Article
Agronomy
Deshui Yu, Renchun Fan, Ling Zhang, Pengya Xue, Libing Liao, Meizhen Hu, Yanjun Cheng, Jine Li, Ting Qi, Shaojuan Jing, Qiuyun Wang, Arvind Bhatt, Qian-Hua Shen
Summary: Plants have a sophisticated immune system that detects pathogen infection and activates immune responses. HvWRKY2 acts as a repressor in barley disease resistance to the powdery mildew fungus. However, the molecular features of HvWRKY2 in its DNA-binding and repressor functions, as well as its target genes, are unknown.
Review
Biochemistry & Molecular Biology
Stefano Amatori, Mirco Fanelli
Summary: Epigenomic aberrations in cancer cells play a role in cancer initiation and progression. Formalin fixation and paraffin embedding (FFPE) is widely used to preserve tissue integrity, and new chromatin immunoprecipitation (ChIP) techniques allow analysis of histone post-translational modifications and transcription factor distribution in FFPE tissues. However, the variability in fixation and storage conditions of clinical specimens can affect the success of ChIP studies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Yu Chen, Weizhu Zeng, Shiqin Yu, Song Gao, Jingwen Zhou
Summary: This study found that chromatin regulation plays an important role in nitrogen metabolism in Saccharomyces cerevisiae. It identified key nitrogen metabolism genes directly regulated by the chromatin regulator Ahc1p and analyzed the interaction between Ahc1p and transcription factors. The study elucidates the regulatory mechanism of nitrogen metabolism in S. cerevisiae from an epigenetic perspective.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Immunology
Thierry Delaveau, Antonin Thiebaut, Medine Benchouaia, Jawad Merhej, Frederic Devaux
Summary: This study revealed the interactions among CBC, Hap4 and Yap5 in Candida glabrata, showing that Yap5 regulation requires specific promoter sequences, and there is competition between Hap4 and Yap5 at the promoter of iron tolerance genes.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Clinical Neurology
Dulika Sumathipala, Petter Stromme, Zohreh Fattahi, Torben Luders, Ying Sheng, Kimia Kahrizi, Ingunn Holm Einarsen, Jennifer L. Sloan, Hossein Najmabadi, Lambert van den Heuvel, Ron A. Wevers, Sergio Guerrero-Castillo, Lars Morkrid, Vassili Valayannopoulos, Paul Hoff Backe, Charles P. Venditti, Clara D. van Karnebeek, Hilde Nilsen, Eirik Frengen, Doriana Misceo
Summary: Mutations in the ZBTB11 gene are associated with intellectual disability. The study found that patients with ZBTB11 mutations showed atrophy in multiple brain regions and had malonic and methylmalonic aciduria as disease markers. In vitro experiments indicated that ZBTB11 regulates mitochondrial functions and RNA processing.
Review
Biochemistry & Molecular Biology
Niamat Khan, Sidra Shahid, Abdul R. Asif
Summary: Chromatin is a dynamic structure consisting of DNA and proteins, playing key roles in DNA packaging, gene expression regulation, and DNA protection. Studying chromatin-associated proteins can enhance our understanding of disease pathophysiology and aid in designing new drugs.
Article
Cell Biology
Gloria Mas, Fabio Santoro, Enrique Blanco, Gianni Paolo Gamarra Figueroa, Francois Le Dily, Gianmaria Frige, Enrique Vidal, Francesca Mugianesi, Cecilia Ballare, Arantxa Gutierrez, Aleksandra Sparavier, Marc A. Marti-Renom, Saverio Minucci, Luciano Di Croce
Summary: In this study, the researchers used primary hematopoietic stem and progenitor cells (HSPCs) and leukemic blasts expressing the fusion protein PML-RARα to investigate the dynamic changes in epigenome, transcriptome, and genome architecture during oncogenic transformation. They identified Klf4 as an early down-regulated gene in PML-RARα-driven leukemogenesis and characterized the dynamic alterations in the Klf4 cis-regulatory network during APL progression. Ectopic overexpression of Klf4 was found to suppress self-renewal and reverse the differentiation block induced by PML-RARα.
GENES & DEVELOPMENT
(2022)
Article
Biochemistry & Molecular Biology
Daniel Gussakovsky, Evan P. Booy, Mira J. F. Brown, Sean A. McKenna
Summary: This study establishes the role of nuclear SRP9/SRP14 in the transcriptional regulation of 7SL and BC200 RNA. Knockdown of SRP9/SRP14 affects the steady-state levels, decay rate, and transcriptional activity of 7SL and BC200 RNA. The findings demonstrate a novel nuclear function of SRP9/SRP14 in transcriptional regulation.
Article
Multidisciplinary Sciences
Mai Nhu Uyen Le, Yichong Ning, Jianlin Zhou
Summary: The tumor suppressor gene p53 acts as a transcription factor and is commonly mutated in human cancers, especially triple negative breast cancer (TNBC). Mutations in the TP53 gene mainly occur in exons 5-8, resulting in changes in the DNA-binding domain of the p53 protein. A chromatin immunoprecipitation followed by DNA microarray (ChIP-chip) experiment was performed to identify target genes and binding motifs of the mutated p53 protein.
Article
Biochemistry & Molecular Biology
Shinnosuke Ueda, Hiroyuki Mizuta, Toshiki Uji
Summary: A ChIP method with modifications has been developed in the red macroalga Neopyropia yezoensis, enabling the identification of histone marks in generation-specific genes. The results show that the acetylation of histone H3 remains relatively high even in generation-repressed gene expression.
MOLECULAR BIOTECHNOLOGY
(2023)
Article
Genetics & Heredity
Ashley B. Reers, Rodriel Bautista, James McLellan, Beatriz Morales, Rolando Garza, Sebastiaan Bol, Kirsten K. Hanson, Evelien M. Bunnik
Summary: The gene expression and histone post-translational modification landscape during the merozoite stage of malaria parasites were investigated. Unique histone modification profiles were identified in a subset of genes, which were upregulated and involved in protein export, translation, and host cell remodeling. Similar regulatory mechanisms may underlie merozoite formation in liver and blood stages. The findings provide insights into the gene regulatory mechanisms in malaria parasite biology and may guide the development of anti-malarial drugs.
EPIGENETICS & CHROMATIN
(2023)
Article
Cell Biology
Enakshi Sinniah, Zhixuan Wu, Sophie Shen, Marina Naval-Sanchez, Xiaoli Chen, Junxian Lim, Abbigail Helfer, Abishek Iyer, Jiahui Tng, Andrew J. Lucke, Robert C. Reid, Meredith A. Redd, Christian M. Nefzger, David P. Fairlie, Nathan J. Palpant
Summary: This study reveals the important roles of HDAC1 and HDAC3 in the differentiation of human pluripotent stem cells into mesendodermal and cardiac progenitors, through chemical perturbation and single-cell RNA sequencing analysis.
Article
Immunology
Meng-Chang Lee, Cheng-Ping Yu, Xing-Hong Chen, Ming-Tsan Liu, Ji-Rong Yang, An-Yu Chen, Chih-Heng Huang
Summary: In this study, it was found that NS1 co-localizes with NF-kappa B and their co-localization at interferon genes, such as IFNL1, was confirmed. NS1 was found to disrupt the binding of NF-kappa B and inhibit the expression of IFNL1. This study reveals how NS1 inhibits the expression of antiviral genes by interfering with the interaction between NF-kappa B and the promoter.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Biology
Juan S. Ramirez-Prado, David Latrasse, Moussa Benhamed
Summary: Characterizing the molecular mechanisms regulating gene expression is crucial for understanding physiological responses in eukaryotes. ChIP-seq has become a key method for determining histone modification profiles, and the described protocol in this study offers a cost-effective approach for performing ChIP-seq of histone modifications in Arabidopsis thaliana plantlets.
Article
Genetics & Heredity
Cheryl A. Keller, Alexander Q. Wixom, Elisabeth F. Heuston, Belinda Giardine, Chris C-S Hsiung, Maria R. Long, Amber Miller, Stacie M. Anderson, April Cockburn, Gerd A. Blobel, David M. Bodine, Ross C. Hardison
Summary: The study focused on the importance of sonication in ChIP-seq experiments, finding that the level of sonication significantly impacts the quality of ChIP-seq signals. Over-sonication consistently reduces quality, while under-sonication affects binding by different transcription factors differently.
G3-GENES GENOMES GENETICS
(2021)
Article
Biotechnology & Applied Microbiology
Xiaolin Zhang, Fang Wen, Zhenyu Xu, Deying Sun, Wee Chew, Jianhua Liu
JOURNAL OF APPLIED PHYCOLOGY
(2019)
Article
Plant Sciences
Leena Thung, Jing He, Qingling Zhu, Zhenyu Xu, Jianhua Liu, Yvonne Chow
Article
Biotechnology & Applied Microbiology
Jibei Liang, Tao Cheng, Yi Huang, Jianhua Liu
Article
Multidisciplinary Sciences
Min Jiang, Chao Niu, Jianmei Cao, Di-an Ni, Zhaoqing Chu
SCIENTIFIC REPORTS
(2018)
Article
Biochemistry & Molecular Biology
Yu Yang, Kai Tang, Tatsiana U. Datsenka, Wenshan Liu, Suhui Lv, Zhaobo Lang, Xingang Wang, Jinghui Gao, Wei Wang, Wenfeng Nie, Zhaoqing Chu, Heng Zhang, Avtar K. Handa, Jian-Kang Zhu, Huiming Zhang
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2019)
Article
Biotechnology & Applied Microbiology
Xingcui Hu, Tao Cheng, Jianhua Liu
Article
Marine & Freshwater Biology
Qing-Ling Zhu, Sai-Nan Guo, Fang Wen, Xiao-Lin Zhang, Cheng-Cheng Wang, Lan-Fang Si, Jia-Lang Zheng, Jianhua Liu
AQUATIC TOXICOLOGY
(2019)
Article
Multidisciplinary Sciences
Jibei Liang, Fang Wen, Jianhua Liu
SCIENTIFIC REPORTS
(2019)
Article
Multidisciplinary Sciences
Wei Wang, Sunil Kumar Singh, Xiwen Li, Hui Sun, Yu Yang, Min Jiang, Hailing Zi, Renyi Liu, Huiming Zhang, Zhaoqing Chu
Article
Marine & Freshwater Biology
Qing-Ling Zhe, Jia-Lang Zheng, Jianhua Liu
AQUATIC TOXICOLOGY
(2020)
Article
Marine & Freshwater Biology
Qing-Ling Zhu, Jingjing Bao, Jianhua Liu, Jia-Lang Zheng
AQUATIC TOXICOLOGY
(2020)
Article
Environmental Sciences
Qingling Zhu, Mengmeng Zhang, Jingjing Bao, Jianhua Liu
Summary: The study reveals that D. salina maintains cellular defense against high cadmium concentration by upregulating ROS-scavenging activities. Additionally, cells produce oxidants and antioxidants through multiple pathways to maintain dynamic redox homeostasis under extended exposure to cadmium.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Article
Microbiology
Qingling Zhu, Mengmeng Zhang, Bingying Liu, Fang Wen, Zhili Yang, Jianhua Liu
Summary: Under mixotrophic growth conditions, high glucose supplementation promotes growth and cell biomass production in Chlorella sorokiniana G32, while photosynthetic efficiency and glucose conversion rate are affected. Transcriptomic and metabolomic analyses reveal the regulatory mechanisms of glucose assimilation and energy metabolism in G32 under mixotrophic conditions.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Zhili Yang, Zengping Zhang, Jiaqi Zhu, Yunhao Ma, Jianxin Wang, Jianhua Liu
Summary: This study presents a three-step protocol for constructing conditional lethal allele of essential genes in Pseudomonas aeruginosa. Using PA0006 as an example, the plasmid-based PA0006(Ts) mutant exhibited defects in regulation of cell morphology, formation of intact core LPS, and attachment of the O-antigen at restrictive temperatures but not at permissive temperatures. A suppressor of PA0006(Ts) was isolated through spontaneous mutations and showed restored cell morphology but not core oligosaccharide or O-antigen. This method should be widely applicable for phenotype and suppressibility analyses of other essential genes of interest in P. aeruginosa.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Microbiology
Juan Ignacio Vilchez, Qiming Tang, Richa Kaushal, Wei Wang, Suhui Lv, Danxia He, Zhaoqing Chu, Heng Zhang, Renyi Liu, Huiming Zhang
GENOME ANNOUNCEMENTS
(2018)