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Research: Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells
- Marcel Tarbier,
- Sebastian D. Mackowiak,
- Vaishnovi Sekar,
- Franziska Bonath,
- Etka Yapar,
- Bastian Fromm,
- Omid R. Faridani,
- Inna Biryukova,
- and Marc R. Friedländer
Genome Res. February 2026 36: 291-302; Published in Advance January 12, 2026, doi:10.1101/gr.279914.124
...covariation between the miRNAs from the mir-17 cluster and the 3p-derived miRNAs from the mir-290 cluster (Fig. 3B) may be induced at the transcriptional level, whereas the negative covariation between the mir-17 cluster and the 5p-derived miRNAs from the mir-290 cluster may be induced post-transcriptionally...
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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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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...-specific gDNA, new predictions in N2-shared gDNA are possibly but not certainly real.Transcription of long tandem repeat regionsIn C. elegans, TRs could be transcriptionally active either because they fall inside regions of transcribed genes that harbor them or because the TRs are themselves actively...
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Research: Endonucleolytic cleavage is the primary mechanism of decay elicited by C. elegans nonsense-mediated mRNA decay
- Marcus J. Viscardi,
- Enisha Sehgal,
- and Joshua A. Arribere
Genome Res. June 2025 35: 1337-1348; Published in Advance May 9, 2025, doi:10.1101/gr.280046.124
...categorized the 5′ ends of RNA reads based on the proximity of their 5′ end to the trans-splicing site (TSS; as many C. elegans gene mRNAs are trans-spliced after transcription, the 5′-most nucleotide of the spliced mRNA differs from the transcription start site). Decapping leaves a 5′ monophosphate (Wang et...
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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
...variants occur in the noncoding (Edwards et al. 2013; Buniello et al. 2019) and likely affect gene regulation (Claringbould and Zaugg 2021). One mechanism by which mutations impact transcriptional programs is through the disruption of transcription factor (TF) binding sites within regulatory elements...
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Review: Navigating the landscape of epitranscriptomics and host immunity
- Elaine Huang,
- Clara Frydman,
- and Xinshu Xiao
Genome Res. April 2024 34: 515-529; Published in Advance May 3, 2024, doi:10.1101/gr.278412.123
...). Because inosines resulting from A-to-I editing are converted to guanosines by reverse transcription, A-to-G mismatches can be indicative of A-to-I editing. Using general linear models, the GIREMI and L-GIREMI methods leverage lack of allelic linkage as a feature to distinguish editing sites from SNPs...
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Research: Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation
- David C.H. Metzger,
- Imogen Porter,
- Brendan Mobley,
- Benjamin A. Sandkam,
- Lydia J.M. Fong,
- Andrew P. Anderson,
- and Judith E. Mank
Genome Res. November 2023 33: 1917-1931; Published in Advance November 21, 2023, doi:10.1101/gr.278127.123
...College, Portland, Oregon 97202, USA; 3Department of Neurobiology and Behavior, Cornell University, Ithaca, New York 14853, USA Corresponding author: dmetzger@zoology.ubc.caAbstractSex chromosome dosage compensation is a model to understand the coordinated evolution of transcription; however, the advanced...
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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
...5 and 6 combine high chromatin accessibility and the presence of either high or low H3K27me3 signal around the transcription start site (TSS) and are labeled “strongly inactive TSS” and “weakly inactive TSS,” respectively (Fig. 1A). For the six states representing active chromatin, state 7 shows...
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Research: Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells
- Belle A. Moyers,
- E. Christopher Partridge,
- Mark Mackiewicz,
- Michael J. Betti,
- Roshan Darji,
- Sarah K. Meadows,
- Kimberly M. Newberry,
- Laurel A. Brandsmeier,
- Barbara J. Wold,
- Eric M. Mendenhall,
- and Richard M. Myers
Genome Res. November 2023 33: 1879-1892; Published in Advance October 18, 2023, doi:10.1101/gr.278205.123
...(DAPs). We used this deep collection to model each TF's impact on gene expression, and identified a cohort of 26 candidate transcriptional repressors. We examine high occupancy target (HOT) sites in the context of three-dimensional organization and show biased motif placement in distal...
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Research: Resetting of the 24-nt siRNA landscape in rice zygotes
- Chenxin Li,
- Jonathan I. Gent,
- Hengping Xu,
- Hong Fu,
- Scott D. Russell,
- and Venkatesan Sundaresan
Genome Res. February 2022 32: 309-323; Published in Advance December 23, 2021, doi:10.1101/gr.275981.121
...significant differences from the egg cell. We produced metagene siRNA coverage plots for seedling, gametes, and zygote, as well as pre- and postfertilization ovaries (Fig. 3A). Seedling had a strong peak upstream of the transcription start site (TSS), corresponding to where short transposons are enriched...

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