Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ATAC-seq and multi-omics analysis of human liver highlight a hepatocyte-specific enhancer for ACOT1 regulating the balance of acyl-CoA and free fatty acids in type 2 diabetes.

ABSTRACT: ATAC-seq (assay for transposase-accessible chromatin followed by sequencing) is widely used to decode chromatin accessibility. Here we performed high-sensitive ATAC-seq in 9 human liver samples from normal and T2D donors, and identified a set of differentially accessible regions (DARs). DARs were overlapped with publicly available CREs databases and integrated with multi-omics data to identify candidates for further experimental validations. We identified 7 DARs that mark putative regulatory elements including a candidate enhancer for the ACOT1 gene that regulates the balance of acyl-CoA and free fatty acids in the cytoplasm. The relevance of ACOT1 regulation in T2D was supported by the analysis of transcriptomics and proteomics data in liver tissue. Conclusions: Our strategy that integrates chromatin accessibility with DNA binding and other types of omics provides novel insights towards the role of genetic regulation in complex multifactorial diseases such as T2D.

ORGANISM(S): Homo sapiens

PROVIDER: GSE173277 | GEO | 2021/09/03

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Liver Chromatin accessibility landscapes during onset of salmon maturation

Project description:We sequenced 12 ATAC-Seq lbraries from four biological replicates before (T1) and after the onset of maturation (T2, T3, T4) from liver. To characterise changes in chromatin state following long light initiation, we defined differentially accessible regions (DARs) where mapping counts differed significantly between T1 and other time points. This revealed a strong early remodelling in the chromatin state landscape, as most DARs were observed at T2 (n=1501) before decreasing in stepwise fashion at T3 (n=477) and T4. The majority of DARs (n=1036 or 57%) exhibit reduced accessibility at T2 compared with T1 and subsequently remained unchanged at later time points (Fig. 5a; Supplementary Figure S14). Similarly, regions that gained accessibility at T2 (n=696 or 38%) also remained unchanged at later timepoints. This left less than 10% of DARs (n=99) that displayed an oscillating pattern following the onset of the maturation. Together, this revealed the ATAC-seq signatures were predominantly stable chromatin state changes.

2020-08-28 | GSE156998 | GEO

Differential analysis of chromatin accessibility and gene expression profiles identifies cis-regulatory elements in rat adipose and muscle

Project description:Chromatin accessibility is a key factor influencing gene expression. We developed a modified protocol, ruptor-ATAC, which together with RNA-seq was used to investigate regulatory elements underlying tissue-specific gene expression in rat white adipose and skeletal muscle, two tissues with contrasting metabolic functions. While promoter accessibility correlated with RNA expression, integration of the two datasets identified tissue-specific differentially accessible regions (DARs) that predominantly localized in intergenic and intron regions. DARs mapped to differentially expressed genes that were enriched in distinct biological processes in each tissue. Motif enrichment analysis on tissue-specific DARs predicted binding sites for transcription factors (TFs), several of which were up-regulated in the corresponding tissue. Positive relationship between DARs and target gene expression further supported a functional role for these TF binding motifs. Our study identifies cis-regulatory regions that likely play a major role in the regulation of tissue-specific gene expression in adipose and muscle.

2022-02-07 | GSE171923 | GEO

ATAC-seq of human monocytes and human monocyte-derived cells.

Project description:ATAC-seq was performed to map changes in chromatin accessibility in monocytes during in vitro differentiation. In addition to control cells, we also studied the impact of siRNA mediated knock-down of key transcription factors on accessible chromatin in monocyte-derived dendritic cells.

2021-02-03 | E-MTAB-9926 | biostudies-arrayexpress

Tissue-specific chromatin accessibility cis-regulatory regions in rat white adipose and muscle

Project description:Chromatin accessibility is a key factor influencing gene expression. We developed a modified protocol, ruptor-ATAC, which with RNA-seq was used to investigate regulatory elements underlying gene expression in rat white adipose and skeletal muscle, two tissues with contrasting metabolic functions. Integration of both datasets showed that promoter accessibility correlated with RNA expression and identified 44,798 tissue-specific differentially accessible regions (DARs), predominantly localized in intergenic and intron regions. Tissue-specific DARs mapped to differentially expressed genes that were enriched in distinct biological processes. Motif enrichment analysis on DARs predicted binding sites for transcription factors (TFs). Significant up-regulation of 11 TFs recognizing enriched cis-motifs in each tissue indicated their functional relevance. Positive correlation between motif accessibility and target gene expression further supported the role of selected TFs as transcriptional regulators. Our study identifies non-promoter cis-regulatory regions that likely play a major role in the control of tissue-specific gene expression in adipose and muscle.

2022-02-07 | GSE168328 | GEO

Multi-omics Analyses Reveal Sex Differences in Mouse Renal Proximal Tubules

Project description:Sex-dependent differences in kidney function have been recognized. However, the molecular mechanisms underlying these differences remain largely unexplored. Advances in genomics and proteomic technologies now allow for an extensive characterization of sex differences. In this study, the authors apply multi-omics approaches integrating RNA-seq, ATAC-seq, and proteomics to investigate gene expression, chromatin accessibility, and protein expression between male and female mouse proximal tubules. This study identifies a large number of sex-biased genes and proteins associated with various kidney functions, including metabolism and transport processes. The authors demonstrate that sex differences may also arise from differences in interaction between transcription factors and accessible chromatin regions. A comprehensive web resource is provided to the research community to advance understanding of sex differences.

2023-05-05 | PXD037098 | Pride

An integrated multi-omics analysis of identiﬁes distinct molecular characteristics in pulmonary infections of Pseudomonas aeruginosa

Project description:Pseudomonas aeruginosa (P. aeruginosa) can cause severe acute infections, including pneumonia and sepsis, and also cause chronic infections commonly in patients with structural respiratory diseases. However, the molecular and pathophysiological mechanisms of P. aeruginosa respiratory infection are largely unknown. Here, we profiled performed to assay for transposase-accessible chromatin using sequencing (ATAC-seq), transcriptomics, and quantitative mass spectrometry-based proteomics and ubiquitin-proteomics in P. aeruginosa-infected lung tissues for multi-omics analysis, while ATAC-seq and transcriptomics were also examined in P. aeruginosa-infected mouse macrophages. To find the pivotal transcription factors that are likely involved in host immune defense, we integrally investigated systematic changes in chromatin accessibility and gene expression in P. aeruginosa-infected lung tissues combined with proteomics and ubiquitin-proteomics studies. We discovered that Stat1 and Stat3 were altered in various omics and found similar results in mouse alveolar macrophages. Taken together, these findings indicate that these crucial transcription factors and their downstream signaling molecules play a critical role in the mobilization of host immune response against P. aeruginosa infection and may serve as potential targets for bacterial infections and inflammatory diseases, as well as provide clear insights and resources for using integrative histological analyses.

2023-07-27 | PXD042381 | Pride

An integrated multi-omics analysis of identiﬁes distinct molecular characteristics in pulmonary infections of Pseudomonas aeruginosa

2023-07-27 | PXD038001 | Pride

Acute depletion of CTCF rewires genome-wide chromatin accessibility

Project description:The transcription factor CTCF appears indispensable in defining topologically associated domain boundaries and maintaining chromatin loop structures within these domains, supported by numerous functional studies. However, acute depletion of CTCF globally reduces chromatin interactions but does not significantly alter transcription. Here we systematically integrated multi-omics data including ATAC-seq, RNA-seq, WGBS, Hi-C, Cut&Run, CRISPR-Cas9 survival dropout screening, time-solved deep proteomic and phosphoproteomic analyses in cells carrying auxin-induced degron at endogenous CTCF locus. Acute CTCF protein degradation markedly rewired genome-wide chromatin accessibility. Increased accessible chromatin regions were largely located adjacent to CTCF-binding sites at promoter regions and insulator sites and were associated with enhanced transcription of nearby genes. In addition, we used CTCF-associated multi-omics data to establish a combinatorial data analysis pipeline to discover CTCF co-regulatory partners in regulating downstream gene expression. We successfully identified 40 candidates, including multiple established partners (i.e., MYC) supported by all layers of evidence. Interestingly, many CTCF co-regulators (e.g., YY1, ZBTB7A) that have evident alterations of respective downstream gene expression do not show changes at their expression levels across the multi-omics measurements upon acute CTCF loss, highlighting the strength of our system to discover hidden co-regulatory partners associated with CTCF-mediated transcription. This study highlights CTCF loss rewires genome-wide chromatin accessibility, which plays a critical role in transcriptional regulation

2021-07-04 | PXD026484 | Pride

ATAC-seq on human pancreatic islets

Project description:We have studied the impact of T2D on open chromatin in human pancreatic islets. We used assay for transposase-accessible chromatin using sequencing (ATAC-seq) to profile open chromatin in islets from T2D and non-diabetic donors. We identified ATAC-seq peaks representing open chromatin regions in islets of non-diabetic and diabetic donors. The majority of ATAC-seq peaks mapped near transcription start sites. Additionally, peaks were enriched in enhancer regions and in regions where islet-specific TFs bind. Islet ATAC-seq peaks overlap with SNPs associated with T2D and with additional SNPs in LD with known T2D SNPs. There was enrichment of open chromatin regions near highly expressed genes in human islets.

2019-04-06 | GSE129383 | GEO

Single Cell Multi-Omics Profiling Using ISSAAC-seq

Project description:Joint profiling of chromatin accessibility and gene expression from the same single cell provides critical information about cell types in a tissue and cell states during a dynamic process. These emerging multi-omics techniques help the investigation of cell-type resolved gene regulatory mechanisms. Here, we developed in situ SHERRY after ATAC-seq (ISSAAC-seq), a highly sensitive and flexible single cell multi-omics method to interrogate chromatin accessibility and gene expression from the same single cell. We demonstrated that ISSAAC-seq is sensitive and provides high quality data with orders of magnitude more features than existing methods. Using the joint profiles from thousands of nuclei from the mouse cerebral cortex, we uncovered major and rare cell types together with their cell-type specific regulatory elements and expression profiles. Finally, we revealed distinct dynamics and relationships of transcription and chromatin accessibility during an oligodendrocyte maturation trajectory.

2022-06-15 | E-MTAB-11264 | biostudies-arrayexpress

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