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Method: Genome-wide cancer-specific chromatin accessibility patterns derived from archival processed xenograft tumors
- Shelsa S. Marcel,
- Austin L. Quimby,
- Melodie P. Noel,
- Oscar C. Jaimes,
- Marjan Mehrab-Mohseni,
- Suud A. Ashur,
- Brian Velasco,
- James K. Tsuruta,
- Sandeep K. Kasoji,
- Charlene M. Santos,
- Paul A. Dayton,
- Joel S. Parker,
- Ian J. Davis,
- and Samantha G. Pattenden
Genome Res. December 2021 31: 2327-2339; Published in Advance November 23, 2021, doi:10.1101/gr.275219.121
...transcriptional and chromatin differences between cells in culture and grown as xenografts.View larger version: In this window In a new window Figure 4. Nanodroplet FAIRE identifies cell-type-specific regions of accessible chromatin from FFPE xenograft tissue. (A) Normalized FAIRE-seq sequencing tracks of EWS894...
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Method: A synergistic DNA logic predicts genome-wide chromatin accessibility
- Tatsunori Hashimoto,
- Richard I. Sherwood,
- Daniel D. Kang,
- Nisha Rajagopal,
- Amira A. Barkal,
- Haoyang Zeng,
- Bart J.M. Emons,
- Sharanya Srinivasan,
- Tommi Jaakkola,
- and David K. Gifford
Genome Res. October 2016 26: 1430-1440; Published in Advance July 25, 2016, doi:10.1101/gr.199778.115
...-mers in the vicinity (Fig. 1A). Once the SCM has discovered the chromatin accessibility code words and their spatial patterns from cell-type–specific training data, it can output predicted chromatin accessibility patterns for any DNA sequence, be it genomic DNA or novel DNA sequence. Since our model is trained...
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Method: Profiling single-cell histone modifications using indexing chromatin immunocleavage sequencing
- Wai Lim Ku,
- Lixia Pan,
- Yaqiang Cao,
- Weiwu Gao,
- and Keji Zhao
Genome Res. October 2021 31: 1831-1842; Published in Advance April 14, 2021, doi:10.1101/gr.260893.120
...cells showed a genomic profile highly similar to that of the corresponding bulk cells at the cell type–specific gene loci including PAX5, CD19, CD14, CD93, CD3D, CD5, TBX21, and NCR1 (Fig. 3C). By comparing the cell type–specific peaks identified from the ENCODE data and cluster-specific peaks...
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Resource: Genome-wide discovery of active regulatory elements and transcription factor footprints in Caenorhabditis elegans using DNase-seq
- Margaret C.W. Ho,
- Porfirio Quintero-Cadena,
- and Paul W. Sternberg
Genome Res. December 2017 27: 2108-2119; Published in Advance October 26, 2017, doi:10.1101/gr.223735.117
...–treated chromatin (DNase-seq) allows high-resolution measurement of chromatin accessibility to DNase I cleavage, permitting identification of de novo active cis-regulatory modules (CRMs) and individual transcription factor (TF) binding sites. We adapted DNase-seq to nuclei isolated from C. elegans embryos and L1...
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Method: Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing
- Shilin Zhang,
- Yichen Wang,
- Lin Jia,
- Xue Wen,
- Zhonghua Du,
- Cong Wang,
- Yajing Hao,
- Dehai Yu,
- Lei Zhou,
- Naifei Chen,
- Jingcheng Chen,
- Huiling Chen,
- Hui Zhang,
- Ilkay Celik,
- Günhan Gülsoy,
- Jianjun Luo,
- Baoming Qin,
- Xueling Cui,
- Zhonghui Liu,
- Songling Zhang,
- Miguel A. Esteban,
- Ferhat Ay,
- Wei Xu,
- Runsheng Chen,
- Wei Li,
- Andrew R. Hoffman,
- Ji-Fan Hu,
- and Jiuwei Cui
Genome Res. September 2019 29: 1521-1532; Published in Advance July 17, 2019, doi:10.1101/gr.244996.118
...is organized as a highly dynamic structure in a cell-type–specific manner and is tightly coupled with gene transcription (Cavalli and Misteli 2013; Sawyer and Dundr 2017; Wang et al. 2017; Watson and Tsai 2017). Chromatin domains can be subdivided into transcriptionally active and inactive territories based...
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Resource: Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis
- Riu Yamashita,
- Nuankanya P. Sathira,
- Akinori Kanai,
- Kousuke Tanimoto,
- Takako Arauchi,
- Yoshiaki Tanaka,
- Shin-ichi Hashimoto,
- Sumio Sugano,
- Kenta Nakai,
- and Yutaka Suzuki
Genome Res. May 2011 21: 775-789; Published in Advance March 3, 2011, doi:10.1101/gr.110254.110
...investigated cell types increased, the frequencywithwhich they were identified in multiple cell types increased (Fig. 1F). Some promoters function at very low levels in a highly cell type-specific manner (Landry et al. 2003; Davuluri et al. 2008). Nevertheless, we were concerned that many of the minor TSCs...
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Research: Genome-wide mapping of human DNA-replication origins: Levels of transcription at ORC1 sites regulate origin selection and replication timing
- Gaetano Ivan Dellino,
- Davide Cittaro,
- Rossana Piccioni,
- Lucilla Luzi,
- Stefania Banfi,
- Simona Segalla,
- Matteo Cesaroni,
- Ramiro Mendoza-Maldonado,
- Mauro Giacca,
- and Pier Giuseppe Pelicci
Genome Res. January 2013 23: 1-11; Published in Advance November 27, 2012, doi:10.1101/gr.142331.112
...IP from low-density chromatin fractions allows ORI purification. Genome-wide validation of the newly identified ORIs Our finding that randomly selected ORC1 binding regions are active ORIs suggests that the ORC1 data set identifies ORIs on a -wide scale. Unfortunately, we could not test this Figure 2...
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Research: PR-DUB maintains the expression of critical genes through FOXK1/2- and ASXL1/2/3-dependent recruitment to chromatin and H2AK119ub1 deubiquitination
- Petros Kolovos,
- Koutarou Nishimura,
- Aditya Sankar,
- Simone Sidoli,
- Paul A. Cloos,
- Kristian Helin,
- and Jesper Christensen
Genome Res. August 2020 30: 1119-1130; Published in Advance August 3, 2020, doi:10.1101/gr.261016.120
...in instructing cell type–specific gene expression patterns (Niwa 2018; Stadhouders et al. 2019). In addition, chromatin undergoes covalent histone modifications and DNA methylation, which further recruit chromatin modifying factors to impart precise catalysis of transcription and enhance or repress gene...
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Research: Differences in firing efficiency, chromatin, and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins
- Joana Sequeira-Mendes,
- Zaida Vergara,
- Ramon Peiró,
- Jordi Morata,
- Irene Aragüez,
- Celina Costas,
- Raul Mendez-Giraldez,
- Josep M. Casacuberta,
- Ugo Bastolla,
- and Crisanto Gutierrez
Genome Res. May 2019 29: 784-797; Published in Advance March 7, 2019, doi:10.1101/gr.240986.118
...stages and types. Our enhanced procedure yielded sufficient amounts of clean NS samples (Methods; Fig. 1A; Supplemental Fig. S1). Briefly, after nuclei purification, NS were purified from DNA replication bubbles by sucrose gradient centrifugation to isolate DNA fragments of appropriate size in several...
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Research: Dynamics of chromatin accessibility and long-range interactions in response to glucocorticoid pulsing
- Diana A. Stavreva,
- Antoine Coulon,
- Songjoon Baek,
- Myong-Hee Sung,
- Sam John,
- Lenka Stixova,
- Martina Tesikova,
- Ofir Hakim,
- Tina Miranda,
- Mary Hawkins,
- John A. Stamatoyannopoulos,
- Carson C. Chow,
- and Gordon L. Hager
Genome Res. June 2015 25: 845-857; Published in Advance February 12, 2015, doi:10.1101/gr.184168.114
...with GR regulatory elements (GREs) for chromatin conformation and for the lifetime of the GR-induced hypersensitivity are largely unknown. Chromatin conformation determines access to a variety of DNA regulatory elements, shaping transcriptional responses in a tissue- and cell-type-specific manner (Stalder...

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