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Chromatin accessibility: methods, mechanisms, and biological insights.
Mansisidor AR, Risca VI. Mansisidor AR, et al. Nucleus. 2022 Dec;13(1):236-276. doi: 10.1080/19491034.2022.2143106. Nucleus. 2022. PMID: 36404679 Free PMC article. Review.
Additional mechanisms that may control DNA accessibility in vivo include chromatin compaction and phase separation - processes that are beginning to be understood. Here, we review the ongoing development of accessibility measurements, we summarize the …
Additional mechanisms that may control DNA accessibility in vivo include chromatin compaction and phase separation - pr …
Spatial epigenome-transcriptome co-profiling of mammalian tissues.
Zhang D, Deng Y, Kukanja P, Agirre E, Bartosovic M, Dong M, Ma C, Ma S, Su G, Bao S, Liu Y, Xiao Y, Rosoklija GB, Dwork AJ, Mann JJ, Leong KW, Boldrini M, Wang L, Haeussler M, Raphael BJ, Kluger Y, Castelo-Branco G, Fan R. Zhang D, et al. Nature. 2023 Apr;616(7955):113-122. doi: 10.1038/s41586-023-05795-1. Epub 2023 Mar 15. Nature. 2023. PMID: 36922587 Free PMC article.
Emerging spatial technologies, including spatial transcriptomics and spatial epigenomics, are becoming powerful tools for profiling of cellular states in the tissue context(1-5). However, current methods capture only one layer of omics information at a time, precluding the …
Emerging spatial technologies, including spatial transcriptomics and spatial epigenomics, are becoming powerful tools for profiling of cellu …
Single-cell chromatin accessibility reveals principles of regulatory variation.
Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf WJ. Buenrostro JD, et al. Nature. 2015 Jul 23;523(7561):486-90. doi: 10.1038/nature14590. Epub 2015 Jun 17. Nature. 2015. PMID: 26083756 Free PMC article.
Here we reveal the landscape and principles of mammalian DNA regulatory variation by developing a robust method for mapping the accessible genome of individual cells by assay for transposase-accessible chromatin using sequencing (ATAC-seq) integrated i …
Here we reveal the landscape and principles of mammalian DNA regulatory variation by developing a robust method for mapping the ac
A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids.
Ramdas S, Judd J, Graham SE, Kanoni S, Wang Y, Surakka I, Wenz B, Clarke SL, Chesi A, Wells A, Bhatti KF, Vedantam S, Winkler TW, Locke AE, Marouli E, Zajac GJM, Wu KH, Ntalla I, Hui Q, Klarin D, Hilliard AT, Wang Z, Xue C, Thorleifsson G, Helgadottir A, Gudbjartsson DF, Holm H, Olafsson I, Hwang MY, Han S, Akiyama M, Sakaue S, Terao C, Kanai M, Zhou W, Brumpton BM, Rasheed H, Havulinna AS, Veturi Y, Pacheco JA, Rosenthal EA, Lingren T, Feng Q, Kullo IJ, Narita A, Takayama J, Martin HC, Hunt KA, Trivedi B, Haessler J, Giulianini F, Bradford Y, Miller JE, Campbell A, Lin K, Millwood IY, Rasheed A, Hindy G, Faul JD, Zhao W, Weir DR, Turman C, Huang H, Graff M, Choudhury A, Sengupta D, Mahajan A, Brown MR, Zhang W, Yu K, Schmidt EM, Pandit A, Gustafsson S, Yin X, Luan J, Zhao JH, Matsuda F, Jang HM, Yoon K, Medina-Gomez C, Pitsillides A, Hottenga JJ, Wood AR, Ji Y, Gao Z, Haworth S, Mitchell RE, Chai JF, Aadahl M, Bjerregaard AA, Yao J, Manichaikul A, Lee WJ, Hsiung CA, Warren HR, Ramirez J, Bork-Jensen J, Kårhus LL, Goel A, Sabater-Lleal M, Noordam R, Mauro P, Matteo F, McDaid AF, Marques-Vidal P, Wielscher M, Trompet S, Sattar N, Møllehave LT, Munz M, Zeng L, Huang J, Yang B, Poved… See abstract for full author list ➔ Ramdas S, et al. Am J Hum Genet. 2022 Aug 4;109(8):1366-1387. doi: 10.1016/j.ajhg.2022.06.012. Am J Hum Genet. 2022. PMID: 35931049 Free PMC article.
A major challenge of genome-wide association studies (GWASs) is to translate phenotypic associations into biological insights. Here, we integrate a large GWAS on blood lipids involving 1.6 million individuals from five ancestries with a wide array of functional geno …
A major challenge of genome-wide association studies (GWASs) is to translate phenotypic associations into biological insights. …
Lineage Tracing and Single-Nucleus Multiomics Reveal Novel Features of Adaptive and Maladaptive Repair after Acute Kidney Injury.
Gerhardt LMS, Koppitch K, van Gestel J, Guo J, Cho S, Wu H, Kirita Y, Humphreys BD, McMahon AP. Gerhardt LMS, et al. J Am Soc Nephrol. 2023 Apr 1;34(4):554-571. doi: 10.1681/ASN.0000000000000057. Epub 2023 Jan 13. J Am Soc Nephrol. 2023. PMID: 36735940
The authors used lineage tracing of cycling cells and single-nucleus multiomics (profiling transcriptome and chromatin accessibility) after AKI. They demonstrated that AKI triggers a cell-cycle response in most epithelial and nonepithelial kidney cell types. ...Howe …
The authors used lineage tracing of cycling cells and single-nucleus multiomics (profiling transcriptome and chromatin accessibili
Chromatin accessibility in neuropsychiatric disorders.
Egervari G. Egervari G. Neurobiol Learn Mem. 2021 May;181:107438. doi: 10.1016/j.nlm.2021.107438. Epub 2021 Apr 15. Neurobiol Learn Mem. 2021. PMID: 33845131 Free PMC article. Review.
Due to the extreme complexity of the epigenetic regulatory landscape, emerging methods that directly assay chromatin accessibility are of particular interest. Here, I review recent insights gained on open and closed chromatin states in the brain …
Due to the extreme complexity of the epigenetic regulatory landscape, emerging methods that directly assay chromatin access
Higher order assembly: folding the chromosome.
Sewitz SA, Fahmi Z, Lipkow K. Sewitz SA, et al. Curr Opin Struct Biol. 2017 Feb;42:162-168. doi: 10.1016/j.sbi.2017.02.004. Epub 2017 Mar 8. Curr Opin Struct Biol. 2017. PMID: 28284913 Free article. Review.
The linear molecules of DNA that constitute a eukaryotic genome have to be carefully organised within the nucleus to be able to correctly direct gene expression. Microscopy and chromosome capture methods have revealed a hierarchical organisation into territories, domains a …
The linear molecules of DNA that constitute a eukaryotic genome have to be carefully organised within the nucleus to be able to correctly di …
Nucleosome remodelling: structural insights into ATP-dependent remodelling enzymes.
Sundaramoorthy R. Sundaramoorthy R. Essays Biochem. 2019 Apr 23;63(1):45-58. doi: 10.1042/EBC20180059. Print 2019 Apr 23. Essays Biochem. 2019. PMID: 30967479 Review.
ATP-dependent chromatin remodelling enzymes play a fundamental role in determining how nucleosomes are organised, and render DNA sequences accessible to interacting proteins, thereby enabling precise regulation of eukaryotic genes. ...In this article, we highlight s …
ATP-dependent chromatin remodelling enzymes play a fundamental role in determining how nucleosomes are organised, and render DNA sequ …
Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping.
Zhao Q, Dacre M, Nguyen T, Pjanic M, Liu B, Iyer D, Cheng P, Wirka R, Kim JB, Fraser HB, Quertermous T. Zhao Q, et al. Genome Biol. 2020 Jun 8;21(1):135. doi: 10.1186/s13059-020-02049-5. Genome Biol. 2020. PMID: 32513244 Free PMC article.
RESULTS: We use a pooling approach with HCASMC lines to map regulatory variants that mediate binding of the CAD-associated transcription factor TCF21 with ChIPseq studies (bQTLs), variants that regulate chromatin accessibility with ATACseq studies (caQTLs), and chro …
RESULTS: We use a pooling approach with HCASMC lines to map regulatory variants that mediate binding of the CAD-associated transcription fac …
Chromatin Accessibility and Transcriptional Landscape during Inhibition of Salmonella enterica by Lactobacillus reuteri in IPEC-J2 Cells.
Qin W, Ren Z, Xu C, Cao YN, Sun MA, Huang R, Bao W. Qin W, et al. Cells. 2023 Mar 22;12(6):968. doi: 10.3390/cells12060968. Cells. 2023. PMID: 36980306 Free PMC article.
Using the porcine intestinal cell line IPEC-J2 as a model, we combined RNA-seq and ATAC-seq methods to delineate the porcine genome-wide changes in biological processes and chromatin accessibility in IPEC-J2 cells stimulated by Salmonella enterica BNCC …
Using the porcine intestinal cell line IPEC-J2 as a model, we combined RNA-seq and ATAC-seq methods to delineate the porcine genome-w …
65 results