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SRX2345843: GSM2390057: ChrRNA-seq-WT-JQ1 - replicate 1; Mus musculus; OTHER
1 ILLUMINA (NextSeq 500) run: 94.3M spots, 7.1G bases, 2.6Gb downloads

Submitted by: NCBI (GEO)
Study: Super-enhancer-mediated RNA processing revealed by integrative microRNA network analysis [ChrRNA-seq]
show Abstracthide Abstract
Super-enhancers are an emerging sub-class of regulatory regions controlling cell identity and disease genes. However, their biological function and impact on miRNA networks are unclear. Here we report that super-enhancers drive the biogenesis of master miRNAs crucial for cell identity by enhancing both transcription and Drosha/DGCR8-mediated primary miRNA processing. Super-enhancers, together with broad H3K4me3 domains, shape a tissue-specific and evolutionarily conserved atlas of miRNA expression and function. CRISPR/Cas9 genomics revealed that super-enhancer constituents act cooperatively and facilitate Drosha/DGCR8 recruitment and pri-miRNA processing to boost cell-specific miRNA production. BET-bromodomain inhibitor JQ1 preferentially inhibited super-enhancer-directed cotranscriptional pri-miRNA processing. Furthermore, super-enhancers are characterized by pervasive interaction with DGCR8/Drosha and DGCR8/Drosha-regulated mRNA stability control, suggesting unique RNA regulation at super-enhancers. Finally, super-enhancers mark multiple miRNAs associated with cancer hallmark traits. This study presents a principle underlying miRNA biology in health and disease and a unrecognized higher-order property of super-enhancers in RNA processing beyond transcription. Overall design: Chromatin-associated RNA sequencing (ChrRNA-seq) in wild type mESCs with/without JQ1 and DGCR8 knockout mESCs.
Sample: ChrRNA-seq-WT-JQ1 - replicate 1
SAMN06014919 • SRS1796548 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: NextSeq 500
Strategy: OTHER
Source: TRANSCRIPTOMIC
Selection: other
Layout: SINGLE
Construction protocol: Cells were trypsinized, washed with cold PBS and resuspended in cold lysis buffer (10 mM Tris pH 7.4; 150 mM NaCl; 0.15% NP-40; RNase inhibitor). After 5 min incubation on ice, the suspension was layered over 1 ml sucrose buffer (10 mM Tris pH 7.4; 150 mM NaCl; 24% sucrose) and centrifuged (5 min, 3500 g). After removal of supernatant, nuclei pellet was briefly rinsed with cold PBS, resuspended in 250 μl Glycerol buffer (20 mM Tris pH 7.4; 75 mM NaCl; 0.5 mM EDTA; 50% Glycerol) and mixed with 250 μl nuclear lysis buffer (10 mM Tris pH 7.4, 7.5 mM MgCl2, 0.2 mM EDTA, 0.3 M NaCl, 1 M Urea, 1% NP-40) by vortexing for 4 sec. After 2 min incubation on ice, samples were centrifuged for 2 min at full speed. The remaining chromatin pellet was rinsed with cold PBS and resuspended in QIAzol lysis agent. RNA was extracted using QIAshredder and miRNeasy Mini Kit (Qiagen). After removal of rRNA by Ribo-Zero rRNA removal kit (Illumina), DNA libraries were generated using TruSeq Stranded Total RNA LT Sample Prep Kit and analyzed by NextSeq.
Experiment attributes:
GEO Accession: GSM2390057
Links:
Runs: 1 run, 94.3M spots, 7.1G bases, 2.6Gb
Run# of Spots# of BasesSizePublished
SRR501745594,297,8937.1G2.6Gb2017-03-09

ID:
3422178

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