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Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
...: 215–233. doi:10.1016/j.cell.2009.01.002 ↵Baskerville S, Bartel DP. 2005. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11: 241–247. doi:10.1261/rna.7240905 ↵Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP...
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Research: Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames
- Peggy Janich,
- Alaaddin Bulak Arpat,
- Violeta Castelo-Szekely,
- Maykel Lopes,
- and David Gatfield
Genome Res. December 2015 25: 1848-1859; Published in Advance October 20, 2015, doi:10.1101/gr.195404.115
...as a novel regulatory mechanism within the clock circuitry. Altogether, our study reveals key features of rhythmic protein biosynthesis and the impact of translational control on gene expression in a solid, highly differentiated mammalian organ with well-studied functions. Results Ribosome profiling in liver...
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Research: Transcription factor activity rhythms and tissue-specific chromatin interactions explain circadian gene expression across organs
- Jake Yeung,
- Jérôme Mermet,
- Céline Jouffe,
- Julien Marquis,
- Aline Charpagne,
- Frédéric Gachon,
- and Felix Naef
Genome Res. February 2018 28: 182-191; Published in Advance December 18, 2017, doi:10.1101/gr.222430.117
..., Zaret KS. 2016. The pioneer transcription factor FoxA maintains an accessible nucleosome configuration at enhancers for tissue-specific gene activation. Mol Cell 62: 79–91. ↵Jouffe C, Cretenet G, Symul L, Martin E, Atger F, Naef F, Gachon F. 2013. The circadian clock coordinates ribosome biogenesis. PLo...
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Research: Post-transcriptional circadian regulation in macrophages organizes temporally distinct immunometabolic states
- Emily J. Collins,
- Mariana P. Cervantes-Silva,
- George A. Timmons,
- James R. O'Siorain,
- Annie M. Curtis,
- and Jennifer M. Hurley
Genome Res. February 2021 31: 171-185; Published in Advance January 12, 2021, doi:10.1101/gr.263814.120
...view of physiological circadian regulation on immunity is via a transcription-translation-based negative-feedback loop, where the heterodimeric transcription factor positive-arm complex regulates the expression of both the negative arm as well as a host of other genes not involved in the feedback loop...
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Research: Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing
- Alaaddin Bulak Arpat,
- Angélica Liechti,
- Mara De Matos,
- René Dreos,
- Peggy Janich,
- and David Gatfield
Genome Res. July 2020 30: 985-999; Published in Advance July 23, 2020, doi:10.1101/gr.257741.119
.... Collectively, our disome profiling approach allows unique insights into gene regulation occurring at the step of translation elongation.The translation of messenger RNA (mRNA) to protein is a central step in gene expression. Knowledge of this process has exploded since the emergence of ribosome profiling (Ribo...
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Research: Diurnal regulation of RNA polymerase III transcription is under the control of both the feeding–fasting response and the circadian clock
- François Mange,
- Viviane Praz,
- Eugenia Migliavacca,
- Ian M. Willis,
- Frédéric Schütz,
- Nouria Hernandez,
- and the CycliX Consortium
Genome Res. June 2017 27: 973-984; Published in Advance March 24, 2017, doi:10.1101/gr.217521.116
...circadian clock genes revealed slightly delayed phases and little changes in amplitude (Supplemental Fig. S4E). Contrasting with the relatively small effects on the control rhythmic data set, the absence of MAF1 resulted in an overall increase in Pol III gene occupancy compared with control mice, similar...
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Resource: Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging
- Jacob C. Kimmel,
- Lolita Penland,
- Nimrod D. Rubinstein,
- David G. Hendrickson,
- David R. Kelley,
- and Adam Z. Rosenthal
Genome Res. December 2019 29: 2088-2103; Published in Advance November 21, 2019, doi:10.1101/gr.253880.119
...of day to limit circadian variation, which affects the expression of nearly half of all murine genes (Zhang et al. 2014). After single-cell isolation, cells were immediately encapsulated and barcoded for library preparation using the 10x Genomics microfluidics system, followed by sequencing (Fig. 1A). We...
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Research: Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation
- Jonathan Neve,
- Kaspar Burger,
- Wencheng Li,
- Mainul Hoque,
- Radhika Patel,
- Bin Tian,
- Monika Gullerova,
- and Andre Furger
Genome Res. January 2016 26: 24-35; Published in Advance November 6, 2015, doi:10.1101/gr.193995.115
...a crucial role in the regulation of gene expression across eukaryotes. Although APA is extensively studied, its regulation within cellular compartments and its physiological impact remains largely enigmatic. Here, we used a rigorous subcellular fractionation approach to compare APA profiles of cytoplasmic...
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Research: Deep sequencing the circadian and diurnal transcriptome of Drosophila brain
- Michael E. Hughes,
- Gregory R. Grant,
- Christina Paquin,
- Jack Qian,
- and Michael N. Nitabach
Genome Res. July 2012 22: 1266-1281; Published in Advance April 3, 2012, doi:10.1101/gr.128876.111
...cycling noncoding RNAs that encode the precursors of more than 50 box-C/D small nucleolar RNAs, key regulators of ribosomal biogenesis. Transcriptional profiling at the level of individual exons reveals alternative splice isoforms for many genes whose relative abundances are regulated by either period...
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Research: Gene duplication and neofunctionalization: POLR3G and POLR3GL
- Marianne Renaud,
- Viviane Praz,
- Erwann Vieu,
- Laurence Florens,
- Michael P. Washburn,
- Philippe l'Hôte,
- and Nouria Hernandez
Genome Res. January 2014 24: 37-51; Published in Advance October 9, 2013, doi:10.1101/gr.161570.113
...relatively more abundant in dividing cells. Genome-wide chromatin immunoprecipitations followed by high-throughput sequencing (ChIP-seq) reveal that both forms of Pol III occupy the same target genes, in very constant proportions within one cell line, suggesting that the two forms of Pol III have a similar...
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