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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
.... Collectively, our integrated transcriptomic, chromatin, and replication data sets provide a comprehensive framework for understanding regulation differences between these in vivo stem-cell populations, demonstrating the power of multiomics in uncovering cell-type-specific regulatory features.Stem cells...
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Research: Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia
- Hao Zhu,
- Jiao Zhang,
- Soumya Rao,
- Matthew D. Durbin,
- Ying Li,
- Ruirui Lang,
- Jiqiang Liu,
- Baichuan Xiao,
- Hailin Shan,
- Ziqiu Meng,
- Jinmo Wang,
- Xiaokai Tang,
- Zhenni Shi,
- Liza L. Cox,
- Shouqin Zhao,
- Stephanie M. Ware,
- Tiong Y. Tan,
- Michelle de Silva,
- Lyndon Gallacher,
- Ting Liu,
- Jie Mi,
- Changqing Zeng,
- Hou-Feng Zheng,
- Qingguo Zhang,
- Stylianos E. Antonarakis,
- Timothy C. Cox,
- and Yong-Biao Zhang
Genome Res. May 2025 35: 1065-1079; Published in Advance April 15, 2025, doi:10.1101/gr.280047.124
.... 2013). This variability is attributed to a multitude of factors, including but not limited to genetic modifiers, environmental conditions, and epigenetic modifications. Variants in regulatory elements that impact gene expression, otherwise known as expression quantitative trait loci (eQTLs), serve...
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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
...chromatin accessibility data from the liver and brain. Retroelements were both the dominant source of TE-CREs and had higher regulatory activity in MPRA experiments compared with DNA elements. A minority of TE subfamilies (16%) accounted for 46% of TE-CREs, but these “CRE superspreaders” were mostly active...
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Method: Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions
- Alicia N. Schep,
- Jason D. Buenrostro,
- Sarah K. Denny,
- Katja Schwartz,
- Gavin Sherlock,
- and William J. Greenleaf
Genome Res. November 2015 25: 1757-1770; Published in Advance August 27, 2015, doi:10.1101/gr.192294.115
...information within regulatory DNA promise to provide insight into the interplay between chromatin organization and transcriptional regulators—a crucial step toward a comprehensive and predictive understanding of how regulatory elements control gene expression. Methods for inferring nucleosome positions...
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Resource: Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors
- Jie Wang,
- Jiali Zhuang,
- Sowmya Iyer,
- XinYing Lin,
- Troy W. Whitfield,
- Melissa C. Greven,
- Brian G. Pierce,
- Xianjun Dong,
- Anshul Kundaje,
- Yong Cheng,
- Oliver J. Rando,
- Ewan Birney,
- Richard M. Myers,
- William S. Noble,
- Michael Snyder,
- and Zhiping Weng
Genome Res. September 2012 22: 1798-1812; doi:10.1101/gr.139105.112
...Consortium 2011). We analyzed this rich collection of data to characterize the sequence features of TF binding sites and determine the local chromatin environment around them. Results Identification of sequence motifs and TF binding sites As described in Supplemental Methods, we built a computational...
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Research: Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains
- Clotilde Garrido,
- Cintia Gómez-Muñoz,
- Etienne Kornobis,
- Nicolas Agier,
- Oana Ilioaia,
- Gilles Fischer,
- and Zhou Xu
Genome Res. March 2026 36: 522-533; Published in Advance January 16, 2026, doi:10.1101/gr.281132.125
...specific suggested the presence of cis regulatory elements. We thus compared extremity-specific TL distributions across strains, with or without elements commonly found at subtelomeres such as X and Y′ elements, as well as Ty5 retrotransposons. To account for different global TL means in different strains...
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Research: Nucleosome repositioning in chronic lymphocytic leukemia
- Kristan V. Piroeva,
- Charlotte McDonald,
- Charalampos Xanthopoulos,
- Chelsea Fox,
- Christopher T. Clarkson,
- Jan-Philipp Mallm,
- Yevhen Vainshtein,
- Luminita Ruje,
- Lara C. Klett,
- Stephan Stilgenbauer,
- Daniel Mertens,
- Efterpi Kostareli,
- Karsten Rippe,
- and Vladimir B. Teif
Genome Res. October 2023 33: 1649-1661; Published in Advance September 12, 2023, doi:10.1101/gr.277298.122
...scale of active chromatin subcompartments.View larger version: In this window In a new window Figure 4. Average nucleosome occupancy and DNA methylation occupancy profiles at cis-regulatory elements. (A) Averaged nucleosome and DNA methylation occupancy profiles at enhancers in NBCs. (B) Same as panel...
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Research: Crossover-active regions of the wheat genome are distinguished by DMC1, the chromosome axis, H3K27me3, and signatures of adaptation
- Andrew J. Tock,
- Daniel M. Holland,
- Wei Jiang,
- Kim Osman,
- Eugenio Sanchez-Moran,
- James D. Higgins,
- Keith J. Edwards,
- Cristobal Uauy,
- F. Chris H. Franklin,
- and Ian R. Henderson
Genome Res. September 2021 31: 1614-1628; Published in Advance August 23, 2021, doi:10.1101/gr.273672.120
...and the chromosome axis protein ASY1 in wheat and investigated their relationships with crossovers, chromatin state, and genetic diversity. DMC1 and ASY1 chromatin immunoprecipitation followed by sequencing (ChIP-seq) revealed strong co-enrichment in the distal, crossover-active regions of the wheat chromosomes...
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Resource: A spatiotemporally resolved atlas of mRNA decay in the C. elegans embryo reveals differential regulation of mRNA stability across stages and cell types
- Felicia Peng,
- C. Erik Nordgren,
- and John Isaac Murray
Genome Res. August 2024 34: 1235-1252; Published in Advance August 14, 2024, doi:10.1101/gr.278980.124
...). Transcripts are often specified for decay through the binding of RNA and protein factors to cis-regulatory elements within the 3′ untranslated region (UTR) (Ray et al. 2013; Vejnar et al. 2019). Cross talk between factors can lead to differential mRNA decay, such as RNA-binding proteins stabilizing...
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Research: Intrinsic DNA binding properties demonstrated for lineage-specifying basic helix-loop-helix transcription factors
- Bradford H. Casey,
- Rahul K. Kollipara,
- Karine Pozo,
- and Jane E. Johnson
Genome Res. April 2018 28: 484-496; Published in Advance March 2, 2018, doi:10.1101/gr.224360.117
...motifs, yet bind largely different genomic sites and regulate distinct transcriptional programs. This suggests that their ability to identify regulatory targets is defined either by the cellular environment of the partially defined lineages in which they are endogenously expressed, or by intrinsic...

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