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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
...mechanisms are likely involved in establishing transcript-specific ribosome occupancies, several simple transcript features have previously been observed to correlate with TEs. In yeast, ORF length and translation rate correlate inversely, presumably due to a selection for faster translation initiation...
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Research: Chromatin-sensitive cryptic promoters putatively drive expression of alternative protein isoforms in yeast
- Wu Wei,
- Bianca P. Hennig,
- Jingwen Wang,
- Yujie Zhang,
- Ilaria Piazza,
- Yerma Pareja Sanchez,
- Christophe D. Chabbert,
- Sophie H. Adjalley,
- Lars M. Steinmetz,
- and Vicent Pelechano
Genome Res. December 2019 29: 1974-1984; Published in Advance November 18, 2019, doi:10.1101/gr.243378.118
...) with the following program: 10 min at 25°C, 50 min at 42°C, and heat inactivated for 15 min at 72°C. Second-strand cDNA synthesis was performed by a single PCR cycle (1 min at 98°C; 2 min at 50°C, and 15 min at 72°C) using a Phusion high-fidelity PCR master mix (NEB). A biotinylated oligo (BioNotI-P5-PET: [Btn...
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Research: Improved redox homeostasis owing to the up-regulation of one-carbon metabolism and related pathways is crucial for yeast heterosis at high temperature
- Liang Song,
- Jun-Yan Shi,
- Shou-Fu Duan,
- Da-Yong Han,
- Kuan Li,
- Ri-Peng Zhang,
- Peng-Yu He,
- Pei-Jie Han,
- Qi-Ming Wang,
- and Feng-Yan Bai
Genome Res. April 2021 31: 622-634; Published in Advance March 15, 2021, doi:10.1101/gr.262055.120
...RT-PCRqRT-PCR was used to validate the gene expression levels determined by RNA-seq analysis. Nineteen RNA samples were randomly selected from the samples subjected to RNA-seq analysis, and cDNA libraries were constructed using the first-strand cDNA synthesis with the PrimeScript RT reagent kit with gDNA Eraser (Ta...
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METHODS: Selecting Open Reading Frames From DNA
- Paola Zacchi,
- Daniele Sblattero,
- Fiorella Florian,
- Roberto Marzari,
- and Andrew R.M. Bradbury
Genome Res. May 1, 2003 13: 980-990; doi:10.1101/gr.861503
...; Crameri and Blaser 1996 ), at the C terminus of p3 ( Fuh and Sidhu 2000 ), p8 ( Fuh et al. 2000 ), p6 ( Jespers et al. 1995 ), or at the C terminus of an artificial protein that is able to replace p8 in filamentous phage ( Weiss and Sidhu 2000 ), although successful display of a cDNA library was recently...
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Research: Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast
- Vahid Aslanzadeh,
- Yuanhua Huang,
- Guido Sanguinetti,
- and Jean D. Beggs
Genome Res. February 2018 28: 203-213; Published in Advance December 18, 2017, doi:10.1101/gr.225615.117
...the transcription rate have been the subject of intensive study in mammalian cells but less is known about effects of splicing on changing the transcription rate in yeast. We present several lines of evidence showing that slow RNA polymerase II elongation increases both cotranscriptional splicing and splicing...
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Research: Turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations
- Éléonore Durand,
- Isabelle Gagnon-Arsenault,
- Johan Hallin,
- Isabelle Hatin,
- Alexandre K. Dubé,
- Lou Nielly-Thibault,
- Olivier Namy,
- and Christian R. Landry
Genome Res. June 2019 29: 932-943; Published in Advance May 31, 2019, doi:10.1101/gr.239822.118
.... (2016; see Supplemental Methods). The rRNAs were depleted in purified ribosome footprints and total mRNA samples using the Ribo-Zero Gold rRNA Removal Kit for yeast (Illumina). Ribosome profiling and total mRNA libraries were constructed using the TruSeq Ribo Profile kit for yeast (Illumina), using...
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Research: The nonessentiality of essential genes in yeast provides therapeutic insights into a human disease
- Piaopiao Chen,
- Dandan Wang,
- Han Chen,
- Zhenzhen Zhou,
- and Xionglei He
Genome Res. October 2016 26: 1355-1362; Published in Advance July 20, 2016, doi:10.1101/gr.205955.116
...for library construction, and samples were sequenced using an Illumina HiSeq 2000 with a paired-end (PE) 125 strategy. Approximately 8million reads were generated for each library, corresponding to an average sequencing depth of ∼80×. Sequence reads were aligned to the yeast by Bowtie 2 (Langmead and Salzberg...
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Research: Heritable variation of mRNA decay rates in yeast
- Jennifer M. Andrie,
- Jon Wakefield,
- and Joshua M. Akey
Genome Res. December 2014 24: 2000-2010; Published in Advance September 25, 2014, doi:10.1101/gr.175802.114
...RNA decay proceeds very rapidly following deadenylation, and that deadenylation, as opposed to decapping or exonucleolytic degradation, is the rate-limiting step in the mRNA decay process (for review, see Wilusz et al. 2001 and Garneau et al. 2007). We created barcoded sequencing libraries from the cDNA...
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Research: Yeast genetic interaction screen of human genes associated with amyotrophic lateral sclerosis: identification of MAP2K5 kinase as a potential drug target
- Myungjin Jo,
- Ah Young Chung,
- Nozomu Yachie,
- Minchul Seo,
- Hyejin Jeon,
- Youngpyo Nam,
- Yeojin Seo,
- Eunmi Kim,
- Quan Zhong,
- Marc Vidal,
- Hae Chul Park,
- Frederick P. Roth,
- and Kyoungho Suk
Genome Res. September 2017 27: 1487-1500; Published in Advance June 8, 2017, doi:10.1101/gr.211649.116
...network analyses focusing on amyotrophic lateral sclerosis (ALS)-associated genes, such as optineurin (OPTN) and angiogenin (ANG), showed that the human orthologs of the yeast toxicity modifiers of these ALS genes are enriched for several biological processes, such as cell death, lipid metabolism...
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RESOURCE: Numerous Novel Annotations of the Human Genome Sequence Supported by a 5′-End–Enriched cDNA Collection
- Betina M. Porcel,
- Olivier Delfour,
- Vanina Castelli,
- Veronique De Berardinis,
- Lucie Friedlander,
- Corinne Cruaud,
- Abel Ureta-Vidal,
- Claude Scarpelli,
- Patrick Wincker,
- Vincent Schächter,
- William Saurin,
- Gabor Gyapay,
- Marcel Salanoubat,
- and Jean Weissenbach
Genome Res. March 2004 14: 463-471; Published in Advance February 12, 2004, doi:10.1101/gr.1481104
...criteria (see Methods). Recently small protein-coding genes (smORFs) were found in Saccharomyces cerevisiae by searching potential budding yeast ORFs against sequences from other related and nonfungal species ( Kessler et al. 2003 ). The CNSLT cDNA resource provides a number of additional candidate sm...

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