Article
Biochemistry & Molecular Biology
Martin S. C. Larke, Ron Schwessinger, Takayuki Nojima, Jelena Telenius, Robert A. Beagrie, Damien J. Downes, A. Marieke Oudelaar, Julia Truch, Bryony Graham, M. A. Bender, Nicholas J. Proudfoot, Douglas R. Higgs, Jim R. Hughes
Summary: Gene transcription is regulated mainly at the level of initiation, with enhancers playing a key role in this process. By evaluating promoter-proximal transcription in the context of differential gene expression, it was shown that changes in transcription initiation, rather than release of Pol II pausing, predominantly control gene expression during differentiation. Using genetically engineered mouse models, it was confirmed that enhancers regulate Pol II recruitment and/or initiation to modulate gene expression.
Article
Plant Sciences
Simon Obermeyer, Richard Stoeckl, Tobias Schnekenburger, Christoph Moehle, Uwe Schwartz, Klaus D. Grasser
Summary: Transcript elongation by RNA polymerase II (RNAPII) plays a significant role in plant development and response to environmental cues. The heterohexameric polymerase-associated factor 1 complex (PAF1C) stabilizes RNAPII elongation complex and promotes efficient transcript synthesis. This study reveals distinct transcriptional responses of PAF1C subunit mutants ELF7 and CDC73 to high salt exposure, suggesting their (partial) specific functions.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
David A. Gallegos, Melyssa Minto, Fang Liu, Mariah F. Hazlett, S. Aryana Yousefzadeh, Luke C. Bartelt, Anne E. West
Summary: This study found that amphetamine regulates the transcription of PV+ interneurons in the NAc and the regulation program is distinct from that of other GABAergic neurons in the NAc. Chromatin accessibility at enhancers predicts cell-type specific gene regulation, providing insight into transcriptional mechanisms. The functional importance of this transcriptional program was explored through expression assessment in a mouse strain with heightened behavioral sensitivity.
MOLECULAR PSYCHIATRY
(2023)
Review
Biochemistry & Molecular Biology
Juntaek Oh, Jun Xu, Jenny Chong, Dong Wang
Summary: This review summarizes recent research progress on the molecular basis of transcriptional pausing and stalling caused by different types of obstacles, and discusses new insights into Pol II-mediated lesion recognition and the roles of CSB in TC-NER.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2021)
Article
Biochemistry & Molecular Biology
Prashant Rawat, Marc Boehning, Barbara Hummel, Fernando Aprile-Garcia, Anwit S. Pandit, Nathalie Eisenhardt, Ashkan Khavaran, Einari Niskanen, Seychelle M. Vos, Jorma J. Palvimo, Andrea Pichler, Patrick Cramer, Ritwick Sawarkar
Summary: Under stress conditions, NELF rapidly forms nuclear condensates, facilitating enhanced recruitment to gene promoters and driving transcriptional downregulation, which is essential for cellular viability under stress. These stress-induced condensates may play a critical role in the coordinated downregulation of transcription and translation as part of the stress survival strategy.
Article
Multidisciplinary Sciences
Chirangini Pukhrambam, Vadim Molodtsov, Mahdi Kooshkbaghi, Ammar Tareen, Hoa Vu, Kyle S. Skalenko, Min Su, Zhou Yin, Jared T. Winkelman, Justin B. Kinney, Richard H. Ebright, Bryce E. Nickels
Summary: In sigma-dependent transcriptional pausing, the presence or absence of GreB determines whether the paused state involves backtracking or scrunched by 2-4 base pairs or 2-3 base pairs respectively. The consensus sequence T(-3)N(-2)Y(-1)G(+1) is associated with pausing in both initial transcription and transcription elongation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Min Liu, Jiafu Zhu, Zhicheng Dong
Summary: Plants have efficient mechanisms for adapting to temperature fluctuations, with primed plants exposed to mild heat stress showing more drastic transcriptional changes compared to naive plants. The study observed accumulation of engaged RNA polymerase II downstream of transcription start sites, with release of 5' pausing being a rate-limiting step for induction of heat shock protein genes.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2021)
Article
Cell Biology
Rebekah Eleazer, Kalpani De Silva, Kalina Andreeva, Zoe Jenkins, Nour Osmani, Eric C. Rouchka, Yvonne Fondufe-Mittendorf
Summary: Circular RNAs (circRNAs), derived from protein-coding genes, play important roles in biology and pathology. The mechanism behind their formation through backsplicing is still unclear. Factors that regulate pre-mRNA transcription and splicing, including RNAPII kinetics, splicing factors, and gene architecture, influence backsplicing decisions. This study investigated the role of PARP1 in circRNA biogenesis and found that PARP1 regulates circRNA production through its influence on RNAPII pausing and gene architecture. This regulation fine-tunes transcriptional output and affects gene function.
Article
Plant Sciences
Lucia Gonzalo, Ileana Tossolini, Tomasz Gulanicz, Damian A. Cambiagno, Anna Kasprowicz-Maluski, Dariusz Jan Smolinski, Maria Florencia Mammarella, Federico D. Ariel, Sebastian Marquardt, Zofia Szweykowska-Kulinska, Artur Jarmolowski, Pablo A. Manavella
Summary: This study demonstrates that plant miRNA biogenesis occurs coupled to transcription, and both co-transcriptional and post-transcriptional processing mechanisms co-exist. R-loops formed near the transcription start site region of MIRNAs promote co-transcriptional pri-miRNA processing.
Article
Multidisciplinary Sciences
Anfeng Luo, Jingwei Kong, Jun Chen, Xue Xiao, Jie Lan, Xiaorong Li, Cuifang Liu, Peng-Ye Wang, Guohong Li, Wei Li, Ping Chen
Summary: This study reveals the mechanism of direct collaboration between ubH2B and FACT at the nucleosome level. The researchers found that ubH2B impairs nucleosome stability and recruits FACT by enhancing its binding on the nucleosome. FACT preferentially binds and deposits H2A-ubH2B dimers to form an intact nucleosome. The stable altered nucleosome state obtained by ubH2B and FACT provides a key platform for gene transcription, as shown by genome-wide and time-course ChIP-qPCR analyses.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Irene Robles-Rebollo, Sergi Cuartero, Adria Canellas-Socias, Sarah Wells, Mohammad M. Karimi, Elisabetta Mereu, Alexandra G. Chivu, Holger Heyn, Chad Whilding, Dirk Dormann, Samuel Marguerat, Inmaculada Rioja, Rab K. Prinjha, Michael P. H. Stumpf, Amanda G. Fisher, Matthias Merkenschlager
Summary: This study demonstrates that inducible genes and enhancers are mainly regulated by transcriptional burst frequency, which is coordinated in single cells and individual alleles. Cohesin is required for coupling burst frequencies of inducible enhancers and promoters, but not for regulating enhancer burst frequencies. The results also suggest that cohesin and BD2 may act on shared pathways in enhancer-mediated inducible gene expression.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Jonathan E. Henninger, Ozgur Oksuz, Krishna Shrinivas, Ido Sagi, Gary LeRoy, Ming M. Zheng, J. Owen Andrews, Alicia Zamudio, Charalampos Lazaris, Nancy M. Hannett, Tong Ihn Lee, Phillip A. Sharp, Ibrahim I. Cisse, Arup K. Chakraborty, Richard A. Young
Summary: This study discusses the mechanisms of feedback control in regulating biological processes, especially in transcription regulation. Research indicates that RNA in transcription initiation promotes condensate formation, while RNA produced during elongation stimulates condensate dissolution. Therefore, transcriptional regulation involves a feedback mechanism where transcribed RNA both stimulates and arrests the process.
Article
Multidisciplinary Sciences
Seungha Hwang, Paul Dominic B. Olinares, Jimin Lee, Jinwoo Kim, Brian T. Chait, Rodney A. King, Jin Young Kang
Summary: In this study, the authors determined the structure of putRNA and its interaction with RNA polymerase using cryo-EM. They found that putRNA can inhibit pausing and termination during transcription, providing insights into the regulation of gene expression.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Kirsten A. Reimer, Claudia A. Mimoso, Karen Adelman, Karla M. Neugebauer
Summary: The study revealed tight coordination between co-transcriptional splicing and transcription elongation and 3' end formation in mammalian cells, with splicing delays possibly taking place between the two catalytic steps. Additionally, inefficient 3' end cleavage was associated with intron retention, highlighting the functional coupling between these co-transcriptional processes.
Article
Biochemistry & Molecular Biology
Yuki Aoi, Avani P. Shah, Sheetal Ganesan, Shimaa H. A. Soliman, Byoung-Kyu Cho, Young Ah Goo, Neil L. Kelleher, Ali Shilatifard
Summary: This study reveals that depletion of SPT6 releases paused RNA Pol II through impaired PAF1C recruitment, and also impairs transcription processivity. Association of NELF with elongating RNA Pol II is observed upon SPT6 depletion, but without functional significance on transcriptional elongation pattern.