Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Dual readout of two histone modifications at the same time with synthetic recombinant proteins reveals H3K36me3-H3K9me3 bivalency at weakly transcribed genes

ABSTRACT: In this proof-of-principle approach we have successfully applied a recombinant heterotypic histone modification interacting domain (HiMID) against H3K9me3 and H3K36me2/3 by using AND logic. We discovered that this new bivalent state is associated with the bodies of weakly transcribed genes and enhancers. Further, we also uncovered that this dual state is enriched in zinc finger coding genes and most likely connected to the zinc finger-Trim28-SetDB1 pathway.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Homo sapiens

SUBMITTER: Goran Kungulovski

PROVIDER: E-MTAB-4216 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Application of dual reading domains as novel reagents in chromatin biology reveals a new H3K9me3 and H3K36me2/3 bivalent chromatin state.

Mauser Rebekka R Kungulovski Goran G Keup Corinna C Reinhardt Richard R Jeltsch Albert A

Epigenetics & chromatin 20170925 1

<h4>Background</h4>Histone post-translational modifications (PTMs) play central roles in chromatin-templated processes. Combinations of two or more histone PTMs form unique interfaces for readout and recruitment of chromatin interacting complexes, but the genome-wide mapping of coexisting histone PTMs remains an experimentally difficult task.<h4>Results</h4>We introduce here a novel type of affinity reagents consisting of two fused recombinant histone modification interacting domains (HiMIDs) fo ...[more]

PMID: 28946896

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Project description:Only a small percentage of human transcription factors (e.g. those associated with a specific differentiation program) are expressed in a given cell type. Thus, cell fate is mainly determined by cell type-specific silencing of transcription factors that drive different cellular lineages. Several histone modifications have been associated with gene silencing, including H3K27me3 and H3K9me3. We have previously shown that the two largest classes of mammalian transcription factors are marked by distinct histone modifications; homeobox genes are marked by H3K27me3 and zinc finger genes are marked by H3K9me3. Several histone methyltransferases (e.g. G9a and SETDB1) may be involved in mediating the H3K9me3 silencing mark. We have used ChIP-chip (GSE24480) and ChIP-seq to demonstrate that SETDB1, but not G9a, is associated with regions of the genome enriched for H3K9me3. A current model is that SETDB1 is recruited to specific genomic locations via interaction with the corepressor TRIM28 (KAP1), which is in turn recruited to the genome via interaction with zinc finger transcription factors that contain a Kruppel-associated box (KRAB) domain. However, specific KRAB-ZNFs that recruit TRIM28 (KAP1) and SETDB1 to the genome have not been identified. We now show that ZNF274 (a KRAB-ZNF that contains 5 C2H2 zinc finger domains), can interact with KAP1 in vitro and, using ChIP-seq, we show that ZNF274 binding sites co-localize with SETDB1, KAP1, and H3K9me3 at the 3’ ends of zinc finger genes. Knockdown of ZNF274 with siRNAs reduced the levels of KAP1 and SETDB1 recruitment to the binding sites. These studies provide the first identification of a KRAB domain-containing ZNFs that is involved in recruitment of the KAP1 and SETDB1 to the human genome. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf 7 total ChIP-seq datasets; 4 ZNF274 datasets done in duplicate from 4 different cell lines; 1 KAP1 duplicate dataset done in duplicate from K562 cells; 1 SetDB1 duplicate dataset from K562 cells; 1 H3K9me3 duplicate dataset from K562 cells

Dataset Information

Dual readout of two histone modifications at the same time with synthetic recombinant proteins reveals H3K36me3-H3K9me3 bivalency at weakly transcribed genes

Publications

Application of dual reading domains as novel reagents in chromatin biology reveals a new H3K9me3 and H3K36me2/3 bivalent chromatin state.

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