Article
Multidisciplinary Sciences
Alfonso Carlos Barragan-Rosillo, Carlos Alberto Peralta-Alvarez, Jonathan Odilon Ojeda-Rivera, Rodrigo G. Arzate-Mejia, Felix Recillas-Targa, Luis Herrera-Estrella
Summary: Plants have evolved strategies to cope with phosphorus scarcity, with genetic approaches identifying key regulators like PHR1 and PHL2 in the transcriptional response to phosphate starvation. Chromatin accessibility undergoes genome-wide remodeling in root cells during Pi starvation, with PHR1 and PHL2 playing a crucial role in this process. These transcription factors directly activate a second wave of epigenetic changes needed for the transcriptional activation of low-Pi-responsive genes in Pi-starved root cells.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Sona Legartova, Alena Svobodova Kovarikova, Jana Behalova Suchankova, Hana Polasek-Sedlackova, Eva Bartova
Summary: RNA methylation, especially 6-methyladenosine (m(6)A)-modified RNAs, play a specific role in DNA damage response (DDR). In this study, researchers observed that RNA modified at 8-methyladenosine (m(8)A) is recruited to DNA lesions after microirradiation and that this recruitment is PARP dependent. The PARP inhibitor Olaparib prevented adenosine methylation at the damaged chromatin and affected the recognition of lesions by the base excision repair factor XRCC1. The study suggests that modified RNAs likely play a role in the BER mechanism accompanied by active DNA demethylation and that R-loops may represent structures recognized by PARP-dependent non-canonical m(6)A/m(8)A-mediated DNA repair pathway.
Article
Biochemistry & Molecular Biology
Chuizheng Kong, Guangyao Zhao, Lifeng Gao, Xiuying Kong, Daowen Wang, Xu Liu, Jizeng Jia
Summary: In this study, the association between transposons (TEs), chromatin states, and chromatin accessibility in Aegilops tauschii was analyzed. It was found that TEs contributed to the diverse distribution of chromatin states and affected the chromatin state and openness of potential regulatory elements. Some TE superfamilies carried active/open chromatin regions. Furthermore, the accessibility shaped by TEs was associated with the histone mark H3K9ac. These findings highlight the role of TEs in shaping the epigenetic landscape and regulating gene expression in Aegilops tauschii.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Zhenhui Zhong, Suhua Feng, Sascha H. Duttke, Magdalena E. Potok, Yiwei Zhang, Javier Gallego-Bartolom, Wanlu Liu, Steven E. Jacobsen
Summary: DNA methylation influences chromatin accessibility, particularly in heterochromatin, in plants. Different sequence contexts of DNA methylation interact with each other, and methylation can impact chromatin structure through mechanisms other than transcription. Increased chromatin accessibility is associated with enhanced long-range chromatin interactions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Immunology
Zewen Kelvin Tuong, Benjamin J. Stewart, Shuang Andrew Guo, Menna R. Clatworthy
Summary: Many immune cell subsets permanently reside in non-lymphoid organs, playing critical roles in tissue homeostasis and defense. Cell interactions and environmental cues shape immune cell function, and dysregulation can lead to inadequate immune responses. Understanding these mechanisms is crucial for studying tissue immunity.
IMMUNOLOGICAL REVIEWS
(2022)
Article
Multidisciplinary Sciences
Shengquan Chen, Guanao Yan, Wenyu Zhang, Jinzhao Li, Rui Jiang, Zhixiang Lin
Summary: RA3 is a computational framework for analyzing chromatin accessibility data at the single-cell level, taking into account previous knowledge and data-specific characteristics. By simultaneously modeling shared and unique biological variations, RA3 identifies distinct subpopulations and demonstrates superior performance on multiple datasets, showing wide applicability.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Liangwei Yin, Gen Xu, Jinliang Yang, Meixia Zhao
Summary: Subgenome dominance after whole-genome duplication has been observed in many plant species, with chromatin environment and cis-regulatory elements playing important roles in shaping the divergence and evolution of duplicated genes. Genes located in chromosomal arms are crucial for maintaining the dominance of one subgenome, while loss of accessible chromatin regions near genes can lead to reduced purifying selection and expression.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Parviz Seifpanahi Shabane, Alexey Onufriev
Summary: The study explores the conformational changes of the H4 tail under different charged states. As the charge of the H4 tail is gradually neutralized, its structure transitions from a random coil to a more compact and stable form. Based on ensemble similarity, K -> M is proposed as a possible alternative to the commonly used K -> Q substitution.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Arsheed H. Sheikh, Kashif Nawaz, Naheed Tabassum, Marilia Almeida-Trapp, Kiruthiga G. Mariappan, Hanna Alhoraibi, Naganand Rayapuram, Manuel Aranda, Martin Groth, Heribert Hirt
Summary: The mutants of Arabidopsis H1 histones, H1.1 and H1.2 double mutants and H1.1, H1.2, and H1.3 triple mutants, were found to be resistant to Pseudomonas syringae and Botrytis cinerea infections. Transcriptome analysis revealed that H1s play a crucial role in regulating the expression of defense genes during pathogen challenge. Overall, the study demonstrates the role of H1 as a molecular gatekeeper in modulating the chromatin landscape of defense genes during plant-pathogen interaction.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Physical
Xiangting Li, Tom Chou
Summary: This study constructs and analyzes monomeric and multimeric models of the stochastic disassembly of a single nucleosome, revealing the factors that affect the detachment time of histones from DNA. The presence of DNA binding proteins or processing molecular motors can facilitate the dissociation process. Competitive DNA binding of remodeling proteins and the speed of motor protein procession play important roles in the detachment rate. The study also extends the model to allow for multimeric nucleosome kinetics, showing additional pathways of disassembly and the influence of histone subunit concentrations on the process.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Multidisciplinary Sciences
Lihua Zhang, Jing Zhang, Qing Nie
Summary: The emergence of single-cell multiomics data provides unprecedented opportunities to study the transcriptional regulatory mechanisms controlling cell identity. DIRECT-NET, a machine-learning method based on gradient boosting, allows us to identify genome-wide cis-regulatory elements (CREs) and their relationship to target genes from single-cell data. DIRECT-NET substantially improves the accuracy of inferring CRE-to-gene relationships and reveals cell subpopulation-specific and dynamic regulatory linkages.
Article
Multidisciplinary Sciences
Jing Wang, Cai Zhou, Shuai Gao, Xiuling Song, Xinyan Yang, Jiaqi Fan, Shaofang Ren, Linzi Ma, Jiexiang Zhao, Manman Cui, Ke Song, Mei Wang, Chaohui Li, Yi Zheng, Fang Luo, Kai Miao, Xiaochun Bai, Andrew P. Hutchins, Lin Li, Gang Chang, Xiao-Yang Zhao
Summary: Round spermatid injection (ROSI) technique shows promise for treating infertility in some men. However, the developmental potential of ROSI embryos is compromised and the mechanisms are not fully understood. This study explores the transcriptome, chromatin accessibility, and DNA methylation patterns of ROSI embryos derived from early-stage round spermatids using single-cell multiomics sequencing. It identifies reprogramming defects in ROSI embryos at the pronuclear stages, primarily associated with misexpression of a group of minor zygotic genome activation genes. The study also discovers a small compound, A366, that can improve the developmental potential of ROSI embryos by correcting epigenetic and transcriptomic states.
Article
Biochemical Research Methods
Yingxin Cao, Laiyi Fu, Jie Wu, Qinke Peng, Qing Nie, Jing Zhang, Xiaohui Xie
Summary: The proposed deep generative model framework SAILER aims to learn a low-dimensional nonlinear latent representation of each cell from scATAC-seq data, ensuring independence from extrinsic confounding factors. Experimental results demonstrate that SAILER outperforms other methods in learning biologically more meaningful cell representations, leading to significant improvements in downstream analyses. SAILER can easily scale to process millions of cells and has been implemented into a software package for large-scale scATAC-seq data analysis.
Article
Biochemical Research Methods
Ankush Sharma, Akshay Akshay, Marie Rogne, Ragnhild Eskeland
Summary: The developed ShinyArchR.UiO application facilitates better understanding of gene regulatory mechanisms and sharing of massive chromatin accessibility data, improving data accessibility. Additionally, it also streamlines collaborative efforts among researchers.
Article
Biochemical Research Methods
Rozemarijn W. D. Kleinendorst, Guido Barzaghi, Mike L. Smith, Judith B. Zaugg, Arnaud R. Krebs
Summary: Precise gene expression control involves multiple factors working together at cis-regulatory elements. Single-molecule footprinting technology developed recently allows simultaneous resolution of protein occupancy on single DNA molecules genome-wide. The technique combines cytosine methyltransferases and bisulfite sequencing to resolve transcription factor binding patterns at cis-regulatory elements.
Article
Gastroenterology & Hepatology
Hannu Huhdanpaa, Darryl Hwang, Steven Cen, Brian Quinn, Megha Nayyar, Xuejun Zhang, Frank Chen, Bhushan Desai, Gangning Liang, Inderbir Gill, Vinay Duddalwar
Article
Biochemistry & Molecular Biology
David Roulois, Helen Loo Yau, Rajat Singhania, Yadong Wang, Arnavaz Danesh, Shu Yi Shen, Han Han, Gangning Liang, Peter A. Jones, Trevor J. Pugh, Catherine O'Brien, Daniel D. De Carvalho
Article
Multidisciplinary Sciences
S. J. Tan, J. Y. Fang, Y. Wu, Z. Yang, G. Liang, B. Han
SCIENTIFIC REPORTS
(2015)
Article
Multidisciplinary Sciences
Jin-Man Kim, Kyunghwan Kim, Vasu Punj, Gangning Liang, Tobias S. Ulmer, Wange Lu, Woojin An
SCIENTIFIC REPORTS
(2015)
Article
Genetics & Heredity
Alexandra Sogaard Helbo, Marianne Treppendahl, Derya Aslan, Konstantinos Dimopoulos, Cecilie Nandrup-Bus, Mette Skov Holm, Mette Klarskov Andersen, Gangning Liang, Lasse Sommer Kristensen, Kirsten Gronbaek
Editorial Material
Medicine, General & Internal
Christopher E. Duymich, Gangning Liang
Article
Oncology
Yoshitomo Chihara, Yae Kanai, Hiroyuki Fujimoto, Kokichi Sugano, Kiyotaka Kawashima, Gangning Liang, Peter A. Jones, Kiyohide Fujimoto, Hiroki Kuniyasu, Yoshihiko Hirao
Article
Oncology
Xiaojing Yang, Han Han, Daniel D. De Carvalho, Fides D. Lay, Peter A. Jones, Gangning Liang
Article
Oncology
Sheng-Fang Su, Andre Luis de Castro Abreu, Yoshitomo Chihara, Yvonne Tsai, Claudia Andreu-Vieyra, Siamak Daneshmand, Eila C. Skinner, Peter A. Jones, Kimberly D. Siegmund, Gangning Liang
CLINICAL CANCER RESEARCH
(2014)
Review
Allergy
Yoshimasa Saito, Hidetsugu Saito, Gangning Liang, Jeffrey M. Friedman
CLINICAL REVIEWS IN ALLERGY & IMMUNOLOGY
(2014)
Article
Biochemistry & Molecular Biology
Fides D. Lay, Timothy J. Triche, Yvonne C. Tsai, Sheng-Fang Su, Sue Ellen Martin, Siamak Daneshmand, Eila C. Skinner, Gangning Liang, Yoshitomo Chihara, Peter A. Jones
Article
Biochemistry & Molecular Biology
S-F Su, Y-W Chang, C. Andreu-Vieyra, J. Y. Fang, Z. Yang, B. Han, A. S. Lee, G. Liang
Article
Multidisciplinary Sciences
Han Han, Xiaojing Yang, Kurinji Pandiyan, Gangning Liang
Article
Urology & Nephrology
In-Seon Choi, Kevin Yu, Jayoung Kim, Erika De Guzman, Daniel J. Weisenberger, Shirley Oghamian, Hee Ju Kim, Kyung Hwa Lee, Cindy Carroll, Binh N. Trinh, Myungjin Kim, Sahar Houshdaran, Peter W. Laird, Peter A. Jones, David Warburton, Gangning Liang, Chester J. Koh
Review
Andrology
Sameer Chopra, Raj Satkunasivam, Chandan Kundavaram, Gangning Liang, Inderbir S. Gill
TRANSLATIONAL ANDROLOGY AND UROLOGY
(2015)