High-resolution profiling of histone methylations in the human genome.

Epigenetic mechanisms are essential for normal development and maintenance of tissue-specific gene expression patterns in mammals. Disruption of epigenetic processes can lead to altered gene function and malignant cellular transformation. Global changes in the epigenetic landscape are a hallmark of cancer. The initiation and progression of cancer, traditionally seen as a genetic disease, is now realized to involve epigenetic abnormalities along with genetic alterations. Recent advancements in the rapidly evolving field of cancer epigenetics have shown extensive reprogramming of every component of the epigenetic machinery in cancer including DNA methylation, histone modifications, nucleosome positioning and non-coding RNAs, specifically microRNA expression. The reversible nature of epigenetic aberrations has led to the emergence of the promising field of epigenetic therapy, which is already making progress with the recent FDA approval of three epigenetic drugs for cancer treatment. In this review, we discuss the current understanding of alterations in the epigenetic landscape that occur in cancer compared with normal cells, the roles of these changes in cancer initiation and progression, including the cancer stem cell model, and the potential use of this knowledge in designing more effective treatment strategies.

/pdf/epigenetics-in-cancer-53kplki7aw.pdf

Epigenetics in Cancer

http://www.people.vcu.edu/~mreimers/SysBio/Li%20-%20Role%20of%20chromatin%20in%20transcription.pdf

The Role of Chromatin during Transcription

'The amino termini of histones extend from the nucleosomal core and are modified by acetyltransferases and deacetylases during the cell cycle These acetylation patterns may direct histone assembly and help regulate the unfolding and activity of genes

Histone acetylation in chromatin structure and transcription

Eukaryotic genomes are packaged into nucleosome particles that occlude the DNA from interacting with most DNA binding proteins. Nucleosomes have higher affinity for particular DNA sequences, reflecting the ability of the sequence to bend sharply, as required by the nucleosome structure. However, it is not known whether these sequence preferences have a significant influence on nucleosome position in vivo, and thus regulate the access of other proteins to DNA. Here we isolated nucleosome-bound sequences at high resolution from yeast and used these sequences in a new computational approach to construct and validate experimentally a nucleosome–DNA interaction model, and to predict the genome-wide organization of nucleosomes. Our results demonstrate that genomes encode an intrinsic nucleosome organization and that this intrinsic organization can explain ∼50% of the in vivo nucleosome positions. This nucleosome positioning code may facilitate specific chromosome functions including transcription factor binding, transcription initiation, and even remodelling of the nucleosomes themselves.

http://absimage.aps.org/image/MAR08/MWS_MAR08-2008-020581.pdf

The Genomic Code for Nucleosome Positioning

H2A.Z is an evolutionary conserved histone variant involved in transcriptional regulation, antisilencing, silencing, and genome stability. The mechanism(s) by which H2A.Z regulates these various biological functions remains poorly defined, in part due to the lack of knowledge regarding its physical location along chromosomes and the bearing it has in regulating chromatin structure. Here we mapped H2A.Z across the yeast genome at an approximately 300-bp resolution, using chromatin immunoprecipitation combined with tiling microarrays. We have identified 4,862 small regions—typically one or two nucleosomes wide—decorated with H2A.Z. Those “Z loci” are predominantly found within specific nucleosomes in the promoter of inactive genes all across the genome. Furthermore, we have shown that H2A.Z can regulate nucleosome positioning at the GAL1 promoter. Within HZAD domains, the regions where H2A.Z shows an antisilencing function, H2A.Z is localized in a wider pattern, suggesting that the variant histone regulates a silencing and transcriptional activation via different mechanisms. Our data suggest that the incorporation of H2A.Z into specific promoter-bound nucleosomes configures chromatin structure to poise genes for transcriptional activation. The relevance of these findings to higher eukaryotes is discussed.

/pdf/variant-histone-h2a-z-is-globally-localized-to-the-promoters-ybj4x6ibel.pdf

Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning.

Eukaryotic DNA is condensed many fold (e.g., 10,000) into chromatin, the basic unit of which contains 146 base pairs (bp) of DNA and an octamer of histone proteins (H2A, H2B, H3, and H4). Due to the high level of compaction, chromatin typically represses certain cellular DNA transactions, including transcription. For successful transcription, it is argued that nucleosomes need to be remodeled or evicted from promoter regions for the transcriptional machinery to be efficiently recruited to a target gene.

The incorporation of histone variants into specific nucleosomes within a promoter region constitutes a mechanism by which promoter region chromatin can become more permissive to transcription initiation and elongation following receipt of a proper physiological cue. One such histone variant is H2A.Z. In Saccharomyces cerevisiae, it can elicit positive effects on gene expression (Santisteban et al. 2000; Adam et al. 2001; Larochelle and Gaudreau 2003). In addition, H2A.Z regulates genes that are proximal to telomeres and acts as a “buffer” to antagonize the spread of heterochromatin into euchromatic regions (Meneghini et al. 2003). Furthermore, recent reports from our laboratory and others (Guillemette et al. 2005; Li et al. 2005; Raisner et al. 2005; Zhang et al. 2005) have shown that H2A.Z is preferentially localized within a few nucleosomes of the initiator regions of multiple promoters in the yeast genome. Interestingly, these H2A.Z-rich loci are largely devoid of transcriptional activity, which suggests that the variant histone prepares genes for activation (Guillemette et al. 2005) and/or operates as a transcriptional repressor. Finally, yeast H2A.Z was shown to regulate nucleosome positioning, which provides mechanistic insight into how its presence can alter promoter transcriptional state (Guillemette et al. 2005).

An ATP-dependent chromatin remodeling complex that specifically loads H2A.Z onto chromatin and exchanges it with H2A exists in yeast (Krogan et al. 2003; Kobor et al. 2004; Mizuguchi et al. 2004). This complex, in which the catalytic subunit is Swr1, also shares essential subunits with the NuA4 histone acetyltransferase complex (Krogan et al. 2003; Kobor et al. 2004). In addition to their importance in gene regulation, the Swr1 complex, H2A.Z, and NuA4 are all involved in the regulation of yeast chromosome stability (Krogan et al. 2004). This is noteworthy because, in mammalian cells, depletion of H2A.Z causes major nuclear and chromosomal abnormalities as witnessed by a high incidence of lagging chromosomes and chromatin bridges (Rangasamy et al. 2004).

There are two homologs of Swr1 in human cells: p400/Domino (herein referred to as p400), and SRCAP (Doyon and Cote 2004; Jin et al. 2005). There are also three uncharacterized p400-type SWI2–SNF2 molecules, including hIno80 (Bakshi et al. 2006). Members of this family of SWI2/SNF2 chromatin remodeling enzymes each contain a spacer region inserted into the SWI2/SNF2 homology region (Smith and Peterson 2005).

p400 was originally isolated as an E1A-associated protein (Fuchs et al. 2001), and it was also shown to interact with p53, Myc, and SV40 large T antigen (Chan et al. 2005). It is also required for E1A to induce p53-mediated apoptosis (Samuelson et al. 2005). SRCAP has been isolated as a CREB-binding protein (Johnston et al. 1999). While one report shows that both p400 and SRCAP constitute part of the same complex (Doyon et al. 2004), a recent study shows that SRCAP and p400 exist in distinct complexes with H2A.Z (Cai et al. 2005; Ruhl et al. 2006). Recently an SRCAP-containing complex was purified, and it was shown to have the ability to exchange H2A–H2B for H2A.Z–H2B in reconstituted mononucleosomes (Ruhl et al. 2006). It remains to be determined whether mammalian homolog(s) of Swr1, such as p400 and SRCAP, also catalyze H2A.Z deposition in vivo.

Depletion of p400 elevates p21 synthesis to initiate premature senescence in primary human fibroblasts (Chan et al. 2005). Senescence was first observed in tissue culture cells as a stable form of cell growth arrest provoked by diverse stresses (Hayflick and Moorhead 1961; Sharpless and DePinho 2005). Recently, oncogene-induced senescence was shown to occur in various precancerous lesions both in humans and mice (Braig et al. 2005; Chen et al. 2005; Collado et al. 2005; Michaloglou et al. 2005), further suggesting that senescence acts as a defense mechanism against malignant cell development (Sager 1991; Hanahan and Weinberg 2000). Importantly, the action of p400 at p21 depends on the function of p53, a key regulator of p21 transcription (el-Deiry et al. 1993).

Given the possibility of a link between p400 and H2A.Z, we questioned whether H2A.Z is also an important regulator of p21 expression. The results of this effort show that H2A.Z depletion induces p21 expression in a p53-dependent fashion, as well as the premature senescence of primary diploid fibroblasts. Similar to senescence induced by p400 depletion, inactivating p53 or p21 blocked the emergence of certain senescent phenotypes following H2A.Z depletion. In a normal setting, H2A.Z is highly enriched at discrete p53-binding sites that lie within the p21 promoter. This distinctive localization pattern depends on the presence of p53, and was detected at other p53 target gene promoters as well. The presence of p400 is required to localize H2A.Z at those loci, and purified recombinant p400 from insect cells can carry out in vitro exchange of H2A.Z–H2B dimers into chromatin. H2A.Z and p400 localization at the p53-binding sites in p21 was severely diminished following p21 induction, and this process was not dependent on active p21 transcription per se. After H2A.Z and p400 eviction from the p53-binding sites in p21, we observed that the Tip60 histone acetyltransferase had been recruited to the distal p53-binding site in the promoter to positively regulate p21 expression. Finally, overexpression of Myc, a known suppressor of p21 synthesis, significantly increased H2A.Z localization at the Myc-binding site in the TATA initiator region of the p21 promoter. This observation is consistent with the view that Myc represses p21 expression by preferentially recruiting H2A.Z-containing nucleosome(s) to this element.

http://genesdev.cshlp.org/content/21/15/1869.full.pdf

p21 transcription is regulated by differential localization of histone H2A.Z.

Evolutionarily conserved variant histone H2A.Z has been recently shown to regulate gene transcription in Saccharomyces cerevisiae. Here we show that loss of H2A.Z in this organism negatively affects the induction of GAL genes. Importantly, fusion of the H2A.Z C-terminal region to S phase H2A without its corresponding C-terminal region can mediate the variant histone's specialized function in GAL1-10 gene induction, and it restores the slow-growth phenotype of cells with a deletion of HTZ1. Furthermore, we show that the C-terminal region of H2A.Z can interact with some components of the transcriptional apparatus. In cells lacking H2A.Z, recruitment of RNA polymerase II and TATA-binding protein to the GAL1-10 promoters is significantly diminished under inducing conditions. Unexpectedly, we also find that H2A.Z is required to globally maintain chromatin integrity under GAL gene-inducing conditions. We hypothesize that H2A.Z can positively regulate gene transcription, at least in part, by modulating interactions with RNA polymerase II-associated factors at certain genes under specific cell growth conditions.

H2A.Z Is Required for Global Chromatin Integrity and for Recruitment of RNA Polymerase II under Specific Conditions

Tuberculosis remains a worldwide threat despite the availability of the BCG vaccine and antibiotic treatment. It is estimated that its etiologic agent, Mycobacterium tuberculosis , infects almost a third of the human population and kills two million people every year ([27][1]). The recent human

σ Factors and Global Gene Regulation in Mycobacterium tuberculosis

Mycobacterium tuberculosis is a remarkable pathogen capable of adapting and surviving in various harsh conditions. Correct gene expression regulation is essential for the success of this process. The reversible association of different σ factors is a common mechanism for reprogramming bacterial RNA polymerase and modulating the transcription of numerous genes. Thirteen putative σ factors are encoded in the M. tuberculosis genome, several being important for virulence. Here, we analyse the latest information available on mycobacterial σ factors and discuss their roles in the physiology and virulence of M. tuberculosis.

Luc Gaudreau

Papers

Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning.

p21 transcription is regulated by differential localization of histone H2A.Z.

H2A.Z Is Required for Global Chromatin Integrity and for Recruitment of RNA Polymerase II under Specific Conditions

σ Factors and Global Gene Regulation in Mycobacterium tuberculosis

The σ factors of Mycobacterium tuberculosis