Article
Immunology
Jing Yang, Edith A. Perez, Changchun Hou, Pin Zhang, Michelle Van Scoyk, Robert A. Winn, Lijun Rong, Jing Liu
Summary: Multiple lines of evidence demonstrate that cigarette smoke or Chronic Obstructive Pulmonary Disease upregulates angiotensin-converting enzyme 2, predisposing individuals to severe Coronavirus disease 2019. Researchers found that loss of function of Miz1 in lung epithelium leads to COPD-like phenotype and upregulation of ACE2, while the binding of Miz1 to ACE2 promoter suppresses its activity.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Microbiology
Meredith B. Finn, Kathryn M. Ramsey, Simon L. Dove, Michael R. Wessels
Summary: The study reveals that the CsrRS system in Group A Streptococcus regulates gene expression by modulating the phosphorylation of CsrR, affecting the bacteria's ability to adapt to the human host. Analysis indicates that CsrR influences the expression of multiple genes by binding to regulated promoters and controlling the expression of intermediate transcription regulators.
Article
Biochemical Research Methods
Priyanka Barman, Amala Kaja, Pritam Chakraborty, Sukesh R. Bhaumik
Summary: Proteins are expressed through transcription, mRNA processing, export and translation, and their interactions with other proteins, DNAs or RNAs play a crucial role in maintaining cellular functions. Studying protein interactions in living cells is important for understanding their mechanisms-of-action in real time. One state-of-the-art approach is formaldehyde crosslinking-based immuno- or chemi-precipitation, which is widely used for analyzing protein-protein and protein-nucleic acid interactions in cellular analysis.
Article
Biotechnology & Applied Microbiology
Ariel Caride, Jin Sung Jang, Geng-Xian Shi, Sam Lenz, Jian Zhong, Kwan Hyun Kim, Mariet Allen, Keith D. Robertson, Gianrico Farrugia, Tamas Ordog, Nilufer Ertekin-Taner, Jeong-Heon Lee
Summary: Chromatin immunoprecipitation (ChIP) is a commonly used antibody-based method in chromatin biology and epigenetics. This study introduces a simple and quick method to quantify chromatin inputs and optimize antibody amounts for ChIP reactions, resulting in improved assay outcomes.
Article
Marine & Freshwater Biology
Yuanyuan Li, Jinbo Li, Yanping Shen, Yiming Xiong, Xinghong Li, Zhanfen Qin
Summary: The study identified ER target genes involved in estrogen-caused gonadal feminization in Xenopus laevis, including pglyrp2, apoa1, fgb, and others. These genes were shown to be responsive to estrogen, either up- or down-regulated by E2, and capable of binding to ER. This contributes to a better understanding of the molecular mechanisms for gonadal feminization caused by estrogenic endocrine disrupting chemicals in X. laevis and potentially other species.
AQUATIC TOXICOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Jing Yang, Leilei Qi, Huai-Chin Chiang, Bin Yuan, Rong Li, Yanfen Hu
Summary: BRCA1 is a tumor suppressor frequently mutated in familial breast and ovarian cancer patients. Many commercial antibodies targeting BRCA1 are poorly characterized, leading to unreliable data. By rigorously validating several commercially available anti-BRCA1 antibodies, researchers identified specific antibodies with high performance, aiming to improve understanding of BRCA1 functions and combat challenges associated with antibody specificity and reproducibility.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2021)
Article
Cell Biology
Filipe A. Monteiro, Rafael M. Miranda, Marta C. Samina, Ana F. Dias, Alexandre A. S. F. Raposo, Patricia Oliveira, Carlos Reguenga, Diogo S. Castro, Deolinda Lima
Summary: The homeobox gene Tlx3 acts as a selector gene in controlling the development of late-born excitatory neurons in the dorsal spinal cord by specifying glutamatergic transmitter fate. Through genomics and validation experiments, it was found that Tlx3 directly activates genes specific to excitatory neurons and also directly represses genes associated with inhibitory neuronal fate. This study provides insight into the regulatory role of Tlx3 in neural development and reveals its novel function in controlling cell identity.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Cardiac & Cardiovascular Systems
Pingzhu Zhou, Yan Zhang, Isha Sethi, Lincai Ye, Michael A. Trembley, Yangpo Cao, Brynn N. Akerberg, Feng Xiao, Xiaoran Zhang, Kai Li, Blake D. Jardin, Neil Mazumdar, Qing Ma, Aibin He, Bin Zhou, William T. Pu
Summary: This study investigated the chromatin occupancy of GATA4 during heart development. The researchers found that GATA4 occupies genomic regions with lineage-specific enhancers in cardiomyocyte and endocardial lineages. They also discovered that non-pioneer transcription factors NKX2-5 and ETS1 guide the activity of GATA4, promoting its binding and opening of chromatin, and regulating endocardial development.
CIRCULATION RESEARCH
(2022)
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
Plant Sciences
Zhibo Wang, Zihang He, Zhujun Liu, Ming Qu, Caiqiu Gao, Chao Wang, Yucheng Wang
Summary: DNA-protein interaction is crucial in biological processes, but current technologies based on DNA hybridization lack specificity and efficiency. To overcome this, we developed a DNA-binding protein capture technology, R-ChIP-dCas9, using the CRISPR-dCas9 system and transient genetic transformation. This method enables the identification of upstream transcription factors, such as BpNAC090 and its potential regulators.
Article
Plant Sciences
Konstantin O. Kutashev, Michal Franek, Klev Diamanti, Jan Komorowski, Marie Olsinova, Martina Dvorackova
Summary: Arabidopsis thaliana's 45S ribosomal genes are located on the termini of chromosomes 2 and 4, encoding rRNA. Not all intranucleolar rDNA is active, with some forming condensed foci marked with repressive histone marks. The condensed foci relate to rDNA folding and contain typical modifications of inactive rDNA.
Article
Biochemistry & Molecular Biology
Annapurna Bhattacharjee, Prabhakar Lal Srivastava, Onkar Nath, Mukesh Jain
Summary: OsHOX24 mediates regulation of desiccation stress response in rice through binding to multiple target genes involved in various biological processes, such as plant development and abiotic stress responses. The involvement of OsHOX24 in complex regulatory networks is indicated by the enrichment of cis-regulatory motifs representing binding sites of other transcription factors.
PLANT MOLECULAR BIOLOGY
(2021)
Article
Agriculture, Dairy & Animal Science
Zhijie Chen, Lu Cui, Li Xu, Zheyi Liu, Yumeng Liang, Xuefeng Li, Yanhui Zhang, Yijing Li, Shengwang Liu, Hai Li
Summary: In this study, the chp53 transcriptional regulatory network was comprehensively characterized through analysis of chromatin occupancy and gene expression, providing insights into the underlying mechanisms of chp53's antiviral functions in chickens. The findings also contribute to a better understanding of p53 transcriptional regulatory mechanisms.
Article
Biochemistry & Molecular Biology
Tomoaki Saito, Shunichi Asai, Nozomi Tanaka, Nijiro Nohata, Chikashi Minemura, Ayaka Koma, Naoko Kikkawa, Atsushi Kasamatsu, Toyoyuki Hanazawa, Katsuhiro Uzawa, Naohiko Seki
Summary: This study utilized ChIP-Seq to analyze active enhancers and identified genes associated with drug resistance and prognosis in oral squamous cell carcinoma, providing crucial genetic information for improving treatment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
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
Genetics & Heredity
Hirotaka Fujita, Toshitsugu Fujita, Hodaka Fujii
Summary: The multitude of molecular interactions with chromatin regulate various chromosomal functions in cells. The locus-specific purification of genomic DNA with the CRISPR system allows for the isolation of target regions and identification of bound interacting molecules, deepening our understanding of regulatory mechanisms and disease pathogenesis.
Article
Oncology
Takashi Takeda, Yuhki Yokoyama, Hidekazu Takahashi, Daisuke Okuzaki, Kaho Asai, Hiroaki Itakura, Norikatsu Miyoshi, Shogo Kobayashi, Mamoru Uemura, Toshitsugu Fujita, Hiroo Ueno, Masaki Mori, Yuichiro Doki, Hodaka Fujii, Hidetoshi Eguchi, Hirofumi Yamamoto
Summary: The study aimed to unravel the regulatory mechanism of the KLF5 gene product in CRC through in vitro methods, revealing that KLF5 protein constructs a core-regulatory circuitry with co-factors in the three-dimensional genome structure and coordinately regulates KLF5 and CCAT1 expression in CRC.
BRITISH JOURNAL OF CANCER
(2022)
Article
Genetics & Heredity
Ashita Sarudate, Toshitsugu Fujita, Takahiro Nakayama, Hodaka Fujii
Summary: This study developed a method called enChIP-Seq to detect physical interactions between genomic regions. It combines engineered DNA-binding molecule-mediated chromatin immunoprecipitation and next-generation sequencing analysis. The researchers also developed enChIP-Seq analyzer software to facilitate the analysis of enChIP-Seq data and identify specific interactions between genomic regions.
Article
Cell Biology
Hirotaka Fujita, Toshitsugu Fujita, Hodaka Fujii
Summary: This study assessed the role of inhibitor of nuclear factor-kappa B kinases (IKKs) in the regulation of interleukin-3 (IL-3)-mediated immediate early gene expression. The results showed that IKK1 and IKK2 are necessary for the immediate expression of c-fos and c-jun induced by IL-3. In addition, IKK2 plays an important role in the activation of c-Jun N-terminal kinase (JNK). The findings suggest that the IKK2-JNK axis regulates IL-3-induced immediate early gene expression in a canonical NF-kappa B-independent manner.
Article
Pathology
Sachiko Imanishi, Shoko Nagata, Toshitsugu Fujita, Hodaka Fujii
Summary: Hepatocellular carcinoma (HCC) is a common and deadly form of liver cancer. Current biomarkers for HCC diagnosis lack specificity, necessitating the search for more specific biomarkers. Recent research has identified circRNA as a potential biomarker for specific HCC diagnosis. Using publicly available RNA-seq data, this study identified eight circRNAs with altered expression levels in HCC tissues. Two circRNAs (hsa_circ_0001438 and hsa_circ_0000417) were identified as potential biomarkers for specific HCC diagnosis.
INTERNATIONAL JOURNAL OF EXPERIMENTAL PATHOLOGY
(2022)
Article
Chemistry, Analytical
Toshitsugu Fujita, Shoko Nagata, Hodaka Fujii
Summary: Blocking PCR is a method to selectively inhibit the amplification of wild-type DNA while amplifying mutated DNA by using a nucleotide sequence complementary to a blocker. Our study demonstrates that an oligoribonucleotide (ORN) can effectively suppress the extension of target DNA by Taq DNA polymerases. This method has been successfully applied for real-time ORNi-PCR and one-step real-time reverse transcriptionORNi-PCR to detect single-nucleotide mutations in DNA and RNA in a sequence-specific manner, providing technical insights for further improvement of blocking PCR.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Minako Yokoyama, Toshitsugu Fujita, Yuka Kadonosawa, Yota Tatara, Daisuke Motooka, Masahito Ikawa, Hodaka Fujii, Yoshihito Yokoayama
Summary: CBR1 is a nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reductase with broad substrate specificity. This study generated transgenic mice overexpressing CBR1 and characterized the expression of CBR1 in various organs, as well as identified changes in protein expression patterns. The transgenic mice may be useful for further understanding the molecular mechanisms regulated by CBR1 and its effects on carcinogenesis and cardiotoxicity of certain cancer drugs.
MOLECULAR BIOLOGY REPORTS
(2023)
Article
Gastroenterology & Hepatology
Xiaolong Zhang, Pankaj Sharma, Patrick Maschmeyer, Yu Hu, Mumeng Lou, Jessica Kim, Hodaka Fujii, Derya Unutmaz, Robert F. Schwabe, Florian Winau
Summary: The expression of GARP on hepatic stellate cells (HSCs) drives the development of liver fibrosis through cell contraction-mediated activation of latent TGF-I3. This finding highlights the potential of GARP on HSCs as a promising target for the treatment of liver fibrosis.
JOURNAL OF HEPATOLOGY
(2023)
Article
Biochemical Research Methods
Hodaka Fujii, Toshitsugu Fujita
Summary: The article describes a method to purify specific genomic regions and identify associated molecules using enChIP technology. By tagging the target genomic region with variants of the CRISPR system, successful expression was achieved in budding yeast. This method has the potential for analyzing genome functions and conducting CRISPR experiments.
BIOLOGY METHODS & PROTOCOLS
(2022)
Review
Biochemical Research Methods
Takeshi Shimizu, Toshitsugu Fujita, Hodaka Fujii
Summary: ORNi-PCR technology utilizes short RNA to interfere with PCR amplification of specific target sequences, effectively suppressing background signal amplification, and can be used for detecting nucleotide mutations and enriching DNA sequences.
BIOLOGY METHODS & PROTOCOLS
(2022)