Depth-corrected multi-factor dissection of chromatin accessibility for scATAC-seq data with PACS by Zhen Miao, Jianqiao Wang, Kernyu Park, Da Kuang, Junhyong Kim

“…Abstract Single cell ATAC-seq (scATAC-seq) experimental designs have become increasingly complex, with multiple factors that might affect chromatin accessibility, including genotype, cell type, tissue of origin, sample location, batch, etc., whose compound effects are difficult to test by existing methods. …”
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Structural and functional characterisation and regulatory mechanisms of SWI/SNF and RSC chromatin remodelling complexes in fungi by Lirong Zhu, Qianqian Liu, Chao Zhao, Meichen Zhu, Xuewei Yang, Jinkui Yang

Subjects: “…Chromatin remodelling…”
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COMPUTER-ASSISTED STUDY OF THE REGULATION OF EUKARYOTIC GENE TRANSCRIPTION ON THE BASE OF DATA ON CHROMATIN SEQUENCING AND PRECIPITATION by Yu. L. Orlov

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ChromaFold predicts the 3D contact map from single-cell chromatin accessibility by Vianne R. Gao, Rui Yang, Arnav Das, Renhe Luo, Hanzhi Luo, Dylan R. McNally, Ioannis Karagiannidis, Martin A. Rivas, Zhong-Min Wang, Darko Barisic, Alireza Karbalayghareh, Wilfred Wong, Yingqian A. Zhan, Christopher R. Chin, William S. Noble, Jeff A. Bilmes, Effie Apostolou, Michael G. Kharas, Wendy Béguelin, Aaron D. Viny, Danwei Huangfu, Alexander Y. Rudensky, Ari M. Melnick, Christina S. Leslie

“…Abstract Identifying cell-type-specific 3D chromatin interactions between regulatory elements can help decipher gene regulation and interpret disease-associated non-coding variants. …”
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Footprint-C reveals transcription factor modes in local clusters and long-range chromatin interactions by Xiaokun Liu, Hanhan Wei, Qifan Zhang, Na Zhang, Qingqing Wu, Chenhuan Xu

“…At pairwise contact level, Footprint-C exhibits higher efficiency in identifying chromatin structural features when compared with other Hi-C methods, segregates chromatin interactions emanating from adjacent TF footprints, and uncovers multiway interactions involving different TFs. …”
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Nuclear DNA Content and Chromatin Pattern of Rat Rhabdomyosarcoma Cell Sublines with Different Metastatic Potentials by Jean Dufer, Marie-France Poupon, Sonia Yatouji

“…Progressive increase in chromatin condensation can be observed in cell sublines with increasing metastatic score. …”
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Altered chromatin landscape and 3D interactions associated with primary constitutional MLH1 epimutations by Paula Climent-Cantó, Marc Subirana-Granés, Mireia Ramos-Rodríguez, Estela Dámaso, Fátima Marín, Covadonga Vara, Beatriz Pérez-González, Helena Raurell, Elisabet Munté, José Luis Soto, Ángel Alonso, GiWon Shin, Hanlee Ji, Megan Hitchins, Gabriel Capellá, Lorenzo Pasquali, Marta Pineda

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Monitoring of single-nucleus chromatin landscape of ischemic stroke in mouse cerebral cortex across time by Ruolin Zhang, Sicheng Guo, Jie Zhou, Xiumei Lin, Ying Wang, Yiqi Wang, Muyang Li, Kaichen Zhao, Wendai Bao, Ke Shui, Chuanyu Liu, Chang Liu, Zhiqiang Dong

“…Abstract Ischemic stroke constitutes a multifaceted neurological affliction that spans various cellular types. Lack of dynamic chromatin accessibility data after stroke is one of the obstacles to understanding this process. …”
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Chromatin environment-dependent effects of DOT1L on gene expression in male germ cells by Manon Coulée, Alberto de la Iglesia, Mélina Blanco, Clara Gobé, Clémentine Lapoujade, Côme Ialy-Radio, Lucia Alvarez-Gonzalez, Guillaume Meurice, Aurora Ruiz-Herrera, Pierre Fouchet, Julie Cocquet, Laïla El Khattabi

“…Here, by producing and integrating epigenomic and spike-in RNA-seq data, we decipher the molecular role of DOT1L during mouse spermatogenesis and show that it has opposite effects on gene expression depending on chromatin environment. On one hand, DOT1L represses autosomal genes that are devoid of H3K79me2 at their bodies and located in H3K27me3-rich/H3K27ac-poor environments. …”
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DNA-Encoded Chromatin Structural Intron Boundary Signals Identify Conserved Genes with Common Function by Justin A. Fincher, Gary S. Tyson, Jonathan H. Dennis

“…Splicing likely occurs cotranscriptionally, with chromatin structure playing a key regulatory role. …”
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Specific Changes of Chromatin Structure in Nuclei of Normal Epithelium Adjacent to Laryngeal Squamous Cell Carcinoma by Thomas Dreyer, Iris Knoblauch, David Garner, Alexei Doudkine, Calum MacAulay, Branko Palcic, Christian Popella

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The Fractal Dimension of Nuclear Chromatin as a Prognostic Factor in Acute Precursor B Lymphoblastic Leukemia by Randall L. Adam, Rosana C. Silva, Fernanda G. Pereira, Neucimar J. Leite, Irene Lorand-Metze, Konradin Metze

“…We investigated the prognostic importance of the fractal dimension (FD) of chromatin in blasts of patients with acute precursor B lymphoblastic leukemia (B-ALL). …”
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Single-cell chromatin accessibility landscape profiling reveals the diversity of epigenetic regulation in the rat nervous system by Peiyao Ma, Shanshan Duan, Wen Ma, Qiuting Deng, Yeya Yu, Peng Gao, Yue Yuan, Chuanyu Liu

“…Single-cell sequencing can provide information on cell-type-specific chromatin structure and regulatory elements, revealing differences in chromatin organization between different cell types and their potential roles of these differences in brain function. …”
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INSTINCT: Multi-sample integration of spatial chromatin accessibility sequencing data via stochastic domain translation by Yuyao Liu, Zhen Li, Xiaoyang Chen, Xuejian Cui, Zijing Gao, Rui Jiang

“…Abstract Recent advances in spatial epigenomic techniques have given rise to spatial assay for transposase-accessible chromatin using sequencing (spATAC-seq) data, enabling the characterization of epigenomic heterogeneity and spatial information simultaneously. …”
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Impact of Long-term Polyvinylpyrrolidone Exposure on Gene Expression, Chromatin Structure, and Malondialdehyde Levels in Human Sperm by Mojdeh Sabour, Mahmood Dehghani Ashkezari, Azam Agharahimi, Seyed Morteza Seifati, Seyed Mehdi Kalantar

“…This study was designed to evaluate the effects of this component on chromatin quality with acridine orange (AO) staining, Malondialdehyde (MDA) levels, and BAX, BCL2, HSP70 (HSPA2), and SOD2 genes expression in different time intervals (0, 15, 30, and 60 minutes). …”
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Copper Imparts a New Therapeutic Property to Resveratrol by Generating ROS to Deactivate Cell-Free Chromatin by Salooni Khanvilkar, Indraneel Mittra

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Mapping chromatin remodelling in glioblastoma identifies epigenetic regulation of key molecular pathways and novel druggable targets by Claire Vinel, James Boot, Weiwei Jin, Nicola Pomella, Alexandra Hadaway, Charles Mein, Nicolae Radu Zabet, Silvia Marino

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TRIM28 is an essential regulator of three-dimensional chromatin state underpinning CD8+ T cell activation by Kun Wei, Ruifeng Li, Xiaohong Zhao, Bowen Xie, Tian Xie, Qinli Sun, Yongzhen Chen, Peng Wei, Wei Xu, Xinyi Guo, Zixuan Zhao, Han Feng, Ling Ni, Chen Dong

“…However, the high-ordered chromatin organization underpinning CD8+ T cell activation is not fully known. …”
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Parent-of-origin effects on nuclear chromatin organization and behavior in a Drosophila model for Williams–Beuren Syndrome by A. V. Medvedeva, E. V. Tokmatcheva, A. N. Kaminskaya, S. A. Vasileva, E. A. Nikitina, A. V. Zhuravlev, G. A. Zakharov, O. G. Zatsepina, E. V. Savvateeva-Popova

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Sir2 and Fun30 regulate ribosomal DNA replication timing via MCM helicase positioning and nucleosome occupancy by Carmina Lichauco, Eric J Foss, Tonibelle Gatbonton-Schwager, Nelson F Athow, Brandon Lofts, Robin Acob, Erin Taylor, James J Marquez, Uyen Lao, Shawna Miles, Antonio Bedalov

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