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Research: Global analysis of transcriptionally engaged yeast RNA polymerase III reveals extended tRNA transcripts
- Tomasz W. Turowski,
- Ewa Leśniewska,
- Clementine Delan-Forino,
- Camille Sayou,
- Magdalena Boguta,
- and David Tollervey
Genome Res. July 2016 26: 933-944; Published in Advance May 20, 2016, doi:10.1101/gr.205492.116
...is rate-limiting during RNAPIII transcription. Down-regulation of RNAPIII transcription under stress conditions was found to be uneven; a subset of tRNA genes showed low response to nutrient shift or loss of the major transcription regulator Maf1, suggesting potential “housekeeping” roles. Many tRNA genes...
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LETTER: Evolutionary turnover of mammalian transcription start sites
- Martin C. Frith,
- Jasmina Ponjavic,
- David Fredman,
- Chikatoshi Kai,
- Jun Kawai,
- Piero Carninci,
- Yoshihide Hayshizaki,
- and Albin Sandelin
Genome Res. June 2006 16: 713-722; Published in Advance May 10, 2006, doi:10.1101/gr.5031006
...implications for phylogenetic footprinting algorithms as well as promoter prediction tools that rely on cross-species comparison. Results Identification of TSS turnover events In order to study TSS evolution, we analyzed alignments of human and mouse mRNAs and CAGE tags to their respective s. Homologous mRNAs...
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Research: Promoter-specific dynamics of TATA-binding protein association with the human genome
- Yuko Hasegawa and
- Kevin Struhl
Genome Res. December 2019 29: 1939-1950; Published in Advance November 15, 2019, doi:10.1101/gr.254466.119
...cells, the TATA-binding protein (TBP) typically displays rapid turnover at RNA polymerase (Pol) II-transcribed promoters, slow turnover at Pol III promoters, and very slow turnover at the Pol I promoter. Turnover rates vary widely among Pol II promoters in a manner that does not correlate with the level...
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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
...in transcript leaders (5′ UTRs), are potent cis-acting regulators of translation and mRNA turnover. Recent -wide ribosome profiling studies suggest that thousands of uORFs initiate with non-AUG start codons. Although intriguing, these non-AUG uORF predictions have been made without statistical control...
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Resource: Pervasive and dynamic transcription initiation in Saccharomyces cerevisiae
- Zhaolian Lu and
- Zhenguo Lin
Genome Res. July 2019 29: 1198-1210; Published in Advance May 10, 2019, doi:10.1101/gr.245456.118
...length and sequence of 5′ UTR are generated. Different lengths of 5′ UTR may have different mRNA folding structures, which would change their thermostability. Modulation of mRNA stability is a critical step in the regulation of gene expression. In eukaryotic cells, the decay rates of individual mRNAs...
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Research: Core promoter T-blocks correlate with gene expression levels in C. elegans
- Vladislav Grishkevich,
- Tamar Hashimshony,
- and Itai Yanai
Genome Res. May 2011 21: 707-717; Published in Advance March 2, 2011, doi:10.1101/gr.113381.110
...characterized SL1 motif involved in trans-splicing. The presence of T-blocks thus correlates with low nucleosome occupancy and the precision of a trans-splicing motif, suggesting its role at both the DNA and RNA levels. Collectively, our results suggest that core promoters may tune gene expression levels...
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Method: Inhibition of transcription leads to rewiring of locus-specific chromatin proteomes
- Deepani W. Poramba-Liyanage,
- Tessy Korthout,
- Christine E. Cucinotta,
- Ila van Kruijsbergen,
- Tibor van Welsem,
- Dris El Atmioui,
- Huib Ovaa,
- Toshio Tsukiyama,
- and Fred van Leeuwen
Genome Res. April 2020 30: 635-646; Published in Advance March 18, 2020, doi:10.1101/gr.256255.119
...to implement gene regulatory programs and ensure the expression of a subset of genes in agreement with the state and environmental cues of the cell. RNA polymerase II (Pol II) is an integral part of this assembly as it catalyzes the DNA-dependent synthesis of messenger RNA (mRNA). Regulation of Pol II occurs...
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Research: Promoter architecture determines cotranslational regulation of mRNA
- Lorena Espinar,
- Miquel Àngel Schikora Tamarit,
- Júlia Domingo,
- and Lucas B. Carey
Genome Res. April 2018 28: 509-518; Published in Advance March 22, 2018, doi:10.1101/gr.230458.117
...of the information encoding regulation of mRNA levels in response to changes in growth rate is encoded in the ORF and not in the promoter. Thus, the ORF sequence is a major regulator of gene expression, and a nonlinear interaction between promoters and ORFs determines mRNA levels.Precise control of gene expression...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
..., which includes ChIP-seq TF annotation (Dréos et al. 2018).Secondary sources that suggest regulators of your GOICorrelating expression of your GOI at the RNA level with known TFs or other target genes, for which regulatory pathways have previously been elucidated, is an important way to generate testable...
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Methods: High-resolution nucleosome mapping reveals transcription-dependent promoter packaging
- Assaf Weiner,
- Amanda Hughes,
- Moran Yassour,
- Oliver J. Rando,
- and Nir Friedman
Genome Res. January 2010 20: 90-100; Published in Advance October 21, 2009, doi:10.1101/gr.098509.109
...-coding region nucleosomes being quite stable. We find evidence for highly sensitive nucleosomes located within “nucleosome-free regions,” suggesting that these regions are not always completely naked but instead are likely associated with easily digested nucleosomes. Finally, since RNA polymerase...
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