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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
..., hinging on the precise binding of transcription factors (TFs) and cofactors to gene regulatory elements such as promoters and enhancers. Although it is relatively routine to profile -wide DNA binding landscapes of proteins, identifying the specific proteins that bind to, and regulate the transcription of...
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Method: Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories
- Borislav Hrisimirov Hristov,
- William Stafford Noble,
- and Alessandro Bertero
Genome Res. October 2024 34: 1610-1623; Published in Advance September 25, 2024, doi:10.1101/gr.278327.123
...such as DNA loops and topologically associating domains. Interchromosomal (trans) contacts have received much less attention, and tools for interrogating potential biologically relevant trans structures are lacking. Here, we develop a computational framework that uses Hi-C data to identify sets of loci...
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Resource: Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish
- Hyung Joo Lee,
- Yiran Hou,
- Ju Heon Maeng,
- Nakul M. Shah,
- Yujie Chen,
- Heather A. Lawson,
- Hongbo Yang,
- Feng Yue,
- and Ting Wang
Genome Res. July 2022 32: 1424-1436; Published in Advance June 1, 2022, doi:10.1101/gr.276052.121
...analysis of zebrafish TEs in the context of gene regulation is lacking. Here, we systematically investigate the epigenomic and transcriptomic landscape of TEs across 11 adult zebrafish tissues using multidimensional sequencing data. We find that TEs contribute substantially to a diverse array of regulatory...
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Research: High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity
- Kaia Mattioli,
- Pieter-Jan Volders,
- Chiara Gerhardinger,
- James C. Lee,
- Philipp G. Maass,
- Marta Melé,
- and John L. Rinn
Genome Res. March 2019 29: 344-355; Published in Advance January 25, 2019, doi:10.1101/gr.242222.118
...of promoters and enhancers (Nguyen et al. 2016; Arnold et al. 2017), but to date a systematic analysis of whether intrinsic features of DNA sequence are responsible for differential activity at lncRNA promoters, protein-coding gene promoters, and enhancers has not been performed.ResultsDivergent lncRNA core...
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Method: Systematic evaluation of the effect of polyadenylation signal variants on the expression of disease-associated genes
- Meng Chen,
- Ran Wei,
- Gang Wei,
- Mingqing Xu,
- Zhixi Su,
- Chen Zhao,
- and Ting Ni
Genome Res. May 2021 31: 890-899; Published in Advance April 19, 2021, doi:10.1101/gr.270256.120
...CS. 2005. A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res 33: 201–212. doi:10.1093/nar/gki158 ↵Tian J, Chang J, Gong J, Lou J, Fu M, Li J, Ke J, Zhu Y, Gong Y, Yang Y. 2019. Systematic functional interrogation of genes in GWAS loci identified ATF1 as a key...
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Resource: The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements
- Stefan Schoenfelder,
- Mayra Furlan-Magaril,
- Borbala Mifsud,
- Filipe Tavares-Cadete,
- Robert Sugar,
- Biola-Maria Javierre,
- Takashi Nagano,
- Yulia Katsman,
- Moorthy Sakthidevi,
- Steven W. Wingett,
- Emilia Dimitrova,
- Andrew Dimond,
- Lucas B. Edelman,
- Sarah Elderkin,
- Kristina Tabbada,
- Elodie Darbo,
- Simon Andrews,
- Bram Herman,
- Andy Higgs,
- Emily LeProust,
- Cameron S. Osborne,
- Jennifer A. Mitchell,
- Nicholas M. Luscombe,
- and Peter Fraser
Genome Res. April 2015 25: 582-597; Published in Advance March 9, 2015, doi:10.1101/gr.185272.114
...interactions in 3C/Hi-C libraries, but a -wide approach enabling the systematic, unbiased, and high-resolution interrogation of chromosomal interactions for tens of thousands of genomic elements simultaneously, independent of their activity or bound proteins, is currently lacking. Here we combine Hi...
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Research: Asymmetric nucleosomes flank promoters in the budding yeast genome
- Srinivas Ramachandran,
- Gabriel E. Zentner,
- and Steven Henikoff
Genome Res. March 2015 25: 381-390; Published in Advance December 9, 2014, doi:10.1101/gr.182618.114
...Asymmetric nucleosomes flank promoters in the budding yeast genome Srinivas Ramachandran 1 , Gabriel E. Zentner 1 and Steven Henikoff 1 , 2 1 Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109...
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Resource: A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination
- Desislava P. Staneva,
- Roberta Carloni,
- Tatsiana Auchynnikava,
- Pin Tong,
- Juri Rappsilber,
- A. Arockia Jeyaprakash,
- Keith R. Matthews,
- and Robin C. Allshire
Genome Res. November 2021 31: 2138-2154; Published in Advance August 18, 2021, doi:10.1101/gr.275368.121
...suggest parallels to RNAPII promoter–associated complexes in conventional eukaryotes. Further, we identify likely components of TbSWR1 and TbNuA4 complexes whose enrichment coincides with the SWR1-C exchange substrate H2A.Z at RNAPII transcription start regions. The systematic approach used provides...
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Research: Recurrent epimutations activate gene body promoters in primary glioblastoma
- Raman P. Nagarajan,
- Bo Zhang,
- Robert J.A. Bell,
- Brett E. Johnson,
- Adam B. Olshen,
- Vasavi Sundaram,
- Daofeng Li,
- Ashley E. Graham,
- Aaron Diaz,
- Shaun D. Fouse,
- Ivan Smirnov,
- Jun Song,
- Pamela L. Paris,
- Ting Wang,
- and Joseph F. Costello
Genome Res. May 2014 24: 761-774; Published in Advance April 7, 2014, doi:10.1101/gr.164707.113
...is assayed by the array at four CpG sites including three in the hypomethylated region that we previously validated with bisulfite sequencing (Fig. 5B,C). In addition, four of nine 59 promoter probes interrogate a region where we observed recurring hypermethylation of ;1 kb of the 3191-bp 59 CGI...
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Research: Epigenetic characterization of pseudogenes across human tissues
- Yunzhe Jiang,
- Beatrice Borsari,
- and Mark Gerstein
Genome Res. April 15, 2026 gr.280768.125; Published in Advance April 15, 2026, doi:10.1101/gr.280768.125
..., relative to other noncoding genomic elements, their promoter architecture and epigenetic regulation remain incompletely understood. Here, we systematically characterize pseudogene promoters and compare them with those of protein-coding genes and long noncoding RNAs. To do this, we integrate matched...
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