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Diverse Heterochromatin-Associated Proteins Repress Distinct Classes of Genes and Repetitive Elements (ChIP-seq)

ABSTRACT: Diverse Heterochromatin-Associated Proteins Repress Distinct Classes of Genes and Repetitive Elements (ChIP-seq)

PROVIDER: PRJNA645434 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12195400_1.fastq.gz	Fastqsanger.gz
	SRR12195400_2.fastq.gz	Fastqsanger.gz
	SRR12195401_1.fastq.gz	Fastqsanger.gz
	SRR12195401_2.fastq.gz	Fastqsanger.gz
	SRR12195402_1.fastq.gz	Fastqsanger.gz

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Diverse Heterochromatin-Associated Proteins Repress Distinct Classes of Genes and Repetitive Elements

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Diverse Heterochromatin-Associated Proteins Repress Distinct Classes of Genes and Repetitive Elements (srHC-seq)

Project description:Heterochromatin, typically marked by H3K9me3 or H3K27me3, is key to the repression of genes and repetitive elements. The mechanisms responsible for establishing and maintaining heterochromatin in a locus specific manner are unclear. Heterochromatin restricts cell identity by preventing activation of alternative lineage genes. This barrier can be partially overcome by inducing ectopic transcription factors (TFs) to activate an alternative transcriptional program. However, TFs are impeded by highly restrictive heterochromatin leading to low reprogramming rates and incomplete activation of the target transcriptome. Previously we utilized the heterochromatin property of sonication resistance to identify 172 proteins associated with sonication resistant heterochromatin (srHC) by mass spectrometry (Becker, et al., 2017). We hypothesized that by functionally assessing the srHC proteins and identifying the genes they repress during reprogramming we could improve our understanding of heterochromatin maintenance and learn how to disrupt heterochromatin to enhance reprogramming. Focusing on reprogramming from fibroblasts to induced human hepatocytes (hiHeps) we conducted an siRNA screen of 97 srHC proteins without reprogramming factors (noTF) and with hiHep reprogramming and assessed the impact on the expression of genes located in srHC domains by RNA-seq. We identified enhancer of rudimentary homolog (ERH) as a key regulator of H3K9me3 heterochromatin maintenance. ERH was found to associate broadly with H3K9me3 domains and when depleted caused global changes in H3K9me3 and srHC. Collectively our screen of srHC protein repressive function demonstrates specific functionality of groups of srHC proteins and increases our understanding of H3K9me3 gene repression.

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Diverse heterochromatin-associated proteins repress distinct classes of genes and repetitive elements.

Project description:Heterochromatin, typically marked by histone H3 trimethylation at lysine 9 (H3K9me3) or lysine 27 (H3K27me3), represses different protein-coding genes in different cells, as well as repetitive elements. The basis for locus specificity is unclear. Previously, we identified 172 proteins that are embedded in sonication-resistant heterochromatin (srHC) harbouring H3K9me3. Here, we investigate in humans how 97 of the H3K9me3-srHC proteins repress heterochromatic genes. We reveal four groups of srHC proteins that each repress many common genes and repeat elements. Two groups repress H3K9me3-embedded genes with different extents of flanking srHC, one group is specific for srHC genes with H3K9me3 and H3K27me3, and one group is specific for genes with srHC as the primary feature. We find that the enhancer of rudimentary homologue (ERH) is conserved from Schizosaccharomyces pombe in repressing meiotic genes and, in humans, now represses other lineage-specific genes and repeat elements. The study greatly expands our understanding of H3K9me3-based gene repression in vertebrates.

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Diverse Heterochromatin-Associated Proteins Repress Distinct Classes of Genes and Repetitive Elements

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