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Resource: Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize
- Laura E. Tibbs-Cortes,
- Tingting Guo,
- Carson M. Andorf,
- Xianran Li,
- and Jianming Yu
Genome Res. August 2024 34: 1253-1263; Published in Advance September 13, 2024, doi:10.1101/gr.279027.124
...). Enriched GO terms for slope included ATPase-coupled intramembrane lipid transporter activity (all traits) and RNA-directed 5′-3′ RNA polymerase activity (flowering time traits). Six GO terms, including plant hormone signal transduction, were identified as significantly enriched for intercept, all of which...
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Research: Genome-wide, integrative analysis of circular RNA dysregulation and the corresponding circular RNA-microRNA-mRNA regulatory axes in autism
- Yen-Ju Chen,
- Chia-Ying Chen,
- Te-Lun Mai,
- Chih-Fan Chuang,
- Yu-Chen Chen,
- Sachin Kumar Gupta,
- Laising Yen,
- Yi-Da Wang,
- and Trees-Juen Chuang
Genome Res. March 2020 30: 375-391; Published in Advance March 3, 2020, doi:10.1101/gr.255463.119
...Taiwan University, Taipei 10617, Taiwan; 3Department of Pathology and Immunology, 4Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA ↵5 These authors contributed equally to this work. Corresponding author: trees@gate.sinica.edu.twAbstractCircular RNAs...
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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
...-seq (scRNA-seq) is widely used to elucidate the biology of complex heterogeneous samples. However, scRNA-seq libraries commonly suffer from high dropouts (false zero expression estimates) and variability owing to both technical variation and the biological stochasticity of gene expression in individual...
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Research: Natural variation of histone modification and its impact on gene expression in the rat genome
- Carola Rintisch,
- Matthias Heinig,
- Anja Bauerfeind,
- Sebastian Schafer,
- Christin Mieth,
- Giannino Patone,
- Oliver Hummel,
- Wei Chen,
- Stuart Cook,
- Edwin Cuppen,
- Maria Colomé-Tatché,
- Frank Johannes,
- Ritsert C. Jansen,
- Helen Neil,
- Michel Werner,
- Michal Pravenec,
- Martin Vingron,
- and Norbert Hubner
Genome Res. June 2014 24: 942-953; Published in Advance May 2, 2014, doi:10.1101/gr.169029.113
...sequence-dependent influence on post-translational histone marks. Recently, two groups identified genetic variants affecting histone modifications in human cells and incorporated TF binding, RNA polymerase II, and DNase I hypersensitvity data to show that in many cases the same variant affects multiple...
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Research: Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells
- Monika S. Kowalczyk,
- Itay Tirosh,
- Dirk Heckl,
- Tata Nageswara Rao,
- Atray Dixit,
- Brian J. Haas,
- Rebekka K. Schneider,
- Amy J. Wagers,
- Benjamin L. Ebert,
- and Aviv Regev
Genome Res. December 2015 25: 1860-1872; Published in Advance October 1, 2015, doi:10.1101/gr.192237.115
...advances in single-cell genomics (Wills et al. 2013), especially single-cell RNA-seq (Hashimshony et al. 2012; Ramskold et al. 2012), have opened the way to characterize distinct 8These authors contributed equally to this work. Corresponding author: aregev@broadinstitute.org Article published online before...
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Research: Extensive protein dosage compensation in aneuploid human cancers
- Klaske M. Schukken and
- Jason M. Sheltzer
Genome Res. July 2022 32: 1254-1270; Published in Advance June 14, 2022, doi:10.1101/gr.276378.121
...copy number changes influence the cancer proteome, we conducted an analysis of hundreds of human cancer cell lines and tumors with matched copy number, RNA expression, and protein expression data. We found that a majority of proteins show dosage compensation and fail to change by the degree expected...
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Research: Independent evolution of transcript abundance and gene regulatory dynamics
- Gat Krieger,
- Offir Lupo,
- Avraham A. Levy,
- and Naama Barkai
Genome Res. July 2020 30: 1000-1011; Published in Advance July 22, 2020, doi:10.1101/gr.261537.120
..., but providing limited information about variation across different conditions. To close this gap, we profiled mRNA levels of two related yeast species in hundreds of conditions and used coexpression analysis to distinguish variation in the dynamic pattern of gene expression from variation in expression levels...
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Research: U2AF1 mutations alter splice site recognition in hematological malignancies
- Janine O. Ilagan,
- Aravind Ramakrishnan,
- Brian Hayes,
- Michele E. Murphy,
- Ahmad S. Zebari,
- Philip Bradley,
- and Robert K. Bradley
Genome Res. January 2015 25: 14-26; Published in Advance September 29, 2014, doi:10.1101/gr.181016.114
...splicing programs. These allelespecific effects are consistent with a computationally predicted model of U2AF1 in complex with RNA. Our findings suggest that U2AF1 mutations contribute to pathogenesis by causing quantitative changes in splicing that affect diverse cellular pathways, and give insight...
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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
...expression. This is followed by a cascade of RNA processing and protein translation, allowing for the newly expressed protein to execute its function, which in turn may contribute to cell signaling. Consequently, one of the main questions that often arises in research is what transcription factors (TFs...
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Resource: Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage
- Daniel E. Goszczynski,
- Michelle M. Halstead,
- Alma D. Islas-Trejo,
- Huaijun Zhou,
- and Pablo J. Ross
Genome Res. April 2021 31: 732-744; Published in Advance March 15, 2021, doi:10.1101/gr.267336.120
...a borderline RQI of 6.9.Following the method described by Batut and Gingeras (2013), DNase-treated RNA was subjected to terminator digestion (TEX enzyme, Epicentre) to degrade 5′-monophosphate RNA (16S and 18S ribosomal RNA). Random primers bearing an adapter sequence overhang were annealed to the RNA, which...

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