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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
...hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res 16: 123–131. doi:10.1101/gr.4074106 ↵Daley T, Smith AD. 2013. Predicting the molecular complexity of sequencing libraries. Nat Methods 10: 325–327. doi:10.1038/nmeth.2375 ↵Dorschner MO, Hawrylycz M, Humbert R, Wallace JC...
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Method: Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles
- Su Wang,
- Chongzhi Zang,
- Tengfei Xiao,
- Jingyu Fan,
- Shenglin Mei,
- Qian Qin,
- Qiu Wu,
- Xujuan Li,
- Kexin Xu,
- Housheng Hansen He,
- Myles Brown,
- Clifford A. Meyer,
- and X. Shirley Liu
Genome Res. October 2016 26: 1417-1429; Published in Advance July 27, 2016, doi:10.1101/gr.201574.115
...at DNase I hypersensitive sites identified from published human and mouse DNase-seq data. We tested the framework on newly generated RNA-seq and H3K27ac ChIP-seq profiles upon siRNA silencing of multiple transcriptional and epigenetic regulators in a prostate cancer cell line, LNCaP-abl. MARGE-cistrome can...
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Methods: Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns
- Tae-young Roh,
- Gang Wei,
- Catherine M. Farrell,
- and Keji Zhao
Genome Res. January 2007 17: 74-81; Published in Advance November 29, 2006, doi:10.1101/gr.5767907
.... , Margulies, E.H. , Chen, Y. , Bernat, J.A. , Ginsburg, D. , et al. ( 2006 ) Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS) Genome Res. 16 : 123 – 131 . ↵ Dorschner, M.O. , Hawrylycz, M. , Humbert, R. , Wallace, J.C. , Shafer, A. , Kawamoto, J. , Mack, J...
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Methods: Identifying gene regulatory elements by genomic microarray mapping of DNaseI hypersensitive sites
- George A. Follows,
- Pawan Dhami,
- Berthold Göttgens,
- Alexander W. Bruce,
- Peter J. Campbell,
- Shane C. Dillon,
- Aileen M. Smith,
- Christoph Koch,
- Ian J. Donaldson,
- Mike A. Scott,
- Ian Dunham,
- Mary E. Janes,
- David Vetrie,
- and Anthony R. Green
Genome Res. October 2006 16: 1310-1319; Published in Advance September 8, 2006, doi:10.1101/gr.5373606
...the region of the α-globin locus in which DNaseI hypersensitive sites have been systematically mapped, only one novel site (+90) was identified as significantly enriched. This region contains conserved DNA sequences and is acetylated in K562 cells, strongly suggesting that it is also a regulatory element...
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Method: Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers
- Aleksander Jankowski,
- Ewa Szczurek,
- Ralf Jauch,
- Jerzy Tiuryn,
- and Shyam Prabhakar
Genome Res. August 2013 23: 1307-1318; Published in Advance April 3, 2013, doi:10.1101/gr.154922.113
.... 2011). Discussion Genome-wide scans for DNase I hypersensitivity are a powerful tool for mapping cis-regulatory elements with high spatial precision in any given cell type (Crawford et al. 2006). One major advantage of this method is that, when combined with TF–DNA affinity models (motifs), DNase...
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Resource: High-resolution mapping of open chromatin in the rice genome
- Wenli Zhang,
- Yufeng Wu,
- James C. Schnable,
- Zixian Zeng,
- Michael Freeling,
- Gregory E. Crawford,
- and Jiming Jiang
Genome Res. January 2012 22: 151-162; Published in Advance November 22, 2011, doi:10.1101/gr.131342.111
...associated with regulatory proteins is a pronounced sensitivity to DNase I digestion. We generated genome-wide high-resolution maps of DNase I hypersensitive (DH) sites from both seedling and callus tissues of rice ( Oryza sativa ). Approximately 25% of the DH sites from both tissues were found in putative...
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Methods: Detection of DNA structural motifs in functional genomic elements
- Jason A. Greenbaum,
- Stephen C.J. Parker,
- and Thomas D. Tullius
Genome Res. June 2007 17: 940-946; doi:10.1101/gr.5602807
.... ( 2006b ) Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS) Genome Res. 16 : 123 – 131 . ↵ Dorschner, M.O. , Hawrylycz, M. , Humbert, R. , Wallace, J.C. , Shafer, A. , Kawamoto, J. , Mack, J. , Hall, R. , Goldy, J. , Sabo, P.J. , et al. ( 2004 ) High...
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Method: Anchor: trans-cell type prediction of transcription factor binding sites
- Hongyang Li,
- Daniel Quang,
- and Yuanfang Guan
Genome Res. February 2019 29: 281-292; Published in Advance December 19, 2018, doi:10.1101/gr.237156.118
...features are extracted and used in our Anchor scheme (416 sequence-based features + 120 DNase-based features + 20 distance features; see below).Genome-wide quantile normalization of cell-type–specific DNase-seq profilesThe original -wide DNase-seq data of multiple technical and biological replicates from...
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Letter: Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers
- Jérôme Eeckhoute,
- Mathieu Lupien,
- Clifford A. Meyer,
- Michael P. Verzi,
- Ramesh A. Shivdasani,
- X. Shirley Liu,
- and Myles Brown
Genome Res. March 2009 19: 372-380; Published in Advance January 7, 2009, doi:10.1101/gr.084582.108
...(FoxA) and GATA-4 . Mol. Cell 9 : 279 – 289 . ↵ Crawford, G.E. , Holt, I.E. , Whittle, J. , Webb, B.D. , Tai, D. , Davis, S. , Margulies, E.H. , Chen, Y. , Bernat, J.A. , Ginsburg, D. , et al. ( 2006 ) Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS...
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Research: Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis
- Hector L. Franco,
- Anusha Nagari,
- Venkat S. Malladi,
- Wenqian Li,
- Yuanxin Xi,
- Dana Richardson,
- Kendra L. Allton,
- Kaori Tanaka,
- Jing Li,
- Shino Murakami,
- Khandan Keyomarsi,
- Mark T. Bedford,
- Xiaobing Shi,
- Wei Li,
- Michelle C. Barton,
- Sharon Y.R. Dent,
- and W. Lee Kraus
Genome Res. February 2018 28: 159-170; Published in Advance December 22, 2017, doi:10.1101/gr.226019.117
...in at least one other cell line. The colored circles indicate the molecular subtype of each cell line. (C) Metaplot analyses showing correlations among enhancer transcription, DNase I hypersensitivity, H3K27ac enrichment, and H3K4me1 enrichment for the uniquely transcribed enhancers identified in ZR-75...

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