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Research: Ribosome profiling reveals an important role for translational control in circadian gene expression
- Christopher Jang,
- Nicholas F. Lahens,
- John B. Hogenesch,
- and Amita Sehgal
Genome Res. December 2015 25: 1836-1847; Published in Advance September 3, 2015, doi:10.1101/gr.191296.115
.../translational negative feedback loop in mammals. Although most core clock factors are transcription factors, post-transcriptional control introduces delays that are critical for circadian oscillations. Little work has been done on circadian regulation of translation, so to address this deficit we conducted ribosome...
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Research: Turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations
- Éléonore Durand,
- Isabelle Gagnon-Arsenault,
- Johan Hallin,
- Isabelle Hatin,
- Alexandre K. Dubé,
- Lou Nielly-Thibault,
- Olivier Namy,
- and Christian R. Landry
Genome Res. June 2019 29: 932-943; Published in Advance May 31, 2019, doi:10.1101/gr.239822.118
...properties was robust to translation detection methods.We observed a stronger post-transcriptional buffering in the tORFs with the highest transcription levels, reflecting either selection against translation or a lack of selection for optimal translation. This buffering was also observed in another ribosome...
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Method: Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation
- Alexander J. Ritter,
- Jolene M. Draper,
- Christopher Vollmers,
- and Jeremy R. Sanford
Genome Res. November 2024 34: 2000-2011; Published in Advance June 5, 2024, doi:10.1101/gr.279170.124
...for the majority of differences between isoforms from the same gene. Random forest classifiers implicated coding sequence (CDS) and untranslated region (UTR) lengths as important determinants of isoform-specific sedimentation profiles, and motif analyses reveal potential cell type–specific and subcellular fraction...
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Research: Conserved non-AUG uORFs revealed by a novel regression analysis of ribosome profiling data
- Pieter Spealman,
- Armaghan W. Naik,
- Gemma E. May,
- Scott Kuersten,
- Lindsay Freeberg,
- Robert F. Murphy,
- and Joel McManus
Genome Res. February 2018 28: 214-222; Published in Advance December 18, 2017, doi:10.1101/gr.221507.117
.... The evolution of transcription-initiation sites. Mol Biol Evol 22: 1137–1146. ↵McManus CJ, May GE, Spealman P, Shteyman A. 2014. Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast. Genome Res 24: 422–430. ↵Medenbach J, Seiler M, Hentze MW. 2011. Translational control...
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Research: Cell type–specific analysis by single-cell profiling identifies a stable mammalian tRNA–mRNA interface and increased translation efficiency in neurons
- William Gao,
- Carlos J. Gallardo-Dodd,
- and Claudia Kutter
Genome Res. January 2022 32: 97-110; Published in Advance December 2, 2021, doi:10.1101/gr.275944.121
...by the codon usage of a single gene, Ttn. When this gene is removed from the tTE calculation, skeletal and cardiac muscle cells have a similar tTE to most other cell types. Whether post-transcriptional regulation resolves the potential translational choke point caused by imbalance of codon demand and anticodon...
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Research: Evolution at two levels of gene expression in yeast
- Carlo G. Artieri and
- Hunter B. Fraser
Genome Res. March 2014 24: 411-421; Published in Advance December 6, 2013, doi:10.1101/gr.165522.113
...acting at both levels of regulation. Finally, we also uncover multiple instances of stop-codon readthrough that are conserved between species. Our analysis reveals the underappreciated complexity of post-transcriptional regulatory divergence and indicates that partitioning the search for the locus...
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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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Method: System-wide analyses of the fission yeast poly(A)⁺ RNA interactome reveal insights into organization and function of RNA–protein complexes
- Cornelia Kilchert,
- Tea Kecman,
- Emily Priest,
- Svenja Hester,
- Ebru Aydin,
- Krzysztof Kus,
- Oliver Rossbach,
- Alfredo Castello,
- Shabaz Mohammed,
- and Lidia Vasiljeva
Genome Res. July 2020 30: 1012-1026; Published in Advance June 18, 2020, doi:10.1101/gr.257006.119
...in gene expression and orchestrate production, function, and turnover of mRNAs. The accuracy and dynamics of RNA–protein interactions within these molecular machines are essential for their function and are mediated by RNA-binding proteins (RBPs). Here, we show that fission yeast whole-cell poly(A)+ RNA...
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Research: Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans
- Can Cenik,
- Elif Sarinay Cenik,
- Gun W. Byeon,
- Fabian Grubert,
- Sophie I. Candille,
- Damek Spacek,
- Bilal Alsallakh,
- Hagen Tilgner,
- Carlos L. Araya,
- Hua Tang,
- Emiliano Ricci,
- and Michael P. Snyder
Genome Res. November 2015 25: 1610-1621; Published in Advance August 21, 2015, doi:10.1101/gr.193342.115
...were consistent with the observation that for many genes, inter-individual RNA expression variation is not reflected in ribosome occupancy. Taken together, our results are consistent with yeast studies that reported translational buffering of divergent RNA expression (Artieri and Fraser 2014; Mc...
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Research: Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol
- Noah Dukler,
- Gregory T. Booth,
- Yi-Fei Huang,
- Nathaniel Tippens,
- Colin T. Waters,
- Charles G. Danko,
- John T. Lis,
- and Adam Siepel
Genome Res. November 2017 27: 1816-1829; Published in Advance October 12, 2017, doi:10.1101/gr.222935.117
...are fundamentally limited in temporal resolution owing to the substantial lag between changes in transcriptional activity and detectable changes in the level of mRNAs. This lag results in part from the time required for transcription and post-transcriptional processing, and in part because pre-existing mRNAs buffer...

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