Identification of chromatin‐accessible domains in non‐alcoholic steatohepatitis‐derived hepatocellular carcinoma

Dechassa, Mekonnen Lemma; Tryndyak, Volodymyr; Conti, Aline de; Xiao, Wenming; Beland, Frederick A.; Pogribny, Igor P.

doi:10.1002/mc.22818

Cited by 23 publications

(15 citation statements)

References 57 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In addition, the ACRs were concentrated at the proximal TSSs, which is consistent with the fact that chromatin around TSSs throughout the genome is more accessible than that in surrounding genomic regions. Overall, our results are in excellent agreement with those of many studies [53,54]. Through ATAC-seq genome-wide identification of peaks in muscle tissue from embryos of different stages, we found that the number of peaks increased with the age of the embryo, indicating that chromatin accessibility is involved in the regulation of embryonic muscle development.…”

Section: Discussionsupporting

confidence: 92%

The Landscape of Chromatin Accessibility in Skeletal Muscle During Embryonic Development in Pigs

Yue

Hou

Liu

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: The development of skeletal muscle during the embryonic stage in pigs is precisely regulated by transcriptional regulation, which depends on chromatin accessibility. However, how chromatin accessibility plays a regulatory role during embryonic skeletal muscle development in pigs has not been reported. To gain insight into the landscape of chromatin accessibility and the associated genome-wide transcriptome during embryonic muscle development, we performed ATAC-seq and RNA-seq on skeletal muscle of pig embryos at 45, 70 and 100 days post coitus (dpc). Results: In total, 21638, 35447 and 60181 unique regions (or peaks) were found across 45 dpc (LW45), 70 dpc (LW70) and 100 dpc (LW100) embryos, respectively. More than 91% of peaks were annotated within -1 kb to 100 bp of transcription start sites (TSSs). First, widespread increases in specific accessible chromatin regions (ACRs) from 45 to 100 dpc embryos suggested that the regulatory mechanisms became increasingly complicated during embryonic development. Second, the findings of integrated ATAC-seq and RNA-seq analyses showed that not only the numbers but also the peak intensities of ACRs could control the expression of associated genes. Finally, motif screening of stage-specific ACRs revealed some transcription factors that regulated muscle development-related genes, such as MyoD, Mef2c, Mef2d and Pax7. Several potential transcriptional repressors, including E2F6, GRHL2, OTX2 and CTCF, were identified among those genes that exhibited different change trends between the ATAC-seq and RNA-seq data. Conclusions: This work indicates that chromatin accessibility plays an important regulatory role in the embryonic muscle development of pigs and regulates the temporal and spatial expression patterns of key genes in muscle development by influencing the binding of transcription factors. Our results contribute to a better understanding of the regulatory dynamics of genes involved in pig embryonic skeletal muscle development.

show abstract

Section: Discussionsupporting

confidence: 92%

The Landscape of Chromatin Accessibility in Skeletal Muscle During Embryonic Development in Pigs

Yue

Hou

Liu

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…However, the mechanism of functional genome alterations in AD requires further investigation. Recent advances in chromatin profiling, especially genome-wide chromatin accessibility profiling methodologies, including MNase-seq, DNase-seq, FAIRE-seq, and ATAC-seq, have made it possible to analyze the alterations in the accessible chromatin state and allow us to better understand the molecular mechanisms of numerous diseases such as cancer, malaria, and metabolic disorders [44][45][46][47]. Although DNase-seq and MNase-seq can provide some subsets of the information obtained by ATAC-seq, they still have some limitations, for example large cell numbers, longer experimental time, and limited applicability to many systems.…”

Section: Discussionmentioning

confidence: 99%

Characterization of the chromatin accessibility in an Alzheimer’s disease (AD) mouse model

et al. 2020

View full text Add to dashboard Cite

Background: The pathological hallmarks of Alzheimer's disease (AD) involve alterations in the expression of numerous genes associated with transcriptional levels, which are determined by chromatin accessibility. Here, the landscape of chromatin accessibility was studied to understand the outline of the transcription and expression of AD-associated metabolism genes in an AD mouse model. Methods: The assay for transposase-accessible chromatin by sequencing (ATAC-seq) was used to investigate the ADassociated chromatin reshaping in the APPswe/PS1dE9 (APP/PS1) mouse model. ATAC-seq data in the hippocampus of 8-month-old APP/PS1 mice were generated, and the relationship between chromatin accessibility and gene expression was analyzed in combination with RNA sequencing. Gene ontology (GO) analysis was applied to elucidate biological processes and signaling pathways altered in APP/PS1 mice. Critical transcription factors were identified; alterations in chromatin accessibility were further confirmed using chromatin immunoprecipitation assays. Results: We identified 1690 increased AD-associated chromatin-accessible regions in the hippocampal tissues of APP/ PS1 mice. These regions were enriched in genes related to diverse signaling pathways, including the PI3K-Akt, Hippo, TGF-β, and Jak-Stat signaling pathways, which play essential roles in regulating cell proliferation, apoptosis, and inflammatory responses. A total of 1003 decreased chromatin-accessible regions were considered to be related with declined AD-associated biological processes including cellular response to hyperoxia and insulin stimulus, synaptic transmission, and positive regulation of autophagy. In the APP/PS1 hippocampus, 1090 genes were found to be upregulated and 1081 downregulated. Interestingly, enhanced ATAC-seq signal was found in approximately 740 genes, with 43 exhibiting upregulated mRNA levels. Several genes involved in AD development were found to have a significantly increased expression in APP/PS1 mice compared to controls, including Sele, Clec7a, Cst7, and Ccr6. The signatures of numerous transcription factors, including Olig2, NeuroD1, TCF4, and NeuroG2, were found enriched in the AD-associated accessible chromatin regions. The transcription-activating marks of H3K4me3 and H3K27ac were also found increased in the promoters of these genes. These results indicate that the mechanism for the upregulation of genes could be attributed to the enrichment of open chromatin regions with transcription factors motifs and the histone marks H3K4me3 and H3K27ac.

show abstract

“…ATAC-seq has applications in the pathogenesis (26), targeted therapy (27), and immunotherapy (28) of leukemia. The type of cancer with the second highest number of included articles that used ATAC-seq was digestive system tumors at 14 articles, including gastric cancer (25), pancreatic cancer (29), liver cancer (30), and colorectal cancer (31). Of the included articles, 6, 3, and 2 were on breast cancer, ovarian cancer, and sarcoma, respectively.…”

Section: Characteristics Of Atac-seq-related Articles In Cancer Biologymentioning

confidence: 99%

Bibliometric Analysis of ATAC-Seq and Its Use in Cancer Biology via Nucleic Acid Detection

et al. 2020

View full text Add to dashboard Cite

Assay for transposase-accessible chromatin using sequencing (ATAC-seq) is associated with significant progress in biological research and has attracted increasing attention. However, the impact of ATAC-seq on cancer biology has not been objectively analyzed. We categorized 440 ATAC-seq publications according to the publication date, type, field, and country. R 3.6.2 was used to analyze the distribution of research fields. VOSviewer was used for country co-authorship and author co-authorship analyses, and GraphPad Prism 8 was used for correlation analyses of the factors that may affect the number of articles published in different countries. We found that ATAC-seq plays roles in carcinogenesis, anticancer immunity, targeted therapy, and metastasis risk predictions and is most frequently used in studies of leukemia among all types of cancer. We found a significantly strong correlation between the top 10 countries in terms of the number of publications and the gross expenditure on research and development (R&D), the number of universities, and the number of researchers. At present, ATAC-seq technology is undergoing a period of rapid development, making it inseparable from the emphasis and investment in scientific research by many countries. Collectively, ATAC-seq has advantages in the study of the cancer mechanisms because it can detect nucleic acids and thus has good application prospects in the field of cancer, especially in leukemia studies. As a country's economic strength increases and the emphasis on scientific research deepens, ATAC-seq will definitely play a more significant role in the field of cancer biology.

show abstract

Identification of chromatin‐accessible domains in non‐alcoholic steatohepatitis‐derived hepatocellular carcinoma

Cited by 23 publications

References 57 publications

The Landscape of Chromatin Accessibility in Skeletal Muscle During Embryonic Development in Pigs

The Landscape of Chromatin Accessibility in Skeletal Muscle During Embryonic Development in Pigs

Characterization of the chromatin accessibility in an Alzheimer’s disease (AD) mouse model

Bibliometric Analysis of ATAC-Seq and Its Use in Cancer Biology via Nucleic Acid Detection

Contact Info

Product

Resources

About