Editorial Material
Cell Biology
Dan Lu, Ashwini Jambhekar, Galit Lahav
Summary: The study reveals that elevated levels of the transcription factor MYC enhance RNA production of target genes by prolonging the duration of transcriptional bursts rather than increasing their frequency.
Article
Endocrinology & Metabolism
Jie Zhang, Peilang Yang, Dan Liu, Min Gao, Jizhuang Wang, Xiqiao Wang, Yan Liu, Xiong Zhang
Summary: Dysfunction in keratinocyte differentiation in diabetic skin is closely related to the overexpression of c-Myc and S100A6, with potential mechanisms including activation of the WNT/beta-catenin pathway and direct regulation of S100A6 expression. These findings suggest that c-Myc and S100A6 may be potential targets for the treatment of chronic diabetic wounds.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Biochemical Research Methods
Zhenjia Wang, Yifan Zhang, Chongzhi Zang
Summary: BART3D is a computational method for inferring TRs associated with genome-wide differential chromatin interactions by comparing Hi-C maps from two states, demonstrating its ability to detect relevant TRs from dynamic Hi-C profiles with TR perturbation or cell differentiation, making it a useful tool in 3D genome data analysis and functional genomics research.
Review
Biochemistry & Molecular Biology
Cristian M. Pis Diez, Maria Juliana Juncos, Matias Villarruel Dujovne, Daiana A. Capdevila
Summary: The movement of bacteria in different niches during their life cycle requires a rapid response to environmental cues. This response is primarily driven by transcriptional regulators, which sense and respond to a wide range of chemical species, ultimately regulating gene transcription. The allosteric-coupling mechanism of sensing and regulation is a central aspect of biological systems and has been a focus of research in recent decades. This review summarizes the state-of-the-art techniques used to understand these mechanisms and provides a roadmap for experimental design based on the desired answers and initial information about the system of study. The review also highlights recent research on allosteric mechanisms of sensing and regulation, discussing the use of multiple strategies and novel experimental techniques. The aim of these experiments is to gain a molecular-level understanding of how bacteria adapt to environmental threats.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Ecology
Casey M. Cosetta, Brittany Niccum, Nick Kamkari, Michael Dente, Matthew Podniesinski, Benjamin E. Wolfe
Summary: Experimental studies have shown that microbial evolution is influenced by interactions with other species in microbial communities. Using a cheese rind model microbial community, this study investigated the evolution of Staphylococcus xylosus, a bacterium associated with food and animals, in the presence of three other microbes. The results indicated that the yeast Debaryomyces hansenii strongly promoted the diversification of S. xylosus, leading to the emergence of novel phenotypic diversity. Whole-genome sequencing revealed unique mutations in specific regulators only in the co-culture with D. hansenii. These findings demonstrate the long-term evolutionary consequences of bacterial-fungal interactions in multispecies microbiomes.
Article
Biochemistry & Molecular Biology
Kyubin Lee, Sohyeong Yun, Jisu Park, Seokchan Lee, Angel M. Carcaboso, Sun-Ju Yi, Kyunghwan Kim
Summary: We investigated the potential of dimethyl alpha-ketoglutarate (DMKG) as an anti-proliferative agent against DIPG and identified its underlying molecular mechanisms. DMKG exhibited robust inhibition of DIPG cell proliferation, colony formation, and neurosphere growth. The inhibition of AKT and ERK signaling pathways by DMKG coincided with decreased expression of the CBP/ p300 coactivator, suggesting the involvement of the c-MYC-p300/ATF1-p300 axis in DIPG.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Xintao Qiu, Nadia Boufaied, Tarek Hallal, Avery Feit, Anna de Polo, Adrienne M. Luoma, Walaa Alahmadi, Janie Larocque, Giorgia Zadra, Yingtian Xie, Shengqing Gu, Qin Tang, Yi Zhang, Sudeepa Syamala, Ji-Heui Seo, Connor Bell, Edward O'Connor, Yang Liu, Edward M. Schaeffer, R. Jeffrey Karnes, Sheila Weinmann, Elai Davicioni, Colm Morrissey, Paloma Cejas, Leigh Ellis, Massimo Loda, Kai W. Wucherpfennig, Mark M. Pomerantz, Daniel E. Spratt, Eva Corey, Matthew L. Freedman, X. Shirley Liu, Myles Brown, Henry W. Long, David P. Labbe
Summary: c-MYC (MYC) is a major driver of prostate cancer tumorigenesis and progression. MYC overexpression diminishes the androgen receptor (AR) transcriptional program, contributing to prostate tumor initiation and progression.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Juliana Cazarin, Rachel E. Derollo, Siti Noor Ain Binti Ahmad Shahidan, Jamison B. Burchett, Daniel Mwangi, Saikumari Krishnaiah, Annie L. Hsieh, Zandra E. Walton, Rebekah Brooks, Stephano S. Mello, Aalim M. Weljie, Chi V. Dang, Brian J. Altman
Summary: MYC disrupts the molecular circadian clock, releasing metabolic and biosynthetic processes from circadian control, which may provide an advantage to cancer cells.
Article
Biotechnology & Applied Microbiology
Thomas E. Speltz, Zeyu Qiao, Colin S. Swenson, Xianghang Shangguan, John S. Coukos, Christopher W. Lee, Deborah M. Thomas, Jesse Santana, Sean W. Fanning, Geoffrey L. Greene, Raymond E. Moellering
Summary: Synthetic transcriptional repressors (STRs) derived from the bHLH domain of MAX have been developed using a chemical strategy. These STRs can bind to MYC/MAX consensus E-box motif with high affinity, show specificity comparable to or better than full-length TFs, compete with MYC/MAX protein for DNA binding, and inhibit MYC-dependent expression and cell proliferation. Co-crystallization and structure determination confirm that STRs retain the DNA recognition capability similar to full-length bHLH TFs. Furthermore, STRs derived from alternative bHLH-TFs can also be designed, enabling the development of highly specific mimetics targeting different gene regulatory elements.
NATURE BIOTECHNOLOGY
(2023)
Article
Cell & Tissue Engineering
Xin Zhou, Yufeng Lu, Fangqi Zhao, Ji Dong, Wenji Ma, Suijuan Zhong, Mengdi Wang, Bosong Wang, Yuqing Zhao, Yingchao Shi, Qiang Ma, Tian Lu, Jun Zhang, Xiaoqun Wang, Qian Wu
Summary: This study reveals the cell-type and spatiotemporal characteristics of human hypothalamus development and finds that different cell fates are produced sequentially with spatial developmental asynchrony. Human hypothalamic gliogenesis occurs at an earlier stage compared to mice and shows different transcription profiles. Early oligodendrocyte cells in humans interact with neuronal cells through Wnt, Hippo, and integrin signals to regulate neuronal maturation.
Article
Gastroenterology & Hepatology
Hua Yu, Jun He, Wei Liu, Shuya Feng, Li Gao, Yingying Xu, Yawei Zhang, Xuyang Hou, Yan Zhou, Leping Yang, Xiongjun Wang
Summary: AF9 protein is up-regulated in liver cancer and correlates with tumor stage and poor prognosis. It forms a complex with HIF1 alpha and acetylated cMyc to promote hypoxia tolerance and glycolysis gene expression.
Article
Fisheries
Caimei Ye, Ningqiu Li, Yinjie Niu, Qiang Lin, Hongru Liang, Lihui Liu, Xiaozhe Fu
Summary: In this study, the transcription factor c-Myc was found to play a critical role in virus replication by regulating glutamine metabolism. The cloned Sc-c-Myc in mandarin fish tissues showed high homology with other species. Overexpression of Sc-c-Myc promoted ISKNV and SCRV replication while knocking it down restrained their replication, indicating it could be a potential target for new therapeutic strategies.
FISH & SHELLFISH IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Nan Liu, Tsuyoshi Konuma, Rajal Sharma, Deyu Wang, Nan Zhao, Lingling Cao, Ying Ju, Di Liu, Shuai Wang, Almudena Bosch, Yifei Sun, Siwei Zhang, Donglei Ji, Satoru Nagatoishi, Noa Suzuki, Masaki Kikuchi, Masatoshi Wakamori, Chengcheng Zhao, Chunyan Ren, Thomas Jiachi Zhou, Yaoyao Xu, Jamel Meslamani, Shibo Fu, Takashi Umehara, Kouhei Tsumoto, Satoko Akashi, Lei Zeng, Robert G. Roeder, Martin J. Walsh, Qiang Zhang, Ming-Ming Zhou
Summary: Histone lysine acylation, such as acetylation and crotonylation, plays a crucial role in gene transcription, but our understanding has been limited to transcriptional activation. This study reveals that histone H3 lysine 27 crotonylation (H3K27cr) is involved in gene transcriptional repression. The YEATS domain of GAS41 selectively recognizes H3K27cr in chromatin and forms a complex with SIN3A-HDAC1 co-repressors. The proto-oncogenic transcription factor MYC recruits the GAS41/SIN3A-HDAC1 complex to repress genes, including the cell-cycle inhibitor p21.
Article
Multidisciplinary Sciences
Vanessa Rousseau, Elias Einig, Chao Jin, Julia Horn, Mathias Riebold, Tanja Poth, Mohamed-Ali Jarboui, Michael Flentje, Nikita Popov
Summary: Replicative stress can contribute to genomic instability and tumorigenesis, but it can also be targeted for therapeutic intervention. This study reveals that the transcription factor E2f4 recruits the DNA helicase Recql to facilitate DNA replication under stress. The ubiquitin ligase Trim33 controls the interaction between E2f4 and Recql by targeting E2f4 for degradation. Under replicative stress, Trim33-mediated ubiquitination of E2f4 is inhibited, leading to transient recruitment of Recql to chromatin and promoting DNA synthesis recovery. However, loss of Trim33 results in chronic recruitment of Recql and accelerated DNA replication under stress, compromising checkpoint signaling and DNA repair. Depletion of Trim33 in Myc-overexpressing cells leads to replication-associated DNA damage accumulation and delays Myc-driven tumorigenesis. The Trim33-E2f4-Recql axis plays a critical role in maintaining genome integrity during DNA replication along transcriptionally active chromatin.
NATURE COMMUNICATIONS
(2023)
Article
Immunology
Emanuela Colombo, Marco Di Dario, Ramesh Menon, Maria Maddalena Valente, Claudia Bassani, Nicole Sarno, Davide Mazza, Federico Montini, Lucia Moiola, Giancarlo Comi, Vittorio Martinelli, Cinthia Farina
Summary: Hepatocyte nuclear factor 4 a (HNF4a), an essential transcription factor for embryonic development, has been found to regulate the expression of inflammatory genes. Blocking HNF4a reduces immune activation and disease severity in multiple sclerosis (MS). Studies on human immune transcriptomes have identified HNF4a, SP1 and c-myc as master transcription factors regulating differential gene expression in MS. These transcription factors are activated by immune cell activation and regulated by environmental risk factors for MS. Targeting their expression or function may provide a potential therapeutic approach for MS and other inflammatory disorders.
JOURNAL OF AUTOIMMUNITY
(2023)
Article
Biochemistry & Molecular Biology
Abhinav Nath, Diana E. Schlamadinger, Elizabeth Rhoades, Andrew D. Miranker
Article
Multidisciplinary Sciences
Ana M. Melo, Juliana Coraor, Garrett Alpha-Cobb, Shana Elbaum-Garfinkle, Abhinav Nath, Elizabeth Rhoades
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2016)
Article
Biophysics
John J. Ferrie, Conor M. Haney, Jimin Yoon, Buyan Pan, Yi-Chih Lin, Zahra Fakhraai, Elizabeth Rhoades, Abhinav Nath, E. James Petersson
BIOPHYSICAL JOURNAL
(2018)
Article
Biochemistry & Molecular Biology
Hannah E. R. Baughman, Amanda F. Clouser, Rachel E. Klevit, Abhinav Nath
JOURNAL OF BIOLOGICAL CHEMISTRY
(2018)
Article
Pharmacology & Pharmacy
Guo Zhong, David Ortiz, Alex Zelter, Abhinav Nath, Nina Isoherranen
MOLECULAR PHARMACOLOGY
(2018)
Article
Biochemistry & Molecular Biology
David W. Baggett, Abhinav Nath
Article
Biochemistry & Molecular Biology
Sunil Kumar, Mark A. Brown, Abhinav Nath, Andrew D. Miranker
CHEMISTRY & BIOLOGY
(2014)
Article
Pharmacology & Pharmacy
Dennis R. Goulet, Michael J. Watson, Susan H. Tam, Adam Zwolak, Mark L. Chiu, William M. Atkins, Abhinav Nath
DRUG METABOLISM AND DISPOSITION
(2018)
Article
Virology
James B. Munro, Abhinav Nath, Michael Faerber, Siddhartha A. K. Datta, Alan Rein, Elizabeth Rhoades, Walther Mothes
JOURNAL OF VIROLOGY
(2014)
Article
Ophthalmology
Catherine M. Lockhart, Travis B. Smith, Paul Yang, Malini Naidu, Allan E. Rettie, Abhinav Nath, Richard Weleber, Edward J. Kelly
BRITISH JOURNAL OF OPHTHALMOLOGY
(2018)
Article
Pharmacology & Pharmacy
Matthew G. McDonald, Sutapa Ray, Clara J. Amorosi, Katherine A. Sitko, John P. Kowalski, Lorela Paco, Abhinav Nath, Byron Gallis, Rheem A. Totah, Maitreya J. Dunham, Douglas M. Fowler, Allan E. Rettie
DRUG METABOLISM AND DISPOSITION
(2017)
Article
Biochemistry & Molecular Biology
Mavis Jiarong Li, Abhinav Nath, William M. Atkins
Article
Biochemistry & Molecular Biology
Dennis R. Goulet, Adam Zwolak, Mark L. Chiu, Abhinav Nath, William M. Atkins
Article
Biophysics
Eri Nakatani-Webster, Abhinav Nath
BIOPHYSICAL JOURNAL
(2017)
Article
Pharmacology & Pharmacy
Jennifer E. Sager, Sasmita Tripathy, Lauren S. L. Price, Abhinav Nath, Justine Chang, Alyssa Stephenson-Famy, Nina Isoherranen
BIOCHEMICAL PHARMACOLOGY
(2017)