Article
Biochemistry & Molecular Biology
Jing Luan, Marit W. Vermunt, Camille M. Syrett, Allison Cote, Jacob M. Tome, Haoyue Zhang, Anran Huang, Jennifer M. Luppino, Cheryl A. Keller, Belinda M. Giardine, Shiping Zhang, Margaret C. Dunagin, Zhe Zhang, Eric F. Joyce, John T. Lis, Arjun Raj, Ross C. Hardison, Gerd A. Blobel
Summary: The study reveals that the transcription factor CTCF specifically suppresses upstream antisense transcription at divergent gene promoters, shedding light on the regulation of antisense transcription and its coordination with sense transcription.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Leonid Serebreni, Lisa-Marie Pleyer, Vanja Haberle, Oliver Hendy, Anna Vlasova, Vincent Loubiere, Filip Nemcko, Katharina Bergauer, Elisabeth Roitinger, Karl Mechtler, Alexander Stark
Summary: Different classes of promoters have distinct mechanisms of transcription initiation, resulting in either focused or dispersed initiation patterns.
Article
Microbiology
Suresh Kumar, Mehak Zahoor Khan, Neha Khandelwal, Chen Chongtham, Biplab Singha, Ankita Dabla, Debashree Behera, Archana Singh, Balasubramanian Gopal, G. Aneeshkumar Arimbasseri, Siddhesh S. Kamat, Vinay Kumar Nandicoori
Summary: EmbR, a transcription factor, plays crucial roles in modulating cellular morphology, antibiotic resistance, and survival in the host. The study highlights EmbR as a key regulator of the hypoxic response in mycobacterial survival.
Article
Biochemistry & Molecular Biology
Anders S. Hansen, Christoph Zechner
Summary: Cells respond to external signals and stresses by activating transcription factors, inducing gene expression changes. Different gene promoters exhibit distinct induction dynamics in response to the same TF input signal, suggesting that promoters can adopt context-dependent manifestations. The full complexity of signal processing by genetic circuits may be significantly underestimated when studied in only specific contexts.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Biology
Qing Liu, Feng Jiang, Jie Zhang, Xiao Li, Le Kang
Summary: The research revealed unique genomic differences in locusts compared to fruit flies, with lower transcription initiation precision and fewer distance constraints. Additionally, stricter exon length constraints and widespread expression of distant core promoters were found in locusts. The study provides new insights into the impact of genome size expansion on distant transcription initiation.
Article
Microbiology
Xi Chen, Xiaojian Cao, Yingying Lei, Aikebaier Reheman, Wei Zhou, Bing Yang, Weipan Zhang, Weize Xu, Shuang Dong, Rohit Tyagi, Zhen F. Fu, Gang Cao
Summary: Mycobacterium tuberculosis can inhibit lysosome acidification in certain cell lines, but in others, it is targeted to acidified phagolysosomes. The gene profile analysis identified the role of ITGB3 in promoting M. tuberculosis clearance in endothelial cells, suggesting a new defense mechanism against the pathogen.
Article
Infectious Diseases
Paulo Ranaivomanana, Marie Sylvianne Rabodoarivelo, Mame Diarra Bousso Ndiaye, Niaina Rakotosamimanana, Voahangy Rasolofo
Summary: The genetic diversity of Mycobacterium tuberculosis complex influences the immune response of the host. This study found that mycobacterial-antigen-stimulated cytokine responses vary with the genotype of the MTBC infecting the patient, with lineage 4 strains inducing a decreased whole-blood pro-inflammatory cytokine response.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Microbiology
Irina Kostyukova, Oksana Pasechnik, Igor Mokrousov
Summary: In this study, the epidemiological situation and drug resistance patterns of Mycobacterium tuberculosis in the Omsk region of Russia were investigated. The TB incidence decreased over time, but the rate of multidrug-resistant tuberculosis (MDR-TB) increased. Drug resistance was found in more than half of the isolates tested, with a significant proportion of MDR cases. Monitoring drug resistance is crucial due to the emergence of M. tuberculosis strains with resistance to multiple drugs.
Article
Multidisciplinary Sciences
Yanjun Zhang, Yuan Fang, Yin Tang, Shixun Han, Junqi Jia, Xinyi Wan, Jiaqi Chen, Ying Yuan, Bin Zhao, Dong Fang
Summary: SETD2 methylates histone H3K36me3 in gene bodies in mammalian cells. In this study, the authors demonstrate that H3K36me3 is also enriched at promoter regions and is catalyzed by SMYD5, recruited by RNA polymerase II. They further show that SMYD5 is elevated in liver cancer, with a correlation to changes in gene expression. These findings provide insights into the localization and function of H3K36me3.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Linda Warfield, Rafal Donczew, Lakshmi Mahendrawada, Steven Hahn
Summary: This study investigates the genome-wide roles of the mediator factor (MED) in transcription. Rapid depletion of the activator-binding domain (Tail) of MED reveals that it only regulates a small subset of genes. The study also classifies genes into tail-dependent and tail-independent categories and discusses their implications for MED, other coactivators, and transcriptional regulation mechanisms.
Article
Cell Biology
Carlos Cordon-Obras, Claudia Gomez-Linan, Sara Torres-Rusillo, Isabel Vidal-Cobo, Diana Lopez-Farfan, Alicia Barroso-del Jesus, Domingo Rojas-Barros, Mark Carrington, Miguel Navarro
Summary: This study reveals the transcription initiation mechanism of genes in trypanosomes, identifying sequence-specific promoters that regulate the transcription of protein-coding genes, and demonstrates the conservation of this promoter-mediated regulation in eukaryotes.
Article
Microbiology
Jin Shi, Yuanyuan Liu, Tuoya Wu, Lu Li, Shujing Han, Xiao Peng, Yuanyuan Shang, Yongli Guo, Yu Pang, Mengqiu Gao, Jie Lu
Summary: This study investigated patterns of spontaneous Mycobacterium tuberculosis mutations associated with acquired bedaquiline (BDQ) and clofazimine (CFZ) resistance. The results revealed differences in acquired BDQ and CFZ resistance mechanisms and provided insights into potential underlying mechanisms. This study enhances our understanding of BDQ/CFZ resistance mechanisms and may facilitate the development of new methods for detecting drug resistance genes.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Ritu Sharma, Travis E. Hartman, Tiago Beites, Jee-Hyun Kim, Hyungjin Eoh, Curtis A. Engelhart, Linnan Zhu, Daniel J. Wilson, Courtney C. Aldrich, Sabine Ehrt, Kyu Young Rhee, Dirk Schnappinger
Summary: The current treatment for tuberculosis (TB) infections is lengthy and requires multiple antibiotics. The development of shorter, simpler treatment regimens is critical to eradicating TB. NadE, an enzyme essential for the synthesis of the cofactor NAD, is considered a promising drug target. Through gene silencing and metabolomics, it has been shown that NADP deficiency is bacteriostatic, while NAD deficiency is bactericidal due to its role in Mtb's respiratory capacity. These findings suggest prioritizing NAD biosynthesis inhibitors in anti-TB drug development.
Article
Microbiology
Valentina Tagliapietra, Maria Beatrice Boniotti, Anna Mangeli, Iyad Karaman, Giovanni Alborali, Mario Chiari, Mario D'Incau, Mariagrazia Zanoni, Annapaola Rizzoli, Maria Lodovica Pacciarini
Summary: This study indicates that wild rodents, particularly Apodemus sylvaticus, Microtus sp., and Apodemus flavicollis, may play essential roles in the maintenance of Mycobacterium microti infections in wild boar by ingestion or contact with infected excreta or contaminated environments at animal aggregation sites.
Article
Immunology
Fergal J. Duffy, Gregory S. Olson, Elizabeth S. Gold, Ana Jahn, Alan Aderem, John Aitchison, Alissa C. Rothchild, Alan H. Diercks, Johannes Nemeth
Summary: The blood RNA signatures derived from a mouse contained tuberculosis model can predict disease and tuberculosis containment in multiple human cohorts, suggesting potential for identification of biomarkers for human tuberculosis. Genes associated with immune defense are up-regulated in mice with CMTI but not in humans with active tuberculosis, indicating their role in bacterial containment. A signature comprising these genes can predict protection from tuberculosis disease and successful treatment at early time points, where current signatures are not predictive.
JOURNAL OF INFECTIOUS DISEASES
(2021)
Article
Medicine, Research & Experimental
Palaniappan Senthilkumar, Murugesan Dinakaran, Perumal Yogeeswari, Arnab China, Valakunja Nagaraja, Dharmarajan Sriram
BIOMEDICINE & PHARMACOTHERAPY
(2009)
Article
Biochemistry & Molecular Biology
Murugesan Dinakaran, Palaniappan Senthilkumar, Perumal Yogeeswari, Arnab China, Valakunja Nagaraja, Dharmarajan Sriram
BIOORGANIC & MEDICINAL CHEMISTRY
(2008)
Article
Biochemistry & Molecular Biology
Palaniappan Senthilkumar, Murugesan Dinakaran, Debjani Banerjee, Ruth Vandana Devakaram, Perumal Yogeeswari, Arnab China, Valakunja Nagaraja, Dharmarajan Sriram
BIOORGANIC & MEDICINAL CHEMISTRY
(2008)
Article
Chemistry, Medicinal
Murugesan Dinakaran, Palaniappan Senthilkumar, Perumal Yogeeswari, Arnab China, Valakunja Nagaraja, Dharmarajan Sriram
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
(2008)
Article
Chemistry, Medicinal
Palaniappan Senthilkumar, Murugesan Dinakaran, Perumal Yogeeswari, Dharmarajan Sriram, Arnab China, Valakunja Nagaraja
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2009)
Article
Infectious Diseases
Dinakaran Murugesan, Senthilkumar Palaniappan, Yogeeswari Perumal, China Arnab, Nagaraja Valakunja, Dharmarajan Sriram
INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS
(2008)
Article
Microbiology
Arnab China, Sonakshi Mishra, Priyanka Tare, Valakunja Nagaraja
JOURNAL OF BACTERIOLOGY
(2012)
Article
Chemistry, Medicinal
Murugesan Dinakaran, Palaniappan Senthilkumar, Perumal Yogeeswari, Arnab China, Valakunja Nagaraja, Dharmarajan Sriram
MEDICINAL CHEMISTRY
(2008)
Article
Microbiology
Vidyasagar Malshetty, Krishna Kurthkoti, Arnab China, Bratati Mallick, Subburaj Yamunadevi, Pau Biak Sang, Narayanaswamy Srinivasan, Valakunja Nagaraja, Umesh Varshney
Article
Microbiology
Arnab China, Priyanka Tare, Valakunja Nagaraja
Article
Multidisciplinary Sciences
Arnab China, Sonakshi Mishra, Valakunja Nagaraja
Article
Biochemical Research Methods
Arnab China, Valakunja Nagaraja
PROTEIN EXPRESSION AND PURIFICATION
(2010)
Article
Chemistry, Medicinal
Dharmarajan Sriram, Palaniappan Senthilkumar, Murugesan Dinakaran, Perumal Yogeeswari, Amab China, Valakunja Nagaraja
JOURNAL OF MEDICINAL CHEMISTRY
(2007)
Article
Biochemistry & Molecular Biology
Vikas Jain, Raspudin Saleem-Batcha, Arnab China, Dipankar Chatterji