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Organization and regulation of gene transcription

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  • Patrick Cramer

    (Max Planck Institute for Biophysical Chemistry)

Abstract

The regulated transcription of genes determines cell identity and function. Recent structural studies have elucidated mechanisms that govern the regulation of transcription by RNA polymerases during the initiation and elongation phases. Microscopy studies have revealed that transcription involves the condensation of factors in the cell nucleus. A model is emerging for the transcription of protein-coding genes in which distinct transient condensates form at gene promoters and in gene bodies to concentrate the factors required for transcription initiation and elongation, respectively. The transcribing enzyme RNA polymerase II may shuttle between these condensates in a phosphorylation-dependent manner. Molecular principles are being defined that rationalize transcriptional organization and regulation, and that will guide future investigations.

Suggested Citation

  • Patrick Cramer, 2019. "Organization and regulation of gene transcription," Nature, Nature, vol. 573(7772), pages 45-54, September.
    • Handle: RePEc:nat:nature:v:573:y:2019:i:7772:d:10.1038_s41586-019-1517-4
    DOI: 10.1038/s41586-019-1517-4
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    Cited by:

    1. Chun-Yi Cho & Patrick H. O’Farrell, 2023. "Stepwise modifications of transcriptional hubs link pioneer factor activity to a burst of transcription," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    2. Hiroaki Ohishi & Seiru Shimada & Satoshi Uchino & Jieru Li & Yuko Sato & Manabu Shintani & Hitoshi Owada & Yasuyuki Ohkawa & Alexandros Pertsinidis & Takashi Yamamoto & Hiroshi Kimura & Hiroshi Ochiai, 2022. "STREAMING-tag system reveals spatiotemporal relationships between transcriptional regulatory factors and transcriptional activity," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    3. Baolei Yuan & Xuan Zhou & Keiichiro Suzuki & Gerardo Ramos-Mandujano & Mengge Wang & Muhammad Tehseen & Lorena V. Cortés-Medina & James J. Moresco & Sarah Dunn & Reyna Hernandez-Benitez & Tomoaki Hish, 2022. "Wiskott-Aldrich syndrome protein forms nuclear condensates and regulates alternative splicing," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
    4. Qiaoqiao Zhang & Kai Deng & Mengyou Liu & Shengye Yang & Wei Xu & Tong Feng & Minwen Jie & Zhiming Liu & Xiao Sheng & Haiyang Chen & Hao Jiang, 2023. "Phase separation of BuGZ regulates gut regeneration and aging through interaction with m6A regulators," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    5. Nathaniel G. Jones & Vincent Geoghegan & Gareth Moore & Juliana B. T. Carnielli & Katherine Newling & Félix Calderón & Raquel Gabarró & Julio Martín & Rab K. Prinjha & Inmaculada Rioja & Anthony J. Wi, 2022. "Bromodomain factor 5 is an essential regulator of transcription in Leishmania," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    6. Michael DeBerardine & Gregory T. Booth & Philip P. Versluis & John T. Lis, 2023. "The NELF pausing checkpoint mediates the functional divergence of Cdk9," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    7. Marta Vicioso-Mantis & Raquel Fueyo & Claudia Navarro & Sara Cruz-Molina & Wilfred F. J. Ijcken & Elena Rebollo & Álvaro Rada-Iglesias & Marian A. Martínez-Balbás, 2022. "JMJD3 intrinsically disordered region links the 3D-genome structure to TGFβ-dependent transcription activation," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    8. Deqiang Kong & Yang Zhou & Yu Wei & Xinyi Wang & Qin Huang & Xianyun Gao & Hang Wan & Mengyao Liu & Liping Kang & Guiling Yu & Jianli Yin & Ningzi Guan & Haifeng Ye, 2024. "Exploring plant-derived phytochrome chaperone proteins for light-switchable transcriptional regulation in mammals," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    9. Lijing Yang & Lei Tu & Shilpa Bisht & Yiqing Mao & Daniel Petkovich & Sara-Jayne Thursby & Jinxiao Liang & Nibedita Patel & Ray-Whay Chiu Yen & Tina Largent & Cynthia Zahnow & Malcolm Brock & Kathy Ga, 2024. "Tissue-location-specific transcription programs drive tumor dependencies in colon cancer," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    10. Tuan Nguyen & Sai Li & Jeremy T-H Chang & John W. Watters & Htet Ng & Adewola Osunsade & Yael David & Shixin Liu, 2022. "Chromatin sequesters pioneer transcription factor Sox2 from exerting force on DNA," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    11. Vladyslava Gorbovytska & Seung-Kyoon Kim & Filiz Kuybu & Michael Götze & Dahun Um & Keunsoo Kang & Andreas Pittroff & Theresia Brennecke & Lisa-Marie Schneider & Alexander Leitner & Tae-Kyung Kim & Cl, 2022. "Enhancer RNAs stimulate Pol II pause release by harnessing multivalent interactions to NELF," Nature Communications, Nature, vol. 13(1), pages 1-22, December.
    12. Katerina Linhartova & Francesco Luca Falginella & Martin Matl & Marek Sebesta & Robert Vácha & Richard Stefl, 2024. "Sequence and structural determinants of RNAPII CTD phase-separation and phosphorylation by CDK7," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    13. Hui Wang & Boyuan Li & Linyu Zuo & Bo Wang & Yan Yan & Kai Tian & Rong Zhou & Chenlu Wang & Xizi Chen & Yongpeng Jiang & Haonan Zheng & Fangfei Qin & Bin Zhang & Yang Yu & Chao-Pei Liu & Yanhui Xu & J, 2022. "The transcriptional coactivator RUVBL2 regulates Pol II clustering with diverse transcription factors," Nature Communications, Nature, vol. 13(1), pages 1-26, December.
    14. Mitsuaki Fujimoto & Ryosuke Takii & Masaki Matsumoto & Mariko Okada & Keiich I. Nakayama & Ryuichiro Nakato & Katsunori Fujiki & Katsuhiko Shirahige & Akira Nakai, 2022. "HSF1 phosphorylation establishes an active chromatin state via the TRRAP–TIP60 complex and promotes tumorigenesis," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    15. Claire Marchal & Nivedita Singh & Zachary Batz & Jayshree Advani & Catherine Jaeger & Ximena Corso-Díaz & Anand Swaroop, 2022. "High-resolution genome topology of human retina uncovers super enhancer-promoter interactions at tissue-specific and multifactorial disease loci," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    16. David Flores-Solis & Irina P. Lushpinskaia & Anton A. Polyansky & Arya Changiarath & Marc Boehning & Milana Mirkovic & James Walshe & Lisa M. Pietrek & Patrick Cramer & Lukas S. Stelzl & Bojan Zagrovi, 2023. "Driving forces behind phase separation of the carboxy-terminal domain of RNA polymerase II," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    17. Tim Krischuns & Benoît Arragain & Catherine Isel & Sylvain Paisant & Matthias Budt & Thorsten Wolff & Stephen Cusack & Nadia Naffakh, 2024. "The host RNA polymerase II C-terminal domain is the anchor for replication of the influenza virus genome," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    18. Shurong Liu & Junhong Huang & Jie Zhou & Siyan Chen & Wujian Zheng & Chang Liu & Qiao Lin & Ping Zhang & Di Wu & Simeng He & Jiayi Ye & Shun Liu & Keren Zhou & Bin Li & Lianghu Qu & Jianhua Yang, 2024. "NAP-seq reveals multiple classes of structured noncoding RNAs with regulatory functions," Nature Communications, Nature, vol. 15(1), pages 1-21, December.

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