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Research: Evidence for compensatory evolution within pleiotropic regulatory elements
- Zane Kliesmete,
- Peter Orchard,
- Victor Yan Kin Lee,
- Johanna Geuder,
- Simon M. Krauß,
- Mari Ohnuki,
- Jessica Jocher,
- Beate Vieth,
- Wolfgang Enard,
- and Ines Hellmann
Genome Res. October 2024 34: 1528-1539; Published in Advance September 10, 2024, doi:10.1101/gr.279001.124
...of the best predictors for protein sequence and expression conservation. In this study, we investigated its effect on the evolution of cis-regulatory elements (CREs). To this end, we carefully reanalyzed the Epigenomics Roadmap data for nine fetal tissues, assigning a measure of pleiotropic degree to nearly...
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Method: Designing realistic regulatory DNA with autoregressive language models
- Avantika Lal,
- David Garfield,
- Tommaso Biancalani,
- and Gokcen Eraslan
Genome Res. September 2024 34: 1411-1420; Published in Advance September 25, 2024, doi:10.1101/gr.279142.124
...characterization of transcriptional regulatory elements in three diverse human cell types. bioRxiv doi:10.1101/2023.03.05.531189 ↵Avsec Ž, Agarwal V, Visentin D, Ledsam JR, Grabska-Barwinska A, Taylor KR, Assael Y, Jumper J, Kohli P, Kelley DR. 2021a. Effective gene expression prediction from sequence...
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Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
- Olga M. Sigalova,
- Mattia Forneris,
- Frosina Stojanovska,
- Bingqing Zhao,
- Rebecca R. Viales,
- Adam Rabinowitz,
- Fayrouz Hammal,
- Benoît Ballester,
- Judith B. Zaugg,
- and Eileen E.M. Furlong
Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
.... 2016) and patient tissues (Cavalli et al. 2016). In addition to pinpointing direct genetic effects within the TF's motif, F1 studies can also give more context by revealing new potential cooperative TF pairs, as shown for three liver-specific factors in mouse F1 hybrids (Wong et al. 2017) and three...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...and total number of subfamilies tested are given in square brackets next to the superfamily codes. Number of regulatory active fragments are given for each category (n). (E–G) TF motif enrichment in transcriptionally inducing MPRA fragments from TE superfamilies enriched in regulatory active fragments. TF...
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Research: Replication timing networks reveal a link between transcription regulatory circuits and replication timing control
- Juan Carlos Rivera-Mulia,
- Sebo Kim,
- Haitham Gabr,
- Abhijit Chakraborty,
- Ferhat Ay,
- Tamer Kahveci,
- and David M. Gilbert
Genome Res. September 2019 29: 1415-1428; Published in Advance August 21, 2019, doi:10.1101/gr.247049.118
...of interactions that form specific functional subnetwork communities. We also constructed directional regulatory networks based on the order of RT changes within cell lineages, and identified master regulators of differentiation pathways. Finally, we explored relationships between RT networks and transcriptional...
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Resource: An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants
- Can Yuan,
- Lijing Tang,
- Thomas Lopdell,
- Vyacheslav A. Petrov,
- Claire Oget-Ebrad,
- Gabriel Costa Monteiro Moreira,
- José Luis Gualdrón Duarte,
- Arnaud Sartelet,
- Zhangrui Cheng,
- Mazdak Salavati,
- D. Claire Wathes,
- Mark A. Crowe,
- GplusE Consortium,
- Wouter Coppieters,
- Mathew Littlejohn,
- Carole Charlier,
- Tom Druet,
- Michel Georges,
- and Haruko Takeda
Genome Res. October 2023 33: 1848-1864; Published in Advance September 26, 2023, doi:10.1101/gr.277947.123
...sequencing (ATAC-seq). We regroup these regulatory elements in 16 components by nonnegative matrix factorization. Correlation between the -wide density of peaks and transcription start sites, correlation between peak accessibility and expression of neighboring genes, and enrichment in transcription factor...
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Method: Dynamic regulatory module networks for inference of cell type–specific transcriptional networks
- Alireza Fotuhi Siahpirani,
- Sara Knaack,
- Deborah Chasman,
- Morten Seirup,
- Rupa Sridharan,
- Ron Stewart,
- James Thomson,
- and Sushmita Roy
Genome Res. July 2022 32: 1367-1384; Published in Advance June 15, 2022, doi:10.1101/gr.276542.121
...-range predictions (Whalen et al. 2016; Zhang et al. 2019). Another direction would be to use more generic sequence features, such as k-mers (Setty and Leslie 2015) or deep learning models (Avsec et al. 2021), to enable the discovery of novel regulatory elements and offer great flexibility in capturing sequence...
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Research: Evolution of transcription factor binding through sequence variations and turnover of binding sites
- Gat Krieger,
- Offir Lupo,
- Patricia Wittkopp,
- and Naama Barkai
Genome Res. June 2022 32: 1099-1111; Published in Advance May 26, 2022, doi:10.1101/gr.276715.122
...attributes such as transcription factor (TF) binding sites. Here, we systematically link variations in cis-regulatory sequences to TF binding by profiling the allele-specific binding of 27 TFs expressed in a yeast hybrid, in which two related s are present within the same nucleus. TFs localize preferentially...
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Method: Evidence of widespread, independent sequence signature for transcription factor cobinding
- Manqi Zhou,
- Hongyang Li,
- Xueqing Wang,
- and Yuanfang Guan
Genome Res. February 2021 31: 265-278; Published in Advance December 10, 2020, doi:10.1101/gr.267310.120
...complexes. We found the motif sequence signatures and the TFs are rarely mutual, corroborating a hierarchical and directional organization of the regulatory network and refuting the possibility of artifacts caused by shared sequence similarity with the TFs under investigation. We modeled such regulatory...
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Research: The logic of transcriptional regulator recruitment architecture at cis-regulatory modules controlling liver functions
- Julie Dubois-Chevalier,
- Vanessa Dubois,
- Hélène Dehondt,
- Parisa Mazrooei,
- Claire Mazuy,
- Aurélien A. Sérandour,
- Céline Gheeraert,
- Penderia Guillaume,
- Eric Baugé,
- Bruno Derudas,
- Nathalie Hennuyer,
- Réjane Paumelle,
- Guillemette Marot,
- Jason S. Carroll,
- Mathieu Lupien,
- Bart Staels,
- Philippe Lefebvre,
- and Jérôme Eeckhoute
Genome Res. June 2017 27: 985-996; Published in Advance April 11, 2017, doi:10.1101/gr.217075.116
...Fig. S17C), which has been described as a distinctive feature of promoters harboring transcriptionally permissive chromatin states and which could provide specific regulatorymechanisms to housekeeping genes (Deaton and Bird 2011; Beck et al. 2014). While our study has allowed us to draw general...

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