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Widespread bidirectional promoters are the major source of cryptic transcripts in yeast

Author

Listed:
  • Helen Neil

    (Institut Pasteur, Unité de Génétique des Interactions Macromoléculaires, CNRS, URA2171, 75015 Paris, France)

  • Christophe Malabat

    (Institut Pasteur, Unité de Génétique des Interactions Macromoléculaires, CNRS, URA2171, 75015 Paris, France)

  • Yves d’Aubenton-Carafa

    (Centre de Génétique Moléculaire, CNRS, Allée de la Terrasse, 91198 Gif-sur-Yvette, France)

  • Zhenyu Xu

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

  • Lars M. Steinmetz

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

  • Alain Jacquier

    (Institut Pasteur, Unité de Génétique des Interactions Macromoléculaires, CNRS, URA2171, 75015 Paris, France)

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

  • Helen Neil & Christophe Malabat & Yves d’Aubenton-Carafa & Zhenyu Xu & Lars M. Steinmetz & Alain Jacquier, 2009. "Widespread bidirectional promoters are the major source of cryptic transcripts in yeast," Nature, Nature, vol. 457(7232), pages 1038-1042, February.
    • Handle: RePEc:nat:nature:v:457:y:2009:i:7232:d:10.1038_nature07747
    DOI: 10.1038/nature07747
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    Citations

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    Cited by:

    1. Benjamin J. E. Martin & LeAnn J. Howe, 2022. "Reply to: Pitfalls in using phenanthroline to study the causal relationship between promoter nucleosome acetylation and transcription," Nature Communications, Nature, vol. 13(1), pages 1-4, December.
    2. Benjamin J. M. Tremblay & Cristina P. Santini & Yajiao Cheng & Xue Zhang & Stefanie Rosa & Julia I. Qüesta, 2024. "Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    3. 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.
    4. 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.
    5. 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.
    6. 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.
    7. Xavier Contreras & David Depierre & Charbel Akkawi & Marina Srbic & Marion Helsmoortel & Maguelone Nogaret & Matthieu LeHars & Kader Salifou & Alexandre Heurteau & Olivier Cuvier & Rosemary Kiernan, 2023. "PAPγ associates with PAXT nuclear exosome to control the abundance of PROMPT ncRNAs," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    8. 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.

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