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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
...gene and may potentially reflect altered RNA polymerase II activity in the absence of PRC1 (Fig. 5). Importantly, the relationship between transcriptional activation and altered nucleosome landscape was not observed in PRC2- cells, highlighting that the transcriptionally repressive function of PRC1...
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Research: Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis
- Catia Attanasio,
- Alex S. Nord,
- Yiwen Zhu,
- Matthew J. Blow,
- Simon C. Biddie,
- Eric M. Mendenhall,
- Jesse Dixon,
- Crystal Wright,
- Roya Hosseini,
- Jennifer A. Akiyama,
- Amy Holt,
- Ingrid Plajzer-Frick,
- Malak Shoukry,
- Veena Afzal,
- Bing Ren,
- Bradley E. Bernstein,
- Edward M. Rubin,
- Axel Visel,
- and Len A. Pennacchio
Genome Res. June 2014 24: 920-929; Published in Advance April 21, 2014, doi:10.1101/gr.168930.113
.... 2011. Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1. Genome Res 21: 1650–1658. Kidder BL, Palmer S, Knott JG. 2009. SWI/SNF-Brg1 regulates self-renewal and occupies core pluripotency-related genes in embryonic stem cells. Stem Cells 27: 317...
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Method: Domain-adaptive neural networks improve cross-species prediction of transcription factor binding
- Kelly Cochran,
- Divyanshi Srivastava,
- Avanti Shrikumar,
- Akshay Balsubramani,
- Ross C. Hardison,
- Anshul Kundaje,
- and Shaun Mahony
Genome Res. March 2022 32: 512-523; Published in Advance January 18, 2022, doi:10.1101/gr.275394.121
...genomic locations in mouse and human livers (Schmidt et al. 2010). On the other hand, the general features of tissue-specific regulatory networks appear to be strongly conserved across mammalian species. The amino acid sequences of TF proteins, their DNA-binding domains, and intrinsic DNA sequence...
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Research: Canonical nucleosome organization at promoters forms during genome activation
- Yong Zhang,
- Nadine L. Vastenhouw,
- Jianxing Feng,
- Kai Fu,
- Chenfei Wang,
- Ying Ge,
- Andrea Pauli,
- Paul van Hummelen,
- Alexander F. Schier,
- and X. Shirley Liu
Genome Res. February 2014 24: 260-266; Published in Advance November 27, 2013, doi:10.1101/gr.157750.113
...DE, Cui K, Ybarra R, NorthrupD, TangQ, Gattinoni L, Restifo NP, Huang S, Zhao K. 2011. Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1. Genome Res 21: 1650–1658. Hughes AL, Jin Y, Rando O, Struhl K. 2012. A functional evolutionary approach...
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Method: Mapping transcription factor occupancy using minimal numbers of cells in vitro and in vivo
- Luca Tosti,
- James Ashmore,
- Boon Siang Nicholas Tan,
- Benedetta Carbone,
- Tapan K. Mistri,
- Valerie Wilson,
- Simon R. Tomlinson,
- and Keisuke Kaji
Genome Res. April 2018 28: 592-605; Published in Advance March 23, 2018, doi:10.1101/gr.227124.117
...expression level in a tissue-specific manner in combination with the GAL4-UAS system (Southall et al. 2013). Translation reinitiation takes place as the eukaryotic ribosome does not always detach from mRNA at the stop codon of a first open reading frame (ORF) and can restart translation of a second...
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Method: DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing
- Kaifu Chen,
- Yuanxin Xi,
- Xuewen Pan,
- Zhaoyu Li,
- Klaus Kaestner,
- Jessica Tyler,
- Sharon Dent,
- Xiangwei He,
- and Wei Li
Genome Res. February 2013 23: 341-351; Published in Advance November 28, 2012, doi:10.1101/gr.142067.112
..., DANPOS, explicitly designed for dynamic nucleosome analysis at single-nucleotide resolution. Using both simulated and real nucleosome data, we demonstrated that bias correction in preliminary data processing and optimal statistical testing significantly enhances the functional interpretation of dynamic...
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Research: DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types
- Deborah R. Winter,
- Lingyun Song,
- Sayan Mukherjee,
- Terrence S. Furey,
- and Gregory E. Crawford
Genome Res. July 2013 23: 1118-1129; Published in Advance May 8, 2013, doi:10.1101/gr.150482.112
...DARNS are positioned over only one side of annotated nucleosomes, suggesting that the periodic digestion pattern attenuates over the nucleosome dyad. DARNS reproduce the arrangement of nucleosomes around transcription start sites and are depleted at ubiquitous DHS sites. We also generated DARNS from...
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Method: Sequence and chromatin determinants of cell-type–specific transcription factor binding
- Aaron Arvey,
- Phaedra Agius,
- William Stafford Noble,
- and Christina Leslie
Genome Res. September 2012 22: 1723-1734; doi:10.1101/gr.127712.111
...# 0.6), including RDBP (NELF-E), SMARCB1 (INI1), POLR3, XRCC4, and WRNIP1 (WHIP); fair accuracy (0.6 < AUC < 0.75), including members of the POLR3 initiation complex (BDP1, BRF1, BRF2, SMARCA4 [BRG1]), members of the POLR2 complex (TBP, TAF1, GTF2B), POLR2 itself, and the histone methyltransferase...
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Method: Cross-species analysis of enhancer logic using deep learning
- Liesbeth Minnoye,
- Ibrahim Ihsan Taskiran,
- David Mauduit,
- Maurizio Fazio,
- Linde Van Aerschot,
- Gert Hulselmans,
- Valerie Christiaens,
- Samira Makhzami,
- Monika Seltenhammer,
- Panagiotis Karras,
- Aline Primot,
- Edouard Cadieu,
- Ellen van Rooijen,
- Jean-Christophe Marine,
- Giorgia Egidy,
- Ghanem-Elias Ghanem,
- Leonard Zon,
- Jasper Wouters,
- and Stein Aerts
Genome Res. December 2020 30: 1815-1834; Published in Advance July 30, 2020, doi:10.1101/gr.260844.120
...to cobind, thereby further stabilizing the nucleosome-depleted region and/or actively enhancing transcription of target genes (Grossman et al. 2018; Jacobs et al. 2018; Dodonova et al. 2020).Because the presence and architecture of TF binding sites within enhancers determines which TFs can bind with high...
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Research: Glucocorticoid receptor quaternary structure drives chromatin occupancy and transcriptional outcome
- Ville Paakinaho,
- Thomas A. Johnson,
- Diego M. Presman,
- and Gordon L. Hager
Genome Res. August 2019 29: 1223-1234; Published in Advance July 23, 2019, doi:10.1101/gr.244814.118
...peak and JUN peak is 10 kb. This analysis suggests that GRtetra is less dependent on AP-1, resembling a “pioneer-like” factor.The mouse harbors millions of putative GREs; however, GR binds only a small subset of them in a highly tissue-specific manner. Chromatin landscape appears to be a major...

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