Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription Analysis of Clustered Essential Genes

ABSTRACT: Transcription Analysis of Clustered Essential Genes

PROVIDER: PRJNA612782 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11310268.fastq.gz	Fastqsanger.gz
	SRR11310269.fastq.gz	Fastqsanger.gz
	SRR11310270.fastq.gz	Fastqsanger.gz
	SRR11310271.fastq.gz	Fastqsanger.gz
	SRR11310272.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 11

Similar Datasets

Transcription Analysis of Clustered Essential Genes

Project description:All 14 essential genes of chrIII were clustered and reordered, and transcription of the genes was tested. We designed and constructed three types of reorganized essential genes into three different plasmids. For the genomic direction (GD) plasmid, the essential genes were arranged according to their natural chromosomal positions and orientations. For the same direction (SD) plasmid, the essential genes were arrayed in the same positions as GD plasmid, but all genes were assembled in the same direction (SD). For the random direction (RD) plasmid, the essential genes were modularly assembled according to the combined length of three individual genes and thus displayed disorderly. The synIII strains bearing the GD/SD/RD plasmids were phenotypically normal despite of the double expression of 14 essential genes.

2020-06-01 | GSE147008 | GEO

Mechanism of REST/NRSF Regulation of Clustered Protocadherin Alpha Genes

Project description:Mechanism of REST/NRSF Regulation of Clustered Protocadherin Alpha Genes

| PRJNA631681 | ENA

Mechanism of REST/NRSF Regulation of Clustered Protocadherin Alpha Genes

Project description:Repressor element-1 silencing transcription factor (REST) or neuron-restrictive silencer factor (NRSF) is a zinc-finger (ZF) containing transcriptional repressor that recognizes thousands of neuron-restrictive silencer elements (NRSEs) in mammalian genomes. How REST/NRSF regulates gene expression remains incompletely understood. Here, we investigate the binding pattern and regulation mechanism of REST/NRSF in the clustered protocadherin (PCDH) genes. We find that REST/NRSF directionally forms base-specific interactions with NRSEs via tandem ZFs in an anti-parallel manner but with striking conformational changes. In addition, REST/NRSF recruitment to the HS5-1 enhancer leads to the decrease of long-range enhancer-promoter interactions and downregulation of the clustered PCDH alpha genes. Thus, REST/NRSF represses PCDH alpha gene expression through directional binding to a repertoire of NRSEs within the distal enhancer and variable target genes.

2021-04-14 | GSE150254 | GEO

Activation of clustered IFNγ target genes drives cohesin-controlled transcriptional memory

Project description:Activation of clustered IFNγ target genes drives cohesin-controlled transcriptional memory

| PRJNA631496 | ENA

Transcriptome analysis of human embryonic stem cells (hESCs) upon siRNA-mediated knockdown of hESC-essential genes

Project description:The maintenance of pluripotency requires the coordinated expression of a set of essential genes. Thorough identification of these genes is vital for gaining a better understanding of the pluripotent state. To this end, we have recently generated a genome-wide loss-of-function library in haploid human pluripotent stem cells utilizing the bacterial clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology using nearly 180,000 single guide RNAs (sgRNAs) and targeting 18,166 protein-coding genes. By combining the results of our high-throughput genetic screening with the analysis of publicly available RNAseq data of pluripotent stem cells and several somatic cells, we have determined the essential genes which have an enriched expression in hESCs and termed these genes as hESC-essential genes. Here, we have individually knocked down four of these hESC-essential genes with siRNAs, namely SALL4, DSCC1, SEPHS1 and VRTN, in human embryonic stem cells and analyzed the transcriptomes of the cells upon downregulation of these transcripts in order to unravel part of the pathways affected by hESC-essential genes.

2018-04-30 | GSE103846 | GEO

Extensive transcriptome analysis identifies essential genes sustaining intestinal invasion by Entamoeba histolytica

Project description:Extensive transcriptome analysis identifies essential genes sustaining intestinal invasion by Entamoeba histolytica

| PRJEB14707 | ENA

Identification of Susceptibility Genes for Essential Tremor

Project description:Identification of Susceptibility Genes for Essential Tremor

| PRJNA290967 | ENA

Spi-1/PU.1 activates transcription through clustered DNA occupancy in erythroleukemia

Project description:Acute leukemia are characterized by deregulation of transcriptional networks that control the lineage specificity of gene expression. The aberrant overexpression of the Spi-1/PU.1 transcription factor leads to erythroleukemia. To determine how Spi-1 mechanistically influences the transcriptional program, we combined a ChIP-seq analysis with transcriptional profiling in cells from an erythroleukemic mouse model. We show that Spi-1 displays a selective DNA-binding that does not often cause transcriptional modulation. We report that Spi-1 controls transcriptional activation and repression through distinct Spi-1 recruitment to chromatin. We revealed several parameters impacting on Spi-1-mediated transcriptional activation. Gene activation is facilitated by Spi-1 occupancy close to transcriptional starting site of genes devoid of CGIs. Moreover, in those regions Spi-1 acts by binding to multiple motifs tightly clustered and with similar orientation. Finally, in contrast to the myeloid and lymphoid B cells in which Spi-1 exerts a physiological activity, in the erythroleukemic cells, lineage-specific cooperating factors do not play a prevalent role in Spi-1-mediated transcriptional activation. Thus, our work describes a new mechanism of gene activation through clustered site occupancy of Spi-1 particularly relevant in regard to the strong expression of Spi-1 in the erythroleukemic cells.

2012-06-30 | GSE33611 | GEO

Spi-1/PU.1 activates transcription through clustered DNA occupancy in erythroleukemia

2012-06-30 | E-GEOD-33611 | biostudies-arrayexpress

Autism risk gene POGZ promotes chromatin accessibility and expression of clustered synaptic genes

Project description:Autism risk gene POGZ promotes chromatin accessibility and expression of clustered synaptic genes

| PRJNA777259 | ENA