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Method: Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle
- Sotiria Milia,
- Alexander S. Leonard,
- Xena Marie Mapel,
- Sandra Milena Bernal Ulloa,
- Cord Drögemüller,
- and Hubert Pausch
Genome Res. April 2025 35: 1041-1052; Published in Advance December 18, 2024, doi:10.1101/gr.279064.124
...assembly path similarities within the graph to reveal an association between two most likely serial alleles of a complex structural variant (SV) 66 kb upstream of KIT and facial depigmentation. The complex SV contains a variable number of tandemly duplicated 14.3 kb repeats, consisting of LTRs, LINEs...
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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
...on potentially misleading predictions.Prediction of potential regulatory sitesThis review focuses on gene-specific transcriptional regulation via direct TF binding to regulatory DNA sites. The initial task is thus to locate candidate DNA regions potentially involved in TF binding, and this starts...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
.... Additionally, although we expected an increase in TF occupancy at the PHO8 promoter because it was upregulated, this increased occupancy extended well into the shared promoter of CWC21–KRE2 (Supplemental Fig. S9). This suggests that the regulation of CWC21–KRE2 may be impacted by the transcriptional mechanisms...
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Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
....We initially used this strategy to analyze the 48 h cellular deamination samples. This analysis revealed high levels of dCPDs within genes but lower levels of dCPDs immediately upstream of the TSS and flanking the TES (Fig. 4A). To test whether this was merely a consequence of differences in DNA 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
...genetic variation impacts transcription factor (TF) binding remains a major challenge, limiting our ability to model disease-associated variants. Here, we used a highly controlled system of F1 crosses with extensive genetic diversity to profile allele-specific binding of four TFs at several time points...
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Resource: Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships
- Michelle Kudron,
- Louis Gevirtzman,
- Alec Victorsen,
- Bridget C. Lear,
- Jiahao Gao,
- Jinrui Xu,
- Swapna Samanta,
- Emily Frink,
- Adri Tran-Pearson,
- Chau Huynh,
- Dionne Vafeados,
- Ann Hammonds,
- William Fisher,
- Martha Wall,
- Greg Wesseling,
- Vanessa Hernandez,
- Zhichun Lin,
- Mary Kasparian,
- Kevin White,
- Ravi Allada,
- Mark Gerstein,
- LaDeana Hillier,
- Susan E. Celniker,
- Valerie Reinke,
- and Robert H. Waterston
Genome Res. December 2024 34: 2319-2334; Published in Advance October 22, 2024, doi:10.1101/gr.279037.124
...more peaks in introns than worms. The distribution of peaks in C. elegans is slightly farther upstream of the TSS than in Drosophila, perhaps reflecting the fact that for many C. elegans gene models the annotated TSS is the site of trans-splicing, with the start of transcription occurring further...
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Method: Resolving the chromatin impact of mosaic variants with targeted Fiber-seq
- Stephanie C. Bohaczuk,
- Zachary J. Amador,
- Chang Li,
- Benjamin J. Mallory,
- Elliott G. Swanson,
- Jane Ranchalis,
- Mitchell R. Vollger,
- Katherine M. Munson,
- Tom Walsh,
- Morgan O. Hamm,
- Yizi Mao,
- Andre Lieber,
- and Andrew B. Stergachis
Genome Res. December 2024 34: 2269-2278; Published in Advance December 9, 2024, doi:10.1101/gr.279747.124
..., this hyper-CpG methylated domain does not include the upstream CTCF element, but rather initiates immediately after it (Fig. 2C). In contrast, CpG methylation downstream from the DMPK CTG repeat is unchanged—indicative of a focal, directional impact of the pathogenic repeat expansion on CpG methylation...
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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
...are bidirectional and lead to the production of highly unstable promoter upstream transcripts (PROMPTs), suggesting that pervasive transcription could also play a role in metazoan replication initiation (Preker et al. 2008; Mayer et al. 2015; Nojima et al. 2015). It has recently been shown that replication...
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Research: Ultraviolet damage and repair maps in Drosophila reveal the impact of domain-specific changes in nucleosome repeat length on repair efficiency
- Benjamin Morledge-Hampton,
- Kathiresan Selvam,
- Manish Chauhan,
- Alan G. Goodman,
- and John J. Wyrick
Genome Res. February 2025 35: 257-267; Published in Advance January 6, 2025, doi:10.1101/gr.279605.124
...(UV) light and are mutagenic unless repaired by nucleotide excision repair (NER). It is known that CPD repair rates vary in different regions owing to transcription-coupled NER and differences in chromatin accessibility; however, the impact of regional chromatin organization on CPD formation remains...
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Research: Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution
- Amit Blumberg,
- Edward J. Rice,
- Anshul Kundaje,
- Charles G. Danko,
- and Dan Mishmar
Genome Res. March 2017 27: 362-373; Published in Advance January 3, 2017, doi:10.1101/gr.209924.116
...similar to that of humans, with transcription initiation occurring right upstream of the tRNA−phe gene (corresponding to the putative HSP1) and termination within the D-Loop. The rhesus macaque heavy-strand TIS mapped downstream from tRNA−phe and likely correspond to HSP2. The light...

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