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Research: Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock
- Akanksha Bafna,
- Gareth Banks,
- Michael H. Hastings,
- and Patrick M. Nolan
Genome Res. May 2023 33: 673-688; Published in Advance May 8, 2023, doi:10.1101/gr.277581.122
...), many of which are transcription factors (TFs) sensitive to the TTFL. Such rhythmic gene transcription depends on the sequential co-ordination of multiple layers of epigenetic events, ranging from chromatin accessibility to TF binding (Yeung et al. 2018). The regulatory enhancer–promoter interactions...
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Research: Post-transcriptional circadian regulation in macrophages organizes temporally distinct immunometabolic states
- Emily J. Collins,
- Mariana P. Cervantes-Silva,
- George A. Timmons,
- James R. O'Siorain,
- Annie M. Curtis,
- and Jennifer M. Hurley
Genome Res. February 2021 31: 171-185; Published in Advance January 12, 2021, doi:10.1101/gr.263814.120
...many different organisms and tissue types, transcriptome profiling studies have found that large proportions of transcripts oscillate circadianly and are highly tissue-specific (Hughes et al. 2009; Abruzzi et al. 2011; Zhang et al. 2014; Mure et al. 2018). However, recent evidence suggests...
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Research: A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility
- Angelo A. Ruggieri,
- Luca Livraghi,
- James J. Lewis,
- Elizabeth Evans,
- Francesco Cicconardi,
- Laura Hebberecht,
- Yadira Ortiz-Ruiz,
- Stephen H. Montgomery,
- Alfredo Ghezzi,
- José Arcadio Rodriguez-Martinez,
- Chris D. Jiggins,
- W. Owen McMillan,
- Brian A. Counterman,
- Riccardo Papa,
- and Steven M. Van Belleghem
Genome Res. October 2022 32: 1862-1875; Published in Advance September 15, 2022, doi:10.1101/gr.276839.122
...in chromatin accessibility between species, 30.4% were within lineage-specific SVs and 9.4% were characterized as TE insertions. These TE insertions were localized closer to gene transcription start sites than expected at random and were enriched for sites with significant resemblance to several transcription...
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Research: Relative contributions of sex hormones, sex chromosomes, and gonads to sex differences in tissue gene regulation
- Montgomery Blencowe,
- Xuqi Chen,
- Yutian Zhao,
- Yuichiro Itoh,
- Caden N. McQuillen,
- Yanjie Han,
- Benjamin L. Shou,
- Rebecca McClusky,
- Karen Reue,
- Arthur P. Arnold,
- and Xia Yang
Genome Res. May 2022 32: 807-824; Published in Advance April 8, 2022, doi:10.1101/gr.275965.121
.... Furthermore, the genes affected by individual sex-biasing factors and interactions among factors are associated with human disease traits such as coronary artery disease, diabetes, and inflammatory bowel disease. Our study offers a tissue-specific account of the individual and interactive contributions...
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Research: Sex differences in human adipose tissue gene expression and genetic regulation involve adipogenesis
- Warren D. Anderson,
- Joon Yuhl Soh,
- Sarah E. Innis,
- Alexis Dimanche,
- Lijiang Ma,
- Carl D. Langefeld,
- Mary E. Comeau,
- Swapan K. Das,
- Eric E. Schadt,
- Johan L.M. Björkegren,
- and Mete Civelek
Genome Res. October 2020 30: 1379-1392; Published in Advance September 23, 2020, doi:10.1101/gr.264614.120
...transcription factor binding motifs. In particular, we observed overlaps with motifs for adipogenic factors including EGR1 and PPARG. To investigate the mechanisms underlying sex-by-SNP interactions, we proposed mechanistic models to explain our results, similar to those proposed for tissue-specific eQTLs (Fu...
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Article: Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation
- Timothy E. Reddy,
- Florencia Pauli,
- Rebekka O. Sprouse,
- Norma F. Neff,
- Kimberly M. Newberry,
- Michael J. Garabedian,
- and Richard M. Myers
Genome Res. December 2009 19: 2163-2171; Published in Advance October 2, 2009, doi:10.1101/gr.097022.109
...factor involved in regulating circadian rhythms. Overall, the genome-wide determination and analysis of GR:DNA binding and transcriptional response to hormone reveals new insights into the complexities of gene regulatory activities managed by GR. Footnotes ↵ 4 Corresponding author. E...
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Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
.... In comparison, Antonaki et al. (2011) allowed for an overlap with any portion of a RELA peak. In the discussion of their study of Alu- associated NF-kB sites, Antonaki et al. (2011) proposed that such sites could serve as transcriptionally inert docking sites of NF-kB which could prevent excessive targeting...
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Resource: Streamlined spatial and environmental expression signatures characterize the minimalist duckweed Wolffia australiana
- Tom Denyer,
- Pin-Jou Wu,
- Kelly Colt,
- Bradley W. Abramson,
- Zhili Pang,
- Pavel Solansky,
- Allen Mamerto,
- Tatsuya Nobori,
- Joseph R. Ecker,
- Eric Lam,
- Todd P. Michael,
- and Marja C.P. Timmermans
Genome Res. July 2024 34: 1106-1120; Published in Advance July 1, 2024, doi:10.1101/gr.279091.124
...distinct subpopulationsWe transcriptionally profiled Wolffia at single-cell resolution to describe, in an unbiased manner, cell types and states within this budding frond system. We first optimized a protoplast isolation method, considering the distinct cell wall composition of Wolffia and the presence...
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Research: Genomic redistribution of GR monomers and dimers mediates transcriptional response to exogenous glucocorticoid in vivo
- Hee-Woong Lim,
- N. Henriette Uhlenhaut,
- Alexander Rauch,
- Juliane Weiner,
- Sabine Hübner,
- Norbert Hübner,
- Kyoung-Jae Won,
- Mitchell A. Lazar,
- Jan Tuckermann,
- and David J. Steger
Genome Res. June 2015 25: 836-844; Published in Advance May 8, 2015, doi:10.1101/gr.188581.114
...repress by tethering to DNA-bound TFs. Our data reveal a strong association between dimeric GR occupancy and activated gene expression on a wide scale in both liver tissue and primary macrophages. However, the discovery of monomeric occupancy near transcriptionally active genes, and the ability...
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Research: Coregulation of ribosomal RNA with hundreds of genes contributes to phenotypic variation
- Bo Li,
- Karl A.G. Kremling,
- Penghao Wu,
- Robert Bukowski,
- Maria C. Romay,
- En Xie,
- Edward S. Buckler,
- and Mingsheng Chen
Genome Res. October 2018 28: 1555-1565; Published in Advance August 30, 2018, doi:10.1101/gr.229716.117
...functionally enriched in ribosome biogenesis. As expected, we identified 1438 coregulated genes (shared by two or more tissues) for gene functional enrichment analysis by excluding tissue-specific genes. To assign these 1438 genes into functional categories, we performed Gene Ontology (GO) analysis. The top...

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