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Research: Transposable element insertions in fission yeast drive adaptation to environmental stress
- Caroline Esnault,
- Michael Lee,
- Chloe Ham,
- and Henry L. Levin
Genome Res. January 2019 29: 85-95; Published in Advance December 12, 2018, doi:10.1101/gr.239699.118
...integration provides a saturated profile of target activity in Schizosaccharomyces pombe. Genome Res 20: 239–248. doi:10.1101/gr.099648.109 ↵Harris MA, Lock A, Bahler J, Oliver SG, Wood V. 2013. FYPO: the fission yeast phenotype ontology. Bioinformatics 29: 1671–1678. doi:10.1093/bioinformatics/btt266...
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Research: Long-read sequencing of nascent RNA reveals coupling among RNA processing events
- Lydia Herzel,
- Korinna Straube,
- and Karla M. Neugebauer
Genome Res. July 2018 28: 1008-1019; Published in Advance June 14, 2018, doi:10.1101/gr.232025.117
...relevant cell signaling. Exponentially growing S. pombe cells were treated with 10 mM caffeine for 15 min (Fig. 6B), which elicits a cellular response similar to nitrogen starvation (Rallis and Bahler 2013). Gene expression and splicing profiles were quantified by nRNA-seq and cytoplasmic mRNA-seq in three...
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Research: Broad domains of histone marks in the highly compact Paramecium macronuclear genome
- Franziska Drews,
- Abdulrahman Salhab,
- Sivarajan Karunanithi,
- Miriam Cheaib,
- Martin Jung,
- Marcel H. Schulz,
- and Martin Simon
Genome Res. April 2022 32: 710-725; Published in Advance March 9, 2022, doi:10.1101/gr.276126.121
...for gene regulation and proper Pol II activity. Histone marks (H3K4me3, H3K9ac, H3K27me3) reveal no narrow peaks but broad domains along gene bodies, whereas intergenic regions are devoid of nucleosomes. Our data implicate H3K4me3 levels inside ORFs to be the main factor associated with gene expression...
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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
...was performed with TRIzol (Invitrogen). The total RNA samples were snap-frozen in liquid nitrogen and stored at −80°C. RNA samples were quantified and evaluated for quality and using the Bioanalyzer 2100 (Agilent Technologies). Five micrograms of total RNA was isolated from each sample. Two biological...
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Research: A novel translational control mechanism involving RNA structures within coding sequences
- Jennifer Jungfleisch,
- Danny D. Nedialkova,
- Ivan Dotu,
- Katherine E. Sloan,
- Neus Martinez-Bosch,
- Lukas Brüning,
- Emanuele Raineri,
- Pilar Navarro,
- Markus T. Bohnsack,
- Sebastian A. Leidel,
- and Juana Díez
Genome Res. January 2017 27: 95-106; Published in Advance November 7, 2016, doi:10.1101/gr.209015.116
.... 2014). In contrast to thewell-establishedDhh1 repressing functions, we and others have found that Dhh1 activates translation of viral RNA s. By using amodel system that allows the replication of the plant Brome mosaic virus (BMV) in yeast, we have previously shown that Dhh1 depletion dramatically...
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Research: Evolutionarily diverse determinants of meiotic DNA break and recombination landscapes across the genome
- Kyle R. Fowler,
- Mariko Sasaki,
- Neta Milman,
- Scott Keeney,
- and Gerald R. Smith
Genome Res. October 2014 24: 1650-1664; Published in Advance July 14, 2014, doi:10.1101/gr.172122.114
...hotspots occur most often at most transcriptional promoters and associated nucleosome-depleted regions (NDRs) (Pan et al. 2011), while in fission yeast and mice, DSB hotspots are generally much farther apart and are infrequently promoter associated (Cromie et al. 2007; Smagulova et al. 2011). Hotspots...

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