Searching journal content for articles similar to Lu and Lin 29 (7): 1198.

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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
.... Whereas much research has focused on the initiation of transcription, regulation of elongation plays an important role not only in transcription dynamics but also in cotranscriptional RNA processing and stability. Despite advances in high-throughput approaches for global quantification of RNA polymerase...
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Method: Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome
- Elisa Oberbeckmann,
- Michael Wolff,
- Nils Krietenstein,
- Mark Heron,
- Jessica L. Ellins,
- Andrea Schmid,
- Stefan Krebs,
- Helmut Blum,
- Ulrich Gerland,
- and Philipp Korber
Genome Res. December 2019 29: 1996-2009; Published in Advance November 6, 2019, doi:10.1101/gr.253419.119
...Absolute nucleosome occupancy map for the Saccharomyces cerevisiae Elisa Oberbeckmann1,8, Michael Wolff2,8, Nils Krietenstein1,3, Mark Heron4,5, Jessica L. Ellins6, Andrea Schmid1, Stefan Krebs7, Helmut Blum7, Ulrich Gerland2 and Philipp Korber1 1Molecular Biology Division, Biomedical Center...
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Research: The origin and evolution of a distinct mechanism of transcription initiation in yeasts
- Zhaolian Lu and
- Zhenguo Lin
Genome Res. January 2021 31: 51-63; Published in Advance November 20, 2020, doi:10.1101/gr.264325.120
...elements in this key process of the central dogma of molecular biology.ResultsEvolutionary dynamics of transcription initiation landscapes in yeastsWe generated high-resolution TSS maps for 10 budding yeast species and two fission yeast species, including S. cerevisiae, S. pombe, and other important...
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Research: Noncoding transcription influences the replication initiation program through chromatin regulation
- Julien Soudet,
- Jatinder Kaur Gill,
- and Françoise Stutz
Genome Res. December 2018 28: 1882-1893; Published in Advance November 6, 2018, doi:10.1101/gr.239582.118
...the parameters that regulate this program in Saccharomyces cerevisiae, chromatin structure has been at the center of attention without considering the contribution of transcription. Here, we revisit the replication initiation program in the light of widespread genomic noncoding transcription. We find...
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Method: Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq
- Robert A. Policastro,
- R. Taylor Raborn,
- Volker P. Brendel,
- and Gabriel E. Zentner
Genome Res. June 2020 30: 910-923; Published in Advance July 6, 2020, doi:10.1101/gr.261545.120
..., current protocols for -wide TSS profiling are laborious and/or expensive. We present Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq), a simple, rapid, and cost-effective protocol for sequencing capped RNA 5′ ends from as little as 50 ng total RNA...
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Research: Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase
- Boning Chen,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. December 2023 33: 2108-2118; Published in Advance December 11, 2023, doi:10.1101/gr.278273.123
...within coding regions throughout the Saccharomyces cerevisiae . PLoS Biol 6: e277. doi:10.1371/journal.pbio.0060277 ↵Churchman LS, Weissman JS. 2011. Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature 469: 368–373. doi:10.1038/nature09652 ↵Clemente-Ruiz M, González...
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Research: Preservation of genetic and regulatory robustness in ancient gene duplicates of Saccharomyces cerevisiae
- Orla M. Keane,
- Christina Toft,
- Lorenzo Carretero-Paulet,
- Gary W. Jones,
- and Mario A. Fares
Genome Res. November 2014 24: 1830-1841; Published in Advance August 22, 2014, doi:10.1101/gr.176792.114
...Preservation of genetic and regulatory robustness in ancient gene duplicates of Saccharomyces cerevisiae Orla M. Keane 1 , 2 , 8 , Christina Toft 3 , 4 , 8 , Lorenzo Carretero-Paulet 5 , Gary W. Jones 6 and Mario A...
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Research: Linking the dynamics of chromatin occupancy and transcription with predictive models
- Trung Q. Tran,
- Heather K. MacAlpine,
- Vinay Tripuraneni,
- Sneha Mitra,
- David M. MacAlpine,
- and Alexander J. Hartemink
Genome Res. June 2021 31: 1035-1046; Published in Advance April 23, 2021, doi:10.1101/gr.267237.120
...in transcription. We used Gaussian process regression to predict the transcription at each time point based solely on chromatin dynamics and initial transcript levels (at 0 min, before cadmium treatment). We constructed four models to evaluate the inclusion of various measures of the chromatin, culminating...
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Research: Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments
- Barbara Dunn,
- Chandra Richter,
- Daniel J. Kvitek,
- Tom Pugh,
- and Gavin Sherlock
Genome Res. May 2012 22: 908-924; Published in Advance February 27, 2012, doi:10.1101/gr.130310.111
...Analysis of the Saccharomyces cerevisiae pan- reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments Barbara Dunn1, Chandra Richter2, Daniel J. Kvitek1, Tom Pugh2 and Gavin Sherlock1,3 1Department of Genetics, Stanford University, Stanford...
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Method: Quantitative proteomic analysis reveals concurrent RNA–protein interactions and identifies new RNA-binding proteins in Saccharomyces cerevisiae
- Daniel M. Klass,
- Marion Scheibe,
- Falk Butter,
- Gregory J. Hogan,
- Matthias Mann,
- and Patrick O. Brown
Genome Res. June 2013 23: 1028-1038; Published in Advance May 1, 2013, doi:10.1101/gr.153031.112
...Quantitative proteomic analysis reveals concurrent RNA–protein interactions and identifies new RNA-binding proteins in Saccharomyces cerevisiae Daniel M. Klass 1 , 2 , Marion Scheibe 3 , Falk Butter 3 , Gregory J. Hogan 1 , 2 , Matthias Mann...
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