Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bidirectional epigenetic editing reveals hierarchies in gene regulation

ABSTRACT: Bidirectional epigenetic editing reveals hierarchies in gene regulation

PROVIDER: PRJNA912205 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR22739500_1.fastq.gz	Fastqsanger.gz
	SRR22739500_2.fastq.gz	Fastqsanger.gz
	SRR22739501_1.fastq.gz	Fastqsanger.gz
	SRR22739501_2.fastq.gz	Fastqsanger.gz
	SRR22739502_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 128

Similar Datasets

Bidirectional epigenetic editing reveals hierarchies in gene regulation

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

2024-03-14 | GSE220976 | GEO

Bidirectional regulation of adenosine-to-inosine (A-to-I) RNA editing by DEAH box helicase 9 (DHX9) in cancer

Project description:Adenosine-to-inosine (A-to-I) RNA editing entails the enzymatic deamination of adenosines to inosines by adenosine deaminases acting on RNA (ADARs). Dysregulated A-to-I editing has been implicated in various diseases, including cancers. However, the precise factors governing the A-to-I editing and their physiopathological implications remain as a long-standing question. Herein, we unravel that DEAH box helicase 9 (DHX9), at least partially dependent of its helicase activity, functions as a bidirectional regulator of A-to-I editing in cancer cells. Intriguingly, the ADAR substrate specificity determines the opposing effects of DHX9 on editing as DHX9 silencing preferentially represses editing of ADAR1-specific substrates, whereas augments ADAR2-specific substrate editing. Analysis of 11 cancer types from The Cancer Genome Atlas (TCGA) reveals a striking overexpression of DHX9 in tumors. Further, tumorigenicity studies demonstrate a helicase-dependent oncogenic role of DHX9 in cancer development. In sum, DHX9 constitutes a bidirectional regulatory mode in A-to-I editing, which is in part responsible for the dysregulated editome profile in cancer.

2018-05-31 | GSE99789 | GEO

CUT&RUN-seq of H3K9me3, H4K20me3 or H3K4me3 in mESC after epigenetic editing and upon release of the trigger

Project description:Enrichment of histone marks was assessed by CUT&RUN-sequencing after epigenetic editing with dCas9::KRAB (or dCas9::GFP as a control) and subsequently upon release of the trigger. Samples were collected after 7 days of DOX induction (epigenetic editing) and after 4 and 7 days of DOX washout (release of the trigger).

2021-11-23 | E-MTAB-10525 | biostudies-arrayexpress

RNAseq of mESC expressing different epigenetic editing machineries

Project description:PolyA RNAseq of mouse ESC carrying a stable integration of an epigenetic editing machinery, consisting of: dCas9-GCN4, individual effectors fused to scFV and gRNA against the Hbby locus. The system is induced by doxycycline addition to the culture media. Total RNA was isolated from cell pellets using NEB Monarch® Total RNA Miniprep Kit and libraries prepared using NEBNext RNA Ultra II kit (NEB E7770S, input: 350 ng of total RNA). Libraries were multiplexed and sequenced on a NextSeq 500 (Paired-End; read length 40). Each sample is present in two biological replicates.

2023-10-01 | E-MTAB-12101 | biostudies-arrayexpress

ATAC-seq of ESC or in vitro differentiated endoderm cells after epigenetic editing and upon release of the trigger

Project description:Chromatin accessibility was assayed in ESC after epigenetic editing with dCas9::KRAB (or dCas9::GFP as a control) and subsequently in ESC and Endoderm differentiated cells upon release of the trigger. Samples were collected in two biological replicates after 7 days of DOX induction in ESC (epigenetic editing) and after 7 days of DOX washout (release of the trigger) in ESC and Endoderm cells.

2021-11-23 | E-MTAB-10523 | biostudies-arrayexpress

Chromatin context-dependent regulation and epigenetic modulation of prime editing

Project description:Chromatin context-dependent regulation and epigenetic modulation of prime editing

| PRJNA949965 | ENA

ATAC-seq of wildtype or Dppa2 knockout ESC upon release of the epigenetic editing trigger

Project description:Chromatin accessibility was assayed in wildtype or Dppa2 knockout ESC after 26 days of release of the trigger imposed by epigenetic editing. Samples were collected in two clonal knockout and wildtype lines after sorting at FACS of cells which maintained a repressive Esg1-tdTomato (TOMneg) reporter expression after 26 days of DOX washout (release of the trigger).

2021-11-23 | E-MTAB-10522 | biostudies-arrayexpress

A Bidirectional Non-Coding RNA Promoter Mediates Long-Range Gene Expression Regulation

Project description:Recent evidence suggests that human gene promoters display gene expression regulatory mechanisms beyond the typical single gene local transcription modulation. In mammalian genomes, genes with an associated bidirectional promoter are abundant; bidirectional promoter architecture serves as a regulatory hub for a gene pair expression. However, it has been suggested that its contribution to transcriptional regulation might exceed local transcription initiation modulation. Despite their abundance, the functional consequences of bidirectional promoter architecture remain largely unexplored. This work studies the long-range gene expression regulatory role of a long-non-coding RNA gene promoter using chromosome conformation capture methods. We found that this particular bidirectional promoter contributes to distal gene expression regulation in a target-specific manner by establishing promoter-promoter interactions. In particular, we validated that bidirectional promoter is contacting multiple gene promoter elements, including BBX promoter, upon loss-of-function assays reduced bidirectional-promoter interactions associated with increased BBX promoter-enhancer and augmented gene expression. Moreover, long-range regulatory functionality is not directly dependent on its associated non-coding gene pair expression levels.

2024-05-26 | GSE264638 | GEO

A Bidirectional Non-Coding RNA Promoter Mediates Long-Range Gene Expression Regulation [4C-seq]

2024-05-26 | GSE264663 | GEO

RNAseq of mESC expressing different epigenetic editing machineries

Project description:RNAseq of mESC expressing different epigenetic editing machineries

| PRJEB55359 | ENA