Mapping cis-regulatory elements in the midgestation mouse placenta
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA744555 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15065800.fastq.gz | Fastqsanger.gz | |||
| SRR15065801.fastq.gz | Fastqsanger.gz | |||
| SRR15065802.fastq.gz | Fastqsanger.gz | |||
| SRR15065803.fastq.gz | Fastqsanger.gz | |||
| SRR15065804.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 77 |
Similar Datasets
Project description:The placenta is a temporary organ that provides the developing fetus with nutrients, oxygen, and protection in utero. Defects in its development, which may be caused by misregulated gene expression, can lead to devastating outcomes for the mother and fetus. In mouse, placental defects during midgestation commonly lead to embryonic lethality. However, the regulatory mechanisms controlling expression of genes during this period have not been thoroughly investigated. Therefore, we generated and analyzed ChIP-seq data for multiple histone modifications known to mark cis-regulatory regions. We annotated active and poised promoters and enhancers, as well as regions generally associated with repressed gene expression. We found that poised promoters were associated with neuronal development genes, while active promoters were largely associated with housekeeping genes. Active and poised enhancers were associated with placental development genes, though only active enhancers were associated with genes that have placenta-specific expression. Motif analysis within active enhancers identified a large network of transcription factors, including those that have not been previously studied in the placenta and are candidates for future studies. The data generated and genomic regions annotated provide researchers with a foundation for future studies, aimed at understanding how specific genes in the midgestation mouse placenta are regulated.
| S-EPMC8595355 | biostudies-literature
Project description:We generated and analyzed ChIP-seq data for H3k4me3, H3k4me1, and H3k27me3. We annotated active and poised promoters and enhancers, as well as regions associated with repressed gene expression and found that poised promoters were associated with neuronal development genes, while active promoters were largely associated with housekeeping genes. Active and poised enhancers were associated with placental development genes, though only active enhancers were associated with genes that have placenta-specific expression.
2021-11-30 | GSE179695 | GEO
Project description:Epigenetic Mapping of Cis-Regulatory Elements in the Developing Mouse and Pig Forelimbs.
| PRJNA1164301 | ENA
Project description:Background Genomic variations contribute to the phenotypic diversity of individuals. A number of polymorphisms in protein-coding regions that alter drug efficacy or lead to adverse reactions have been characterized; however, noncoding regions that affect drug responses are largely overlooked, except for a limited number of well-studied enhancers. Results We conducted a quantitative assessment of cis-regulatory elements (CREs) based on transcription initiation profiling of mRNAs and noncoding RNAs, including enhancer RNAs, by using CAGE (Cap Analysis of Gene Expression). Candidate CREs identified in a hepatocellular carcinoma HepG2 cell line with stable expression of drug-responsive transcription factor pregnane X receptor (PXR) were further narrowed down by integrating data of PXR-binding sites in human primary hepatocytes and genome-wide association studies. We found more than 100-fold enrichments of the candidates to genetically associated loci with circulating levels of bilirubin and vitamin D, which implicated a link to adverse reactions of PXR ligands. We uncovered novel enhancers of UGT1A1 and TSKU through CRISPR/Cas9 knockout experiments. We identified alleles altering regulatory activities of UGT1A1 and CYP24A1enhancers by using luciferase reporter assay. Furthermore, our siRNA experiments revealed an unexpected impact of TSKU on the expression of vitamin D-metabolizing enzymes. Conclusions Our transcriptome-based assessment of CREs expanded the list of drug-inducible and PXR-mediated enhancers and super-enhancers. We identified regulatory alleles that alter drug-induced gene expressions, and discovered a novel molecular cascade associated with an adverse reaction. Our results contribute a precise understanding of the noncoding elements of the human genome underlying drug responses.
2025-04-17 | PXD060446 | Pride
Project description:mRNA molecules are generally thought to be messengers of genetic information in the cell. Stretches of RNA that are complementary in sequence have a propensity to pair, forming elements of secondary structure within RNA molecules. Although these structures will exist in every mRNA molecule, the role they play in gene regulation is not well understood. Currently two techniques are available to profile the cell RNA structure, in-vivo, in an unbiased manner. We applied one of those techniques, DMS-seq, for probing the human mRNA structure in primary foreskin fibroblasts (HFFs) along human cytomegalovirus (HCMV) infection. As a proof of concept, using DMS-seq, we managed to predict the already solved human 28S rRNA structure with high accuracy. Using our data, we are able to show for the first time in-vivo, that human coding sequences (CDSs) are less structured relative to UTRs. Additionally, we provide systematic in-vivo evidences for unwinding of the mRNA by the ribosomes during translation. Intriguingly, we also found structural changes in human CDSs around the start and stop codon, and also in 3’UTRs. The combination of accurate measurements of translation regulation and mapping changes in mRNA structure along a dynamic process can be used as a platform for deciphering cis-regulatory elements that control gene expression in various cell types, organisms and biological processes.
2018-10-03 | GSE102069 | GEO
Project description:Predictable Engineering of Signal-Dependent Cis-Regulatory Elements
| PRJNA1232713 | ENA
Project description:Although most disease-causing variants are within coding region of genes, it is now well established that cis-acting regulatory sequences, depending on 3D-chromatin organization, are required for temporal and spatial control of gene expression. Disruptions of such regulatory elements and/or chromatin conformation are likely to play a critical role in human genetic disease. Hence, recurrent monoallelic cases of the most common hereditary type of nonsyndromic hearing loss (i.e. DFNB1) carrying out only one identified pathogenic allele, led to strongly suggest the presence of uncharacterized distal cis-acting elements in the missing allele. Herewith, we study the spatial organization of a large DFNB1 locus encompassing the gap junction protein beta 2 (GJB2) gene, the most frequently mutated gene in this inherited hearing loss, with the chromosome conformation capture carbon copy technology (5C). By combining this approach with functional activity reporter assays and mapping of CCCTC-binding factor (CTCF) along the DFNB1 locus by quantitative real-time PCR chromatin immunoprecipitation, we identify a novel set of cooperating GJB2 cis-acting elements and propose a DFNB1 three-dimensional looping regulation model. A loop chromatin forming, allows bringing closer enhancers to the GJB2 promoter, but also avoids GJB2 silencing with an enhancer-blocking insulator activity.
2020-03-26 | GSE128881 | GEO
Project description:The goal of this study is to improve the quality, efficiency, and sustainability of milk production by improving the understanding of the function of cis-regulatory elements in regulating the bovine mammary gland. To this end, we have characterized the non-lactating and lactating mammary gland transcriptomes by whole transcriptome shotgun sequencing (RNA-seq). We will identify cis-regulatory elements in the non-lactating and lactating bovine mammary gland genome-wide. Finally, we will annotate and characterize mammary gland cis-regulatory elements by computational analysis and identify high-resolution genome-wide in vivo footprints of diverse trans-acting-factors (TF), over-represented TF bindings sites and overlapping SNPs.
2021-04-06 | GSE116079 | GEO
Project description:We investigated the transcriptional activation and cis-regulatory elements of effector ISGs in CD8+ murine dendritic cells (DCs) stimulated with IFN-beta. We analysed gene repression changes and characterized activated cis-regulatory regions. Binding of ISGF3 subunits (IRF9, Stat1, and Stat2) and other transcription factors, DNA motifs, and chromatin status were also determined.
2022-04-01 | GSE172376 | GEO
Project description:High-throughput discovery of post-transcriptional cis-regulatory elements
| PRJNA302654 | ENA