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

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

This article reviews the mechanisms of gene silencing in cancer and clinical applications of this phenomenon. The silencing of genes, especially tumor-suppressor genes, is a key event in the development of cancer. The silencing can be effected by a disabling mutation or by a shutting down of the promoter region, the site at which transcription of the gene begins.

Gene Silencing in Cancer in Association with Promoter Hypermethylation

https://www.chem.uwec.edu/Chem412_S05/Pages/presentations/giesemc/Shi_et_al_2004.pdf

Histone demethylation mediated by the nuclear amine oxidase homolog lsd1

DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers and locus control regions. Here we present the first extensive map of human DHSs identified through genome-wide profiling in 125 diverse cell and tissue types. We identify ∼2.9 million DHSs that encompass virtually all known experimentally validated cis-regulatory sequences and expose a vast trove of novel elements, most with highly cell-selective regulation. Annotating these elements using ENCODE data reveals novel relationships between chromatin accessibility, transcription, DNA methylation and regulatory factor occupancy patterns. We connect ∼580,000 distal DHSs with their target promoters, revealing systematic pairing of different classes of distal DHSs and specific promoter types. Patterning of chromatin accessibility at many regulatory regions is organized with dozens to hundreds of co-activated elements, and the transcellular DNase I sensitivity pattern at a given region can predict cell-type-specific functional behaviours. The DHS landscape shows signatures of recent functional evolutionary constraint. However, the DHS compartment in pluripotent and immortalized cells exhibits higher mutation rates than that in highly differentiated cells, exposing an unexpected link between chromatin accessibility, proliferative potential and patterns of human variation. An extensive map of human DNase I hypersensitive sites, markers of regulatory DNA, in 125 diverse cell and tissue types is described; integration of this information with other ENCODE-generated data sets identifies new relationships between chromatin accessibility, transcription, DNA methylation and regulatory factor occupancy patterns. This paper describes the first extensive map of human DNaseI hypersensitive sites — markers of regulatory DNA — in 125 diverse cell and tissue types. Integration of this information with other data sets generated by ENCODE (Encyclopedia of DNA Elements) identified new relationships between chromatin accessibility, transcription, DNA methylation and regulatory-factor occupancy patterns. Evolutionary-conservation analysis revealed signatures of recent functional constraint within DNaseI hypersensitive sites.

/pdf/the-accessible-chromatin-landscape-of-the-human-genome-2cq94d4b48.pdf

The accessible chromatin landscape of the human genome

Recruitment of Histone Modifications by USF Proteins at a Vertebrate Barrier Element

Although it is now well-established that boundary elements/insulators function to subdivide eukaryotic chromosomes into autonomous regulatory domains, the underlying mechanisms remain elusive. One idea is that boundaries act as barriers, preventing the processive spreading of "active" or "silenced" chromatin between domains. Another is that the partitioning into autonomous functional units is a consequence of an underlying structural subdivision of the chromosome into higher order "looped" domains. In this view, boundaries are thought to delimit structural domains by interacting with each other or with some other nuclear structure. The studies reported here provide support for the looped domain model. We show that the Drosophila scs and scs' boundary proteins, Zw5 and BEAF, respectively, interact with each other in vitro and in vivo. Moreover, consistent with idea that this protein:protein interaction might facilitate pairing of boundary elements, we find that that scs and scs' are in close proximity to each other in Drosophila nuclei.

/pdf/protein-protein-interactions-and-the-pairing-of-boundary-wqyocckgi9.pdf

Protein:protein interactions and the pairing of boundary elements in vivo.

The scs and scs′ elements were proposed to function as chromatin domain boundaries for the 87A7 heat shock locus in Drosophila melanogaster. Here we report the identification and characterization of SBP (scs binding protein), a component of the scs nucleoprotein complex. SBP binds specifically to a 24-bp region of scs in vitro and is associated with scs in vivo. Multiple copies of an oligonucleotide containing the SBP recognition sequence are capable of blocking enhancer–promoter interactions in transgene assays. Mutations in the oligonucleotide that disrupt SBP binding in vitro also eliminate enhancer-blocking activity in vivo. We show that SBP is encoded by the zeste-white 5 gene and that mutations in zeste-white 5 reduce the enhancer-blocking activity of the multimerized oligonucleotides.

/pdf/the-zw5-protein-a-component-of-the-scs-chromatin-domain-4sclojyldv.pdf

The Zw5 protein, a component of the scs chromatin domain boundary, is able to block enhancer–promoter interaction

There is growing consensus that genome organization and long-range gene regulation involves partitioning of the genome into domains of distinct epigenetic chromatin states. Chromatin insulator or barrier elements are key components of these processes as they can establish boundaries between chromatin states. The ability of elements such as the paradigm β-globin HS4 insulator to block the range of enhancers or the spread of repressive histone modifications is well established. Here we have addressed the hypothesis that a barrier element in vertebrates should be capable of defending a gene from silencing by DNA methylation. Using an established stable reporter gene system, we find that HS4 acts specifically to protect a gene promoter from de novo DNA methylation. Notably, protection from methylation can occur in the absence of histone acetylation or transcription. There is a division of labor at HS4; the sequences that mediate protection from methylation are separable from those that mediate CTCF-dependent enhancer blocking and USF-dependent histone modification recruitment. The zinc finger protein VEZF1 was purified as the factor that specifically interacts with the methylation protection elements. VEZF1 is a candidate CpG island protection factor as the G-rich sequences bound by VEZF1 are frequently found at CpG island promoters. Indeed, we show that VEZF1 elements are sufficient to mediate demethylation and protection of the APRT CpG island promoter from DNA methylation. We propose that many barrier elements in vertebrates will prevent DNA methylation in addition to blocking the propagation of repressive histone modifications, as either process is sufficient to direct the establishment of an epigenetically stable silent chromatin state.

/pdf/vezf1-elements-mediate-protection-from-dna-methylation-1ab9ngayau.pdf

VEZF1 elements mediate protection from DNA methylation.

Insulator elements were first described in Drosophila, but subsequent studies have shown that they are present in vertebrates as well (for review, see West et al. 2002). Over the past several years we have focused our attention on the properties of an insulator at the 5end of the chicken β-globin locus that has begun to provide an understanding of how such elements function. This work, as well as studies in other laboratories, has revealed that there are two distinct kinds of insulator activities, which are different in their function. The first of these is the en-hancer-blocking activity, which can prevent interaction between a distal enhancer and a promoter when placed between them (Fig. 1A). This has the effect of preventing an incorrect interaction between regulatory elements in adjacent, but separately regulated, gene systems. The second insulator function is connected with barrier activity, which prevents condensed heterochromatin from extending into adjacent chromatin domains carrying transcrip-tionally active genes (Fig. 1B). The chicken β-globin locus extends over 30 kb. It contains four members of the globin gene family, with different programs of expression during development (Fig. 2), which have been studied extensively (Felsenfeld 1993). Strong positive regulatory elements, components of the locus control region (LCR), are distributed both upstream of the gene cluster and within it. Further upstream is a DNase I " hypersensitive site, " 5´HS4, which, unlike others in the locus, is not erythroid-specific, but is nucle-ase sensitive in all cells that have been tested (Reitman and Felsenfeld 1990). It seemed an attractive possibility that this marked the 5end of the open chromatin domain; in fact, it was shown not long afterward that immediately upstream of 5´HS4 there is an abrupt decrease of nucle-ase sensitivity and histone acetylation in globin-expressing cells, consistent with a transition from the open chro-matin of the globin locus to a more inactive, condensed chromatin structure (Hebbes et al. 1994). We explored the possibility that this element might have the properties of an insulator (Chung et al. 1997).

/pdf/chromatin-boundaries-and-chromatin-domains-ziro039vtl.pdf

Miklos Gaszner

Papers

Recruitment of Histone Modifications by USF Proteins at a Vertebrate Barrier Element

Protein:protein interactions and the pairing of boundary elements in vivo.

The Zw5 protein, a component of the scs chromatin domain boundary, is able to block enhancer–promoter interaction

VEZF1 elements mediate protection from DNA methylation.

Chromatin Boundaries and Chromatin Domains