline is silenced from early leptotene onwards, similar to the W chromosome in avian oocytes. The GRC remains largely unsynapsed throughout meiotic prophase I, although patches of SYCP1 staining indicate that part of the GRC may self-synapse. In addition, the GRC is largely devoid of meiotic double strand breaks. We observed a lack of the inner centromere protein INCENP on the GRC and elimination of the GRC following metaphase I. Subsequently, the GRC forms a micronucleus in which the DNA is fragmented. We conclude that in contrast to MSUC in mammals, meiotic silencing of this single chromosome in the avian germline occurs prior to, and independent of DNA double strand breaks and chromosome pairing, hence we have named this phenomenon meiotic silencing prior to synapsis (MSPS).

Genetically modified mice-successes and failures of a widely used technology

Genetically modified mice, created by random integration of a transgene into the genome or by targeted mutation of a specific gene, have proven to be extremely powerful tools for studying gene function in vivo. In this article, we give (1) a short overview of the traditional methods in mouse transgenesis and (2) a discussion of the problems with these methods, (3) more recent methods that were developed to overcome these problems, and (4) an outlook on future directions in gene targeting.

Polycomb group protein gene silencing, non-coding RNA, stem cells, and cancer

Epigenetic programming is an important facet of biology, controlling gene expression patterns and the choice between developmental pathways. The Polycomb group proteins (PcGs) silence gene expression, allowing cells to both acquire and maintain identity. PcG silencing is important for stemness, X chromosome inactivation (XCI), genomic imprinting, and the abnormally silenced genes in cancers. Stem and cancer cells commonly share gene expression patterns, regulatory mechanisms, and signalling pathways. Many microRNA species have oncogenic or tumor suppressor activity, and disruptions in these networks are common in cancer; however, long non-coding (nc)RNA species are also important. Many of these directly guide PcG deposition and gene silencing at the HOX locus, during XCI, and in examples of genomic imprinting. Since inappropriate HOX expression and loss of genomic imprinting are hallmarks of cancer, disruption of long ncRNA-mediated PcG silencing likely has a role in oncogenesis. Aberrant silencing of coding and non-coding loci is critical for both the genesis and progression of cancers. In addition, PcGs are commonly abnormally overexpressed years prior to cancer pathology, making early PcG targeted therapy an option to reverse tumor formation, someday replacing the blunt instrument of eradication in the cancer therapy arsenal.

Life without RNAi: noncoding RNAs and their functions in Saccharomyces cerevisiae

There are a number of well-characterized and fundamental roles for noncoding RNAs (ncRNAs) in gene regulation in all kingdoms of life. ncRNAs, such as ribosomal RNAs, transfer RNAs, small nuclear RNAs, small nucleolar RNAs, and small interfering RNAs, can serve catalytic and scaffolding functions in transcription, messenger RNA processing, translation, and RNA degradation. Recently, our understanding of gene expression has been dramatically challenged by the identification of large and diverse populations of novel ncRNAs in the eukaryotic genomes surveyed thus far. Studies carried out using the budding yeast Saccharomyces cerevisiae indicate that at least some coding genes are regulated by these novel ncRNAs. S. cerevisiae lacks RNA interference (RNAi) and, thus, provides an ideal system for studying the RNAi-independent mechanisms of ncRNA-based gene regulation. The current picture of gene regulation is one of great unknowns, in which the transcriptional environment surrounding a given locus may have as much to do with its regulation as its DNA sequence or local chromatin structure. Drawing on the recent research in S. cerevisiae and other organisms, this review will discuss the identification of ncRNAs, their origins and processing, and several models that incorporate ncRNAs into the regulation of gene expression and chromatin structure.

A comparative approach for the investigation of biological information processing: an examination of the structure and function of computer hard drives and DNA

BACKGROUND

The robust storage, updating and utilization of information are necessary for the maintenance and perpetuation of dynamic systems. These systems can exist as constructs of metal-oxide semiconductors and silicon, as in a digital computer, or in the "wetware" of organic compounds, proteins and nucleic acids that make up biological organisms. We propose that there are essential functional properties of centralized information-processing systems; for digital computers these properties reside in the computer's hard drive, and for eukaryotic cells they are manifest in the DNA and associated structures.

METHODS

Presented herein is a descriptive framework that compares DNA and its associated proteins and sub-nuclear structure with the structure and function of the computer hard drive. We identify four essential properties of information for a centralized storage and processing system: (1) orthogonal uniqueness, (2) low level formatting, (3) high level formatting and (4) translation of stored to usable form. The corresponding aspects of the DNA complex and a computer hard drive are categorized using this classification. This is intended to demonstrate a functional equivalence between the components of the two systems, and thus the systems themselves.

RESULTS

Both the DNA complex and the computer hard drive contain components that fulfill the essential properties of a centralized information storage and processing system. The functional equivalence of these components provides insight into both the design process of engineered systems and the evolved solutions addressing similar system requirements. However, there are points where the comparison breaks down, particularly when there are externally imposed information-organizing structures on the computer hard drive. A specific example of this is the imposition of the File Allocation Table (FAT) during high level formatting of the computer hard drive and the subsequent loading of an operating system (OS). Biological systems do not have an external source for a map of their stored information or for an operational instruction set; rather, they must contain an organizational template conserved within their intra-nuclear architecture that "manipulates" the laws of chemistry and physics into a highly robust instruction set. We propose that the epigenetic structure of the intra-nuclear environment and the non-coding RNA may play the roles of a Biological File Allocation Table (BFAT) and biological operating system (Bio-OS) in eukaryotic cells.

CONCLUSIONS

The comparison of functional and structural characteristics of the DNA complex and the computer hard drive leads to a new descriptive paradigm that identifies the DNA as a dynamic storage system of biological information. This system is embodied in an autonomous operating system that inductively follows organizational structures, data hierarchy and executable operations that are well understood in the computer science industry. Characterizing the "DNA hard drive" in this fashion can lead to insights arising from discrepancies in the descriptive framework, particularly with respect to positing the role of epigenetic processes in an information-processing context. Further expansions arising from this comparison include the view of cells as parallel computing machines and a new approach towards characterizing cellular control systems.

Histone variant H2A.Z regulates centromere silencing and chromosome segregation in fission yeast

The incorporation of histone variant H2A.Z into nucleosomes plays essential roles in regulating chromatin structure and gene expression. A multisubunit complex containing chromatin remodeling protein Swr1 is responsible for the deposition of H2A.Z in budding yeast and mammals. Here, we show that the JmjC domain protein Msc1 is a novel component of the fission yeast Swr1 complex and is required for Swr1-mediated incorporation of H2A.Z into nucleosomes at gene promoters. Loss of Msc1, Swr1, or H2A.Z results in loss of silencing at centromeres and defective chromosome segregation, although centromeric levels of CENP-A, a centromere-specific histone H3 variant that is required for setting up the chromatin structure at centromeres, remain unchanged. Intriguingly, H2A.Z is required for the expression of another centromere protein, CENP-C, and overexpression of CENP-C rescues centromere silencing defects associated with H2A.Z loss. These results demonstrate the importance of H2A.Z and CENP-C in maintaining a silenced chromatin state at centromeres.

Phylogenetic footprinting of non-coding RNA: hammerhead ribozyme sequences in a satellite DNA family of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae)

BACKGROUND

The great variety in sequence, length, complexity, and abundance of satellite DNA has made it difficult to ascribe any function to this genome component. Recent studies have shown that satellite DNA can be transcribed and be involved in regulation of chromatin structure and gene expression. Some satellite DNAs, such as the pDo500 sequence family in Dolichopoda cave crickets, have a catalytic hammerhead (HH) ribozyme structure and activity embedded within each repeat.

RESULTS

We assessed the phylogenetic footprints of the HH ribozyme within the pDo500 sequences from 38 different populations representing 12 species of Dolichopoda. The HH region was significantly more conserved than the non-hammerhead (NHH) region of the pDo500 repeat. In addition, stems were more conserved than loops. In stems, several compensatory mutations were detected that maintain base pairing. The core region of the HH ribozyme was affected by very few nucleotide substitutions and the cleavage position was altered only once among 198 sequences. RNA folding of the HH sequences revealed that a potentially active HH ribozyme can be found in most of the Dolichopoda populations and species.

CONCLUSIONS

The phylogenetic footprints suggest that the HH region of the pDo500 sequence family is selected for function in Dolichopoda cave crickets. However, the functional role of HH ribozymes in eukaryotic organisms is unclear. The possible functions have been related to trans cleavage of an RNA target by a ribonucleoprotein and regulation of gene expression. Whether the HH ribozyme in Dolichopoda is involved in similar functions remains to be investigated. Future studies need to demonstrate how the observed nucleotide changes and evolutionary constraint have affected the catalytic efficiency of the hammerhead.

Silent mysteries: epigenetic paradigms could hold the key to conquering the epidemic of allergy and immune disease

Epigenetic mechanisms provide new insights into how environmental changes may mediate the increasing propensity for complex immune diseases such as allergic disease. There is now strong evidence that early environmental exposures play a key role in activating or silencing genes by altering DNA and histone methylation, histone acetylation and chromatin structure. These modifications determine the degree of DNA compaction and accessibility for gene transcription, altering gene expression, phenotype and disease susceptibility. While there is already evidence that a number of early environmental exposures are associated with an increased risk of allergic disease, several new studies indicate in utero microbial and dietary exposures can modify gene expression and allergic disease propensity through epigenetic modification. This review explores the evidence that immune development is under clear epigenetic regulation, including the pattern of T helper (Th)1 and Th2 cell differentiation, regulatory T cell differentiation, and more recently, Th17 development. It also considers the mechanisms of epigenetic regulation and early immune defects in allergy prone neonates. The inherent plasticity conferred by epigenetic mechanisms clearly also provides opportunities for environmental strategies that can re-programme gene expression for disease prevention. Identifying genes that are differentially silenced or activated in relation to subsequent disease will not only assist in identifying causal pathways, but may also help identify the contributing environmental factors.

Structure and epigenetics of nucleoli in comparison with non-nucleolar compartments

The nucleolus is a nuclear compartment that plays an important role in ribosome biogenesis. Some structural features and epigenetic patterns are shared between nucleolar and non-nucleolar compartments. For example, the location of transcriptionally active mRNA on extended chromatin loop species is similar to that observed for transcriptionally active ribosomal DNA (rDNA) genes on so-called Christmas tree branches. Similarly, nucleolus organizer region-bearing chromosomes located a distance from the nucleolus extend chromatin fibers into the nucleolar compartment. Specific epigenetic events, such as histone acetylation and methylation and DNA methylation, also regulate transcription of both rRNA- and mRNA-encoding loci. Here, we review the epigenetic mechanisms and structural features that regulate transcription of ribosomal and mRNA genes. We focus on similarities in epigenetic and structural regulation of chromatin in nucleoli and the surrounding non-nucleolar region and discuss the role of proteins, such as heterochromatin protein 1, fibrillarin, nucleolin, and upstream binding factor, in rRNA synthesis and processing.

AURKB-mediated effects on chromatin regulate binding versus release of XIST RNA to the inactive chromosome

How XIST RNA strictly localizes across the inactive X chromosome is unknown; however, prophase release of human XIST RNA provides a clue. Tests of inhibitors that mimic mitotic chromatin modifications implicated an indirect role of PP1 (protein phosphatase 1), potentially via its interphase repression of Aurora B kinase (AURKB), which phosphorylates H3 and chromosomal proteins at prophase. RNA interference to AURKB causes mitotic retention of XIST RNA, unlike other mitotic or broad kinase inhibitors. Thus, AURKB plays an unexpected role in regulating RNA binding to heterochromatin, independent of mechanics of mitosis. H3 phosphorylation (H3ph) was shown to precede XIST RNA release, whereas results exclude H1ph involvement. Of numerous Xi chromatin (chromosomal protein) hallmarks, ubiquitination closely follows XIST RNA retention or release. Surprisingly, H3S10ph staining (but not H3S28ph) is excluded from Xi and is potentially linked to ubiquitination. Results suggest a model of multiple distinct anchor points for XIST RNA. This study advances understanding of RNA chromosome binding and the roles of AURKB and demonstrates a novel approach to manipulate and study XIST RNA.

Transmission héréditaire de l’information épigénétique par le gamète mâle

Comment est déterminé un phénotype ? Historiquement, on pensait que ce dernier résultait de l’information génétique reçue par les parents. Mais de nombreuses études ont révélé l’existence de modifications épigénétiques qui ne sont pas portées sur la séquence nucléotidique d’un gène, mais dont la présence est indispensable à l’expression normale d’un gène. Point important, ces modifications épigénétiques peuvent être héritées par les enfants, indiquant clairement que le gamète femelle mais aussi le gamète mâle contiennent des informations épigénétiques transmissibles à la descendance.

Epigenetics: deciphering how environmental factors may modify autoimmune type 1 diabetes

Type 1 diabetes (T1D) is an autoimmune disease that has increased two- to threefold over the past half century by as yet unknown means. It is generally accepted that T1D is the result of gene-environment interactions, but such rapid increases in incidence are not explained by Mendelian inheritance. There have been numerous advances in our knowledge of the pathogenesis of T1D. Indeed, there has been a large number of genes identified that contribute to risk for this disease and several environmental factors have been proposed. The complexity of such interactions is yet to be understood for any major chronic disease. Epigenetic regulation is one way to explain the rapid increase in incidence and could be a central mechanism by which environmental factors influence development of diabetes. However, there is remarkably little known about the contribution of epigenetics to T1D pathogenesis. Here we speculate on various candidate processes and molecules of the immune and endocrine systems that could modify risk for T1D through epigenetic regulation.

Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome

Transcriptome studies are revealing that the eukaryotic genome actively transcribes a diverse repertoire of large noncoding RNAs (ncRNAs), many of which are unannotated and distinct from the small RNAs that have garnered much attention in recent years. Why are they so pervasive, and do they have a function? X-chromosome inactivation (XCI) is a classic epigenetic phenomenon associated with many large ncRNAs. Here, I provide a perspective on how XCI is achieved in mice and suggest how this knowledge can be applied to the rest of the genome. Emerging data indicate that long ncRNAs can function as guides and tethers, and may be the molecules of choice for epigenetic regulation: First, unlike proteins and small RNAs, large ncRNAs remain tethered to the site of transcription, and can therefore uniquely direct allelic regulation. Second, ncRNAs command a much larger sequence space than proteins, and can therefore achieve very precise spatiotemporal control of development. These properties imply that long noncoding transcripts may ultimately rival small RNAs and proteins in their versatility as epigenetic regulators, particularly for locus- and allele-specific control.

Histone modifications within the human X centromere region

Human centromeres are multi-megabase regions of highly ordered arrays of alpha satellite DNA that are separated from chromosome arms by unordered alpha satellite monomers and other repetitive elements. Complexities in assembling such large repetitive regions have limited detailed studies of centromeric chromatin organization. However, a genomic map of the human X centromere has provided new opportunities to explore genomic architecture of a complex locus. We used ChIP to examine the distribution of modified histones within centromere regions of multiple X chromosomes. Methylation of H3 at lysine 4 coincided with DXZ1 higher order alpha satellite, the site of CENP-A localization. Heterochromatic histone modifications were distributed across the 400–500 kb pericentromeric regions. The large arrays of alpha satellite and gamma satellite DNA were enriched for both euchromatic and heterochromatic modifications, implying that some pericentromeric repeats have multiple chromatin characteristics. Partial truncation of the X centromere resulted in reduction in the size of the CENP-A/Cenp-A domain and increased heterochromatic modifications in the flanking pericentromere. Although the deletion removed ∼1/3 of centromeric DNA, the ratio of CENP-A to alpha satellite array size was maintained in the same proportion, suggesting that a limited, but defined linear region of the centromeric DNA is necessary for kinetochore assembly. Our results indicate that the human X centromere contains multiple types of chromatin, is organized similarly to smaller eukaryotic centromeres, and responds to structural changes by expanding or contracting domains.

Regulatory roles of natural antisense transcripts

Mammalian genomes encode numerous natural antisense transcripts, but the function of these transcripts is not well understood. Functional validation studies indicate that antisense transcripts are not a uniform group of regulatory RNAs but instead belong to multiple categories with some common features. Recent evidence indicates that antisense transcripts are frequently functional and use diverse transcriptional and post-transcriptional gene regulatory mechanisms to carry out a wide variety of biological roles.

Silent chromatin at the middle and ends: lessons from yeasts

Eukaryotic centromeres and telomeres are specialized chromosomal regions that share one common characteristic: their underlying DNA sequences are assembled into heritably repressed chromatin. Silent chromatin in budding and fission yeast is composed of fundamentally divergent proteins tat assemble very different chromatin structures. However, the ultimate behaviour of silent chromatin and the pathways that assemble it seem strikingly similar among Saccharomyces cerevisiae (S. cerevisiae), Schizosaccharomyces pombe (S. pombe) and other eukaryotes. Thus, studies in both yeasts have been instrumental in dissecting the mechanisms that establish and maintain silent chromatin in eukaryotes, contributing substantially to our understanding of epigenetic processes. In this review, we discuss current models for the generation of heterochromatic domains at centromeres and telomeres in the two yeast species.

A 'higher order' of telomere regulation: telomere heterochromatin and telomeric RNAs

Protection of chromosome ends from DNA repair and degradation activities is mediated by specialized protein complexes bound to telomere repeats. Recently, it has become apparent that epigenetic regulation of the telomric chromatin template critically impacts on telomere function and telomere-length homeostasis from yeast to man. Across all species, telomeric repeats as well as the adjacent subtelomeric regions carry features of repressive chromatin. Disruption of this silent chromatin environment results in loss of telomere-length control and increased telomere recombination. In turn, progressive telomere loss reduces chromatin compaction at telomeric and subtelomeric domains. The recent discoveries of telomere chromatin regulation during early mammalian development, as well as during nuclear reprogramming, further highlights a central role of telomere chromatin changes in ontogenesis. In addition, telomeres were recently shown to generate long, non-coding RNAs that remain associated to telomeric chromatin and will provide new insights into the regulation of telomere length and telomere chromatin. In this review, we will discuss the epigenetic regulation of telomeres across species, with special emphasis on mammalian telomeres. We will also discuss the links between epigenetic alterations at mammalian telomeres and telomere-associated diseases.

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

We recently showed that the mammalian genome encodes >1,000 large intergenic noncoding (linc)RNAs that are clearly conserved across mammals and, thus, functional. Gene expression patterns have implicated these lincRNAs in diverse biological processes, including cell-cycle regulation, immune surveillance, and embryonic stem cell pluripotency. However, the mechanism by which these lincRNAs function is unknown. Here, we expand the catalog of human lincRNAs to approximately 3,300 by analyzing chromatin-state maps of various human cell types. Inspired by the observation that the well-characterized lincRNA HOTAIR binds the polycomb repressive complex (PRC)2, we tested whether many lincRNAs are physically associated with PRC2. Remarkably, we observe that approximately 20% of lincRNAs expressed in various cell types are bound by PRC2, and that additional lincRNAs are bound by other chromatin-modifying complexes. Also, we show that siRNA-mediated depletion of certain lincRNAs associated with PRC2 leads to changes in gene expression, and that the up-regulated genes are enriched for those normally silenced by PRC2. We propose a model in which some lincRNAs guide chromatin-modifying complexes to specific genomic loci to regulate gene expression.

MLL associates with telomeres and regulates telomeric repeat-containing RNA transcription

Mammalian telomeres consist of TTAGGG repeats organized in nucleosomes and associated with a six-protein complex known as shelterin, which preserves telomere structure and protects chromosome ends from the cellular DNA damage response. Recent studies have found that telomeres are transcribed into telomeric UUAGGG repeat-containing RNA (TERRA) starting from subtelomeric regions. TERRA binding at telomeres appears to be involved in cis-based mechanisms of telomeric chromatin organization and maintenance. A number of histone methyltransferases (HMTs) are known to influence telomeric chromatin status; however, the regulatory mechanisms of telomere transcription are poorly understood. Here, we show that the histone 3/lysine 4 (H3/K4) HMT and the transcriptional regulator MLL associate with telomeres and contribute to their H3/K4 methylation and transcription in a telomere length-dependent manner. In human diploid fibroblasts, RNA interference-mediated MLL depletion affects telomere chromatin modification and transcription and induces the telomere damage response. Telomere uncapping through either TRF2 shelterin protein knockdown or exposure to telomere G-strand DNA oligonucleotides significantly increases the transcription of TERRA, an effect mediated by the functional cooperation between MLL and the tumor suppressor p53. In total, our findings identify a previously unrecognized role of MLL in modifying telomeric chromatin and provide evidence for the functional interaction between MLL, p53, and the shelterin complex in the regulation of telomeric transcription and stability.

Developmental origins of adult disease

Intrauterine growth retardation (IUGR) has been linked to development of type 2 diabetes in adulthood. Using a rat model, we tested the hypothesis that uteroplacental insufficiency disrupts the function of the electron transport chain in the fetal beta-cell and leads to a debilitating cascade of events. The net result is progressive loss of beta-cell function and eventual development of type 2 diabetes in the adult. Studies in the IUGR rat demonstrate that an abnormal intrauterine environment induces epigenetic modifications of key genes regulating beta-cell development; experiments directly link chromatin remodeling with suppression of transcription. Future research will be directed at elucidating the mechanisms underlying epigenetic modifications in offspring.

Riboactivators: transcription activation by noncoding RNA

The paradigm of gene regulation was forever changed by the discovery that short RNA duplexes could directly regulate gene expression. Most regulatory roles attributed to noncoding RNA were often repressive. Recent observations are beginning to reveal that duplex RNA molecules can stimulate gene transcription. These RNA activators employ a wide array of mechanisms to up-regulate transcription of target genes, including functioning as DNA-tethered activation domains, as coactivators and modulators of general transcriptional machinery, and as regulators of other noncoding transcripts. The discoveries over the past few years defy "Moore's law" in the breath-taking rapidity with which new roles for noncoding RNA in gene expression are being revealed. As gene regulatory networks are reconstructed to accommodate the influence of noncoding RNAs, their importance in maintenance of cellular health will become increasingly apparent. In fact, a new generation of therapeutic agents will focus on modulating the function of noncoding RNA.

Constitutive heterochromatin: a surprising variety of expressed sequences

The organization of chromosomes into euchromatin and heterochromatin is amongst the most important and enigmatic aspects of genome evolution. Constitutive heterochromatin is a basic yet still poorly understood component of eukaryotic chromosomes, and its molecular characterization by means of standard genomic approaches is intrinsically difficult. Although recent evidence indicates that the presence of transcribed genes in constitutive heterochromatin is a conserved trait that accompanies the evolution of eukaryotic genomes, the term heterochromatin is still considered by many as synonymous of gene silencing. In this paper, we comprehensively review data that provide a clearer picture of transcribed sequences within constitutive heterochromatin, with a special emphasis on Drosophila and humans.

Coding DNA repeated throughout intergenic regions of the Arabidopsis thaliana genome: evolutionary footprints of RNA silencing

Pyknons are non-random sequence patterns significantly repeated throughout non-coding genomic DNA that also appear at least once among coding genes. They are interesting because they portend an unforeseen connection between coding and non-coding DNA. Pyknons have only been discovered in the human genome, so it is unknown whether pyknons have wider biological relevance or are simply a phenomenon of the human genome. To address this, DNA sequence patterns from the Arabidopsis thaliana genome were detected using a probability-based method. 24 654 statistically significant sequence patterns, 16 to 24 nucleotides long, repeating 10 or more times in non-coding DNA also appeared in 46% of A. thaliana protein-coding genes. A. thaliana pyknons exhibit features similar to human pyknons, including being distinct sequence patterns, having multiple instances in genes and having remarkable similarity to small RNA sequences with roles in gene silencing. Chromosomal position mapping revealed that genomic pyknon density has concordance with siRNA and transposable element positioning density. Because the A. thaliana and human genomes have approximately the same number of genes but drastically different amounts of non-coding DNA, these data reveal that pyknons represent a biologically important link between coding and non-coding DNA. Because of the association of pyknons with siRNAs and localization to silenced regions of heterochromatin, we postulate that RNA-mediated gene silencing leads to the accumulation of gene sequences in non-coding DNA regions.

Decoding the epigenetic language of neuronal plasticity

Neurons are submitted to an exceptional variety of stimuli and are able to convert these into high-order functions, such as storing memories, controlling behavior, and governing consciousness. These unique properties are based on the highly flexible nature of neurons, a characteristic that can be regulated by the complex molecular machinery that controls gene expression. Epigenetic control, which largely involves events of chromatin remodeling, appears to be one way in which transcriptional regulation of gene expression can be modified in neurons. This review will focus on how epigenetic control in the mature nervous system may guide dynamic plasticity processes and long-lasting cellular neuronal responses. We outline the molecular pathways underlying chromatin transitions, propose the presence of an "epigenetic indexing code," and discuss how central findings accumulating at an exponential pace in the field of epigenetics are conceptually changing our perspective of adult brain function.

Tackling the epigenome in the pluripotent stem cells

Embryonic stem cells are unique in their abilities of self-renewal and to differentiate into many, if not all, cellular lineages. Transcriptional regulation, epigenetic modifications and chromatin structures are the key modulators in controlling such pluripotency nature of embryonic stem cell genomes, particularly in the developmental decisions and the maintenance of cell fates. Among them, epigenetic regulation of gene expression is mediated partly by covalent modifications of core histone proteins including methylation, phosphorylation and acetylation. Moreover, the chromatins in stem cell genome appear as a highly organized structure containing distinct functional domains. Recent rapid progress of new technologies enables us to take a global, unbiased and comprehensive view of the epigenetic modifications and chromatin structures that contribute to gene expression regulation and cell identity during diverse developmental stages. Here, we summarized the latest advances made by high throughput approaches in profiling epigenetic modifications and chromatin conformations, with an emphasis on genome-wide analysis of histone modifications and their implications in pluripotency nature of embryonic stem cells.

Nested Ty3-gypsy retrotransposons of a single Beta procumbens centromere contain a putative chromodomain

LTR retrotransposons belong to a major group of DNA sequences that are often localized in plant centromeres. Using BAC inserts originating from the centromere of a monosomic wild beet (Beta procumbens) chromosome fragment in Beta vulgaris, two complete LTR retrotransposons were identified. Both elements, designated Beetle1 and Beetle2, possess a coding region with genes in the order characteristic for Ty3-gypsy retrotransposons. Beetle1 and Beetle2 have a chromodomain in the C-terminus of the integrase gene and are highly similar to the centromeric retrotransposons (CRs) of rice, maize, and barley. Both retroelements were localized in the centromeric region of B. procumbens chromosomes by fluorescence in-situ hybridization. They can therefore be classified as centromere-specific chromoviruses. PCR analysis using RNA as template indicated that Beetle1 and Beetle2 are transcriptionally active. On the basis of the sequence diversity between the LTR sequences, it was estimated that Beetle1 and Beetle2 transposed within the last 60,000 years and 130,000 years, respectively. The centromeric localization of Beetle1 and Beetle2 and their transcriptional activity combined with high sequence conservation within each family play an important structural role in the centromeres of B. procumbens chromosomes.

Radiation-induced bystander effects in vivo are epigenetically regulated in a tissue-specific manner

Exposure of animal body parts to ionizing radiation (IR) can lead to molecular changes in distant shielded "bystander" tissues and organs. Nevertheless, tissue specificity of bystander responses within the same organism has not been examined in detail. Studies on in vivo bystander effect conducted so far analyzed changes induced by single-dose exposure. The potential of fractionated irradiation to induce bystander effects in vivo has never been studied. We analyzed changes in global DNA methylation and microRNAome in skin and spleen of animals subjected to single-dose (acute or fractionated) whole-body or cranial exposure to 0.5 Gy of X-rays. We found that IR-induced DNA methylation changes in bystander spleen and skin were distinct. Acute radiation exposure resulted in a significant loss of global DNA methylation in the exposed and bystander spleen 6 hr, 96 hr, and 14 days after irradiation. Fractionated irradiation led to hypomethylation in bystander spleen 6 hr after whole-body exposure, and 6 hr, 96 hr, and 14 days after cranial irradiation. Contrarily, changes in the skin of the same animals were seen only 6 hr after acute whole-body and head exposure. DNA hypomethylation observed in spleen was paralleled by a reduction of methyl-binding protein MeCP2 expression. Irradiation also induced tissue-specific microRNAome alterations in skin and spleen. For the first time, we have shown that IR-induced epigenetic bystander effects that occur in the same organism are triggered by both acute and fractionated exposure and are very distinct in different bystander organs. Future studies are clearly needed to address organismal and carcinogenic repercussions of those changes.

Epigenetic regulation of mammalian stem cells

Two critical properties of stem cells are self-renewal and multipotency. The maintenance of their "stemness" state and commitment to differentiation are therefore tightly controlled by intricate molecular networks. Epigenetic mechanisms, including DNA methylation, chromatin remodeling and the noncoding RNA-mediated process, have profound regulatory roles in mammalian gene expression. Recent studies have shown that epigenetic regulators are key players in stem cell biology and their dysfunction can result in human diseases such as cancer and neurodevelopmental disorders. Here, we review the recent evidences that advance our knowledge in epigenetic regulations of mammalian stem cells, with focus on embryonic stem cells and neural stem cells.

Chromatin condensation in terminally differentiating mouse erythroblasts does not involve special architectural proteins but depends on histone deacetylation

Terminal erythroid differentiation in vertebrates is characterized by progressive heterochromatin formation and chromatin condensation and, in mammals, culminates in nuclear extrusion. To date, although mechanisms regulating avian erythroid chromatin condensation have been identified, little is known regarding this process during mammalian erythropoiesis. To elucidate the molecular basis for mammalian erythroblast chromatin condensation, we used Friend virus-infected murine spleen erythroblasts that undergo terminal differentiation in vitro. Chromatin isolated from early and late-stage erythroblasts had similar levels of linker and core histones, only a slight difference in nucleosome repeats, and no significant accumulation of known developmentally regulated architectural chromatin proteins. However, histone H3(K9) dimethylation markedly increased while histone H4(K12) acetylation dramatically decreased and became segregated from the histone methylation as chromatin condensed. One histone deacetylase, HDAC5, was significantly upregulated during the terminal stages of Friend virus-infected erythroblast differentiation. Treatment with histone deacetylase inhibitor, trichostatin A, blocked both chromatin condensation and nuclear extrusion. Based on our data, we propose a model for a unique mechanism in which extensive histone deacetylation at pericentromeric heterochromatin mediates heterochromatin condensation in vertebrate erythroblasts that would otherwise be mediated by developmentally-regulated architectural proteins in nucleated blood cells.

HP1 proteins form distinct complexes and mediate heterochromatic gene silencing by nonoverlapping mechanisms

HP1 proteins are a highly conserved family of eukaryotic proteins that bind to methylated histone H3 lysine 9 (H3K9) and are required for heterochromatic gene silencing. In fission yeast, two HP1 homologs, Swi6 and Chp2, function in heterochromatic gene silencing, but their relative contribution to silencing remains unknown. Here we show that Swi6 and Chp2 exist in nonoverlapping complexes and make distinct contributions to silencing. Chp2 associates with the SHREC histone deacetylase complex (SHREC2), is required for histone H3 lysine 14 (H3K14) deacetylation, and mediates transcriptional repression by limiting RNA polymerase II access to heterochromatin. In contrast, Swi6 associates with a different set of nuclear proteins and with noncoding centromeric transcripts and is required for efficient RNAi-dependent processing of these transcripts. Our findings reveal an unexpected role for Swi6 in RNAi-mediated gene silencing and suggest that different HP1 proteins ensure full heterochromatic gene silencing through largely nonoverlapping inhibitory mechanisms.

Identification and quantification of protein posttranslational modifications

Posttranslational modifications (PTMs) of proteins perform crucial roles in regulating the biology of the cell. PTMs are enzymatic, covalent chemical modifications of proteins that typically occur after the translation of mRNAs. These modifications are relevant because they can potentially change a protein's physical or chemical properties, activity, localization, or stability. Some PTMs can be added and removed dynamically as a mechanism for reversibly controlling protein function and cell signaling. Extensive investigations have aimed to identify PTMs and characterize their biological functions. This chapter will discuss the existing and emerging techniques in the field of mass spectrometry and proteomics that are available to identify and quantify PTMs. We will focus on the most frequently studied modifications. In addition, we will include an overview of the available tools and technologies in tandem mass spectrometry instrumentation that affect the ability to identify specific PTMs.

The fast chromatin immunoprecipitation method

The chromatin immunoprecipitation assay (ChIP assay) has greatly facilitated the recent, dramatic expansion of our knowledge of the protein-DNA interactions involved in regulating gene expression, DNA repair, and cell division. The power of the assay is that it gives a researcher the ability to not only detect a specific protein-DNA interaction in vivo but also determine the relative density of factors along genes or the entire genome. Though powerful, the traditional assay is time consuming (involving 2 days or more) and laborious. With Fast ChIP, we simplified the assay to greatly reduce the time and labor involved. The improved assay is especially useful for studies which involve many samples, including the probing of multiple chromatin factors simultaneously and/or looking at genomic events over several time points. Using Fast ChIP, 24 sheared chromatin samples can be processed to yield PCR-ready DNA in 5 h.

Centromere-competent DNA: structure and evolution

Although extant data favour centromere being an epigenetic structure, it is also clear that centromere formation is based on DNA, in particular, tandemly repeated satellite DNA and its transcripts. Presence of conserved structural motifs within satellite DNAs such as periodically distributed AT tracts, protein binding sites, or promoter elements indicate that despite sequence flexibility, there are structural determinants that are prerequisite for centromere function. In addition, existence of functional centromeric DNA transcripts indicates possible importance of structural elements at the level of RNA secondary or tertiary structure. Rapid centromere evolution is explained by homologous recombination followed by extrachromosomal rolling circle replication. This could lead to amplification of different satellite sequences within a genome. However, only those satellites that have inherent centromere-competence in the form of structural requirements necessary for centromere function are after amplification fixed in a population as a new centromere.

Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation

Recent investigations have implicated long antisense noncoding RNAs in the epigenetic regulation of chromosomal domains. Here we show that Kcnq1ot1 is an RNA polymerase II-encoded, 91 kb-long, moderately stable nuclear transcript and that its stability is important for bidirectional silencing of genes in the Kcnq1 domain. Kcnq1ot1 interacts with chromatin and with the H3K9- and H3K27-specific histone methyltransferases G9a and the PRC2 complex in a lineage-specific manner. This interaction correlates with the presence of extended regions of chromatin enriched with H3K9me3 and H3K27me3 in the Kcnq1 domain in placenta, whereas fetal liver lacks both chromatin interactions and heterochromatin structures. In addition, the Kcnq1 domain is more often found in contact with the nucleolar compartment in placenta than in liver. Taken together, our data describe a mechanism whereby Kcnq1ot1 establishes lineage-specific transcriptional silencing patterns through recruitment of chromatin remodeling complexes and maintenance of these patterns through subsequent cell divisions occurs via targeting the associated regions to the perinucleolar compartment.

Epigenetic transcriptional gene silencing in Entamoeba histolytica

The human intestinal pathogen Entamoeba histolytica has a number of virulence factors which can cause damage to the host. Transcriptional silencing of the gene coding for one of its major toxic molecules, the amoebapore (Ehap-a), occurred following the transfection of amoebic trophozoites with a plasmid containing the 5' promoter region of Ehap-a as well as a truncated segment of a neighboring, upstream SINE1 element that is transcribed from the opposite strand. Silencing was dependent on the presence of the truncated SINE1 sequences. Small amounts of short (approximately 140 n), ssRNA molecules with homology to SINE1 were detected in the silenced amoeba but no siRNA. The silenced Ehap-a gene domain had a chromatin modification indicating transcriptional inactivation without any DNA methylation. Removal of the plasmid did not restore transcription of Ehap-a. Transcription analysis by microarrays revealed that a number of additional genes were silenced and some were also up-regulated. Transfections of amoeba which already had a silenced Ehap-a, with a plasmid containing a second gene ligated to the 5' upstream region of Ehap-a, enabled the silencing, in-trans, of other genes of choice. The nonvirulent phenotype of the gene-silenced amoeba was demonstrated in various assays and the results suggest that they may have a potential use for vaccination.

Regulation of the mammalian epigenome by long noncoding RNAs

Genomic analyses have demonstrated that although less than 2% of the mammalian genome encodes proteins, at least two thirds is transcribed. Many nontranslated RNAs have now been characterized, and several long transcripts, ranging from 0.5 to over 100 kb, have been shown to regulate gene expression by modifying chromatin structure. Functions uncovered at a few well characterized loci demonstrate a wide diversity of mechanisms by which long noncoding RNAs can regulate chromatin over a single promoter, a gene cluster, or an entire chromosome, in order to activate or silence genes in cis or in trans. In reviewing the activities of these ncRNAs, we will look for common features in their interactions with the chromatin modifying machinery, and highlight new experimental approaches by which to address outstanding issues in ncRNA-dependent regulation of gene expression in development, disease and evolution.

Noncoding RNA in development

Non-protein-coding sequences increasingly dominate the genomes of multicellular organisms as their complexity increases, in contrast to protein-coding genes, which remain relatively static. Most of the mammalian genome and indeed that of all eukaryotes is expressed in a cell- and tissue-specific manner, and there is mounting evidence that much of this transcription is involved in the regulation of differentiation and development. Different classes of small and large noncoding RNAs (ncRNAs) have been shown to regulate almost every level of gene expression, including the activation and repression of homeotic genes and the targeting of chromatin-remodeling complexes. ncRNAs are involved in developmental processes in both simple and complex eukaryotes, and we illustrate this in the latter by focusing on the animal germline, brain, and eye. While most have yet to be systematically studied, the emerging evidence suggests that there is a vast hidden layer of regulatory ncRNAs that constitutes the majority of the genomic programming of multicellular organisms and plays a major role in controlling the epigenetic trajectories that underlie their ontogeny.

Mutually exclusive var gene expression in the malaria parasite: multiple layers of regulation

As a major factor in Plasmodium falciparum malaria pathogenesis, the var gene family has been the focus of extensive research, which has contributed to our current understanding of Plasmodium antigenic variation. In recent years, sophisticated molecular tools have enabled the generation of interesting data regarding the regulation of mutually exclusive var expression. Although their results are still inconclusive, these studies have demonstrated the existence of multiple layers of control over gene activation, silencing, memory and 'counting'. This review attempts to summarize recent findings and dissect the different layers of var regulation.

Integration of cytological features with molecular and epigenetic properties of rice chromosome 4

It has been reported that rice chromosome 4 has eight major heterochromatic knobs within the heterochromatic half and that this organization correlates with chromosomal-level transcriptional activity. To better understand this chromosomal organization, we created a model based on the statistical distribution of various types of gene models to divide chromosome 4 into 17 euchromatic and heterochromatic regions that correspond with the cytological staining. Fluorescence in-situ hybridization (FISH) experiments using a set of bacterial artificial chromosome (BAC) clones from chromosome 4 placed all 18 clones in the region predicted by the model. Elevated levels of H3K4 di- and tri-methylation detected by chromatin-immunoprecipitation (ChIP) on chip were correlated with euchromatic regions whereas lower levels of these two modifications were detected in heterochromatic regions. Small RNAs were more abundant in the heterochromatic regions. To validate these findings, H3K4 trimethylation, H3K9 acetylation, H4K12 acetylation, and H3K9 di- and tri-methylation of 19 individual genes were measured by ChIP-PCR. Genes in heterochromatic regions had elevated H3K9 di- and tri-methylation while genes in euchromatic regions had elevated levels of the other three modifications. We also assayed cytosine methylation of these genes using the restriction enzymes McrBC, HapII, and Msp I. This analysis indicated that cytosines of transposable elements and some genes located in heterochromatic regions were methylated while cytosines of the other genes were unmethylated. These results suggest that local transcriptional activity may reflect the organization of the corresponding part of the chromosome. They also indicate that epigenetic regulation plays an important role in correlating chromosomal organization with transcriptional activity.