Molecular architecture of human polycomb repressive complex 2.

Polycomb Repressive Complex 2 (PRC2) is essential for gene silencing, establishing transcriptional repression of specific genes by tri-methylating Lysine 27 of histone H3, a process mediated by cofactors such as AEBP2. In spite of its biological importance, little is known about PRC2 architecture and subunit organization. Here, we present the first three-dimensional electron microscopy structure of the human PRC2 complex bound to its cofactor AEBP2. Using a novel internal protein tagging-method, in combination with isotopic chemical cross-linking and mass spectrometry, we have localized all the PRC2 subunits and their functional domains and generated a detailed map of interactions. The position and stabilization effect of AEBP2 suggests an allosteric role of this cofactor in regulating gene silencing. Regions in PRC2 that interact with modified histone tails are localized near the methyltransferase site, suggesting a molecular mechanism for the chromatin-based regulation of PRC2 activity.DOI:http://dx.doi.org/10.7554/eLife.00005.001

EZH2 RIP-seq Identifies Tissue-specific Long Non-coding RNAs.

BackgroundPolycomb Repressive Complex 2 (PRC2) catalyzes histone methylation at H3 Lys27, and plays crucial roles during development and diseases in numerous systems. Its catalytic subunit EZH2 represents a key nuclear target for long non-coding RNAs (lncRNAs) that emerging to be a novel class of epigenetic regulator and participate in diverse cellular processes. LncRNAs are characterized by high tissue-specificity; however, little is known about the tissue profile of the EZH2- interacting lncRNAs.ObjectiveHere we performed a global screening for EZH2-binding lncRNAs in tissues including brain, lung, heart, liver, kidney, intestine, spleen, testis, muscle and blood by combining RNA immuno- precipitation and RNA sequencing. We identified 1328 EZH2-binding lncRNAs, among which 470 were shared in at least two tissues while 858 were only detected in single tissue. An RNA motif with specific secondary structure was identified in a number of lncRNAs, albeit not in all EZH2-binding lncRNAs. The EZH2-binding lncRNAs fell into four categories including intergenic lncRNA, antisense lncRNA, intron-related lncRNA and promoter-related lncRNA, suggesting diverse regulations of both cis and trans-mechanisms. A promoter-related lncRNA Hnf1aos1 bound to EZH2 specifically in the liver, a feature same as its paired coding gene Hnf1a, further confirming the validity of our study. In addition to the well known EZH2-binding lncRNAs like Kcnq1ot1, Gas5, Meg3, Hotair and Malat1, majority of the lncRNAs were firstly reported to be associated with EZH2.ConclusionOur findings provide a profiling view of the EZH2-interacting lncRNAs across different tissues, and suggest critical roles of lncRNAs during cell differentiation and maturation

Role of enhancer of zeste homolog 2 polycomb protein and its significance in tumor progression and cell differentiation

Epigenetics is a branch of genetics that focuses on the heritable changes of DNA or associated proteins, other than DNA sequence variations, which carry information content during cell division [1,2]. These heritable changes are ascribed to chromatin, which constitutes the ultrastructure of DNA and whose modifications affect the genetic material functionality. Differences in chromatin structure have been associated to transcription regulation [3-5] and chromosome stability [6,7], affecting both gene’s information, expression and heritability. Noteworthy, these epigenetic modifications are involved in both transcriptional activation and repression, indicating their widespread role as modulators of gene expression in numerous biological processes [8,9]. Chromatin is subjected to numerous modifications roughly classified in two groups: DNA and histone post-translational modifications (histone-PTMs). DNA methylation is the most studied epigenetic modification of DNA and corresponds to the covalent addition of a methyl (CH3) group to the nucleotide cytosine within CG dinucleotides or CNG trinucleotides where N can be C, A, G or T. Usually, DNA methylation induces decreased protein-DNA binding of transcription factors and leads to the repression of gene expression [10]. DNA “methylable” sequences are not uniform across the human genome but restricted in CpG rich DNA regions termed CpG islands (CGI). CGI are localized at repetitive sequences, heavy methylated, to prevent the reactivation of endoparasitic sequences such as transposons, and at gene promoter sequences, which are normally refractory to methylation in normal somatic cells [8,11].</br

Biphasic euchromatin-to-heterochromatin transition on the KSHV genome following de novo infection.

The establishment of latency is an essential step for the life-long persistent infection and pathogenesis of Kaposi's sarcoma-associated herpesvirus (KSHV). While the KSHV genome is chromatin-free in the virions, the viral DNA in latently infected cells has a chromatin structure with activating and repressive histone modifications that promote latent gene expression but suppress lytic gene expression. Here, we report a comprehensive epigenetic study of the recruitment of chromatin regulatory factors onto the KSHV genome during the pre-latency phase of KSHV infection. This demonstrates that the KSHV genome undergoes a biphasic chromatinization following de novo infection. Initially, a transcriptionally active chromatin (euchromatin), characterized by high levels of the H3K4me3 and acetylated H3K27 (H3K27ac) activating histone marks, was deposited on the viral episome and accompanied by the transient induction of a limited number of lytic genes. Interestingly, temporary expression of the RTA protein facilitated the increase of H3K4me3 and H3K27ac occupancy on the KSHV episome during de novo infection. Between 24-72 hours post-infection, as the levels of these activating histone marks declined on the KSHV genome, the levels of the repressive H3K27me3 and H2AK119ub histone marks increased concomitantly with the decline of lytic gene expression. Importantly, this transition to heterochromatin was dependent on both Polycomb Repressive Complex 1 and 2. In contrast, upon infection of human gingiva-derived epithelial cells, the KSHV genome underwent a transcription-active euchromatinization, resulting in efficient lytic gene expression. Our data demonstrate that the KSHV genome undergoes a temporally-ordered biphasic euchromatin-to-heterochromatin transition in endothelial cells, leading to latent infection, whereas KSHV preferentially adopts a transcriptionally active euchromatin in oral epithelial cells, resulting in lytic gene expression. Our results suggest that the differential epigenetic modification of the KSHV genome in distinct cell types is a potential determining factor for latent infection versus lytic replication of KSHV

Coordinated actions of microRNAs with other epigenetic factors regulate skeletal muscle development and adaptation

Epigenetics plays a pivotal role in regulating gene expression in development, in response to cellular stress or in disease states, in virtually all cell types. MicroRNAs (miRNAs) are short, non-coding RNA molecules that mediate RNA silencing and regulate gene expression. miRNAs were discovered in 1993 and have been extensively studied ever since. They can be expressed in a tissue-specific manner and play a crucial role in tissue development and many biological processes. miRNAs are responsible for changes in the cell epigenome because of their ability to modulate gene expression post-transcriptionally. Recently, numerous studies have shown that miRNAs and other epigenetic factors can regulate each other or cooperate in regulating several biological processes. On the one hand, the expression of some miRNAs is silenced by DNA methylation, and histone modifications have been demonstrated to modulate miRNA expression in many cell types or disease states. On the other hand, miRNAs can directly target epigenetic factors, such as DNA methyltransferases or histone deacetylases, thus regulating chromatin structure. Moreover, several studies have reported coordinated actions between miRNAs and other epigenetic mechanisms to reinforce the regulation of gene expression. This paper reviews multiple interactions between miRNAs and epigenetic factors in skeletal muscle development and in response to stimuli or disease

Targeting of polycombs to DNA in EMT

We here describe the conceptual advance provided by the study by Battistelli and coworkers (PMID: 27452518), that shed light on a molecular mechanism of Polycomb targeting in the biological process known as Epithelial-to-Mesenchymal Transition (EMT). In this paper, different working hypotheses of how EZH2 gets to its genomic targets have been reconciled and a new paradigm of function for a lncRNA is highlighted. The interest may also arise from the clarification of the role of a lncRNA as a new molecular player in EMT regulation. This evidence holds promise for the development of novel therapeutic targets in carcinoma progression

The Snail repressor recruits EZH2 to specific genomic sites through the enrollment of the lncRNA HOTAIR in epithelial-to-mesenchymal transition

The transcription factor Snail is a master regulator of cellular identity and epithelial-to-mesenchymal transition (EMT) directly repressing a broad repertoire of epithelial genes. How chromatin modifiers instrumental to its activity are recruited to Snail-specific binding sites is unclear. Here we report that the long non-coding RNA (lncRNA) HOTAIR (for HOX Transcript Antisense Intergenic RNA) mediates a physical interaction between Snail and enhancer of zeste homolog 2 (EZH2), an enzymatic subunit of the polycomb-repressive complex 2 and the main writer of chromatin-repressive marks. The Snail-repressive activity, here monitored on genes with a pivotal function in epithelial and hepatic morphogenesis, differentiation and cell-type identity, depends on the formation of a tripartite Snail/HOTAIR/EZH2 complex. These results demonstrate an lncRNA-mediated mechanism by which a transcriptional factor conveys a general chromatin modifier to specific genes, thereby allowing the execution of hepatocyte transdifferentiation; moreover, they highlight HOTAIR as a crucial player in the Snail-mediated EMT.Oncogene advance online publication, 25 July 2016; doi:10.1038/onc.2016.260

From Linear Genes to Epigenetic Inheritance of Three-dimensional Epigenomes

Fifty years ago Jacob and Monod reported their findings on the regulation of gene activity. Working on lambda bacteriophage lysogeny and the regulation of the production of an enzyme that cleaves lactose, they observed that its production was induced by the presence of lactose in the medium and came to general conclusions about gene expression that still hold true today. Thanks to decades of intense multidisciplinary research, these conclusions have been extended by several fundamental discoveries. In particular, gene regulatory circuits include the ability to propagate the memory of a specific gene regulatory state long after being established and even when the original inducer is no longer present. Furthermore, in addition to being regulated by binding of regulators such as RNAs or proteins in the vicinity of the site of transcription initiation, genes can be regulated by factor binding at incredible distances from their transcriptional start sites. Prominent among the regulatory components involved in these processes are Polycomb and Trithorax group proteins, pleiotropic gene regulators of critical importance in development, physiology and disease