Review
Biochemistry & Molecular Biology
Chao Yu, Fenghuan Yang, Dingrong Xue, Xiuna Wang, Huamin Chen
Summary: Sigma(54) factor (RpoN) is a transcriptional regulatory factor widely found in pathogenic bacteria, regulating the transcription of various functional genes in an enhancer-binding protein (EBP)-dependent manner. RpoN plays a crucial regulatory role in bacterial growth and pathogenesis by binding to different EBPs. The complex regulatory network of RpoN in bacteria needs further investigation for better understanding.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Cell Biology
Qianhui Li, Xin Liu, Jingtao Wen, Xi Chen, Bumin Xie, Yang Zhao
Summary: With the advancement of high-throughput sequencing technology, an increasing number of non-coding RNAs have been discovered, including miRNAs, lncRNAs, circRNAs, snoRNAs, and piRNAs. The identification of eRNAs in 2010 has expanded the diversity of non-coding RNAs. eRNAs are non-coding RNA molecules transcribed from enhancer fragments of DNA cis-acting elements. Recent studies have revealed that eRNA transcription may serve as a biological marker for enhancer activity and can participate in the regulation of coding gene transcription. This review discusses the biological characteristics of eRNAs, their functions in transcriptional regulation, the factors regulating eRNA production, and the research progress of eRNAs in different diseases.
CELL COMMUNICATION AND SIGNALING
(2023)
Review
Neurosciences
Erick Sousa, Nuria Flames
Summary: Neuronal diversity is an intrinsic feature of the nervous system, with transcription factors playing key roles in establishing different neuronal identities. Common features in transcription factor categories can be identified in both mammals and nematodes, highlighting their pleiotropic functions. Transcriptional repression is crucial in controlling neuronal diversity, and the acquisition of neuronal identities is considered a metastable process.
EUROPEAN JOURNAL OF NEUROSCIENCE
(2022)
Article
Plant Sciences
Ho-Wen Yang, Jae-Hoon Lee, Youfu Zhao
Summary: Erwinia amylovora, the causal agent of fire blight disease, activates the RpoN-HrpL sigma factor cascade to regulate the hypersensitive response (HR) and pathogenicity (hrp)-type III secretion system (T3SS). This study identified the RpoN regulon in E. amylovora using RNA-seq transcriptomic analysis and in silico binding site analysis. RpoN directly regulates genes associated with virulence, nitrogen assimilation, the PspF system, motility, and the YfhA/YfhK two-component regulatory system.
Article
Genetics & Heredity
Amarni L. Thomas, Judith Marsman, Jisha Antony, William Schierding, Justin M. O'Sullivan, Julia A. Horsfield
Summary: This study used bioinformatic methods and functional data to characterize the regulatory landscape of vertebrate Runx1 gene. It identified conserved REs between human and mouse, some of which have single nucleotide polymorphisms associated with gene expression. The study suggests that REs may be variant in haematological malignancies.
Article
Biotechnology & Applied Microbiology
Yunha Hwang, Jeong-Geol Na, Seung Jae Lee
Summary: This study provides biochemical evidence of transcriptional regulation of soluble methane monooxygenase (sMMO) in methanotrophs that control methane levels in ecological systems. The purified enhancer-binding protein (MmoR) and transcription factor (s54) were used to elucidate the mechanism of transcription regulation in sMMO. Characterization studies identified the promoter binding sites and enhancer-binding sequences essential for sMMO expression. The findings demonstrate that MmoR functions as a trigger for sMMO expression due to its high specificity and selectivity for enhancer-binding sequences. The binding events of both MmoR and s54 are influenced by copper ion concentration.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Philippe J. Batut, Xin Yang Bing, Zachary Sisco, Joao Raimundo, Michal Levo, Michael S. Levine
Summary: Past studies have provided contradictory claims about the role of genome organization in gene activity regulation. This study demonstrates that the Drosophila genome is organized by two independent classes of regulatory sequences, tethering elements and insulators. These two levels of genome organization operate independently to ensure precise transcriptional dynamics and reliable complex patterning processes.
Review
Biochemistry & Molecular Biology
Yanna Shi, Bai-Jun Li, Guanqing Su, Mengxue Zhang, Donald Grierson, Kun-Song Chen
Summary: Fleshy fruit texture is an important quality characteristic of ripe fruit, and softening is an irreversible process mainly caused by changes in cell wall, starch degradation, and flavonoid levels. Lignification of certain fruits negatively affects eating quality, and excessive softening can lead to physical damage and infection. Transcription factors play a crucial role in regulating fruit texture by controlling genes related to cell wall and starch metabolism. This review focuses on the transcriptional regulatory mechanisms governing fruit textural change and discusses potential targets for breeding and future research directions.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2022)
Review
Immunology
Shengbo Zhang, Cindy Audiger, Michael Chopin, Stephen L. Nutt
Summary: This review summarizes recent advances in understanding the transcriptional networks that regulate the development of different subsets of dendritic cells (DCs). It discusses the heterogeneity of cDC2s, the ontogeny of pDCs, and the newly described DC subset, DC3. The review also examines critical transcription factors such as IRF8, PU.1, and E2-2, and highlights their regulatory mechanisms and downstream targets. The complex interplay between these transcription factors shapes the DC transcriptome and influences their function in response to environmental stimuli. The information presented in this review provides essential insights into the regulation of DC development and function, with potential implications for developing novel therapeutic strategies for immune-related diseases.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Microbiology
Muqing Ma, Anthony G. Garza, David J. Lemon, Eduardo A. Caro, Linnea Ritchie, Charles Ryan, Victoria M. Spearing, Kimberly A. Murphy, Roy D. Welch
Summary: In this study, we aimed to better understand the gene regulatory network associated with starvation in Myxococcus xanthus. We identified Nla28 as a key regulator of the early starvation response and determined its mechanism of action. Our findings suggest that Nla28 regulates a large network of genes involved in metabolic and defense-related functions. Furthermore, we discovered several target promoters of Nla28 and showed that they play important roles in starvation-induced development.
JOURNAL OF BACTERIOLOGY
(2022)
Article
Multidisciplinary Sciences
Anil K. Panigrahi, David M. Lonard, Bert W. O'Malley
Summary: This study demonstrates the interdependence of transcription between enhancers and target promoters. The results suggest that transcriptional concurrence and coordination throughout the genome are based on the transcriptional interdependence of enhancers and promoters. The study proposes a model where enhancers and promoters are entangled in the form of enhancer-promoter contact, reside in a proteinaceous bubble, and utilize shared transcriptional resources and regulatory inputs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Cell Biology
Tiegh Taylor, Natalia Sikorska, Virlana M. Shchuka, Sanjay Chahar, Chenfan Ji, Neil N. Macpherson, Sakthi D. Moorthy, Marit A. C. de Kort, Shanelle Mullany, Nawrah Khader, Zoe E. Gillespie, Lida Langroudi, Ian C. Tobias, Tineke L. Lenstra, Jennifer A. Mitchell, Tom Sexton
Summary: The connection between transcriptional control and chromatin architecture is not clearly understood. This study using genome editing and chromatin interaction analysis in mouse embryonic stem cells found a disconnect where Sox2 transcriptional activation is traced back to a few key transcription factor binding sites that have no effect on promoter-enhancer interaction frequencies or topological domain organization. Maintenance of local chromatin architecture, including at the topologically associating domain boundary downstream from the Sox2 enhancer, is distributed across multiple transcription factor-bound regions and is independent of CTCF. Additionally, disruption of promoter-enhancer interactions has no effect on Sox2 transcription. These findings suggest that many transcription factors can modulate chromatin architecture independently of CTCF.
GENES & DEVELOPMENT
(2022)
Article
Developmental Biology
James D. Price, Susan Lindtner, Athena Ypsilanti, Fadya Binyameen, Jeffrey R. Johnson, Billy W. Newton, Nevan J. Krogan, John L. R. Rubenstein
Summary: This study reveals the crucial role of transcription factors Dlx1/2 and Olig1/2 in determining the fate of subpallium cells. Dlx1/2 interacts with the NuRD complex to regulate gene transcription and cell differentiation. Loss of Dlx1/2 leads to dysregulation of regulatory elements near genes such as Olig2, resulting in increased production of OLIG2(+) cells.
Article
Biochemistry & Molecular Biology
Shatabdi Bhattacharjee, Eswar Prasad R. Iyer, Srividya Chandramouli Iyer, Sumit Nanda, Myurajan Rubaharan, Giorgio A. Ascoli, Daniel N. Cox
Summary: This study reveals the important role of a previously uncharacterized gene, CG3995, in cell type-specific dendritic development in Drosophila. The gene encodes a zinc-finger BED-type protein that regulates proportional growth and branching of dendritic arbors. It functions in both transcriptional and translational cellular pathways, promoting protein translation and ribosome trafficking along the dendritic arbor.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Virology
Dania Lavysh, Vladimir Mekler, Evgeny Klimuk, Konstantin Severinov
Summary: This study investigated the temporal pattern of gene expression during Salmonella enterica serovar Newport bacteriophage 7-11 infection and compared it to the previously determined transcription strategy of Escherichia coli phage phiEco32. The results revealed the presence of eight promoters in 7-11 phage and the absence of middle promoters and shut-off of sigma(70)-dependent transcription.
Article
Microbiology
L. Rajeev, M. E. Garber, G. M. Zane, M. N. Price, I Dubchak, J. D. Wall, P. S. Novichkov, A. Mukhopadhyay, A. E. Kazakov
ENVIRONMENTAL MICROBIOLOGY
(2019)
Article
Microbiology
Xiaoxuan Ge, Brian J. Vaccaro, Michael P. Thorgersen, Farris L. Poole, Erica L. Majumder, Grant M. Zane, Kara B. De Leon, W. Andrew Lancaster, Ji Won Moon, Charles J. Paradis, Frederick von Netzer, David A. Stahl, Paul D. Adams, Adam P. Arkin, Judy D. Wall, Terry C. Hazen, Michael W. W. Adams
ENVIRONMENTAL MICROBIOLOGY
(2019)
Article
Ecology
Hans K. Carlson, Morgan N. Price, Mark Callaghan, Alex Aaring, Romy Chakraborty, Hualan Liu, Jennifer Kueh, Adam P. Arkin, Adam M. Deutschbauer
Article
Multidisciplinary Sciences
Vivek K. Mutalik, Pavel S. Novichkov, Morgan N. Price, Trenton K. Owens, Mark Callaghan, Sean Carim, Adam M. Deutschbauer, Adam P. Arkin
NATURE COMMUNICATIONS
(2019)
Article
Microbiology
Ankita Kothari, Yu-Wei Wu, John-Marc Chandonia, Marimikel Charrier, Lara Rajeev, Andrea M. Rocha, Dominique C. Joyner, Terry C. Hazen, Steven W. Singer, Aindrila Mukhopadhyay
Article
Microbiology
Luke J. McKay, Mensur Dlakic, Matthew W. Fields, Tom O. Delmont, A. Murat Eren, Zackary J. Jay, Korinne B. Klingelsmith, Douglas B. Rusch, William P. Inskeep
NATURE MICROBIOLOGY
(2019)
Article
Microbiology
Morgan N. Price, Jayashree Ray, Anthony T. Iavarone, Hans K. Carlson, Elizabeth M. Ryan, Rex R. Malmstrom, Adam P. Arkin, Adam M. Deutschbauer
Article
Multidisciplinary Sciences
Lara Rajeev, Eric G. Luning, Grant M. Zane, Thomas R. Juba, Alexey E. Kazakov, Pavel S. Novichkov, Judy D. Wall, Aindrila Mukhopadhyay
Correction
Genetics & Heredity
Morgan N. Price, Grant M. Zane, Jennifer V. Kuehl, Ryan A. Melnyk, Judy D. Wall, Adam M. Deutschbauer, Adam P. Arkin
Article
Multidisciplinary Sciences
Estelle Couradeau, JoeIle Sasse, Danielle Goudeau, Nandita Nath, Terry C. Hazen, Ben P. Bowen, Romy Chakraborty, Rex R. Malmstrom, Trent R. Northen
NATURE COMMUNICATIONS
(2019)
Article
Microbiology
Zhou Shi, Huaqun Yin, Joy D. Van Nostrand, James W. Voordeckers, Qichao Tu, Ye Deng, Mengting Yuan, Aifen Zhou, Ping Zhang, Naijia Xiao, Daliang Ning, Zhili He, Liyou Wu, Jizhong Zhou
Article
Multidisciplinary Sciences
Daliang Ning, Ye Deng, James M. Tiedje, Jizhong Zhou
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Engineering, Environmental
Anna J. Zelaya, Albert E. Parker, Kathryn L. Bailey, Ping Zhang, Joy Van Nostrand, Daliang Ning, Dwayne A. Elias, Jizhong Zhou, Terry C. Hazen, Adam P. Arkin, Matthew W. Fields