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Method: KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
- Samuel H. Kim,
- Georgi K. Marinov,
- and William J. Greenleaf
Genome Res. January 2025 35: 124-134; Published in Advance November 21, 2024, doi:10.1101/gr.279621.124
...of regulatory elements and chromatin states in the human , as well as to estimate the absolute abundance of transcribed and accessible/single-stranded structures. In addition, we map nucleosomal and subnucleosomal structures associated with active transcription and comprehensively measure TF footprints...
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Research: Orc4 spatiotemporally stabilizes centromeric chromatin
- Lakshmi Sreekumar,
- Kiran Kumari,
- Krishnendu Guin,
- Asif Bakshi,
- Neha Varshney,
- Bhagya C. Thimmappa,
- Leelavati Narlikar,
- Ranjith Padinhateeri,
- Rahul Siddharthan,
- and Kaustuv Sanyal
Genome Res. April 2021 31: 607-621; Published in Advance January 29, 2021, doi:10.1101/gr.265900.120
...in 50 regions, 49 of which were found to be located within tRNA gene bodies (tDNAs) and one within the tDNA regulatory region. The most enriched nucleotides of mode A correspond to the third hairpin loop of the tRNA clover structure. The other three modes were low complexity motifs, TGATGA (mode B), CAn...
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Method: Orientation-aware plasma cell-free DNA fragmentation analysis in open chromatin regions informs tissue of origin
- Kun Sun,
- Peiyong Jiang,
- Suk Hang Cheng,
- Timothy H.T. Cheng,
- John Wong,
- Vincent W.S. Wong,
- Simon S.M. Ng,
- Brigette B.Y. Ma,
- Tak Y. Leung,
- Stephen L. Chan,
- Tony S.K. Mok,
- Paul B.S. Lai,
- Henry L.Y. Chan,
- Hao Sun,
- K.C. Allen Chan,
- Rossa W.K. Chiu,
- and Y.M. Dennis Lo
Genome Res. March 2019 29: 418-427; Published in Advance February 26, 2019, doi:10.1101/gr.242719.118
...connected to each other by a relatively short linker DNA, except in active regulatory elements (e.g., open chromatin regions), where nucleosomes are evicted and the nearby nucleosomes will be connected by a much longer stretch of DNA. It is believed that a significant proportion of cfDNA molecules...
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Research: Polycomb repressive complex 1 shapes the nucleosome landscape but not accessibility at target genes
- Hamish W. King,
- Nadezda A. Fursova,
- Neil P. Blackledge,
- and Robert J. Klose
Genome Res. October 2018 28: 1494-1507; Published in Advance August 28, 2018, doi:10.1101/gr.237180.118
.... The position of nucleosomes on DNA and the organization of nucleosomes into higher-order chromatin structures also plays major roles in gene regulation (Kouzarides 2007; Li et al. 2007). For example, nucleosomes can occlude sequence-specific transcription factors and the transcriptional machinery from...
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Research: Distinctive regulatory architectures of germline-active and somatic genes in C. elegans
- Jacques Serizay,
- Yan Dong,
- Jürgen Jänes,
- Michael Chesney,
- Chiara Cerrato,
- and Julie Ahringer
Genome Res. December 2020 30: 1752-1765; Published in Advance October 22, 2020, doi:10.1101/gr.265934.120
...-active promoters have well-positioned +1 and −1 nucleosomes associated with a periodic 10-bp WW signal (W = A/T). Somatic tissue–specific promoters lack positioned nucleosomes and this signal, have wide nucleosome-depleted regions, and are more enriched for core promoter elements, which largely differ between...
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Research: Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation
- Răzvan V. Chereji,
- Peter R. Eriksson,
- Josefina Ocampo,
- Hemant K. Prajapati,
- and David J. Clark
Genome Res. December 2019 29: 1985-1995; Published in Advance September 11, 2019, doi:10.1101/gr.249326.119
...such as promoters and enhancers, blocking access to transcription factors (Fig. 1A). Activation is thought to occur when an ATP-dependent chromatin remodeler removes the blocking nucleosome, allowing transcription factors to bind, although precisely how remodelers are targeted to regulatory elements is still...
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Method: Single-molecule long-read sequencing reveals the chromatin basis of gene expression
- Yunhao Wang,
- Anqi Wang,
- Zujun Liu,
- Andrew L. Thurman,
- Linda S. Powers,
- Meng Zou,
- Yue Zhao,
- Adam Hefel,
- Yunyi Li,
- Joseph Zabner,
- and Kin Fai Au
Genome Res. August 2019 29: 1329-1342; Published in Advance June 14, 2019, doi:10.1101/gr.251116.119
...in two different chromatin accessibility statuses: open (accessible and active genomic regions with sparse nucleosome occupancy); and closed (inaccessible and inactive genomic regions with dense nucleosome occupancy). Positioning of nucleosomes and dynamic changes of chromatin status play important...
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Resource: Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans
- Aaron C. Daugherty,
- Robin W. Yeo,
- Jason D. Buenrostro,
- William J. Greenleaf,
- Anshul Kundaje,
- and Anne Brunet
Genome Res. December 2017 27: 2096-2107; Published in Advance November 15, 2017, doi:10.1101/gr.226233.117
...for the interpretation of chromatin structure in complex multitissue systems in vivo.ResultsHigh-resolution chromatin accessibility profiles from three C. elegans life stagesTo sensitively measure high-resolution chromatin accessibility at different life stages in C. elegans, we used the Assay for Transposase Accessible...
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Research: Ligand-induced native G-quadruplex stabilization impairs transcription initiation
- Conghui Li,
- Honghong Wang,
- Zhinang Yin,
- Pingping Fang,
- Ruijing Xiao,
- Ying Xiang,
- Wen Wang,
- Qiuzi Li,
- Beili Huang,
- Jian Huang,
- and Kaiwei Liang
Genome Res. September 2021 31: 1546-1560; Published in Advance August 16, 2021, doi:10.1101/gr.275431.121
...transcription and may be involved in development processes (Creyghton et al. 2010; Rada-Iglesias et al. 2011; Local et al. 2018). Distribution of G4 in transcription regulatory regions has been associated with chromatin relaxation, because the treatment of cells with the histone deacetylase inhibitor entinostat...
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Research: ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm
- Marta Bozek,
- Roberto Cortini,
- Andrea Ennio Storti,
- Ulrich Unnerstall,
- Ulrike Gaul,
- and Nicolas Gompel
Genome Res. May 2019 29: 771-783; Published in Advance April 8, 2019, doi:10.1101/gr.242362.118
...reduced, does not decrease to the level of background inaccessible regions. Instead, axis patterning enhancers are characterized by an open chromatin structure in both their active and inactive states, although the absolute level of accessibility is unique to each enhancer.Well-positioned nucleosomes...
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