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Research: Genome-wide oscillations in G + C density and sequence conservation
- Zarmik Moqtaderi,
- Susan Brown,
- and Welcome Bender
Genome Res. November 2021 31: 2050-2057; Published in Advance October 14, 2021, doi:10.1101/gr.274332.120
...on the evolution of genomic sequences. J Biol Phys 30: 33–81. doi:10.1023/B:JOBP.0000016438.86794.8e ↵Barrière A, Gordon KL, Ruvinsky I. 2011. Distinct functional constraints partition sequence conservation in a cis-regulatory element. PLoS Genet 7: e1002095. doi:10.1371/journal.pgen.1002095 ↵Beltran M, Tavares M...
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Resource: Native RNA sequencing in fission yeast reveals frequent alternative splicing isoforms
- José Carlos Montañés,
- Marta Huertas,
- Simone G. Moro,
- William R. Blevins,
- Mercè Carmona,
- José Ayté,
- Elena Hidalgo,
- and M. Mar Albà
Genome Res. June 2022 32: 1215-1227; Published in Advance May 26, 2022, doi:10.1101/gr.276516.121
...et al. 2005; Moldón et al. 2008). At the same time, the intron retention (IR) isoform results in a 17-kDa protein with a role in recombination in the premeiotic S phase. Other possible examples of functional AS events are three exon skipping (ES) transcripts that have been reported to be conserved...
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Research: Ribosomal DNA harbors an evolutionarily conserved clock of biological aging
- Meng Wang and
- Bernardo Lemos
Genome Res. March 2019 29: 325-333; Published in Advance February 14, 2019, doi:10.1101/gr.241745.118
...in Drosophila melanogaster but absent in Saccharomyces cerevisiae, Schizosaccharomyces pombe, and other yeast species. Anal Chem 86: 3697–3702. doi:10.1021/ac500447w ↵Carlson KA, Gardner K, Pashaj A, Carlson DJ, Yu F, Eudy JD, Zhang C, Harshman LG. 2015. Genome-wide gene expression in relation to age in large...
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Research: The frequent evolutionary birth and death of functional promoters in mouse and human
- Robert S. Young,
- Yoshihide Hayashizaki,
- Robin Andersson,
- Albin Sandelin,
- Hideya Kawaji,
- Masayoshi Itoh,
- Timo Lassmann,
- Piero Carninci,
- The FANTOM Consortium,
- Wendy A. Bickmore,
- Alistair R. Forrest,
- and Martin S. Taylor
Genome Res. October 2015 25: 1546-1557; Published in Advance July 30, 2015, doi:10.1101/gr.190546.115
...currently have limited insight intowhichDNA sequence changes impact transcriptional regulation or how such regulatory networks evolve (Stolfi et al. 2014). The core promoter is the 150–200 nt of DNA on which the RNA polymerase II pre-initiation complex is assembled and where transcription initiates...
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Research: Polygenic cis-regulatory adaptation in the evolution of yeast pathogenicity
- Hunter B. Fraser,
- Sasha Levy,
- Arun Chavan,
- Hiral B. Shah,
- J. Christian Perez,
- Yiqi Zhou,
- Mark L. Siegal,
- and Himanshu Sinha
Genome Res. October 2012 22: 1930-1939; Published in Advance May 29, 2012, doi:10.1101/gr.134080.111
...gene set to remain significant after this multiple test correction. Because adjacent genes can share cis-regulatory information and thus may not be independent in terms of our test, we examined the genomic locations of the genes in the endocytosis complex. The closest pair was separated by over 20...
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Research: The identification and functional annotation of RNA structures conserved in vertebrates
- Stefan E. Seemann,
- Aashiq H. Mirza,
- Claus Hansen,
- Claus H. Bang-Berthelsen,
- Christian Garde,
- Mikkel Christensen-Dalsgaard,
- Elfar Torarinsson,
- Zizhen Yao,
- Christopher T. Workman,
- Flemming Pociot,
- Henrik Nielsen,
- Niels Tommerup,
- Walter L. Ruzzo,
- and Jan Gorodkin
Genome Res. August 2017 27: 1371-1383; Published in Advance May 9, 2017, doi:10.1101/gr.208652.116
...to the regulatory function of the genomic site (Rinn and Chang 2012). One crucial role of bidirectionally transcribed promoters and enhancers may be in transcript stabilization (Goodarzi et al. 2012). This process is relatively independent from the primary sequence and instead may be linked to RNAstructure, e...
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ARTICLE: Genome-wide identification of direct targets of the Drosophila retinal determination protein Eyeless
- Edwin J. Ostrin,
- Yumei Li,
- Kristi Hoffman,
- Jing Liu,
- Keqing Wang,
- Li Zhang,
- Graeme Mardon,
- and Rui Chen
Genome Res. April 2006 16: 466-476; Published in Advance March 13, 2006, doi:10.1101/gr.4673006
...to this work. Abstract The discovery of direct downstream targets of transcription factors (TFs) is necessary for understanding the genetic mechanisms underlying complex, highly regulated processes such as development. In this report, we have used a combinatorial strategy to conduct a genome-wide...
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Research: Tempo and mode of regulatory evolution in Drosophila
- Joseph D. Coolon,
- C. Joel McManus,
- Kraig R. Stevenson,
- Brenton R. Graveley,
- and Patricia J. Wittkopp
Genome Res. May 2014 24: 797-808; Published in Advance February 24, 2014, doi:10.1101/gr.163014.113
...); it is essential for organismal form, fitness, and function, and frequently varies within and between species. Comparative studies using genomic surveys of gene expression in yeast (Busby et al. 2011), Drosophila (Rifkin et al. 2003), and mammalian species (Brawand et al. 2011) with a range of divergence times...
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Research: Drought responsive gene expression regulatory divergence between upland and lowland ecotypes of a perennial C₄ grass
- John T. Lovell,
- Scott Schwartz,
- David B. Lowry,
- Eugene V. Shakirov,
- Jason E. Bonnette,
- Xiaoyu Weng,
- Mei Wang,
- Jenifer Johnson,
- Avinash Sreedasyam,
- Christopher Plott,
- Jerry Jenkins,
- Jeremy Schmutz,
- and Thomas E. Juenger
Genome Res. April 2016 26: 510-518; Published in Advance March 7, 2016, doi:10.1101/gr.198135.115
...×E) of fitness. Selection upon gene expression regulatory variation can contribute to adaptive phenotypic diversity; however, surprisingly few studies have examined how genome-wide patterns of gene expression G×E are manifested in response to environmental stress and other selective agents that cause climatic...
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Method: Sasquatch: predicting the impact of regulatory SNPs on transcription factor binding from cell- and tissue-specific DNase footprints
- Ron Schwessinger,
- Maria C. Suciu,
- Simon J. McGowan,
- Jelena Telenius,
- Stephen Taylor,
- Doug R. Higgs,
- and Jim R. Hughes
Genome Res. October 2017 27: 1730-1742; Published in Advance September 13, 2017, doi:10.1101/gr.220202.117
...and the genes whose expression they affect are not known. Regulation of gene expression occurs via the binding of tissue-specific and general transcription factors (TFs) to regulatory sequences (promoters, enhancers, and boundary elements). Whereas promoters can be easily linked to the genes they regulate...

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