Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Widespread Long-range Cis-Regulatory Elements in the Maize Genome

ABSTRACT: Widespread Long-range Cis-Regulatory Elements in the Maize Genome

PROVIDER: PRJNA492464 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10964901_1.fastq.gz	Fastqsanger.gz
	SRR10964901_2.fastq.gz	Fastqsanger.gz
	SRR10964902_1.fastq.gz	Fastqsanger.gz
	SRR10964902_2.fastq.gz	Fastqsanger.gz
	SRR10964903_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 101

Similar Datasets

Widespread Long-range Cis-Regulatory Elements in the Maize Genome

Project description:Genetic mapping studies on crops suggest that agronomic traits can be controlled by loci within the gene-distal intergenic space. Despite the biological importance and the potential agronomic utility of these intergenic loci, they remain virtually uncharacterized in all crop species to date. Here, we provide genetic, epigenomic, and functional molecular evidence supporting the widespread existence of gene-distal (hereafter, distal) loci which act as long-range transcriptional cis-regulatory elements (CREs) in the maize genome. Such loci are enriched for euchromatic chromatin features that suggest their regulatory functions. Chromatin loops link together putative CREs with genes and recapitulate eQTL-gene interactions. Additionally, putative CREs display elevated transcriptional enhancer activities, as measured by STARR-seq. These results provide functional support for the widespread existence of CREs which act over large genomic distances to modulate gene expression.

2019-09-19 | GSE120304 | GEO

Widespread long-range cis-regulatory elements in the maize genome.

Project description:Genetic mapping studies on crops suggest that agronomic traits can be controlled by gene-distal intergenic loci. Despite the biological importance and the potential agronomic utility of these loci, they remain virtually uncharacterized in all crop species to date. Here, we provide genetic, epigenomic and functional molecular evidence to support the widespread existence of gene-distal (hereafter, distal) loci that act as long-range transcriptional cis-regulatory elements (CREs) in the maize genome. Such loci are enriched for euchromatic features that suggest their regulatory functions. Chromatin loops link together putative CREs with genes and recapitulate genetic interactions. Putative CREs also display elevated transcriptional enhancer activities, as measured by self-transcribing active regulatory region sequencing. These results provide functional support for the widespread existence of CREs that act over large genomic distances to control gene expression.

| S-EPMC6904520 | biostudies-literature

Conserved Cis-Acting Range Extender Elements Mediate Long-Range Developmental Enhancer Activity in Mammals

Project description:Conserved Cis-Acting Range Extender Elements Mediate Long-Range Developmental Enhancer Activity in Mammals

| PRJNA1019308 | ENA

The Role of cis Regulatory Evolution in Maize Domestication

Project description:Modification of cis regulatory elements to produce differences in gene expression level, localization, and timing is an important mechanism by which organisms evolve divergent adaptations. To examine gene regulatory change during the domestication of maize from its wild progenitor, teosinte, we assessed allele-specific expression in a collection of maize and teosinte inbreds and their F1 hybrids using three tissues from different developmental stages. Our use of F1 hybrids represents the first study in a domesticated crop and wild progenitor that dissects cis and trans regulatory effects to examine characteristics of genes under various cis and trans regulatory regimes. We find evidence for consistent cis regulatory divergence that differentiates maize from teosinte in approximately 4% of genes. These genes are significantly correlated with genes under selection during domestication and crop improvement, suggesting an important role for cis regulatory elements in maize evolution.

2014-11-06 | GSE61810 | GEO

MAPT expression is mediatedd by long-range interactions with cis-regulatory elements.

Project description:MAPT expression is mediatedd by long-range interactions with cis-regulatory elements.

| PRJNA948130 | ENA

MAPT expression is mediated by long-range interactions with cis-regulatory elements [RNA_timecourse]

Project description:MAPT expression is mediated by long-range interactions with cis-regulatory elements [RNA_timecourse]

| PRJNA948135 | ENA

MAPT expression is mediated by long-range interactions with cis-regulatory elements [scMultiomics]

Project description:MAPT expression is mediated by long-range interactions with cis-regulatory elements [scMultiomics]

| PRJNA948138 | ENA

MAPT expression is mediated by long-range interactions with cis-regulatory elements [ATAC-seq]

Project description:MAPT expression is mediated by long-range interactions with cis-regulatory elements [ATAC-seq]

| PRJNA948136 | ENA

MAPT expression is mediated by long-range interactions with cis-regulatory elements [RNA-seq]

Project description:MAPT expression is mediated by long-range interactions with cis-regulatory elements [RNA-seq]

| PRJNA948134 | ENA

MAPT expression is regulated by long-range interactions with cis-regulatory elements [ChIP-seq]

Project description:MAPT expression is regulated by long-range interactions with cis-regulatory elements [ChIP-seq]

| PRJNA948133 | ENA

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