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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 nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat Genet 46: 1311–1320. doi:10.1038/ng.3142 ↵Crawford GE, Holt IE, Whittle J, Webb BD, Tai D, Davis S, Margulies EH, Chen Y, Bernat JA, Ginsburg D, et al. 2006. Genome-wide mapping of DNase...
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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
...and methylome analyses in oocytes revealed that DNA methylation is primarily restricted to transcribed regions (Kobayashi et al. 2012). These transcription events reshape the histone methylation landscape, guiding the DNMT complex to specific genomic regions. Specifically, the transcription-coupled loss of H3K4...
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Research: Genome-wide promoter assembly in E. coli measured at single-base resolution
- Jordan John,
- Javaid Jabbar,
- Nitika Badjatia,
- Matthew J. Rossi,
- William K.M. Lai,
- and B. Franklin Pugh
Genome Res. May 2022 32: 878-892; Published in Advance April 28, 2022, doi:10.1101/gr.276544.121
...). Although mechanisms for how sigma factors direct RNAP to promoters and initiate transcription have been well established through biochemical assays, supporting evidence for the applicability of such models on a genomic scale in vivo is limited, owing in part to the low resolution of -wide assays.Genome-wide...
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Research: Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation
- Vanessa L. Porter,
- Michelle Ng,
- Kieran O'Neill,
- Signe MacLennan,
- Richard D. Corbett,
- Luka Culibrk,
- Zeid Hamadeh,
- Marissa Iden,
- Rachel Schmidt,
- Shirng-Wern Tsaih,
- Carolyn Nakisige,
- Martin Origa,
- Jackson Orem,
- Glenn Chang,
- Jeremy Fan,
- Ka Ming Nip,
- Vahid Akbari,
- Simon K. Chan,
- James Hopkins,
- Richard A. Moore,
- Eric Chuah,
- Karen L. Mungall,
- Andrew J. Mungall,
- Inanc Birol,
- Steven J.M. Jones,
- Janet S. Rader,
- and Marco A. Marra
Genome Res. April 2025 35: 653-670; Published in Advance December 5, 2024, doi:10.1101/gr.279041.124
...-like integration events (Supplemental Tables S9, S10). The integration events are oriented according to the direction of HPV transcription. In transcribed events, we observed that human regions upstream of HPV transcription were methylated, while human regions downstream from HPV transcription were unmethylated...
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Research: Genome-wide uniformity of human ‘open’ pre-initiation complexes
- William K.M. Lai and
- B. Franklin Pugh
Genome Res. January 2017 27: 15-26; Published in Advance November 10, 2016, doi:10.1101/gr.210955.116
.... The initiation and pause regions are highlighted in gray and yellow, respectively. Genome-wide human transcription initiation Genome Research 21 www..org state. If true, INRs (focused initiation) might utilize globally nonspecific sequences embedded in an “anti-INR” environment, thereby making them locally...
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Research: Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans
- Kristina Krassovsky,
- Rajarshi P. Ghosh,
- and Barbara J. Meyer
Genome Res. July 2021 31: 1187-1202; Published in Advance June 24, 2021, doi:10.1101/gr.270082.120
...overwind or underwind DNA, creating DNA supercoils (Kouzine and Levens 2007). Supercoils can, in turn, induce formation of single-stranded DNA (ssDNA, hereafter SS DNA) or other non-B DNA structures.Genome-wide mapping of alternative DNA structures in cell lines and computational predictions in s suggested...
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Research: Genome wide analysis of 3′ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish
- Charles E. Vejnar,
- Mario Abdel Messih,
- Carter M. Takacs,
- Valeria Yartseva,
- Panos Oikonomou,
- Romain Christiano,
- Marlon Stoeckius,
- Stephanie Lau,
- Miler T. Lee,
- Jean-Denis Beaudoin,
- Damir Musaev,
- Hiba Darwich-Codore,
- Tobias C. Walther,
- Saeed Tavazoie,
- Daniel Cifuentes,
- and Antonio J. Giraldez
Genome Res. July 2019 29: 1100-1114; Published in Advance June 21, 2019, doi:10.1101/gr.245159.118
...transcription (2 and 6 hpf) in wild-type, α-amanitin, or LNA430-injected zebrafish embryos. Depletion or enrichment of sequences over developmental time revealed 1404 destabilizing and 295 stabilizing regions, respectively, across 3456 genes. Destabilizing regions were modulated by the maternal (593), zygotic...
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Research: Noncoding transcription influences the replication initiation program through chromatin regulation
- Julien Soudet,
- Jatinder Kaur Gill,
- and Françoise Stutz
Genome Res. December 2018 28: 1882-1893; Published in Advance November 6, 2018, doi:10.1101/gr.239582.118
...initiation takes place at several dispersed locations termed replication origins. Origins are defined by a specific chromatin structure consisting of a nucleosome-depleted region (NDR) and the binding of specific replication initiation factors. In Saccharomyces cerevisiae, replication origins or ARSs...
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Research: Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution
- Chang Liu,
- Congmao Wang,
- George Wang,
- Claude Becker,
- Maricris Zaidem,
- and Detlef Weigel
Genome Res. August 2016 26: 1057-1068; Published in Advance May 25, 2016, doi:10.1101/gr.204032.116
...Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution Chang Liu 1 , 2 , Congmao Wang 1 , 3 , George Wang 1 , Claude Becker 1 , Maricris Zaidem 1 and Detlef Weigel 1 1...
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Research: Rtt109 promotes nucleosome replacement ahead of the replication fork
- Felix Jonas,
- Gilad Yaakov,
- and Naama Barkai
Genome Res. June 2022 32: 1089-1098; Published in Advance May 24, 2022, doi:10.1101/gr.276674.122
...al. 2021).The fact that Rtt109 acts on unbound H3 suggests that it plays a role in H3 incorporation. Consistent with such a role, H3K56 acetylation increases the affinity of H3 toward CAF1, the histone chaperone incorporating histones at the replication fork (Li et al. 2008; Han et al. 2013). Genome-wide...

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