Article
Multidisciplinary Sciences
Chun-Ping Yu, Chen-Hao Kuo, Chase W. Nelson, Chi-An Chen, Zhi Thong Soh, Jinn-Jy Lin, Ru-Xiu Hsiao, Chih-Yao Chang, Wen-Hsiung Li
Summary: By developing a computational pipeline for analyzing ChIP-seq data, this study discovered and characterized a large number of previously unknown TFBSs, providing insights into the biological and genomic features of TFBSs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Plant Sciences
Maaike R. Boersma, Ryan M. Patrick, Sonia L. Jillings, Nur Fariza M. Shaipulah, Pulu Sun, Michel A. Haring, Natalia Dudareva, Ying Li, Robert C. Schuurink
Summary: ODO1 has been identified as a key regulator in controlling the production of floral scents in Petunia spp., by activating specific metabolic pathways to generate floral volatile compounds.
Article
Green & Sustainable Science & Technology
Naveenarani Murugan, Ravinder Kumar, Shashi Kant Pandey, Pooja Dhansu, Mahadevaiah Chennappa, Saranya Nallusamy, Hemaprabha Govindakurup, Appunu Chinnaswamy
Summary: This study investigated the characteristics and regulatory mechanisms of phosphate transporter gene promoters through computer analysis. It found that one of the gene promoters can enhance gene expression under salt stress conditions, which is of great significance for the development of salt-tolerant transgenic crops.
Article
Microbiology
Shima Shahbaz, Isobel Okoye, Gregg Blevins, Shokrollah Elahi
Summary: CD8(+) T cells play an important role in chronic viral infections, but the expression of CD73 is compromised and its function impaired in HIV infection. CD73 expression is decreased in HIV-infected individuals at both cell surface and gene levels. CD73(+) T cells exhibit functional impairments while showing enhanced migration capabilities.
Article
Chemistry, Physical
Emmanuelle Bignon, Angelo Spinello, Tom Miclot, Luisa D'Anna, Cosimo Ducani, Stephanie Grandemange, Giampaolo Barone, Antonio Monari, Alessio Terenzi
Summary: This article investigates the interplay among three G4 sequences in the c-KIT proto-oncogene promoter and finds that their structural linkage favors the formation of a parallel structure for WSP. Using molecular dynamics simulations and enhanced sampling methods, they provide the first computationally resolved structure of a well-organized G4 cluster in the promoter of a crucial gene involved in cancer development. The study suggests that neighboring G4s influence their mutual three-dimensional arrangement and provide a powerful tool for predicting and interpreting complex DNA structures, which can be used as a starting point for drug discovery.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Biochemistry & Molecular Biology
Ruoyao Lin, Xiaoming Zhong, Yongli Zhou, Huichao Geng, Qingxi Hu, Zhihao Huang, Jun Hu, Xiang-Dong Fu, Liang Chen, Jia-Yu Chen
Summary: R-loopBase integrates high-quality genome-wide R-loop mapping datasets and comprehensive literature information to provide high-confidence R-loop localization and a comprehensive list of regulatory proteins, helping to reveal a global regulatory network of R-loop dynamics and its potential links to cancer and neurological diseases.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Sarvesh Nikumbh, Boris Lenhard
Summary: Core promoters are DNA sequences at the beginning of genes that contain motifs facilitating the binding of transcription initiation complexes. This study introduces a new method, seqArchR, based on non-negative matrix factorisation (NMF), for clustering promoter sequences according to their near-fixed-distance motifs from a reference point, such as transcription start sites (TSS). seqArchR efficiently identifies TSS-directing motifs and reveals changes in the relative usage of promoter architectures over time. It is a powerful tool for genome-wide classification and functional characterisation of promoters.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Plant Sciences
Anton V. Tsukanov, Victoria V. Mironova, Victor G. Levitsky
Summary: The study examined the role of motif models in direct TF-DNA interactions, finding that traditional PWM and alternative models BaMM and SiteGA can detect sites with different affinities, with SiteGA having higher proportions of enriched genes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Paola Pellanda, Mattia Dalsass, Marco Filipuzzi, Alessia Loffreda, Alessandro Verrecchia, Virginia Castillo Cano, Hugo Thabussot, Mirko Doni, Marco J. Morelli, Laura Soucek, Theresia Kress, Davide Mazza, Marina Mapelli, Marie-Eve Beaulieu, Bruno Amati, Arianna Sabo
Summary: Eukaryotic transcription factors have both specific DNA sequence motif recognition and non-specific DNA-binding activity. Non-specific DNA binding is essential for engaging with genomic regulatory regions, while sequence recognition contributes to transcriptional activation by stabilizing Myc onto DNA and unexpectedly promoting its transcriptional activity. The seemingly pervasive genome interaction profiles detected by ChIP-seq actually encompass diverse DNA-binding modes driving defined, sequence-dependent transcriptional responses.
Article
Biochemistry & Molecular Biology
Xianjin Zhou
Summary: Reduction of Sp4 expression leads to age-dependent hippocampal vacuolization and other schizophrenia-related phenotypes in mice. Human genetic studies have validated SP4 as a significant schizophrenia-risk gene, with truncation of the human SP4 gene having a high odds ratio for schizophrenia. Analysis suggests that SP4 may act as a hub in the regulation of various schizophrenia-risk genes through GC-boxes in the pathogenesis of schizophrenia.
MOLECULAR PSYCHIATRY
(2022)
Review
Biochemical Research Methods
Manuel Tognon, Rosalba Giugno, Luca Pinello
Summary: Transcription factors (TFs) are regulatory proteins that control transcriptional rate by binding to DNA sequences called transcription factor binding sites (TFBS) or motifs. Experimental and computational methods have been developed to identify and characterize TFBS motifs in DNA sequences. This review article discusses these methods, highlighting their advantages, drawbacks, open challenges, and future perspectives.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Jun Yuan, Xiaomei He, Yinsheng Wang
Summary: High-order chromatin organization is crucial for biological processes and disease development. This study investigated the role of guanine quadruplex (G4) structures in RNA polymerase II (RNAPII)-mediated DNA interactions and transcription activity. Data analysis revealed a strong positive correlation between RNAPII-linked DNA loops and G4 structures in chromatin. Treatment with PDS, a G4-binding ligand, was found to diminish RNAPII-linked long-range DNA contacts, especially those involving G4 structure loci, leading to changes in gene expression.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Yongqing Zhang, Zixuan Wang, Yuanqi Zeng, Jiliu Zhou, Quan Zou
Summary: Research has shown that deep learning models can predict TFBSs at the base-pair level, but there is a need for improvement to integrate information more effectively for increased accuracy.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Plant Sciences
Malgorzata Majewska, Lukasz Kuzma, Piotr Szymczyk
Summary: Salvia miltiorrhiza synthesises tanshinones with multidirectional therapeutic effects. In this study, a new sequence of the HMGR4 gene in S. miltiorrhiza was isolated and characterised, providing valuable information for understanding the transcription regulation of this gene and further exploring the medicinal value of S. miltiorrhiza.
Article
Microbiology
Canfeng Hua, Jiadai Huang, Tingting Wang, Yue Sun, Jingui Liu, Linfeng Huang, Xin Deng
Summary: This study reveals that bacterial transcription factors have the same binding pattern in both coding and promoter regions. Additionally, three regulatory mechanisms of CDS-bound transcription factors are identified, demonstrating the complexity of bacterial TF regulation and the prevalence of internal cryptic promoters in CDS.
Article
Biochemistry & Molecular Biology
Xiaoyu Zhang, Qin Xia, Rui Wei, Hongfei Song, Jiaqi Mi, Zhaoyu Lin, Yang Yang, Zijie Sun, Kang Zou
FREE RADICAL BIOLOGY AND MEDICINE
(2019)
Article
Cell & Tissue Engineering
Qin Xia, Danchen Zhang, Jingjing Wang, Xiaoyu Zhang, Weixiang Song, Rong Chen, Hua Li, Wenhai Xie, Kang Zou
STEM CELLS AND DEVELOPMENT
(2020)
Article
Cell Biology
Sitong Liu, Rui Wei, Hongyang Liu, Ruiqi Liu, Pengxiao Li, Xiaoyu Zhang, Wei Wei, Xiaodong Zhao, Xiaomeng Li, Yang Yang, Xueqi Fu, Kang Zou
Summary: This study demonstrates the connection between p53 and pluripotency-associated factors in the transformation of SSCs, with SMAD3 identified as a key factor. However, an unknown event is required to activate SMAD3, serving as a prerequisite for SSCs reprogramming in long-term culture.
CELL PROLIFERATION
(2022)
Article
Biochemistry & Molecular Biology
Ning Zhou, Yong Tian, Hongzhi Wu, Yongqing Cao, Ruiqing Li, Kang Zou, Wenwu Xu, Lizhi Lu
Summary: Resveratrol has antioxidant effects on duck intestinal epithelial cells, potentially alleviating oxidative stress and inhibiting cell apoptosis through the PI3K/AKT and P38 MAPK signaling pathways. These findings have important implications for studying the health benefits of resveratrol.
Review
Endocrinology & Metabolism
Wen Zhang, Ruotian Nie, Yihui Cai, Wenhai Xie, Kang Zou
Summary: This review summarizes the current knowledge of germline stem cells (GSCs) transplantation and its application in mammals, as well as discusses the prospects in reproductive medicine and animal science.
REPRODUCTIVE BIOLOGY AND ENDOCRINOLOGY
(2022)
Article
Veterinary Sciences
Ning Zhou, Yong Tian, Wenchao Liu, Bingjiang Tu, Wenwu Xu, Tiantian Gu, Kang Zou, Lizhi Lu
Summary: This study demonstrates that dietary supplementation with resveratrol and apigenin can alleviate oxidative stress in the small intestine of diquat-challenged pullets. These findings are valuable for the chicken industry and the applications of resveratrol and apigenin in animal husbandry.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
Ning Zhou, Yong Tian, Wenchao Liu, Bingjiang Tu, Tiantian Gu, Wenwu Xu, Kang Zou, Lizhi Lu
Summary: This study investigated the effects of dietary supplementation with quercetin and coated sodium butyrate on oxidative stress in the small intestine of diquat-challenged pullets. The results showed that supplementation with these additives could relieve oxidative stress and protect the intestinal barrier of the pullets over time.
Article
Biochemistry & Molecular Biology
Weixiang Song, Danchen Zhang, Jiaqi Mi, Wenfei Du, Yang Yang, Rong Chen, Cong Tian, Xiaodong Zhao, Kang Zou
Summary: E-cadherin and Cadherin-22 synergistically maintain the undifferentiation of SPCs through the pivotal intermediate molecule beta-catenin. LEF1, TCF3, STAT3, and HDAC4 were identified as co-regulatory factors of beta-catenin in regulating SPC fate.
CELL AND BIOSCIENCE
(2022)
Article
Reproductive Biology
Yulu Cao, Jingjing Wang, Xiaoxiao Li, Biyun Liu, Chongjun Li, Yijin Sun, Kang Zou
Summary: This study investigated the toxic effects of Zearalenone (ZEA) on porcine Sertoli cells and porcine spermatogonial stem cells (pSSCs). It was found that low concentration ZEA inhibited cell apoptosis while high concentration induced cell apoptosis. The expression levels of certain genes associated with cell function were significantly affected by ZEA treatment, and the NOTCH signaling pathway played a role in these effects.
REPRODUCTIVE BIOLOGY
(2023)
Article
Reproductive Biology
Wen Zhang, Yang Cheng, Shu Zhang, Rui Wei, Kang Zou
Summary: Female germline stem cells (FGSCs) are rare undifferentiated cells in the ovarian cortex that can self-renew and differentiate. We conducted experiments using a Matrigel-based 3-D culture system to establish a suitable in vitro microenvironment for FGSCs, testing different dilution ratios, medium compositions, and co-culture cells. Our results showed that Matrigel can be used as a FGSCs 3-D culture media, and co-culturing FGSCs with certain cells in Matrigel-based system had the potential to form ovarian organoids. The safety of Matrigel was confirmed in vivo through transplantation experiment, suggesting its potential for clinical research.
REPRODUCTIVE BIOLOGY
(2023)
Article
Reproductive Biology
Jingjing Wang, Hairui Tian, Hongyang Liu, Jian Wen, Ruihua Huang, Kang Zou, Liming Hou, Pinghua Li
Summary: Exposure to Zearalenone (ZEA) inhibits the proliferation of porcine germline stem cells and causes multiple cellular damages, which may harm the health and fertility of animals.
Article
Cell & Tissue Engineering
Rui Wei, Xiaoyu Zhang, Yihui Cai, Hongyang Liu, Bingyuan Wang, Xiaodong Zhao, Kang Zou
STEM CELL REVIEWS AND REPORTS
(2020)
Article
Zoology
Dan-Chen Zhang, Rong Chen, Yi-Hui Cai, Jing-Jing Wang, Chang Yin, Kang Zou
ZOOLOGICAL RESEARCH
(2020)
Article
Cell & Tissue Engineering
Yihui Cai, Jingjing Wan, Kang Zou
STEM CELL REVIEWS AND REPORTS
(2020)
