Review
Biochemistry & Molecular Biology
Araceli Gonzalez-Jimenez, Adrian Campos, Francisco Navarro, Andres Clemente-Blanco, Olga Calvo
Summary: Phosphorylation can regulate the function of RNA polymerases and affect the coordination with other nuclear processes. Apart from Rpb1-CTD, other RNAPII subunits are phosphorylated, but little is known about phosphorylation of RNAPI and RNAPIII. Different subunits of RNAPI and RNAPIII may be susceptible to phosphorylation, indicating a potential coordination mechanism among the three RNAPs.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Izabela Rudzinska, Malgorzata Ciesla, Tomasz W. Turowski, Alicja Armatowska, Ewa Lesniewska, Magdalena Boguta
Summary: The study showed that the rpc128-1007 mutant disrupts Pol III assembly, affecting mRNA expression levels, particularly through modulation of the general transcription factor Gcn4. Additionally, regardless of suppressor genes, the rpc128-1007 mutation leads to a slight increase in the expression of ribosome biogenesis genes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
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
Biology
Shao-Pei Chou, Adriana K. Alexander, Edward J. Rice, Lauren A. Choate, Charles G. Danko
Summary: This study investigates how DNA sequence differences affect the dynamics and position of RNA polymerase II (Pol II) during transcription. The researchers found that DNA sequence motifs are key determinants of Pol II initiation and pause positions, and that initiation site selection follows a stochastic process similar to Brownian motion. Additionally, they discovered that differences in transcription termination impact the structure and stability of mature mRNA, and that allelic changes in transcription affect mRNA and ncRNA expression across genomic domains.
Article
Biochemistry & Molecular Biology
Anna Sawicka, Gabriel Villamil, Michael Lidschreiber, Xavier Darzacq, Claire Dugast-Darzacq, Bjoern Schwalb, Patrick Cramer
Summary: In human cells, shortening CTD by half does not affect pre-mRNA synthesis and processing, but it does impact Pol II pausing, enhancer element transcription, and transcription activation after MAP kinase pathway stimulation. This suggests that a long CTD is necessary for efficient recruitment of Pol II to target genes for rapid activation.
Article
Multidisciplinary Sciences
Hadar Medini, Amit Zirman, Dan Mishmar
Summary: Mitochondrial dysfunction has been found to play a central role in COVID-19, with significantly reduced mtDNA gene expression in patients observed, suggesting a potential link to the disease. Additionally, elevated expression of ROS-response genes and glycolysis enzymes in patients may indicate a shift towards glycolysis, creating conditions beneficial for SARS-CoV-2 replication.
Review
Cell Biology
Arianna Mangiavacchi, Gabriele Morelli, Valerio Orlando
Summary: Non-coding DNA makes up about 98.5% of the human genome and has been re-evaluated to reveal its importance in cell regulation through the presence of non-coding RNAs (ncRNAs). This review focuses on the relationship between chromatin-interacting RNAs, such as long non-coding RNA (lncRNA), enhancer RNA (eRNA), non-coding natural antisense transcript (ncNAT), circular RNA (circRNA), and the epigenome, highlighting their role in regulating gene expression and their impact on human diseases, particularly cancer.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Bianca Cesaro, Marco Tarullo, Alessandro Fatica
Summary: The field of RNA modification, known as epitranscriptomics, is attracting more attention from scientists. Over 160 chemical modifications have been found in RNA molecules, but their functions are still unclear. This review focuses on the role of N-6,2'-O-dimethyladenosine (m(6)A(m)) in gene expression regulation. While the role of m(6)A(m) in splicing regulation has been supported by studies, conflicting data exist regarding its role in mRNA stability and translation. Nonetheless, promising results have been obtained by modulating regulators in cancer cells. Further investigation on m(6)A(m) is expected to yield significant findings.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Microbiology
Robert Landick
Summary: RNA polymerase plays a crucial role in expressing genetic information through transcription of DNA, and has evolved to sense and process environmental information. Transcriptional pauses, which occur during transcript elongation, play a key role in regulatory decisions. After decades of study, four classes of transcriptional pause signals have been identified, raising numerous questions about how RNA polymerase responds to these signals and the broader regulation of transcript elongation.
ANNUAL REVIEW OF MICROBIOLOGY, VOL 75, 2021
(2021)
Article
Multidisciplinary Sciences
Benedict Shi Xiang Lian, Takumi Kawasaki, Norisuke Kano, Daisuke Ori, Moe Ikegawa, Ayako Isotani, Taro Kawai
Summary: This study demonstrates that DNA methylation at specific CpG dinucleotides plays an important regulatory role in Il6 gene expression. Hypomethylation of CpG+286 promotes Il6 expression, while deletion of CpG+348 leads to a reduction in Il6 expression associated with enhanced CTCF binding to the Il6 locus. Moreover, hypomethylation of CpG+286 in alveolar macrophages from aged mice results in higher Il6 expression in response to LPS compared to young mice.
Review
Biochemistry & Molecular Biology
Yuqiu Wang, Xing Wang Deng, Danmeng Zhu
Summary: Gene regulation mediated by noncoding RNAs (ncRNAs) plays an important role in plant development and environmental responses. This review summarizes the current understanding of the roles of small nucleolar RNA (snoRNA) and regulatory long noncoding RNA (lncRNA) in plants, as well as the potential of these ncRNAs as genetic resources for improving agronomic traits and molecular breeding.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Christian Sudfeld, Ana Pozo-Rodriguez, Sara A. Manjavacas Diez, Rene H. Wijffels, Maria J. Barbosa, Sarah D'Adamo
Summary: This study reports a novel gene expression system discovered in the oleaginous microalga Nannochloropsis, utilizing the highly efficient transcriptional activity of RNA polymerase I and an internal ribosome entry site for translation. By identifying the nucleolus as a genomic safe harbor for Pol I transcription and constructing transformant strains, consistently strong transgene expression was achieved, providing a powerful tool for genetic and metabolic engineering of microalgae and potential significant contributions to microalgal research.
Article
Cell Biology
Jia Fei, Jun Xu, Ziwei Li, Kevin Xu, Dong Wang, George A. Kassavetis, James T. Kadonaga
Summary: NDF is a transcription elongation factor that binds to Pol II and enhances gene expression elongation by a different mechanism than TFIIS.
GENES & DEVELOPMENT
(2022)
Editorial Material
Cell Biology
Alexander Hoffmann
Summary: The study focuses on understanding the function and species-specificity of short sequence elements in the core promoter that determine gene transcription activity. Through massively parallel measurements of synthetic core promoters, a statistical learning model was developed to identify the sequence differences between human and Drosophila core promoters. This model was then used to design gene core promoters that are specifically recognized by the human transcriptional machinery.
GENES & DEVELOPMENT
(2023)
Article
Cell Biology
Long Vo Ngoc, Torrey E. Rhyne, James T. Kadonaga
Summary: In this study, machine learning was used to compare DPR region, a DNA motif involved in transcription initiation, in humans and Drosophila. A distinct human-specific version of DPR was identified and machine learning models were used to predict synthetic DPR motifs with specificity for human transcription factors. These findings demonstrate the potential of machine learning in designing synthetic DNA elements with specific functional properties.
GENES & DEVELOPMENT
(2023)
Correction
Chemistry, Physical
Zaixing Jiang, Shuai Zhang, Chuanxu Yang, Reza M. Zadegan, Jorgen Kjems, Yudong Huang, Flemming Besenbacher, Mingdong Dong
Article
Chemistry, Multidisciplinary
Reza M. Zadegan, Mette D. E. Jepsen, Lasse L. Hildebrandt, Victoria Birkedal, Jorgen Kjems
Article
Chemistry, Physical
Victor Zhirnov, Reza M. Zadegan, Gurtej S. Sandhu, George M. Church, William L. Hughes
Article
Chemistry, Multidisciplinary
Christopher M. Green, Kelly Schutt, Noah Morris, Reza M. Zadegan, William L. Hughes, Wan Kuang, Elton Graugnard
Article
Multidisciplinary Sciences
Deepak K. Prusty, Volker Adam, Reza M. Zadegan, Stephan Irsen, Michael Famulok
NATURE COMMUNICATIONS
(2018)
Article
Chemistry, Multidisciplinary
Reza M. Zadegan, Mette D. E. Jepsen, Karen E. Thomsen, Anders H. Okholm, David H. Schaffert, Ebbe S. Andersen, Victoria Birkedal, Jorgen Kjems
Article
Chemistry, Multidisciplinary
Zhao Zhang, Eva M. Olsen, Mille Kryger, Niels V. Voigt, Thomas Torring, Eda Gultekin, Morten Nielsen, Reza MohammadZadegan, Ebbe S. Andersen, Morten M. Nielsen, Jorgen Kjems, Victoria Birkedal, Kurt V. Gothelf
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2011)
Review
Biochemistry & Molecular Biology
Reza M. Zadegan, Michael L. Norton
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2012)
Article
Multidisciplinary Sciences
Reza M. Zadegan, Elias G. Lindau, William P. Klein, Christopher Green, Elton Graugnard, Bernard Yurke, Wan Kuang, William L. Hughes
SCIENTIFIC REPORTS
(2017)
Article
Nanoscience & Nanotechnology
William P. Klein, Brian S. Rolczynski, Sean M. Oliver, Reza Zadegan, Susan Buckhout-White, Mario G. Ancona, Paul D. Cunningham, Joseph S. Melinger, Patrick M. Vora, Wan Kuang, Igor L. Medintz, Sebastian A. Diaz
ACS APPLIED NANO MATERIALS
(2020)