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An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo

ABSTRACT: An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo

PROVIDER: PRJNA529893 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8286570.fastq.gz	Fastqsanger.gz
	SRR8286571.fastq.gz	Fastqsanger.gz
	SRR8286572.fastq.gz	Fastqsanger.gz
	SRR8286567.fastq.gz	Fastqsanger.gz
	SRR8286568.fastq.gz	Fastqsanger.gz

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An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo (Hi-C)

Project description:High-resolution chromosome conformation capture-sequencing of RE6-9 heterozygous mutants. We investigated the three-dimensional organization of the Scn5a-Scn10a locus in whole hearts of RE6-9 heterozyous mutants and wildtype littermates. Viewpoint were set on enhancer 1 (enh1, located in the intronic region of Scn10a) and the Scn5a promoter (P1_2). The liver of FVB mice was used as controle tissue to determine the specificity of the Scn5a-Scn10a interaction domain in the heart.

2019-10-04 | GSE129062 | GEO

An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo (RNA-Seq)

Project description:An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo (RNA-Seq)

| PRJNA508757 | ENA

An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo (Hi-C)

Project description:An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo (Hi-C)

| PRJNA529888 | ENA

An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo.

Project description:Mutations and variations in and around SCN5A, encoding the major cardiac sodium channel, influence impulse conduction and are associated with a broad spectrum of arrhythmia disorders. Here, we identify an evolutionary conserved regulatory cluster with super enhancer characteristics downstream of SCN5A, which drives localized cardiac expression and contains conduction velocity-associated variants. We use genome editing to create a series of deletions in the mouse genome and show that the enhancer cluster controls the conformation of a >0.5?Mb genomic region harboring multiple interacting gene promoters and enhancers. We find that this cluster and its individual components are selectively required for cardiac Scn5a expression, normal cardiac conduction and normal embryonic development. Our studies reveal physiological roles of an enhancer cluster in the SCN5A-SCN10A locus, show that it controls the chromatin architecture of the locus and Scn5a expression, and suggest that genetic variants affecting its activity may influence cardiac function.

| S-EPMC6821807 | biostudies-literature

An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-10-04 | GSE129067 | GEO

An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo (RNA-Seq)

Project description:Whole transcriptome analysis of RE6-9 heterozygous mutants

2019-10-04 | GSE123440 | GEO

Chromatin topology and the timing of enhancer function at the HoxD locus [ChIP-seq]

Project description:The HoxD gene cluster is critical for proper limb formation in tetrapods. In the emerging limb buds, different sub-groups of Hoxd genes respond first to a proximal regulatory signal, then to a distal signal that organizes digits. These two regulations are exclusive from one another and emanate separately from two TADs flanking HoxD, both containing a range of appropriate enhancer sequences. The telomeric TAD (T-DOM) contains several enhancers active in presumptive forearm cells and is divided into two sub-TADs separated by a CTCF-rich boundary, which defines two regulatory sub-modules. To understand the importance of this particular regulatory topology to control Hoxd gene transcription in time and space, we either deleted or inverted this sub-TAD boundary, eliminated the CTCF binding sites or inverted the entire T-DOM to exchange the respective positions of the two sub-TADs. The effects of such perturbations on the transcriptional regulation of Hoxd genes illustrates the requirement of this regulatory topology for the precise timing of gene activation. However, the spatial distribution of transcripts is eventually resumed, showing that the presence of enhancers sequences, rather than either their exact topology or a particular chromatin architecture, is the key factor. We also show that the affinity of enhancers to find their natural target genes can overcome the presence of both a strong TAD border and an unfavourable orientation of CTCF sites.

2020-11-10 | GSE154187 | GEO

Chromatin topology and the timing of enhancer function at the HoxD locus [RNA-seq]

2020-11-10 | GSE154188 | GEO

Voltage-gated Sodium Channel SCN5A Promotes Tumor Progression and Enhances Chemosensitivity to 5-Fluorouracil in Colorectal Cancer

Project description:SCN5A was reported to promote proliferation and invasiveness potential in colorectal cancer, yet the mechanism was not clarified, and little was known about its association with chemosensitivity to 5-fluorouracil. In the current study, elevated SCN5A expression were associated with poor prognosis and metastasis in colorectal cancers, whereas stage II-III patients with up-regulated SCN5A expression were more likely to benefit from 5-fluorouracil-based adjuvant chemotherapy. SCN5A could promote proliferation and invasiveness potential through regulating cell cycle and epithelial-mesenchymal transition in colorectal cancer cells. Furthermore, SCN5A regulated Ras signaling by stabilizing KRas-calmodulin complex through Ca2+ influx. Apart from that, under 5-fluorouracil treatment, SCN5A promoted calmodulin-dependent apoptosis in colorectal cancers.

2020-05-09 | GSE150134 | GEO

miR-452-5p mediates SCN5A dependent fibrosis via TGF-beta/SMAD4 axis

Project description:SCN5A coding for sodium channels in the heart and its reduced activity implicated various biological processes including fibrogenesis. However, the mechanistic interplay between loss of SCN5A activity and cardiac fibrosis pertinence remains elusive. In-vitro knockdown of the SCN5A gene activates fibroblasts and increases TGF-β signaling with small-RNA sequencing indicating its impact on miR-452-5P expression in human cardiac fibroblasts (HCF). Mechanistically, miR-452-5p acts as a direct regulator of TGF-β signaling by inhibiting SMAD4 expression, maintaining cellular homeostasis in normal physiological conditions. SCN5A knockdown limits miR-452-5p regulatory function on SMAD4, which further promotes cardiac fibrosis (CF). These results clarify the significant involvement of miR-452-5p in CF development and propose a promising target for potential therapeutic intervention.

2024-06-20 | GSE261598 | GEO

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