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Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
- Prashanthi Ravichandran,
- Princy Parsana,
- Rebecca Keener,
- Kasper D. Hansen,
- and Alexis Battle
Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
...-specific networks. Central genes in consensus networks are enriched for evolutionarily constrained genes and ubiquitous biological pathways, whereas context-specific central nodes include tissue-specific transcription factors. The increased statistical power from data aggregation facilitates the derivation...
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Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
- Bertille Montibus,
- James A. Cain,
- Rocio T. Martinez-Nunez,
- and Rebecca J. Oakey
Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
...that transcriptional co-occurrence is often tissue specific. This coexpression was especially prevalent within the transcriptionally permissive tissue, testis. We use this developmental system and scRNA-seq analysis to demonstrate that the coexpression of pairs can occur in single cells and transcription in the same...
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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
...indirect or secondary effects. Compared with RNAi or CRISPR knockout, degrons can thus reveal more immediate transcriptional dependencies on the TF of interest.In practice, combining depletion strategies with the precise transcriptional readouts discussed in this section provides a robust framework...
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Research: Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F₁ hybrids
- Carina F. Mugal,
- Mi Wang,
- Niclas Backström,
- David Wheatcroft,
- Murielle Ålund,
- Marie Sémon,
- S. Eryn McFarlane,
- Ludovic Dutoit,
- Anna Qvarnström,
- and Hans Ellegren
Genome Res. December 2020 30: 1727-1739; Published in Advance November 3, 2020, doi:10.1101/gr.254508.119
...analysis of mtDNA sequences revealed that all three F1 hybrids were the result of crosses between a female pied flycatcher and a male collared flycatcher (Supplemental Fig. S1).Tissue-specific patterns of gene expression evolutionPrincipal component analysis (PCA) of gene expression patterns across tissues...
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Method: Targeted single-cell RNA sequencing of transcription factors enhances the identification of cell types and trajectories
- Alexandra Pokhilko,
- Adam E. Handel,
- Fabiola Curion,
- Viola Volpato,
- Emma S. Whiteley,
- Sunniva Bøstrand,
- Sarah E. Newey,
- Colin J. Akerman,
- Caleb Webber,
- Michael B. Clark,
- Rory Bowden,
- and M. Zameel Cader
Genome Res. June 2021 31: 1069-1081; Published in Advance May 19, 2021, doi:10.1101/gr.273961.120
...and their targets from neuron and astrocyte networks (https://github.com/marbach/genecircuits) (Marbach et al. 2016), in which the tissue-specific gene regulatory networks had been inferred by combining transcription factor sequence motifs with activity data for promoters and enhancers from the FANTOM5 project...
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Research: Population and single-cell genomics reveal the Aire dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia
- Stephen N. Sansom,
- Noriko Shikama-Dorn,
- Saule Zhanybekova,
- Gretel Nusspaumer,
- Iain C. Macaulay,
- Mary E. Deadman,
- Andreas Heger,
- Chris P. Ponting,
- and Georg A. Holländer
Genome Res. December 2014 24: 1918-1931; Published in Advance September 15, 2014, doi:10.1101/gr.171645.113
...TEC that mostly co-expressed Aire as identified by immunohistochemistry (Fig. 1B) and by high cell surface concentrations of MHC class II molecules as verified by flow cytometry (Supplemental Figs. 1, 2A). We inspected residual transcription from themodified Aire locus and confirmed it to be largely limited...
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Method: Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding
- J. Omar Yáñez-Cuna,
- Huy Q. Dinh,
- Evgeny Z. Kvon,
- Daria Shlyueva,
- and Alexander Stark
Genome Res. October 2012 22: 2018-2030; Published in Advance April 25, 2012, doi:10.1101/gr.132811.111
...), for which time-, celltype-, or tissue-specific chromatin immunoprecipitation (ChIP) data sets were available. Figure 1. Context-specific Twist binding sites display differential motif content. (A) Twist binding sites identified by ChIP-chip in D. melanogaster embryos (Zinzen et al. 2009) differ between...
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Research: Combinatorial binding of transcription factors in the pluripotency control regions of the genome
- Luciana Ferraris,
- Allan P. Stewart,
- Jinsuk Kang,
- Alec M. DeSimone,
- Matthew Gemberling,
- Dean Tantin,
- and William G. Fairbrother
Genome Res. July 2011 21: 1055-1064; Published in Advance April 28, 2011, doi:10.1101/gr.115824.110
...of cooperativity and competition in the pluripotency network. The most prominent pattern is a pervasive binding competition between POU5F1 and the forkhead transcription factors. Like many transcription factors, POU5F1 is co-expressed with a paralog, POU2F1, that shares an apparently identical binding specificity...
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Research: NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors
- Joseph D. Fleming,
- Giulio Pavesi,
- Paolo Benatti,
- Carol Imbriano,
- Roberto Mantovani,
- and Kevin Struhl
Genome Res. August 2013 23: 1195-1209; Published in Advance April 17, 2013, doi:10.1101/gr.148080.112
...of NF-Y sites are located at enhancers, many of which are tissue specific, and nearly half of the NF-Y sites are in select subclasses of HERV LTR repeats. Unlike most TFs, NF-Y can access its target DNA motif in inactive (nonmodified) or polycomb-repressed chromatin domains. Unexpectedly, NF...
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LETTER: Human gene organization driven by the coordination of replication and transcription
- Maxime Huvet,
- Samuel Nicolay,
- Marie Touchon,
- Benjamin Audit,
- Yves d'Aubenton-Carafa,
- Alain Arneodo,
- and Claude Thermes
Genome Res. September 2007 17: 1278-1285; Published in Advance August 3, 2007, doi:10.1101/gr.6533407
...Fig. S4c–f), since transcription always generates positive S values on the coding strand (and negative ones on the noncoding strand) ( Green et al. 2003 ; Touchon et al. 2003 , 2004 ). Recent studies have revealed the existence of complex networks of unannotated transcripts ( Cheng et al. 2005...

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