Article
Biochemistry & Molecular Biology
Jie Bai, Takako Yokomizo-Nakano, Sho Kubota, Yuqi Sun, Akinori Kanai, Mihoko Iimori, Hironori Harada, Atsushi Iwama, Goro Sashida
Summary: High Mobility Group AT-hook 2 (HMGA2) is found to be overexpressed in patients with myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML), with its expression level finely tuned by Lin28b-Let-7 axis and Polycomb Repressive Complex 2. The overexpression of HMGA2 can activate the oncogene Igf2bp2 and enhance self-renewal of Tet2-deficient stem cells, affecting the transcriptional program and differentiation of myeloid cells. These findings highlight the potential therapeutic target of HMGA2-Igf2bp2 axis in the transformation of stem cells.
Article
Biochemistry & Molecular Biology
Mirjana Lilic, Seth A. Darst, Elizabeth A. Campbell
Summary: The study reveals the crucial role of WhiB7 in induced antibiotic resistance in mycobacteria, showing its interaction with RNA polymerase and AT-rich DNA sequences to activate gene expression. These findings provide new insights into the molecular mechanism of antibiotic resistance in bacteria.
Article
Biochemistry & Molecular Biology
Yuan-Chao Lou, Hsuan-Yu Huang, Hsin-Hong Yeh, Wei-Hung Chiang, Chinpan Chen, Kuen-Phon Wu
Summary: This study reports the structure of a bacterial PmrA-dependent transcription activation complex, which reveals that RNAPH interacts with the C-terminal DNA-binding domain of PmrA via electrostatic interactions and reorients the DBD, resulting in a dynamic TAC conformation. In vivo assays show that substitution of the DNA-recognition residue eliminates its transcriptional activity, while variants with altered RNAPH-interacting residues result in enhanced transcriptional activity. These findings suggest the importance of both PmrA recognition-induced DNA distortion and promoter escape in its transcriptional activation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Genetics & Heredity
Michel G. Tremblay, Dany S. Sibai, Melissa Valere, Jean-Clement Mars, Frederic Lessard, Roderick T. Hori, Mohammad Moshahid Khan, Victor Y. Stefanovsky, Mark S. LeDoux, Tom Moss
Summary: The translation discusses the cellular mechanisms involved in the transcription of mouse and human ribosomal RNA genes, the cooperative relationship between UBTF and SL1 in cell growth and gene activation, and the impact of gene mutations on gene expression and cellular development.
Article
Biochemistry & Molecular Biology
Eunho Song, Seungha Hwang, Palinda Ruvan Munasingha, Yeon-Soo Seo, Jin Young Kang, Changwon Kang, Sungchul Hohng
Summary: In this study on bacterial Rho factor-dependent terminators, it was found that the three Rho-dependent termination routes operate compatibly and their efficiency depends on the termination pauses. The most abundant route involves Rho catching up with a paused RNA polymerase, leading to simultaneous release of transcript RNA and template DNA. The fastest route results in RNA-only release and recycling of RNAP, while the slowest route facilitates simultaneous releases. The termination efficiency of stand-by Rho positively correlates with pause duration, contrary to previous speculation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
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, Juntao Gao, Zhi Qi, Wulan Deng, Xiong Ji
Summary: This study reveals that AAA+ ATPase RUVBL2 co-occupies promoters with Pol II and different transcription factors, promoting RPB1 CTD clustering and transcription initiation. Depletion of RUVBL2 leads to a decrease in Pol II clusters and inhibits RNA synthesis, while tethering RUVBL2 to active promoters enhances Pol II clustering. Target genes directly linked to the RUVBL2-Pol II axis are identified, many of which are involved in cancer and cellular functions.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Renjie Wu, Bangyan Zhou, Wei Wang, Feng Li
Summary: This study categorizes the states of single eukaryotic genes, identifies 6 essential transcriptional events, and reveals how transcriptional bursting is modulated by various regulators. The results provide insights into transcriptional sensitivity, burst profiles, intrinsic transcriptional noise, and gene induction requirements.
Article
Biochemistry & Molecular Biology
Saurabh Sharma, Ramesh Kumar, Ayushi Jain, Manoj Kumar, Rahul Gauttam, Rajdeep Banerjee, Jayanta Mukhopadhyay, Jaya Sivaswami Tyagi
Summary: The DevR/DosR response regulator is involved in virulence, dormancy adaptation, and antibiotic tolerance mechanisms of Mycobacterium tuberculosis by regulating the expression of dormancy regulon genes. The study developed an in vivo transcription system specific to M. tuberculosis to investigate the interaction between DevR and RNA polymerase, providing insights into potential strategies to target DevR function. Additionally, the system proved useful for screening anti-DevR compounds.
BIOCHEMICAL JOURNAL
(2021)
Article
Multidisciplinary Sciences
Chung-Chi Liao, Yi-Sen Wang, Wen-Chieh Pi, Chun-Hsiung Wang, Yi-Min Wu, Wei-Yi Chen, Kuo-Chiang Hsia
Summary: The authors present a cryo-EM structure of Kap114p, revealing a non-canonical function beyond nuclear transport that modulates yTBP-dependent transcription.
NATURE COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Zhijian Ke, Yidong Zhou, Wankui Jiang, Mingliang Zhang, Hui Wang, Yijun Ren, Jiguo Qiu, Minggen Cheng, Qing Hong
Summary: This study identified McbG as a transcriptional activator of the mcbBCDEF cluster, belonging to the LysR family of transcriptional regulators. McbG regulates the transcription of the enzyme gene cluster by binding to a 25-bp motif in the mcbBCDEF promoter area. The findings reveal the regulatory mechanism for the upstream pathway of carbaryl degradation in strain XWY-1.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Akio Masuda, Toshihiko Kawachi, Kinji Ohno
Summary: This article discusses the importance of protein-RNA interactions in mRNA transcription and processing, as well as the methods for detecting these interactions and their applications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Tim Krischuns, Maria Lukarska, Nadia Naffakh, Stephen Cusack
Summary: The influenza virus RNA-dependent RNA polymerase (FluPol) transcribes the viral RNA genome by snatching capped oligomers from host RNA polymerase II transcripts. Understanding the exact mechanisms of this cap-snatching process and how FluPol targets active RNA polymerase II for transcription remains a topic of ongoing research.
ANNUAL REVIEW OF BIOCHEMISTRY, VOL 90, 2021
(2021)
Article
Biochemical Research Methods
Marleen Beentjes, Ana-Sofia Ortega-Arbulu, Hannes Loewe, Katharina Pflueger-Grau, Andreas Kremling
Summary: This study established a T7 RNA polymerase-based system for heterologous protein production in P. putida and overcame the limitations of the initial system setup. By replacing the T7 phage-inherent terminator and utilizing a ribosome binding site library, the system achieved high expression levels and predictability. The experimental data were integrated into a model that can predict protein production rates.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Toray S. Akcan, Sergey Vilov, Matthias Heinig
Summary: DNA and RNA-binding trans-acting factors play a crucial role in regulating promoter-proximal RNA polymerase II (Pol II) pausing, which is a rate-limiting step in gene expression. In this study, we developed a machine learning model that accurately predicts the extent of Pol II pausing based on genomic and transcriptomic data, and identified previously unknown regulators of pausing.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Malik Affar, Stefania Bottardi, Norreen Quansah, Maud Lemarie, Ailyn C. Ramon, El Bachir Affar, Eric Milot
Summary: IKAROS is a crucial regulator involved in determining the fate of lymphoid and other hematopoietic cells. It plays a role in the association of epigenetic regulators with chromatin, ensuring the proper expression of target genes during development and lineage specification. Disruption of IKAROS function has been linked to the development of various blood malignancies and immune disorders. Interestingly, while IKAROS acts as a tumor suppressor, it is also considered a key therapeutic target for the treatment of hematological malignancies, including multiple myeloma. The mechanisms by which IKAROS functions are not fully understood, but it is known to interact with various proteins and complexes involved in chromatin organization and transcriptional regulation. IKAROS can promote gene repression or activation by interacting with the RNA polymerase II machinery. The expression levels and isoform production of IKAROS are variable and may play a role in the seemingly opposite effects of its absence. This review summarizes the current understanding of IKAROS' biological roles and mechanisms, with a focus on its post-translational modifications. Additionally, potential explanations for how IKAROS destruction may be beneficial in the treatment of certain hematological malignancies are explored.
CELL DEATH AND DIFFERENTIATION
(2023)