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3D genome organization during TGFB-induced transcription requires nuclear microRNA and G-quadruplexes [ChIRP_seq]

ABSTRACT: 3D genome organization during TGFB-induced transcription requires nuclear microRNA and G-quadruplexes [ChIRP_seq]

PROVIDER: PRJNA1026482 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26332869.fastq.gz	Fastqsanger.gz
	SRR26332870.fastq.gz	Fastqsanger.gz

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3D genome organization during TGFB-induced transcription requires nuclear microRNA and G-quadruplexes

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3D genome organization during TGFB-induced transcription requires nuclear microRNA and G-quadruplexes

Project description:Studying the dynamics of three-dimensional (3D) chromatin structure is essential to the understanding of biological processes in the nucleus. Integrative analysis of multi-omics data in recent publications have provided comprehensive and multilevel insight into 3D genome organization emphasizing its role for transcriptional regulation. While enhancers are regulatory elements that play a central role in the spatiotemporal control of gene expression, chromatin looping has been broadly accepted as a means for enhancer-promoter interactions yieldingcell-type-specific gene expression signatures. On the other hand, G-quadruplexes (G4s) are non-canonical DNA secondary structures that are enriched at promoters and related to increased gene expression, both. A role for G4s in promoter-distal regulatory elements, such as super-enhancers (SE), as well as in 3D genome organization and chromatin looping mediating long-range enhancer-promoter interactions has, however, remained elusive. Here we show that mature microRNA 9 (miR-9) is enriched at promoters and SE of genes that are inducible by tissue growth factor beta 1 (TGFB1) signaling. Further, we find that nuclear miR-9 is required for chromatin features related to increased transcriptional activity, such as broad domains of the euchromatin histone mark H3K4me3 (histone 3 tri-methylated lysine 4) and G4s. Moreover, we show that nuclear miR-9 is required for promoter-super-enhancer looping. Our study places a nuclear microRNA in the same structural and functional context with G4s and promoter-enhancer interactions during 3D genome organization and transcriptional activation induced by TGFB1 signaling, a critical regulator of proliferation programs in cancer and fibrosis.

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3D genome organization during TGFB-induced transcription requires nuclear microRNA and G-quadruplexes [HICHIP_seq]

Project description:Chromatin is the physiological template for all biological processes in the eukaryotic cell nucleus. In addition, the structure of chromatin is intrinsically related to its function. Thus, studying the dynamics of three-dimensional (3D) chromatin structure is essential to understand these biological processes. Recent publications based on integrative analysis of multi-omics studies have provided comprehensive and multilevel insights into 3D genome organization emphasizing its role during transcriptional regulation. However, the function of nuclear microRNAs in 3D genome organization has remained elusive. Here we show that mature microRNA 9 (miR-9) is enriched at promoters and super-enhancers (SE) of genes that are inducible by tissue growth factor beta 1 (TGFB1) signaling. Further, we found that nuclear miR-9 is required for broad domains of the euchromatin histone mark H3K4me3 (histone 3 tri-methylated lysine 4), as well as the nucleic acid secondary structure G-quadruplexes (G4s), both are chromatin features related to increased transcriptional activity. Moreover, we show that nuclear miR-9 is required for promoter-super-enhancer looping. Our study places a nuclear microRNA in the same structural and functional context with G4s and promoter-enhancer interactions during 3D genome organization and transcriptional activation induced by TGFB1 signaling, a pathway that plays important role in hyperproliferative diseases, such as cancer and fibrosis.

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3D genome organization during TGFB-induced transcription requires nuclear microRNA and G-quadruplexes [ChIRP_seq]

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3D genome organization during TGFB-induced transcription requires nuclear microRNA and G-quadruplexes [Cut&Tag]

Project description:Studying the dynamics of three-dimensional (3D) chromatin structure is essential to the understanding of biological processes in the nucleus. Integrative analysis of multi-omics data in recent publications have provided comprehensive and multilevel insight into 3D genome organization emphasizing its role for transcriptional regulation. While enhancers are regulatory elements that play a central role in the spatiotemporal control of gene expression, chromatin looping has been broadly accepted as a means for enhancer-promoter interactions yielding cell-type-specific gene expression signatures. On the other hand, G-quadruplexes (G4s) are non-canonical DNA secondary structures that are enriched at promoters and related to increased gene expression. However, the role of G4s in promoter-distal regulatory elements, such as super-enhancers (SE), as well as in 3D genome organization and chromatin looping mediating long-range enhancer-promoter interactions has remained elusive. Here we show that mature microRNA 9 (miR-9) is enriched at promoters and SE of genes that are inducible by tissue growth factor beta 1 (TGFB1) signaling. Further, we find that nuclear miR-9 is required for chromatin features related to increased transcriptional activity, such as broad domains of the euchromatin histone mark H3K4me3 (histone 3 tri-methylated lysine 4) and G4s. Moreover, we show that nuclear miR-9 is required for promoter-super-enhancer looping. Our study places a nuclear microRNA in the same structural and functional context with G4s and promoter-enhancer interactions during 3D genome organization and transcriptional activation induced by TGFB1 signaling, a critical regulator of proliferation programs in cancer and fibrosis.

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