Article
Genetics & Heredity
Magdalena Boguta
Summary: The control of assembly of yeast RNA polymerases (RNAPs) is not well understood. A recent study suggests that the early-stage assembly of RNAP III complex may occur through a co-translational mechanism, with the involvement of the Rbs1 protein.
Article
Multidisciplinary Sciences
Zhong Chen, William Hankey, Yue Zhao, Jeff Groth, Furong Huang, Hongyan Wang, Alexandre Rosa Campos, Jiaoti Huang, Robert G. Roeder, Qianben Wang
Summary: RNA Polymerase II (Pol II) recycling can impact transcription efficiency. An approach has been described to facilitate the identification of factors involved in Pol II recycling, with PAF1 complex components identified as mediators of recycling.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Mustafa Malik Ghulam, Mathieu Catala, Gaspard Reulet, Michelle S. Scott, Sherif Abou Elela
Summary: We demonstrate that gene duplication in yeast serves as a stress-adaptation mechanism by modulating the global proteome through differential expression of ribosomal protein paralogs. This mechanism controls translation through differential acetylation of ribosomal proteins, favoring the translation of genes with short open reading frames under normal conditions and increasing translation of genes with long open reading frames after exposure to drugs. This study identifies a natural program where changing the ratio of proteins produced from duplicated genes modifies translation in response to drugs, regardless of ribosome number.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Alison C. Greenlaw, Kris G. Alavattam, Toshio Tsukiyama
Summary: To ensure cell survival during quiescence, cells modulate their gene expression and transcription. By studying the nascent transcriptome, researchers identified over a thousand noncoding RNAs in quiescent and G1 yeast cells, revealing that noncoding transcription plays a larger role in the quiescent state. Furthermore, post-transcriptional regulation is increased in quiescence, affecting both mRNA and ncRNA. The nuclear exosome-NNS pathway was found to regulate the abundance of mRNAs involved in various cellular processes during quiescent entry, highlighting its important biological role in mRNA regulation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Alejandro Collin, Araceli Gonzalez-Jimenez, Maria del Carmen Gonzalez-Jimenez, Manuel J. Alfonso, Olga Calvo
Summary: Saccharomyces cerevisiae Sub1 is a transcriptional stimulatory protein that shares homology with the ssDNA binding domain (ssDBD) of human PC4. This study reveals the key residues responsible for DNA-ScSub1 interaction in vivo, localized in the ssDBD, and demonstrates that the carboxyl-terminal (CT) region is required for transcription elongation. These findings indicate that Sub1 plays a dual role in transcription, participating in initiation through the ssDBD and in elongation through the CT region.
Article
Biochemistry & Molecular Biology
Ana I. Garrido-Godino, Abel Cuevas-Bermudez, Francisco Gutierrez-Santiago, Maria del Carmen Mota-Trujillo, Francisco Navarro
Summary: Rtr1 plays a critical role in RNA pol II assembly and mRNA decay regulation by mediating the association between RNA pol II and Rpb4/7. This study reveals new mechanisms in gene regulation and the crosstalk between mRNA synthesis and decay.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Nouhou Haidara, Marta Giannini, Odil Porrua
Summary: Pervasive transcription is a common occurrence that leads to the production of numerous non-coding RNAs. It can have harmful effects on genome expression and stability if left uncontrolled, but it can also play important regulatory roles through transcriptional interference. This study focuses on the mechanisms that regulate the termination of non-coding transcription in response to environmental cues, specifically by investigating the helicase Sen1 in budding yeast. The findings reveal that phosphorylation at a specific site in Sen1 reduces its efficiency in transcription termination, highlighting a novel gene regulatory mechanism.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
A. I. Garrido-Godino, I. Gupta, F. Gutierrez-Santiago, A. B. Martinez-Padilla, A. Alekseenko, L. M. Steinmetz, J. E. Perez-Ortin, V. Pelechano, F. Navarro
Summary: The study identified the molecular mechanisms mediated by Rpb4 in regulating posttranscriptional events of mRNA imprinting and stability. Rpb4 interacts with a large population of mRNAs and collaborates with Puf3 to affect the stability and imprinting of a common group of mRNAs. This suggests that Rpb4 may play a key role in coordinating mRNA synthesis, imprinting, and stability in cooperation with RNA binding proteins.
Review
Biochemistry & Molecular Biology
Agnes Baudin-Baillieu, Olivier Namy
Summary: Ribosomal RNA is a crucial component of ribosomes, playing a key role in peptide bond formation and accurate genetic code decoding. Recent research suggests that ribosomal RNA modifications are not 100% complete, leading to heterogeneous populations of ribosomes. Accumulated knowledge from yeast is valuable in understanding the role of ribosomal RNA modifications in humans.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Ioannis Tsirkas, Daniel Dovrat, Manikandan Thangaraj, Ineke Brouwer, Amit Cohen, Zohar Paleiov, Michael M. Meijler, Tineke Lenstra, Amir Aharoni
Summary: The coexistence of DNA replication and transcription during S-phase requires tight coordination to prevent conflicts. This study developed a live-cell imaging approach to monitor the real-time progression of replisomes and transcription dynamics during a transcription-replication encounter. The findings showed a wave of partial transcriptional repression ahead of the moving replication fork, and revealed the negative impact of conflicts on both processes.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Trevor van Eeuwen, Tao Li, Hee Jong Kim, Jose J. Gorbea Colon, Mitchell Parker, Roland L. Dunbrack, Benjamin A. Garcia, Kuang-Lei Tsai, Kenji Murakami
Summary: During transcription initiation, TFIIH marks RNA polymerase II by phosphorylating Ser5 of Rpb1's CTD, followed by modifications related to transcription elongation, mRNA processing, and histone dynamics. The structure of TFIIK helps extend the proposed model of the CTD path to TFIIH's active site.
Article
Biology
Shu-Hao Liou, Sameer K. Singh, Robert H. Singer, Robert A. Coleman, Wei-Li Liu
Summary: Liou et al. report a 4.6 angstrom resolution structure of the human p53/RNA polymerase II assembly, using single particle cryoelectron microscopy. This study suggests that p53's functional domains regulate the DNA binding activity of RNA polymerase II, providing insights into p53-regulated gene expression.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Alan M. Tartakoff, Lan Chen, Shashank Raghavachari, Daria Gitiforooz, Akshyasri Dhinakaran, Chun-lun Ni, Cassandra Pasadyn, Ganapati H. Mahabeleshwar, Vanessa Pasadyn, John L. Woolford
Summary: In yeast cells, the coaxial organization of ribosomal DNA allows for continuous transcription and assembly processes. Inhibition of subunit production leads to differential relocation of nucleolar assembly factors between inner and outer layers, indicating the presence of assembly intermediates and cotranscriptional assembly of subunits. This cycling of assembly factors also facilitates vectorial 2-phase partitioning for relocation of nascent ribonucleoproteins.
Article
Microbiology
Yan Yang, Ganglong Yang, Zi-Jie Li, Yi-Shi Liu, Xiao-Dong Gao, Hideki Nakanishi
Summary: The surface of Saccharomyces cerevisiae spore wall has a ridged appearance. The outermost layer, believed to be a dityrosine layer composed of crosslinked dipeptide bisformyl dityrosine, is impervious to protease digestion. However, the ridged structure is removed by protease treatment. Hydrophilin proteins present in the spore wall, such as Sip18, Gre1, and Hsp12, are required for the proper organization of the ridged and proteinaceous structure.
Article
Biochemistry & Molecular Biology
Hong Zhang, Parker Murphy, Jason Yu, Sukyeong Lee, Francis T. F. Tsai, Ambro van Hoof, Jiqiang Ling
Summary: Aminoacyl-tRNA synthetases (aaRSs), essential enzymes for protein synthesis, can cause neurological disorders when mutated. This study investigates the mechanism behind these mutations and found that combined defects in aminoacylation and editing result in severe proteotoxicity. The results show that aminoacylation deficiency predisposes cells to proteotoxic stress and impairs ribosome-associated quality control.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Kyle P. Eagen, Tom A. Hartl, Roger D. Kornberg
Article
Multidisciplinary Sciences
Kyle P. Eagen, Erez Lieberman Aiden, Roger D. Kornberg
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2017)
Review
Biochemistry & Molecular Biology
Kyle P. Eagen
TRENDS IN BIOCHEMICAL SCIENCES
(2018)
Article
Biochemistry & Molecular Biology
Ryan W. Lewis, John Mabry, Jason G. Polisar, Kyle P. Eagen, Bruce Ganem, George P. Hess
Editorial Material
Biochemistry & Molecular Biology
Tiffany Ge, Celeste D. Rosencrance, Kyle P. Eagen
TRENDS IN BIOCHEMICAL SCIENCES
(2019)
Article
Biochemistry & Molecular Biology
Celeste D. Rosencrance, Haneen N. Ammouri, Qi Yu, Tiffany Ge, Emily J. Rendleman, Stacy A. Marshall, Kyle P. Eagen
Review
Biochemistry & Molecular Biology
Kyle P. Eagen, Christopher A. French
Summary: NUT carcinoma is an extremely aggressive squamous cancer driven by the BRD4-NUT fusion oncoprotein, offering potential therapeutic targets such as BET inhibitors. The BRD4-NUT complex recruits and activates histone acetyltransferase p300, forming hyperacetylated chromatin foci known as megadomains that regulate stem cell-related transcription factors. These megadomains also create a novel nuclear sub-compartment, called subcompartment M, with implications for 3D genome organization and gene regulation. Leveraging knowledge of BRD4-NUT function has led to the development of targeted therapies.
Article
Biochemistry & Molecular Biology
Ann K. Hogan, Kizhakke M. Sathyan, Alexander B. Willis, Sakshi Khurana, Shashank Srivastava, Ewelina Zasadzinska, Alexander S. Lee, Aaron O. Bailey, Matthew N. Gaynes, Jiehuan Huang, Justin Bodner, Celeste D. Rosencrance, Kelvin A. Wong, Marc A. Morgan, Kyle P. Eagen, Ali Shilatifard, Daniel R. Foltz
Summary: Histone chaperones, such as UBR7, play a crucial role in regulating the stability and supply of post-nucleosomal histone complexes. UBR7 interacts with NASP and histones to promote reincorporation of post-nucleosomal H3 complexes, opposing the histone storage functions of NASP. The absence of UBR7 leads to accumulation of NASP-bound post-nucleosomal histones and depletion of H3K4me3-modified histones in chromatin.
Editorial Material
Genetics & Heredity
Kyle P. Eagen
Summary: Two new studies demonstrate the involvement of BET proteins, particularly BRD4, in both loop extrusion and compartmentalization processes, where BRD4 facilitates one while surprisingly inhibiting the other.
Article
Biotechnology & Applied Microbiology
Celestia Fang, Zhenjia Wang, Cuijuan Han, Stephanie L. Safgren, Kathryn A. Helmin, Emmalee R. Adelman, Valentina Serafin, Giuseppe Basso, Kyle P. Eagen, Alexandre Gaspar-Maia, Maria E. Figueroa, Benjamin D. Singer, Aakrosh Ratan, Panagiotis Ntziachristos, Chongzhi Zang
Article
Biochemistry & Molecular Biology
Brian A. Kelch, Kyle P. Eagen, F. Pinar Erciyas, Elisabeth L. Humphris, Adam R. Thomason, Shinji Mitsuiki, David A. Agard
JOURNAL OF MOLECULAR BIOLOGY
(2007)