Author Correction: 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

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scaDA: A novel statistical method for differential analysis of single-cell chromatin accessibility sequencing data. by Fengdi Zhao, Xin Ma, Bing Yao, Qing Lu, Li Chen

“…Single-cell ATAC-seq sequencing data (scATAC-seq) has been widely used to investigate chromatin accessibility on the single-cell level. One important application of scATAC-seq data analysis is differential chromatin accessibility (DA) analysis. …”
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Restriction Enzyme Analysis of DNA Methylation in “Condensed” Chromatin of Ha-Ras-Transformed NIH 3T3 Cells by Maria Luiza S. Mello, Ann F. Chambers, Benedicto C. Vidal, Wolfgang Planding, Ulrich Schenck

“…Increased amounts of chromatin condensation (i.e., localized areas of high DNA density, or chromatin higher order packing state) have been described in NIH 3T3 cells transformed with the Ha‐ras oncogene. …”
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The role of chromatin state in intron retention: A case study in leveraging large scale deep learning models. by Ahmed Daoud, Asa Ben-Hur

“…Our work also demonstrates the impact of chromatin state on the regulation of intron retention. …”
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Aberrant c-AMP signalling in richter syndrome revealed by single-cell transcriptome and 3D chromatin analysis by Heng Li, Cheng Xing, Ji Li, Yihao Zhan, Ming Luo, Peilong Wang, Yue Sheng, Hongling Peng

“…Hi-C sequencing exposed a unique chromatin architecture in RS, with increased proximal and decreased distal interactions. …”
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Nongenetic evolution of the tumor: from challenges to new therapeutic opportunities by Elisa Oricchio

Subjects: “…chromatin…”
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Identification of alterations in the nucleotide sequence of the chromatin remodeling gene PBRM1 in clear cell renal cell carcinoma patients by E. A. Klimentova, I. R. Gilyazova, A. A. Izmailov, I. M. Sultanov, M. A. Bermisheva, V. N. Pavlov, E. K. Khusnutdinova

“…One of these genes, which are inactivated in the case of ccRCC is the PBRM1 gene encoding the PBAF SWI/SNF subunit of the chromatin remodeling complex, BAF180. The PBRM1 gene is located on the short arm of the third chromosome in the 3p21 region near the von Hippel-Lindau gene (VHL), the mutation in which is the main event in the occurrence of ccRCC. …”
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Effect of Chromatin-Remodeling Agents in Hepatic Differentiation of Rat Bone Marrow-Derived Mesenchymal Stem Cells In Vitro and In Vivo by Danna Ye, Tong Li, Philip Heraud, Rangsun Parnpai

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Protocol for visualizing the chromatin assembly properties of epigenetic protein complexes via an HTM module-mediated artificial tethering system by Shanli Guan, Jiajia Tang, Cuixia Di, Bo Cheng

“…Summary: The detailed chromatin assembly processes for many epigenetic regulatory complexes are largely unknown. …”
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Transcriptome and chromatin accessibility landscape of ovarian development at different egg-laying stages in taihe black-bone silky fowls by Jingyi Zhang, Yong Cui, Jiming Ruan, Haiyan Zhu, Haiping Liang, Ji Cao, Qing Wei, Jianzhen Huang

“…This study aims to explore the ovarian development status, as well as the changes in the transcriptome and chromatin accessibility landscape at different egg-laying stages of SF, in order to reveal the epigenetic regulatory mechanisms underlying ovarian development in laying hens. …”
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ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning by Wouter Saelens, Olga Pushkarev, Bart Deplancke

“…Abstract Gene regulation is inherently multiscale, but scale-adaptive machine learning methods that fully exploit this property in single-nucleus accessibility data are still lacking. Here, we develop ChromatinHD, a pair of scale-adaptive models that uses the raw accessibility data, without peak-calling or windows, to link regions to gene expression and determine differentially accessible chromatin. …”
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Chronological Reorganization of Microtubules, Actin Microfilaments, and Chromatin during the First Cell Cycle in Swamp Buffalo (Bubalus bubalis) Embryos by Vibuntita Chankitisakul, Theerawat Tharasanit, Kriengsak Tasripoo, Mongkol Techakumphu

“…This paper aimed to study the dynamics of early embryonic development, in terms of redistribution of cytoskeleton (microtubules, actin microfilaments) and chromatin configurations during the first cell cycle in swamp buffalo embryos. …”
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The added value of coupling anti-dsDNA and anti-chromatin antibodies in follow-up monitoring of systemic lupus erythematosus patients by Caroline Carlé, Françoise Fortenfant, Chloé Bost, Julie Belliere, Stanislas Faguer, Dominique Chauveau, Antoine Huart, David Ribes, Laurent Alric, Gregory Pugnet, Laurent Sailler, Yves Renaudineau

Subjects: “…anti-Chromatin…”
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The Lyn/RUVBL1 Complex Promotes Colorectal Cancer Liver Metastasis by Regulating Arachidonic Acid Metabolism Through Chromatin Remodeling by Zhenyu Zhang, Yina Gao, Yuanyuan Qian, Bowen Wei, Kexin Jiang, Zhiwei Sun, Feifan Zhang, Mingming Yang, Salem Baldi, Xiaoqi Yu, Yunfei Zuo, Shuangyi Ren

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Fluo-Cast-Bright: a deep learning pipeline for the non-invasive prediction of chromatin structure and developmental potential in live oocytes by Xiangyu Zhang, Claudia Baumann, Rabindranath De La Fuente

“…Abstract In mammalian oocytes, large-scale chromatin organization regulates transcription, nuclear architecture, and maintenance of chromosome stability in preparation for meiosis onset. …”
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Disruption of erythroid nuclear opening and histone release in myelodysplastic syndromes by Baobing Zhao, Hui Liu, Yang Mei, Yijie Liu, Xu Han, Jing Yang, Amittha Wickrema, Peng Ji

Subjects: “…chromatin condensation…”
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Editorial: Current insights in Epigenetics and Epigenomics by Steven Henikoff, Steven Henikoff, Sharon Y. R. Dent, Sharon Y. R. Dent, Raul Mostoslavsky, Raul Mostoslavsky, Ting Wang, Luca Comai

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The role of genetic diversity, epigenetic regulation, and sex-based differences in HIV cure research: a comprehensive review by Punitha Letchumanan, Kumitaa Theva Das

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Chromatin Structure and U2AF1-RS1 Gene Expression in Embryonic Stem Cells following RA-Induced Apoptosis by N. Andollo, M.D. Boyano, M. Garcia-Sanz, A. Asumendi, M.M. Zalduendo, J. Arechaga

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Chromatin accessibility and differentially expressed genes profiling in large yellow croaker (Larimichthys crocea) head kidney cells following iridovirus infection by Chaowei Song, Ying Huang, Fang Han, Zhiyong Wang, Zhiyong Wang

Subjects: “…chromatin accessibility…”
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