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Resource: Isoform- and pathway-specific regulation of post-transcriptional RNA processing in human cells
- Ishwarya Venkata Narayanan,
- Karan Bedi,
- Brian Magnuson,
- Ariel McShane,
- Mario Ashaka,
- Michelle Paulsen,
- Thomas E Wilson,
- and Mats Ljungman
Genome Res. March 26, 2026 gr.280892.125; Published in Advance March 26, 2026, doi:10.1101/gr.280892.125
...periods 62 of time has minimal effects on transcription, post-transcriptional processing, and cell 63 viability (Tani et al. 2012; Bedi et al. 2021; Huang et al. 2025). In approach-to-64 equilibrium experiments, actively synthesizing RNAs in cells are labeled for increasing 65 durations until the labeled...
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Research: Post-transcriptional cross- and auto-regulation buffer expression of the human RNA helicases DDX3X and DDX3Y
- Shruthi Rengarajan,
- Jason Derks,
- Daniel W. Bellott,
- Nikolai Slavov,
- and David C. Page
Genome Res. January 2025 35: 20-30; Published in Advance January 10, 2025, doi:10.1101/gr.279707.124
...cells and by negative auto-regulation of DDX3X in 46,XX cells. DDX3X–DDX3Y cross-regulation is mediated through mRNA destabilization—as shown by metabolic labeling of newly transcribed RNA—and buffers total levels of DDX3X and DDX3Y protein in human cells. We infer that post-transcriptional auto...
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Method: Robust and efficient annotation of cell states through gene signature scoring
- Laure Ciernik,
- Agnieszka Kraft,
- Florian Barkmann,
- Josephine Yates,
- and Valentina Boeva
Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
..., particularly for unsupervised cellular state annotation based on maximum signature score values. However, this application requires robust and comparable score distributions across diverse signatures and experimental conditions. Our systematic evaluation of established scoring methodologies—Seurat, SCANPY...
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Research: Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans
- Jun Kim,
- Haoyu Wang,
- and Sevinç Ercan
Genome Res. May 2025 35: 1108-1123; Published in Advance April 10, 2025, doi:10.1101/gr.279365.124
...Jun Kim, Haoyu Wang and Sevinç Ercan Department of Biology, Center for Genomics and Systems Biology, New York University, New York, New York 10003, USA Corresponding author: sevinc@nyu.eduAbstractIn mammals, cohesin and CTCF organize the 3D into topologically associating domains (TADs) to regulate...
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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
...necessary to orchestrate daily timekeeping in mammals.Most organisms possess intrinsic circadian (∼1-d) clocks that align their molecular, behavioral, and physiological processes to changing daily environmental conditions. In mammals, the phase and amplitude of circadian processes are directed...
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Research: Extensive cross-regulation of post-transcriptional regulatory networks in Drosophila
- Marcus H. Stoiber,
- Sara Olson,
- Gemma E. May,
- Michael O. Duff,
- Jan Manent,
- Robert Obar,
- K.G. Guruharsha,
- Peter J. Bickel,
- Spyros Artavanis-Tsakonas,
- James B. Brown,
- Brenton R. Graveley,
- and Susan E. Celniker
Genome Res. November 2015 25: 1692-1702; Published in Advance August 20, 2015, doi:10.1101/gr.182675.114
..., particularly in higher eukaryotic organisms, where ∼3% of genes encode proteins that have either known or predicted RNA-binding domains (Glisovic et al. 2008). RBPs participate in many essential post-transcriptional functions, including premRNA splicing, 3′ end formation, RNA localization, turnover...
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Resource: Global compositional and functional states of the human gut microbiome in health and disease
- Sunjae Lee,
- Theo Portlock,
- Emmanuelle Le Chatelier,
- Fernando Garcia-Guevara,
- Frederick Clasen,
- Florian Plaza Oñate,
- Nicolas Pons,
- Neelu Begum,
- Azadeh Harzandi,
- Ceri Proffitt,
- Dorines Rosario,
- Stefania Vaga,
- Junseok Park,
- Kalle von Feilitzen,
- Fredric Johansson,
- Cheng Zhang,
- Lindsey A. Edwards,
- Vincent Lombard,
- Franck Gauthier,
- Claire J. Steves,
- David Gomez-Cabrero,
- Bernard Henrissat,
- Doheon Lee,
- Lars Engstrand,
- Debbie L. Shawcross,
- Gordon Proctor,
- Mathieu Almeida,
- Jens Nielsen,
- Adil Mardinoglu,
- David L. Moyes,
- Stanislav Dusko Ehrlich,
- Mathias Uhlen,
- and Saeed Shoaie
Genome Res. June 2024 34: 967-978; Published in Advance July 22, 2024, doi:10.1101/gr.278637.123
...of nonwesternized and European samples of subjects connected by a mixture of western/nonwestern samples belonging to China or Japan and to the United States (Fig. 1E; Supplemental Fig. S1B). Based on a comparative analysis across different regions, we identified 742 MSPs specifically enriched in certain regions...
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Research: Characterization of the distribution and dynamics of chromatin states in the C. elegans germline reveals substantial H3K4me3 remodeling during oogenesis
- Mariateresa Mazzetto,
- Lauren E. Gonzalez,
- Nancy Sanchez,
- and Valerie Reinke
Genome Res. January 2024 34: 57-69; Published in Advance December 26, 2023, doi:10.1101/gr.278247.123
....Using chromatin states to understand germline regulatory mechanismsThe C. elegans germline is characterized by an organized trajectory along which proliferating germ cells enter meiosis I and either differentiate into sperm at the L4 stage or into oocytes as adults. These temporal and spatial dynamics result...
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Research: Circadian gene variants and the skeletal muscle circadian clock contribute to the evolutionary divergence in longevity across Drosophila populations
- Liam C. Hunt,
- Jianqin Jiao,
- Yong-Dong Wang,
- David Finkelstein,
- Deepti Rao,
- Michelle Curley,
- Maricela Robles-Murguia,
- Abbas Shirinifard,
- Vishwajeeth R. Pagala,
- Junmin Peng,
- Yiping Fan,
- and Fabio Demontis
Genome Res. August 2019 29: 1262-1276; Published in Advance June 27, 2019, doi:10.1101/gr.246884.118
...preponderance of post-transcriptional mechanisms in the determination of proteome composition in old age. r2 correlation coefficients are indicated.Disconnect of the muscle transcriptome and proteome with agingPrevious studies in different model organisms have shown that the correlation between mRNA and protein...
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Research: Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population
- Agnese Viluma,
- Øystein Flagstad,
- Mikael Åkesson,
- Camilla Wikenros,
- Håkan Sand,
- Petter Wabakken,
- and Hans Ellegren
Genome Res. March 2022 32: 449-458; Published in Advance February 8, 2022, doi:10.1101/gr.276070.121
...Whole- resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population Agnese Viluma1, Øystein Flagstad2, Mikael Åkesson3, Camilla Wikenros3, Håkan Sand3, Petter Wabakken4 and Hans Ellegren1 1Department of Evolutionary...
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