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Research: Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy
- Dhanur P. Iyer,
- Lambert Moyon,
- Lars Wittler,
- Chieh-Yu Cheng,
- Francisca R. Ringeling,
- Stefan Canzar,
- Annalisa Marsico,
- and Aydan Bulut-Karslioğlu
Genome Res. April 2024 34: 572-589; Published in Advance May 6, 2024, doi:10.1101/gr.278662.123
...cells from proliferation to dormancy.DiscussionmiRNAs are critical regulators of cellular transitions, mediating prompt target down-regulation mostly via translational interference or mRNA decay. The prominent role of miRNAs in regulation of growth and proliferation led us to hypothesize that they may...
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Resource: The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
- Hsin-Yen Larry Wu,
- Isaiah D. Kaufman,
- and Polly Yingshan Hsu
Genome Res. September 2025 35: 2130-2142; Published in Advance July 22, 2025, doi:10.1101/gr.280480.125
...the mechanism of mRNA translation (Guydosh and Green 2014; Chothani et al. 2023; Wu et al. 2024a).Although several Ribo-seq software packages generate aggregate plots to examine 3 nt periodicity at a global level (Ji et al. 2015; Calviello et al. 2016, 2020; Zhang et al. 2017; Xiao et al. 2018; Choudhary et al...
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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
...and other mammalian species remains to be characterized. Here, we address the global contribution of TEs to mammalian NF-kB binding by performing a comparative genomic analysis of TNF-induced NF-kB binding in primary human, mouse, and cow aortic endothelial cells.ResultsTransposable elements contribute...
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Research: Global loss of cellular m⁶A RNA methylation following infection with different SARS-CoV-2 variants
- Roshan Vaid,
- Akram Mendez,
- Ketan Thombare,
- Rebeca Burgos-Panadero,
- Rémy Robinot,
- Barbara F. Fonseca,
- Nikhil R. Gandasi,
- Johan Ringlander,
- Mohammad Hassan Baig,
- Jae-June Dong,
- Jae Yong Cho,
- Björn Reinius,
- Lisa A. Chakrabarti,
- Kristina Nystrom,
- and Tanmoy Mondal
Genome Res. March 2023 33: 299-313; Published in Advance March 1, 2023, doi:10.1101/gr.276407.121
...is known to be compromised in SARS-CoV-2-infected cells, and KD of the stress granule protein G3BP1 enhances SARS-CoV-2 infection (Zheng et al. 2021). We reasoned that the inactivation of stress granule formation by SARS-CoV-2 could be mediated by the global loss of m6A in cellular mRNAs that we uncovered...
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Research: Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay
- Jessica A. Hurt,
- Alex D. Robertson,
- and Christopher B. Burge
Genome Res. October 2013 23: 1636-1650; Published in Advance June 13, 2013, doi:10.1101/gr.157354.113
...Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay Jessica A. Hurt , Alex D. Robertson and Christopher B. Burge 1 Department of Biology, Massachusetts Institute of Technology, Cambridge...
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Method: Analysis of alternative polyadenylation from single-cell RNA-seq using scDaPars reveals cell subpopulations invisible to gene expression
- Yipeng Gao,
- Lei Li,
- Christopher I. Amos,
- and Wei Li
Genome Res. October 2021 31: 1856-1866; Published in Advance May 25, 2021, doi:10.1101/gr.271346.120
...indicate that scDaPars can robustly recover missing APA events caused by the low amounts of mRNA sequenced in single cells. When applied to cancer and human endoderm differentiation data, scDaPars not only revealed cell-type-specific APA regulation but also identified cell subpopulations that are otherwise...
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Research: Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomes
- Matthew R. Gazzara,
- Michael J. Mallory,
- Renat Roytenberg,
- John P. Lindberg,
- Anupama Jha,
- Kristen W. Lynch,
- and Yoseph Barash
Genome Res. August 2017 27: 1360-1370; Published in Advance May 16, 2017, doi:10.1101/gr.220517.117
...machinery with substrate, resulting in inclusion or skipping of specific exons in the final mRNA. Importantly, pre-mRNA transcripts are often bound by multiple proteins that cooperate or compete in their regulation of the splicingmachinery. Thus, the final splicing pattern of a gene in any given cell...
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Resource: A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation
- Andreas J. Gruber,
- Ralf Schmidt,
- Andreas R. Gruber,
- Georges Martin,
- Souvik Ghosh,
- Manuel Belmadani,
- Walter Keller,
- and Mihaela Zavolan
Genome Res. August 2016 26: 1145-1159; Published in Advance July 5, 2016, doi:10.1101/gr.202432.115
...and Bartel 2009). However, -wide measurements of mRNA and protein levels in dividing and resting cells revealed that systematic 3′ UTR shortening has a relatively minor impact on mRNA stability, translation, and protein output (Spies et al. 2013; Gruber et al. 2014). Instead, evidence has started to emerge...
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Research: Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition
- Håvard Aanes,
- Cecilia L. Winata,
- Chi Ho Lin,
- Jieqi P. Chen,
- Kandhadayar G. Srinivasan,
- Serene G.P. Lee,
- Adrian Y.M. Lim,
- Hajira Shreen Hajan,
- Philippe Collas,
- Guillaume Bourque,
- Zhiyuan Gong,
- Vladimir Korzh,
- Peter Aleström,
- and Sinnakaruppan Mathavan
Genome Res. August 2011 21: 1328-1338; Published in Advance May 9, 2011, doi:10.1101/gr.116012.110
...(A) tail measurement revealed that this increase was not due to de novo transcription of poly(A)+ RNA, but rather reflected an extension of the poly(A) tail of existing maternal mRNAs. Furthermore, results from the 39-dA experiment strongly suggest that the two cohorts of maternal mRNAs have specific...
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Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
- Haiyue Liu and
- Lea H. Gregersen
Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
...was observed among lncRNA subgroups classified according to their genomic locations relative to mRNAs (Supplemental Fig. S5C). Analysis of active enhancer-associated histone modifications, including H3K4me1 and H3K27ac, revealed greater enrichment of these marks in the promoter regions and reduced enrichment...
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