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Bidirectional promoters generate pervasive transcription in yeast

Author

Listed:
  • Zhenyu Xu

    (European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany)

  • Wu Wei

    (European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany)

  • Julien Gagneur

    (European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany)

  • Fabiana Perocchi

    (European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany)

  • Sandra Clauder-Münster

    (European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany)

  • Jurgi Camblong

    (Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK)

  • Elisa Guffanti

    (Sciences III, University of Geneva, 30 Quai E. Ansermet, 1211 Geneva 4, Switzerland)

  • Françoise Stutz

    (Sciences III, University of Geneva, 30 Quai E. Ansermet, 1211 Geneva 4, Switzerland)

  • Wolfgang Huber

    (European Molecular Biology Laboratory, European Bioinformatics Institute)

  • Lars M. Steinmetz

    (European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany)

Abstract

Small RNAs make the CUT Two papers in this issue reveal the prevalence of cryptic or hidden transcription in the yeast genome. Cryptic unstable transcripts (CUTs) are a major class of RNA polymerase II transcripts in budding yeast and are degraded immediately after being synthesized. They had therefore escaped detection until recently. In the current papers, high-resolution genome analyses reveal that CUTs arise predominantly from promoter regions and in an antisense direction. There is therefore a widespread occurrence of inherently bidirectional promoters in yeast, which hints at a regulatory function for these non-coding transcripts.

Suggested Citation

  • Zhenyu Xu & Wu Wei & Julien Gagneur & Fabiana Perocchi & Sandra Clauder-Münster & Jurgi Camblong & Elisa Guffanti & Françoise Stutz & Wolfgang Huber & Lars M. Steinmetz, 2009. "Bidirectional promoters generate pervasive transcription in yeast," Nature, Nature, vol. 457(7232), pages 1033-1037, February.
    • Handle: RePEc:nat:nature:v:457:y:2009:i:7232:d:10.1038_nature07728
    DOI: 10.1038/nature07728
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    1. Charlotte Cautereels & Jolien Smets & Peter Bircham & Dries De Ruysscher & Anna Zimmermann & Peter De Rijk & Jan Steensels & Anton Gorkovskiy & Joleen Masschelein & Kevin J. Verstrepen, 2024. "Combinatorial optimization of gene expression through recombinase-mediated promoter and terminator shuffling in yeast," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    2. Reiner-Benaim Anat & Davis Ronald W. & Juneau Kara, 2014. "Scan statistics analysis for detection of introns in time-course tiling array data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 13(2), pages 173-190, April.
    3. Kotchaphorn Mangkalaphiban & Lianwu Fu & Ming Du & Kari Thrasher & Kim M. Keeling & David M. Bedwell & Allan Jacobson, 2024. "Extended stop codon context predicts nonsense codon readthrough efficiency in human cells," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    4. Bingnan Li & Patrice Zeis & Yujie Zhang & Alisa Alekseenko & Eliska Fürst & Yerma Pareja Sanchez & Gen Lin & Manu M. Tekkedil & Ilaria Piazza & Lars M. Steinmetz & Vicent Pelechano, 2023. "Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    5. Jan Zrimec & Xiaozhi Fu & Azam Sheikh Muhammad & Christos Skrekas & Vykintas Jauniskis & Nora K. Speicher & Christoph S. Börlin & Vilhelm Verendel & Morteza Haghir Chehreghani & Devdatt Dubhashi & Ver, 2022. "Controlling gene expression with deep generative design of regulatory DNA," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    6. Haiqing Xu & Chuan Li & Chuan Xu & Jianzhi Zhang, 2023. "Chance promoter activities illuminate the origins of eukaryotic intergenic transcriptions," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    7. Komal Soni & Anusree Sivadas & Attila Horvath & Nikolay Dobrev & Rippei Hayashi & Leo Kiss & Bernd Simon & Klemens Wild & Irmgard Sinning & Tamás Fischer, 2023. "Mechanistic insights into RNA surveillance by the canonical poly(A) polymerase Pla1 of the MTREC complex," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
    8. Ying Xiong & Weijing Han & Chunhua Xu & Jing Shi & Lisha Wang & Taoli Jin & Qi Jia & Ying Lu & Shuxin Hu & Shuo-Xing Dou & Wei Lin & Terence R. Strick & Shuang Wang & Ming Li, 2024. "Single-molecule reconstruction of eukaryotic factor-dependent transcription termination," Nature Communications, Nature, vol. 15(1), pages 1-12, December.

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