Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation [histone marks]

ABSTRACT: Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation [histone marks]

PROVIDER: PRJNA510815 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8354670_1.fastq.gz	Fastqsanger.gz
	SRR8354670_2.fastq.gz	Fastqsanger.gz
	SRR8354680_1.fastq.gz	Fastqsanger.gz
	SRR8354680_2.fastq.gz	Fastqsanger.gz
	SRR8354690_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 60

Similar Datasets

Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation [histone marks]

Project description:Recent work suggests extensive adaptation of transposable elements (TEs) for host gene regulation. However, high numbers of integrations typical of TEs, coupled with sequence divergence within families, have made systematic interrogation of the regulatory contributions of TEs challenging. Here, we employ CARGO, our recent method for CRISPR gRNA multiplexing, to facilitate targeting of LTR5HS, a higher primate-specific class of HERVK (HML-2) LTRs that is active during early development and present in ~700 copies throughout the human genome. We combine CARGO with CRISPR activation or interference to, respectively, induce or silence LTR5HS en masse, and demonstrate that this system robustly targets the vast majority of LTR5HS insertions. Remarkably, activation/silencing of LTR5HS is associated with reciprocal up- and down-regulation of hundreds of human genes. These effects require presence of retroviral sequences, but occur over long genomic distances, consistent with a pervasive function of LTR5HS elements as early embryonic enhancers in higher primates.

2018-12-19 | GSE124128 | GEO

Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation

Project description:Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation

| PRJNA436649 | ENA

Systematic Perturbation of Thousands of Retroviral LTRs in Mouse Embryos

Project description:Systematic Perturbation of Thousands of Retroviral LTRs in Mouse Embryos

| PRJNA1011387 | ENA

Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation [ChIP-seq]

Project description:Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation [ChIP-seq]

| PRJNA436641 | ENA

Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation [RNA-seq]

Project description:Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation [RNA-seq]

| PRJNA436643 | ENA

Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation [RNA-seq]

2018-08-16 | GSE111332 | GEO

Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation [ChIP-seq]

2018-08-16 | GSE111331 | GEO

Systematic Perturbation of Thousands of Retroviral LTRs in Mouse Embryos [ChIP-Seq]

Project description:Systematic Perturbation of Thousands of Retroviral LTRs in Mouse Embryos [ChIP-Seq]

| PRJNA1011394 | ENA

Systematic Perturbation of Thousands of Retroviral LTRs in Mouse Embryos [RNA-Seq]

Project description:Systematic Perturbation of Thousands of Retroviral LTRs in Mouse Embryos [RNA-Seq]

| PRJNA1011393 | ENA

Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation.

Project description:Recent work suggests extensive adaptation of transposable elements (TEs) for host gene regulation. However, high numbers of integrations typical of TEs, coupled with sequence divergence within families, have made systematic interrogation of the regulatory contributions of TEs challenging. Here, we employ CARGO, our recent method for CRISPR gRNA multiplexing, to facilitate targeting of LTR5HS, an ape-specific class of HERVK (HML-2) LTRs that is active during early development and present in ~700 copies throughout the human genome. We combine CARGO with CRISPR activation or interference to, respectively, induce or silence LTR5HS en masse, and demonstrate that this system robustly targets the vast majority of LTR5HS insertions. Remarkably, activation/silencing of LTR5HS is associated with reciprocal up- and down-regulation of hundreds of human genes. These effects require the presence of retroviral sequences, but occur over long genomic distances, consistent with a pervasive function of LTR5HS elements as early embryonic enhancers in apes.

| S-EPMC6158008 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data