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Candidate silencer elements in the human and mouse genome

ABSTRACT: Candidate silencer elements in the human and mouse genome

PROVIDER: PRJNA596216 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10721036.fastq.gz	Fastqsanger.gz
	SRR10721037.fastq.gz	Fastqsanger.gz
	SRR10721038.fastq.gz	Fastqsanger.gz
	SRR10721039.fastq.gz	Fastqsanger.gz
	SRR10721040.fastq.gz	Fastqsanger.gz

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Candidate silencer elements in the human and mouse genome

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Project description:The study of gene regulation is dominated by a focus on the control of gene activation or increase in the level of expression. Just as critical is the process of gene repression or silencing. Chromatin signatures have identified enhancers, however, genome-wide identification of silencers by computational or experimental approaches are lacking. Here, we first define uncharacterized cis-regulatory elements likely containing silencers and find that 41.5% of ~7500 tested elements show silencer activity using massively parallel reporter assay (MPRA). We trained a support vector machine classifier based on MPRA data to predict candidate silencers in over 100 human and mouse cell or tissue types. The predicted candidate silencers exhibit characteristics expected of silencers. Leveraging promoter-capture HiC data, we find that over 50% of silencers are interacting with gene promoters having very low to no expression. Our results suggest a general strategy for genome-wide identification and characterization of silencer elements.

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Project description:The role of non-coding regulatory elements and how they might contribute to tissue type specificity of disease phenotypes is poorly understood. Autosomal Dominant Leukodystrophy (ADLD) is a fatal, adult-onset, neurological disorder that is characterized by extensive CNS demyelination. Most cases of ADLD are caused by tandem genomic duplications involving the lamin B1 gene (LMNB1) while a small subset are caused by genomic deletions upstream of the gene. Utilizing data from recently identified families that carry LMNB1 gene duplications but that do not exhibit demyelination, ADLD patient tissues, CRISPR modified cell lines and mouse models, we have identified a novel silencer element that is lost in ADLD patients and that specifically targets overexpression only to oligodendrocytes. This element consists of CTCF binding sites that mediate three-dimensional chromatin looping involving the LMNB1 and the recruitment of the PRC2 repressor complex. Loss of the silencer element in ADLD identifies a previously unknown role for silencer elements in tissue specificity and disease causation.

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An anti-silencer- and SATB1-dependent chromatin hub regulates Rag1 and Rag2 gene expression during thymocyte development

Project description:Rag1 and Rag2 gene expression in CD4+CD8+ double positive (DP) thymocytes depends on the activity of a distant anti-silencer element (ASE) that counteracts the activity of an intergenic silencer. However, the mechanistic basis for ASE activity is unknown. Here we show that the ASE physically interacts with the distant Rag1 and Rag2 gene promoters in DP thymocytes, bringing the two promoters together to form an active chromatin hub. Moreover, we show that the ASE functions as a classical enhancer that can potently activate these promoters in the absence of the silencer or other locus elements. In thymocytes lacking the chromatin organizer SATB1, we identified a partial defect in Tcra gene rearrangement that was associated with reduced expression of Rag1 and Rag2 at the DP stage. SATB1 binds to the ASE and Rag promoters, facilitating inclusion of Rag2 in the chromatin hub and the loading of RNA polymerase II to both the Rag1 and Rag2 promoters. Our results provide a novel framework for understanding ASE function and demonstrate a novel role for SATB1 as a regulator of Rag locus organization and gene expression in DP thymocytes. Sequencing of Satb1-ChIP and input control from 6 wk old thymus

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Project description:Dual-function regulatory elements (REs), acting as enhancers in some cellular contexts and as silencers in others, have been reported to facilitate the precise gene regulatory response to developmental signals in Drosophila melanogaster However, with few isolated examples detected, dual-function REs in mammals have yet to be systematically studied. We herein investigated this class of REs in the human genome and profiled their activity across multiple cell types. Focusing on enhancer-silencer transitions specific to the development of T cells, we built an accurate deep learning classifier of REs and identified about 12,000 silencers active in primary peripheral blood T cells that act as enhancers in embryonic stem cells. Compared with regular silencers, these dual-function REs are evolving under stronger purifying selection and are enriched for mutations associated with disease phenotypes and altered gene expression. In addition, they are enriched in the loci of transcriptional regulators, such as transcription factors (TFs) and chromatin remodeling genes. Dual-function REs consist of two intertwined but largely distinct sets of binding sites bound by either activating or repressing TFs, depending on the type of RE function in a given cell line. This indicates the recruitment of different TFs for different regulatory modes and a complex DNA sequence composition of these REs with dual activating and repressive encoding. With an estimated >6% of cell type-specific human silencers acting as dual-function REs, this overlooked class of REs requires a specific investigation on how their inherent functional plasticity might be a contributing factor to human diseases.

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