Article
Multidisciplinary Sciences
Soohwan Oh, Jiaofang Shao, Joydeep Mitra, Feng Xiong, Matteo D'Antonio, Ruoyu Wang, Ivan Garcia-Bassets, Qi Ma, Xiaoyu Zhu, Joo-Hyung Lee, Sreejith J. Nair, Feng Yang, Kenneth Ohgi, Kelly A. Frazer, Zhengdong D. Zhang, Wenbo Li, Michael G. Rosenfeld
Summary: The study shows that when a preferred promoter is functionally lost, its partner enhancer may be released and activate another nearby promoter. This process of target-switching may be determined by CTCF binding at promoters, in line with the model of 'enhancer scanning'. Additionally, the mechanism of enhancer release and retargeting is found to underlie the activation of disease-susceptibility genes.
Article
Multidisciplinary Sciences
Ralph S. Grand, Lukas Burger, Cathrin Grawe, Alicia K. Michael, Luke Isbel, Daniel Hess, Leslie Hoerner, Vytautas Iesmantavicius, Sevi Durdu, Marco Pregnolato, Arnaud R. Krebs, Sebastien A. Smallwood, Nicolas Thoma, Michiel Vermeulen, Dirk Schubeler
Summary: The study reveals that BANP is a critical transcription activator that binds to the CGCG element, controlling essential metabolic genes in pluripotent stem cells and neuronal cells. BANP binding is influenced by DNA methylation, restricting most binding to CGIs and explaining differential binding at CGI promoters in cancer cells. Additionally, BANP's binding to unmethylated motifs leads to chromatin opening and nucleosome phasing.
Article
Gastroenterology & Hepatology
Noga Korenfeld, Maya Finkel, Nufar Buchshtab, Meirav Bar-Shimon, Meital Charni-Natan, Ido Goldstein
Summary: The study reveals that glucagon and glucocorticoids play a role in the transcriptional regulation of amino acid catabolism genes, and their synergistic effect can enhance gluconeogenesis.
CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY
(2021)
Article
Plant Sciences
Weinan Sun, Bing Zhang, Jinwu Deng, Lin Chen, Abid Ullah, Xiyan Yang
Summary: This study identified and analyzed the CBL and CIPK gene families in upland cotton, revealing complex interactions and potential functional redundancy within the GhCBL-GhCIPK networks. Some of these genes were found to be differentially expressed under abiotic stress conditions, especially drought stress. These findings provide insights into the structural features and potential functions of the GhCBL-GhCIPK networks in stress response mechanisms in plants.
PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS
(2021)
Article
Plant Sciences
Liping Wang, Jingye Fu, Qinqin Shen, Qiang Wang
Summary: Phytoalexin is the main chemical weapon in plants to defend against pathogens. A transcription factor, OsWRKY10, has been identified to positively regulate rice diterpenoid phytoalexin biosynthesis, enhancing resistance to rice blast. OsWRKY10 directly binds to the promoters of rice diterpenoid phytoalexin biosynthesis genes, regulating gene expression.
Article
Biochemistry & Molecular Biology
Min-Jeong Jang, Woo-Jong Hong, Young-Soo Park, Ki-Hong Jung, Seungill Kim
Summary: Gene families evolve divergently and give rise to different genes with specific structures and functions. A comprehensive analysis of Zinc-finger homeodomain genes (ZF-HDs) revealed the competitive functions of Mini zinc-finger genes (MIFs) and Zinc-finger with homeodomain genes (ZHDs). Further analyses showed that MIFs (MIF-Is) had distinct motif compositions from ZHDs, while some MIFs (MIF-Zs) contained ZHD-specific motifs. Phylogenetic analyses suggested a common origin for MIF-Zs and ZHDs, while MIF-Is emerged from a separate progenitor. Additionally, the study uncovered a novel function of MIF-Is in rice, regulating surface material patterns in anthers and pollen through transcriptional regulation by interacting ZHDs.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Plant Sciences
Patricia Abril-Urias, Virginia Ruiz-Ferrer, Javier Cabrera, Rocio Olmo, Ana Claudia Silva, Fernando Evaristo Diaz-Manzano, Jose Dominguez-Figueroa, Angela Martinez-Gomez, Almudena Gomez-Rojas, Miguel Angel Moreno-Risueno, Carmen Fenoll, Carolina Escobar
Summary: Cysts and root-knot nematodes induce specialized feeding cells, syncytia and giant cells, respectively, within plant roots. The formation of these feeding sites involves different processes and signaling pathways, but both are related to the plant hormone auxin. However, there is limited information on the molecular differences and similarities between the formation of these feeding sites and the auxin-responsive genes involved.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Lei Gu, Xuanxuan Chen, Yunyan Hou, Heyan Wang, Hongcheng Wang, Bin Zhu, Xuye Du
Summary: In this study, a maize WRKY transcription factor gene, ZmWRKY70, was cloned and found to be accumulated under submergence stress in maize seedlings. ZmWRKY70 was localized in the nucleus and had transcriptional activation activity. Overexpression of ZmWRKY70 in Arabidopsis and maize increased the tolerance to submergence stress by upregulating the expression of key genes involved in anaerobic respiration. ZmWRKY70 enhanced the expression of ZmERF148 by binding to its promoter region. These findings suggest that ZmWRKY70 plays a significant role in submergence stress tolerance.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Review
Immunology
Noemi Yokobori, Beatriz Lopez, Viviana Ritacco
Summary: Multidrug-resistant tuberculosis is a major obstacle to global tuberculosis eradication efforts. In Argentina, the HIV/AIDS epidemic fueled the spread of the M strain, causing a large outbreak. Research indicates that the successful transmission of the M strain is due to its unchanged virulence, low immune response, low fitness cost of resistance mutations, and high resistance to host-related stress. However, improvements in management, diagnosis, and treatment, as well as decreased patient mobility, have contributed to the containment of the outbreak.
Article
Biochemistry & Molecular Biology
Yujin Kang, Jin Kang, AeRi Kim
Summary: The study revealed that histone H3K4me1 is a marker for DNase I hypersensitive sites in super-enhancers, and its loss significantly impacts the activation levels of super-enhancers and the expression of eRNA/mRNA transcripts.
BIOSCIENCE REPORTS
(2021)
Review
Genetics & Heredity
Laura Huning, Gary R. Kunkel
Summary: Zinc Finger Protein 143 (ZNF143) is a widespread transcriptional activator protein that regulates the efficiency of eukaryotic promoter regions. It can activate transcription at both protein coding genes and small RNA genes transcribed by different polymerases. ZNF143 plays a key role in regulating gene expression and may also be involved in chromatin looping and establishing higher order structure within the genome.
Article
Biology
Hina Khan, Partha Paul, Ritesh Rajesh Sevalkar, Sangita Kachhap, Balvinder Singh, Dibyendu Sarkar
Summary: This study identifies a new set of genes regulated by cyclic AMP (cAMP) in Mycobacterium tuberculosis, including virulence factors controlled by the major regulator PhoP. The results show that PhoP, as a DNA binding transcription factor, impacts gene expression and phosphorylated PhoP promotes recruitment of cAMP receptor protein (CRP) at target promoters. Additionally, a novel regulatory mechanism is uncovered, where activation of these genes requires direct recruitment of both PhoP and CRP at their target promoters.
Review
Genetics & Heredity
Biguang Huang, Weiren Wu, Zonglie Hong
Summary: Multiple genes control the diversity and development of barley awns, resulting in various shapes and lengths. Complexity of gene interactions poses challenges in genetic mapping, necessitating specific strategies for mapping genes with interactive effects.
Article
Biochemistry & Molecular Biology
Edio Maldonado, Sebastian Morales-Pison, Fabiola Urbina, Claudia Arias, Christian Castillo, Lilian Jara, Aldo Solari
Summary: In this study, we identified a protein called HEBP that binds to the HomolE box and activates transcription of RPGs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Medicine, General & Internal
Zhezhe Cui, Jun Liu, Yue Chang, Dingwen Lin, Dan Luo, Jing Ou, Liwen Huang
Summary: The study found that Beijing family strains had a significantly higher proportion in hot spots compared to cold spots, and mutations in related genes showed significant differences between the two. Additionally, age, BMI, and polymorphisms in the Rv0210 gene were identified as significant factors in the transmission and development of M. tb.
Article
Biochemistry & Molecular Biology
Kautilya Kumar Jena, Srinivasa Prasad Kolapalli, Subhash Mehto, Parej Nath, Biswajit Das, Pradyumna Kumar Sahoo, Abdul Ahad, Gulam Hussain Syed, Sunil K. Raghav, Shantibhusan Senapati, Swati Chauhan, Santosh Chauhan
Article
Biochemistry & Molecular Biology
Subhash Mehto, Kautilya Kumar Jena, Parej Nath, Swati Chauhan, Srinivasa Prasad Kolapalli, Saroj Kumar Das, Pradyumna Kumar Sahoo, Ashish Jain, Gregory A. Taylor, Santosh Chauhan
Editorial Material
Cell Biology
Kautilya Kumar Jena, Subhash Mehto, Srinivasa Prasad Kolapalli, Parej Nath, Rinku Sahu, Nishant Ranjan Chauhan, Pradyumna Kumar Sahoo, Kollori Dhar, Saroj Kumar Das, Swati Chauhan, Santosh Chauhan
Editorial Material
Cell Biology
Subhash Mehto, Swati Chauhan, Kautilya Kumar Jena, Nishant Ranjan Chauhan, Parej Nath, Rinku Sahu, Kollori Dhar, Saroj Kumar Das, Santosh Chauhan
Article
Oncology
Subha Saha, Krushna Chandra Murmu, Mayukh Biswas, Sohini Chakraborty, Jhinuk Basu, Swati Madhulika, Srinivasa Prasad Kolapalli, Santosh Chauhan, Amitava Sengupta, Punit Prasad
FRONTIERS IN ONCOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Kautilya Kumar Jena, Subhash Mehto, Parej Nath, Nishant Ranjan Chauhan, Rinku Sahu, Kollori Dhar, Saroj Kumar Das, Srinivasa Prasad Kolapalli, Krushna C. Murmu, Ashish Jain, Sivaram Krishna, Bhabani Sankar Sahoo, Soma Chattopadhyay, Tor Erik Rusten, Punit Prasad, Swati Chauhan, Santosh Chauhan
Article
Cell Biology
Parej Nath, Kautilya Kumar Jena, Subhash Mehto, Nishant Ranjan Chauhan, Rinku Sahu, Kollori Dhar, Kolapalli Srinivas, Swati Chauhan, Santosh Chauhan
Summary: IRGM serves as a genetic risk factor for autoimmune diseases and acts as a master suppressor of interferon response, preventing the aberrant activation of the immune system and autoimmunity.
Article
Oncology
Srinivasa P. Kolapalli, Rinku Sahu, Nishant R. Chauhan, Kautilya K. Jena, Subhash Mehto, Saroj K. Das, Ashish Jain, Manaswini Rout, Rupesh Dash, Rajeeb K. Swain, David Y. Lee, Tor Erik Rusten, Santosh Chauhan, Swati Chauhan
Summary: This study demonstrates, for the first time, that DZIP3 uses a unique two-pronged mechanism to stabilize Cyclin D1 and drive cell-cycle progression and cancer progression. DZIP3 controls Cyclin D1 mRNA and protein stability in a cell-cycle phase-dependent manner, making it a novel driver of cell-cycle and cancer progression.
Article
Biochemistry & Molecular Biology
Parej Nath, Nishant Ranjan Chauhan, Kautilya Kumar Jena, Ankita Datey, Nilima Dinesh Kumar, Subhash Mehto, Saikat De, Tapas Kumar Nayak, Swatismita Priyadarsini, Kshitish Rout, Ramyasingh Bal, Krushna C. Murmu, Manjula Kalia, Srinivas Patnaik, Punit Prasad, Fulvio Reggiori, Soma Chattopadhyay, Santosh Chauhan
Summary: The research demonstrates that IRGM negatively regulates viral infection, and depletion of IRGM can enhance the cell-intrinsic antiviral immune state, resulting in resistance to multiple viruses.
Review
Biochemistry & Molecular Biology
Swati Chauhan, Kautilya Kumar Jena, Subhash Mehto, Nishant Ranjan Chauhan, Rinku Sahu, Kollori Dhar, Rina Yadav, Sivaram Krishna, Pundrik Jaiswal, Santosh Chauhan
Summary: There is extensive crosstalk between autophagy and innate immune signaling pathways, where increased autophagy aims to eliminate stimuli and regulate inflammatory pathways by targeted degradation of proteins. This interplay helps maintain immune homeostasis and protect against inflammatory and autoimmune diseases. Further systematic studies are needed to fully understand the mechanisms of this interaction.
Letter
Hematology
Subha Saha, Priyanka Samal, Swati Madhulika, Krushna Chandra Murmu, Sohini Chakraborty, Jhinuk Basu, Subhabrata Barik, Kautilya Kumar Jena, Asima Das, Santosh Chauhan, Punit Prasad
Article
Biochemistry & Molecular Biology
Subhash Mehto, Kautilya Kumar Jena, Rina Yadav, Swatismita Priyadarsini, Pallavi Samal, Sivaram Krishna, Kollori Dhar, Ashish Jain, Nishant Ranjan Chauhan, Krushna C. Murmu, Ramyasingh Bal, Rinku Sahu, Pundrik Jaiswal, Bhabani Sankar Sahoo, Srinivas Patnaik, Thomas A. Kufer, Tor Erik Rusten, Swati Chauhan, Punit Prasad, Santosh Chauhan
Summary: This study reveals a unique mechanism where bacterial infection induces the formation of endogenous RIPK2 oligomers (RIPosomes) that coat the bacteria to induce NF-kappa B response. Autophagy proteins IRGM and p62/SQSTM1 physically interact with NOD1/2, RIPK2 and RIPosomes to promote their selective autophagy and limit NF-kappa B activation. This study highlights the involvement of innate immune proteins and autophagy machinery in bacterial defense and immune homeostasis maintenance.
Editorial Material
Cell Biology
Subhash Mehto, Soumya Kundu, Swati Chauhan, Santosh Chauhan
Summary: The NOD1-NOD2-RIPK2-NFKB/NF-kappa B pro-inflammatory axis is important for regulating the immune response to bacterial infection. Our recent study showed that degradation of RIPosomes through selective autophagy can limit the inflammatory response and maintain innate immune balance.
Article
Oncology
Kautilya Kumar Jena, Srinivasa Prasad Kolapalli, Subhash Mehto, Swati Chauhan, Santosh Chauhan
MOLECULAR & CELLULAR ONCOLOGY
(2018)
Article
Cell Biology
Kautilya Kumar Jena, Subhash Mehto, Srinivasa Prasad Kolapalli, Parej Nath, Swati Chauhan, Santosh Chauhan