Article
Biochemistry & Molecular Biology
Dingdang Yu, Guoyu Chen, Yuci Wang, Yining Wang, Risheng Lin, Nanbo Liu, Ping Zhu, Hang Liu, Tao Hu, Rui Feng, Haizhong Feng, Fei Lan, Jiabin Cai, Hao Chen
Summary: PDS5A and PDS5B proteins co-localize with RAD21 and CTCF at loop anchors, playing important roles in the formation and size regulation of chromatin loops. Rapid degradation of PDS5A or PDS5B in liver cancer cells results in reduced chromatin loops and increased loop size. PDS5B loss has a stronger impact on RAD21 and CTCF signals at loop anchors compared to PDS5A.
Article
Biochemistry & Molecular Biology
Yezhang Zhu, Jiali Yu, Jiahui Gu, Chaoran Xue, Long Zhang, Jiekai Chen, Li Shen
Summary: The 3D genome organization plays a critical role in acquiring totipotency, as demonstrated in a study using mouse embryonic stem cells. The transition from pluripotent to totipotent-like state involves changes in chromatin architecture, enhancer-promoter interactions, and gene regulation, highlighting the importance of chromatin organization in cell fate determination. Disruption of chromatin structure promotes the ESC to 2CLC transition, emphasizing the functional significance of 3D genome organization in totipotency acquisition.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Bart J. H. Dequeker, Matthias J. Scherr, Hugo B. Brandao, Johanna Gassler, Sean Powell, Imre Gaspar, Ilya M. Flyamer, Aleksandar Lalic, Wen Tang, Roman Stocsits, Iain F. Davidson, Jan-Michael Peters, Karl E. Duderstadt, Leonid A. Mirny, Kikue Tachibana
Summary: This study reveals that the minichromosome maintenance (MCM) complex acts as a barrier in G1 phase for loop extrusion, reducing the number of CTCF-anchored loops and weakening TAD boundary insulation. The study also demonstrates that MCMs are physical barriers that frequently constrain cohesin translocation. The findings suggest that loop extrusion barriers, including MCMs, play a crucial role in shaping the three-dimensional genome.
Article
Cell Biology
Magdalena A. Karpinska, Aukje Marieke Oudelaar
Summary: Gene expression patterns in complex multicellular organisms are regulated by enhancers, which communicate with their target gene promoters in three-dimensional (3D) chromatin structures. Loop extrusion has been identified as an important process that controls enhancer-promoter communication, but the molecular mechanism behind this regulation is not well understood. This review provides an overview of recent evidence and insights into how loop extrusion contributes to enhancer-mediated gene activation.
CURRENT OPINION IN GENETICS & DEVELOPMENT
(2023)
Article
Biochemistry & Molecular Biology
Runxia Lin, Ziwei Zhai, Junqi Kuang, Chuman Wu, Yuxiang Yao, Ruona Shi, Jiangping He, Shuyang Xu, Pengli Li, Yixin Fan, Wei Li, Zichao Wu, Xiaoxi Li, Jin Ming, Jing Guo, Bo Wang, Dongwei Li, Shangtao Cao, Xiaofei Zhang, Yi Li, Duanqing Pei, Jing Liu
Summary: This study investigates the key events in early mammalian embryonic development using a JUN-induced pluripotent-somatic transition (PST) model. The results reveal a rapid transfer of chromatin remodeling complexes from pluripotent loci to somatic loci during PST, facilitating chromatin opening and gene activation.
CELL AND BIOSCIENCE
(2022)
Article
Biochemical Research Methods
Shuzhen Kuang, Liangjiang Wang
Summary: The study developed a deep learning model called DeepCTCFLoop to predict chromatin loop formation between pairs of CTCF motifs, revealing complex sequence patterns that may impact chromatin architecture. The model significantly outperforms other machine learning models in predicting loop formation based solely on DNA sequences.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2021)
Review
Cell Biology
Christopher M. Uyehara, Effie Apostolou
Summary: The spatiotemporal control of gene expression depends on the activity of regulatory sequences known as enhancers, which regulate target genes over varying distances in the genome. Recent advancements in genomics and imaging technologies have revealed complex networks of enhancer-promoter interactions. This review summarizes our current understanding of enhancer-promoter communication and discusses highly connected enhancer-promoter hubs and their functions in signal integration and gene regulation.
Correction
Geosciences, Multidisciplinary
Ellen Cliff, Samar Khatiwala, Andreas Schmittner
Summary: An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Review
Cell Biology
Jan-Michael Peters
Summary: Structural maintenance of chromosomes' complexes play a crucial role in folding genomic DNA into loops, especially in V(D)J recombination of antigen receptor genes in B and T cells. Regulating the formation and recombination of chromatin loops ensures the diversity of B-cell receptors and antibodies.
CURRENT OPINION IN CELL BIOLOGY
(2021)
Review
Biology
Aktan Alpsoy, Surbhi Sood, Emily C. Dykhuizen
Summary: The packaging of DNA in the nucleus plays a crucial role in gene expression, with long-range interactions through physical loops in the genome influencing transcription. The hierarchy of chromatin folding in the nucleus is tightly regulated, allowing for dynamic shifts to accommodate changes in transcription, DNA replication, and repair. Chromatin remodeling is essential for maintaining and regulating the 3D genome organization, particularly in relation to the regulation of architectural proteins CTCF and cohesin.
Article
Multidisciplinary Sciences
Nikolay Postika, Paul Schedl, Pavel Georgiev, Olga Kyrchanova
Summary: The autonomy of segment-specific regulatory domains in the Bithorax complex is conferred by boundary elements and associated Polycomb response elements (PREs). The role of HS1 and HS2 in boundary function suggests that the boundary function of Fab-6 HS1 must be bolstered by a second element that has PRE activity.
SCIENTIFIC REPORTS
(2021)
Review
Cell Biology
Mateusz Chilinski, Kaustav Sengupta, Dariusz Plewczynski
Summary: The three-dimensional structure of the human genome has a significant impact on gene expression, and genetic variation can affect this structure. Current methods for evaluating the functional effect include eQTLs analysis and evaluating non-coding DNA sequence changes based on BIN. Studying chromatin interactions and the impact of genetic variation on the spatial organization of the genome and cellular function using the BIN model is important.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Woei Shyuan Ng, Hendrik Sielaff, Ziqing Winston Zhao
Summary: Phase separation is an effective strategy to compartmentalize cellular components, particularly those involving chromatin. Advanced imaging-based approaches have enabled the quantitative characterization of chromatin-based phase condensates. The complex interplay between chromatin and other molecular species mediated by phase separation regulates the genome within the dynamic nuclear space at multiple scales and modes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Correction
Mathematics, Applied
Hongyu Miao, Alan S. Perelson, Hulin Wu
Summary: This erratum corrects an error in the coefficients of an equation in the original paper.
Correction
Mathematics
David Scheinker
Summary: Theorem 1.5 of the paper incorrectly claimed the existence of a k-dimensional inner variety in the n-disc where all solutions to a Nevanlinna-Pick problem are equal. The correct statement is that there exists a k-dimensional inner analytic disc where all solutions to a Nevanlinna-Pick problem are equal. The proof does not need to be modified.
JOURNAL OF FUNCTIONAL ANALYSIS
(2022)
Article
Biochemistry & Molecular Biology
Qiangwei Zhou, Sheng Cheng, Shanshan Zheng, Zhenji Wang, Pengpeng Guan, Zhixian Zhu, Xingyu Huang, Cong Zhou, Guoliang Li
Summary: The study developed a comprehensive database called ChromLoops, which integrated 1030 ChIA-PET, HiChIP, and PLAC-Seq datasets from 13 species, and documented 1,491,416,813 high-quality chromatin loops. The database provided annotations for genes and regions overlapping with chromatin loop anchors, and included rich functional annotations. Additionally, it identified genes with high-frequency chromatin interactions in different species and cancer samples.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Enkhjin Batdorj, Najla AlOgayil, Qinwei Kim-Wee Zhuang, Jose Hector Galvez, Klara Bauermeister, Kei Nagata, Tohru Kimura, Monika A. Ward, Teruko Taketo, Guillaume Bourque, Anna K. Naumova
Summary: Several lines of evidence suggest that the presence of the Y chromosome influences DNA methylation of autosomal loci. In this study, we identified Y chromosome dependent differentially methylated regions (yDMRs) in mice and found that most of the yDMRs were located in transposable elements (TEs) and had lower methylation in XY mice compared to XX or XO mice. Further analyses showed that genetic variation in the Y chromosome influenced methylation levels of autosomal regions.
Article
Chemistry, Multidisciplinary
Yigeng Shang, Zhigang Hao, Chao Yao, Guoliang Li
Summary: Graph neural network (GNN) is a widely used deep learning model for processing graph-structured data and has been applied to link prediction task. However, randomly sampling unobserved edges as negative samples has limitations. We propose a policy-based training method (PbTRM) to improve the quality of negative samples.
APPLIED SCIENCES-BASEL
(2023)
Article
Cell Biology
Sabrina Daniela da Silva, Gregoire B. Morand, Luciana Diesel, Jefferson Muniz de Lima, Krikor Bijian, Senthilkumar Kailasam, Francois Lefebvre, Guillaume Bourque, Michael Hier, Moulay A. Alaoui-Jamali
Summary: In this study, a high-throughput RNA sequencing technology was used to investigate a group of papillary thyroid carcinomas (PTCs) with an unusually aggressive phenotype. It was found that metastatic PTCs with mutated BRAF (V600E) expressed an up-regulation of RSPO4 and genes involved in focal adhesion and cell-extracellular matrix signaling. Further validation confirmed the upregulation of these target genes in metastatic PTC cases. Preclinical studies supported the association between RSPO4 overexpression and BRAF V600E mutation, indicating the potential for co-targeting B-Raf, RSPO, and focal adhesion proteins as a pharmacological approach for aggressive BRAF V600E PTC.
Article
Virology
Xi Zeng, Yuyouye Wang, Binghan Liu, Xinjie Rao, Canhui Cao, Fang Peng, Wenhua Zhi, Ping Wu, Ting Peng, Ye Wei, Tian Chu, Miaochun Xu, Yashi Xu, Wencheng Ding, Guoliang Li, Shitong Lin, Peng Wu
Summary: Integration of human papilloma virus (HPV) DNA into the human genome may progressively contribute to cervical carcinogenesis. We analyzed multiomics data from 50 patients with cervical cancer to explore how HPV integration affects gene expression by altering DNA methylation. High-frequency HPV-integrated genes, including five novel recurrent genes, were identified. HPV integrations occurring in exons were associated with altered gene expression in tumor tissues. Our study provides novel insights into HPV-induced cervical cancer at the biological and clinical level.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Multidisciplinary Sciences
Ramesh Rajaby, Dong-Xu Liu, Chun Hang Au, Yuen-Ting Cheung, Amy Yuet Ting Lau, Qing-Yong Yang, Wing-Kin Sung
Summary: This article introduces a new method called INSurVeyor for detecting insertions and compares its sensitivity with other methods. It also provides updated catalogues of insertions in Arabidopsis and human genomes based on INSurVeyor.
NATURE COMMUNICATIONS
(2023)
Article
Cell Biology
Weizhi Ouyang, Xiwen Zhang, Minrong Guo, Jing Wang, Xiaoting Wang, Runxin Gao, Xu Xiang, Shiping Luan, Feng Xing, Zhilin Cao, Meng Ma, Jiapei Yan, Guoliang Li, Xingwang Li
Summary: In this study, high-resolution 3D genome maps were constructed using long-read chromatin interaction analysis, and the H3K27me3-associated chromatin interactions in an elite rice hybrid, Shanyou 63, were characterized. It was found that many H3K27me3-marked regions may function as silencer-like regulatory elements and can come into proximity with distal target genes via forming chromatin loops in the nuclei's 3D space. Additionally, genetic variations were identified to alter allelic chromatin topology and modulate allelic gene imprinting in rice hybrids.
Article
Computer Science, Artificial Intelligence
Zhigang Hao, Wolfgang Mayer, Jingbo Xia, Guoliang Li, Li Qin, Zaiwen Feng
Summary: This paper proposes a new method based on ontology embedding incorporating the semantic and structural features for ontology alignment. The method is used to align two widely used food ontologies and three Chinese food classification ontologies. Experimental results show that this method enhances the performance compared to other advanced alignment systems, demonstrating the importance of learning semantic representation and structural representation.
JOURNAL OF WEB SEMANTICS
(2023)
Editorial Material
Biochemistry & Molecular Biology
Zhenji Wang, Minghao Liu, Fuming Lai, Qiangqiang Fu, Liang Xie, Yaping Fang, Qiangwei Zhou, Guoliang Li
Article
Biochemistry & Molecular Biology
Zhixian Zhu, Qiangwei Zhou, Yuanhui Sun, Fuming Lai, Zhenji Wang, Zhigang Hao, Guoliang Li
Summary: DNA methylation plays a crucial role in tumorigenesis and tumor progression. The MethMarkerDB database integrates WGBS data and DNA methylation biomarker genes, providing valuable resources for identifying novel biomarkers.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Adda-Lee Graham-Paquin, Deepak Saini, Jacinthe Sirois, Ishtiaque Hossain, Megan S. Katz, Qinwei Kim-Wee Zhuang, Sin Young Kwon, Yojiro Yamanaka, Guillaume Bourque, Maxime Bouchard, William A. Pastor
Summary: Zmym2(-/-) mice exhibit embryonic lethality and fail to undergo proper DNA methylation, resulting in upregulation of germline genes and abnormal expression of transposon-gene fusion transcripts. It suggests that ZMYM2 plays a crucial role in early embryonic development and DNA methylation patterning.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Li Deng, Qiangwei Zhou, Jie Zhou, Qing Zhang, Zhibo Jia, Guangfeng Zhu, Sheng Cheng, Lulu Cheng, Caijun Yin, Chao Yang, Jinxiong Shen, Junwei Nie, Jian-Kang Zhu, Guoliang Li, Lun Zhao
Summary: The fine scale genome organization of Arabidopsis was revealed through high-resolution chromatin interaction analysis, showing that distant active cis-regulatory elements are linked to target genes through long-range chromatin interactions with increased expression, while poised cis-regulatory elements are linked to target genes through long-range chromatin interactions with depressed expression. Transcription factor MYC2 plays a critical role in chromatin spatial organization, and MYC2 occupancy and MYC2-mediated chromatin interactions facilitate transcription within 3D chromatin architecture. Functionally related gene-defined chromatin connectivity networks indicated that genes involved in flowering-time control are compartmentalized into separate subdomains based on their spatial activity, linking chromatin conformation with coordinated gene expression.
Article
Biochemical Research Methods
Sean Upchurch, Emilio Palumbo, Jeremy Adams, David Bujold, Guillaume Bourque, Jared Nedzel, Keenan Graham, Meenakshi S. Kagda, Pedro Assis, Benjamin Hitz, Emilio Righi, Roderic Guigo, Barbara J. Wold
Summary: Large-scale sharing of genomic quantification data requires standardized access interfaces. In this project, RNAget, an API for secure access to genomic quantification data in matrix form, was developed. RNAget allows for slicing matrices to extract desired subsets of data and can be applied to various expression matrix-format data, including RNA sequencing and microarrays. It can also be extended to other sequence-based genomics quantification matrices such as ATAC-seq and ChIP-seq.
Article
Cell Biology
Cristian Groza, Xun Chen, Alain Pacis, Marie-Michelle Simon, Albena Pramatarova, Katherine A. Aracena, Tomi Pastinen, Luis B. Barreiro, Guillaume Bourque
Summary: This study demonstrates that genome graphs can reveal regulatory regions that would have been overlooked by other approaches, providing important insights into the impact of genetic variants on processes such as immunity.
Meeting Abstract
Oncology
Elena Kuzmin, Jean Monlong, Mathieu Bourgey, Jarry Barber, Tom Lesluyes, Toby Baker, Genevieve Morin, Dongmei Zou, Michael Schwartz, Yang Yang, Alain Pacis, Constanza Martinez, Hellen Kuasne, Anne-Marie Fortier, Rui Li, Claudia Kleinman, Sidong Huang, Peter van Loo, Quaid Morris, Jiannis Ragoussis, Guillaume Bourque, Morag Park
