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

Eukaryotic genomes are organized into domains containing individual genes and gene clusters that have distinct patterns of expression both during development and in differentiated cells. These genomes contain regulatory elements such as enhancers that are able to activate target genes in cis over considerable distances. They may also contain extended regions of condensed chromatin capable of encroaching on adjacent domains to perturb gene expression. There are a number of ways in which individual domains could be maintained independent of their surroundings through the establishment of boundaries. These boundaries might be variable in position, and established through a balance between countervail

/pdf/insulators-many-functions-many-mechanisms-q3lgryqg31.pdf

Insulators: many functions, many mechanisms

Insulators are DNA sequence elements that prevent inappropriate interactions between adjacent chromatin domains. One type of insulator establishes domains that separate enhancers and promoters to block their interaction, whereas a second type creates a barrier against the spread of heterochromatin. Recent studies have provided important advances in our understanding of the modes of action of both types of insulator. These new insights also suggest that the mechanisms of action of both enhancer blockers and barriers might not be unique to these types of element, but instead are adaptations of other gene-regulatory mechanisms.

/pdf/insulators-exploiting-transcriptional-and-epigenetic-40hca3r7sk.pdf

Insulators: exploiting transcriptional and epigenetic mechanisms

Methylation of histones at specific residues plays an important role in transcriptional regulation. Chromatin immunoprecipitation of dimethylated lysine 9 on histone H3 across 53 kilobases of the chicken β-globin locus during erythropoiesis shows an almost complete anticorrelation between regions of elevated lysine 9 methylation and acetylation. Lysine 9 is methylated most over constitutive condensed chromatin and developmentally inactive globin genes. In contrast, lysine 4 methylation of histone H3 correlates with H3 acetylation. These results lead us to propose a mechanism by which the insulator in the β-globin locus can protect the globin genes from being silenced by adjacent condensed chromatin.

/pdf/correlation-between-histone-lysine-methylation-and-577idc916f.pdf

Correlation Between Histone Lysine Methylation and Developmental Changes at the Chicken β-Globin Locus

The 1.2-kb DNA sequence element (5′HS4) at the 5′ end of the chicken β-globin locus has the two defining properties of an insulator: it prevents an “external” enhancer from acting on a promoter when placed between them (“enhancer blocking”) and acts as a barrier to chromosomal position effect (CPE) when it surrounds a stably integrated reporter. We previously reported that a single CTCF-binding site in 5′HS4 is necessary and sufficient for enhancer blocking. We show here that a 250-bp “core” element from within 5′HS4 is sufficient to confer protection against silencing of transgenes caused by CPE. Further dissection of the core reveals that 5′HS4 is a compound element in which it is possible to separate enhancer blocking and barrier activities. We demonstrate that full protection against CPE is conferred by mutant 5′HS4 sequences from which the CTCF-binding site has been deleted. In contrast, mutations of four other protein binding sites within 5′HS4 result in varying reductions in the ability to protect against CPE. We find that binding sites for CTCF are neither necessary nor sufficient for protection against CPE. Comparison of the properties of 5′HS4 with those of other CTCF-binding enhancer-blocking elements suggests that CPE protection is associated with maintenance of a high level of histone acetylation near the insulator, conferred by insulator binding-proteins other than CTCF.

Position-effect protection and enhancer blocking by the chicken β-globin insulator are separable activities

Insulators are DNA sequence elements that can serve in some cases as barriers to protect a gene against the encroachment of adjacent inactive condensed chromatin. Some insulators also can act as blocking elements to protect against the activating influence of distal enhancers associated with other genes. Although most of the insulators identified so far derive from Drosophila, they also are found in vertebrates. An insulator at the 5′ end of the chicken β-globin locus marks a boundary between an open chromatin domain and a region of constitutively condensed chromatin. Detailed analysis of this element shows that it possesses both enhancer blocking activity and the ability to screen reporter genes against position effects. Enhancer blocking is associated with binding of the protein CTCF; sites that bind CTCF are found at other critical points in the genome. Protection against position effects involves other properties that appear to be associated with control of histone acetylation and methylation. Insulators thus are complex elements that can help to preserve the independent function of genes embedded in a genome in which they are surrounded by regulatory signals they must ignore.

/pdf/the-insulation-of-genes-from-external-enhancers-and-42lfp2gw9d.pdf

Miklos Gaszner

Papers

Insulators: many functions, many mechanisms

Insulators: exploiting transcriptional and epigenetic mechanisms

Correlation Between Histone Lysine Methylation and Developmental Changes at the Chicken β-Globin Locus

Position-effect protection and enhancer blocking by the chicken β-globin insulator are separable activities

The insulation of genes from external enhancers and silencing chromatin