LDB1 establishes multi-enhancer networks to regulate gene expression

Authors: Aboreden, Nicholas G. ^{1, 2}, Lam, Jessica C. ^{1, 2}, Goel, Viraat Y. ^{3, 4, 5}, Wang, Siqing ², Wang, Xiaokang ², Midla, Susannah C. ², Quijano, Alma ^{1, 2}, Keller, Cheryl A. ⁶, Giardine, Belinda M. ⁶, Hardison, Ross C. ⁶, Zhang, Haoyue ⁷, Hansen, Anders S. ^{3, 4, 5}, Blobel, Gerd A. ^{1, 2, 8, ∗}

Source: In Molecular Cell 16 January 2025 85(2):376-393

Long non-coding RNAs: roles in cellular stress responses and epigenetic mechanisms regulating chromatin

Authors: Jeffrey A. Nickerson, Fatemeh Momen-Heravi

Source: Nucleus, Vol 15, Iss 1 (2024)

Subject Terms: Building RNA structures, chromatin architecture, genome-wide lncRNA screens, lncRNA, RNP networks, stress response, Genetics, QH426-470, Cytology, QH573-671

File Description: electronic resource

Relation: https://doaj.org/toc/1949-1034; https://doaj.org/toc/1949-1042

Access URL: https://doaj.org/article/8acae4493f48405193dc0c3f98af9457

Interaction of CTCF and CTCFL in genome regulation through chromatin architecture during the spermatogenesis and carcinogenesis

Authors: Xin Tong, Yang Gao, Zhongjing Su

Source: PeerJ, Vol 12, p e18240 (2024)

Subject Terms: CTCF, CTCFL, Chromatin architecture, Spermatogenesis, Carcinogenesis, Medicine, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://peerj.com/articles/18240.pdf; https://peerj.com/articles/18240/; https://doaj.org/toc/2167-8359

Access URL: https://doaj.org/article/a7a8aac687414a9fb6b07c194921e671

Beyond interacting with Rap1: Dissecting the roles of Rif1

Authors: Wei, Jiyu ^{a, 1}, Sun, Hao ^{a, 1}, Huang, Zhihong ^{a, b, 1}, Yang, Liqian ^{a, b}, Wu, Jiaxing ^{a, b}, Zhang, Jiaqi ^{a, b}, Liu, Minghui ^c, Li, Meiting ^c, Luo, Jianyuan ^{a, c}, Wang, Haiying ^{a, b, ⁎}

Source: In International Journal of Biological Macromolecules May 2025 306 Part 3

Regulatory landscape enrichment analysis (RLEA): a computational toolkit for non-coding variant enrichment and cell type prioritization

Authors: Samuel Rosean, Eric A. Sosa, Dónal O’Shea, Srilakshmi M. Raj, Cathal Seoighe, John M. Greally

Source: BMC Bioinformatics, Vol 25, Iss 1, Pp 1-18 (2024)

Subject Terms: Cell-type prioritization, Non-coding enrichment, Chromatin architecture, GWAS, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/4060e01f1a0740f48e1cf9011cdeebb1

Su(Hw) interacts with Combgap to establish long-range chromatin contacts

Authors: Nadezhda E. Vorobyeva, Alexey N. Krasnov, Maksim Erokhin, Darya Chetverina, Marina Mazina

Source: Epigenetics & Chromatin, Vol 17, Iss 1, Pp 1-13 (2024)

Subject Terms: Insulator binding protein, Su(Hw), Combgap, Chromatin architecture, Transcription, Long-range interactions, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1756-8935

Access URL: https://doaj.org/article/2603cbab3c9243ada237a07846d5c50f

Reorganization of 3D genome architecture provides insights into pathogenesis of early fatty liver disease in laying hens

Authors: Yanli Liu, Zhuqing Zheng, Chaohui Wang, Yumeng Wang, Xi Sun, Zhouzheng Ren, Xin Yang, Xiaojun Yang

Source: Journal of Animal Science and Biotechnology, Vol 15, Iss 1, Pp 1-15 (2024)

Subject Terms: 3D chromatin architecture, Fatty liver disease, Folate, H3K27ac profiling, Transcription reprogramming, Animal culture, SF1-1100, Veterinary medicine, SF600-1100

File Description: electronic resource

Relation: https://doaj.org/toc/2049-1891

Access URL: https://doaj.org/article/6d04ce502b264b3d9340bbe64eb2e355

How Chromatin Motor Complexes Influence the Nuclear Architecture: A Review of Chromatin Organization, Cohesins, and Condensins with a Focus on C. elegans

Authors: Bahaar Chawla, Györgyi Csankovszki

Source: DNA, Vol 4, Iss 1, Pp 84-103 (2024)

Subject Terms: chromatin architecture, SMC proteins, condensin, cohesin, TADs, C. elegans, Biochemistry, QD415-436

File Description: electronic resource

Relation: https://www.mdpi.com/2673-8856/4/1/5; https://doaj.org/toc/2673-8856

Access URL: https://doaj.org/article/66064a7107f04ec98978d8e496938d4e

Advances in DNA methylation and its role in cytoplasmic male sterility in higher plants

Authors: Atiqur Rahman, Md. Hasan Sofiur Rahman, Md. Shakil Uddin, Naima Sultana, Shirin Akhter, Ujjal Kumar Nath, Shamsun Nahar Begum, Md. Mazadul Islam, Afroz Naznin, Md. Nurul Amin, Sharif Ahmed, Akbar Hossain

Source: Journal of Integrative Agriculture, Vol 23, Iss 1, Pp 1-19 (2024)

Subject Terms: DNA methylation, epigenetics, CMS male sterility, chromatin architecture, gene expression, higher plants, Agriculture (General), S1-972

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2095311923001156; https://doaj.org/toc/2095-3119

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3D organization of regulatory elements for transcriptional regulation in Arabidopsis

Authors: 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

Source: Genome Biology, Vol 24, Iss 1, Pp 1-30 (2023)

Subject Terms: Chromatin architecture, Transcriptional regulation, ChIA-PET, Arabidopsis, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/04c34c22e5ed4651874c861dc3f57f10

Editorial: Epigenetics in prostate cancer

Authors: Aria Baniahmad, Mustafa Ozen

Source: Frontiers in Oncology, Vol 13 (2023)

Subject Terms: lncRNA, chromatin architecture, immune escape, anoikis, higher order chromatin architecture, prostate cancer, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fonc.2023.1268519/full; https://doaj.org/toc/2234-943X

Access URL: https://doaj.org/article/133d9961bf8c40ab9575d91ced90c712

NSD2 E1099K drives relapse in pediatric acute lymphoblastic leukemia by disrupting 3D chromatin organization

Authors: Sonali Narang, Nikki A. Evensen, Jason Saliba, Joanna Pierro, Mignon L. Loh, Patrick A. Brown, Pandurang Kolekar, Heather Mulder, Ying Shao, John Easton, Xiaotu Ma, Aristotelis Tsirigos, William L. Carroll

Source: Genome Biology, Vol 24, Iss 1, Pp 1-25 (2023)

Subject Terms: Relapsed acute lymphoblastic leukemia, NSD2, Clonal evolution, Chromatin architecture, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/2fa3e7fe8efc458a83cdfba95749aef0

Genomic rearrangements and evolutionary changes in 3D chromatin topologies in the cotton tribe (Gossypieae)

Authors: Xiaochong Li, Jinbin Wang, Yanan Yu, Guo Li, Jinpeng Wang, Changping Li, Zixian Zeng, Ning Li, Zhibin Zhang, Qianli Dong, Yiyang Yu, Xiaofei Wang, Tianya Wang, Corrinne E. Grover, Bin Wang, Bao Liu, Jonathan F. Wendel, Lei Gong

Source: BMC Biology, Vol 21, Iss 1, Pp 1-17 (2023)

Subject Terms: Chromatin architecture, Gossypieae, Chromosome rearrangement, Hi-C, Epigenetic modifications, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1741-7007

Access URL: https://doaj.org/article/4043ed3c9df94ab4a0a4923fe3d73898

Consistencies and contradictions in different polymer models of chromatin architecture

Authors: Amanda Souza Câmara, Martin Mascher

Source: Computational and Structural Biotechnology Journal, Vol 21, Iss , Pp 1084-1091 (2023)

Subject Terms: Chromatin architecture, Chromatin dynamics, Copolymer models, Mechanistic models, Polymer physics, Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2001037023000326; https://doaj.org/toc/2001-0370

Access URL: https://doaj.org/article/9057ce4960344b85bab7db59f732941d

Epigenetic control and genomic imprinting dynamics of the Dlk1-Dio3 domain

Authors: Ariella Weinberg-Shukron, Neil A. Youngson, Anne C. Ferguson-Smith, Carol A. Edwards

Source: Frontiers in Cell and Developmental Biology, Vol 11 (2023)

Subject Terms: Dlk1-Dio3 domain, genomic imprinting, CTCF, chromatin architecture, DNA methylation, long non-coding RNA, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fcell.2023.1328806/full; https://doaj.org/toc/2296-634X

Access URL: https://doaj.org/article/830e3195b57543f98f3c604b36e574b8

Editorial: Chromatin architecture in gene regulation and disease

Authors: Xiang Wang

Source: Frontiers in Genetics, Vol 14 (2023)

Subject Terms: chromatin architecture, human disease, genome organization, gene expression, enhancer-promoter interaction, Genetics, QH426-470

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fgene.2023.1254865/full; https://doaj.org/toc/1664-8021

Access URL: https://doaj.org/article/6b76dfaf005b4ef8bac11bcebf36c87c

Aging is associated with increased chromatin accessibility and reduced polymerase pausing in liver

Authors: Mihaela Bozukova, Chrysa Nikopoulou, Niklas Kleinenkuhnen, Dora Grbavac, Katrin Goetsch, Peter Tessarz

Source: Molecular Systems Biology, Vol 18, Iss 9, Pp 1-21 (2022)

Subject Terms: aging, chromatin architecture, nascent transcription, promoter‐proximal pausing, Biology (General), QH301-705.5, Medicine (General), R5-920

File Description: electronic resource

Relation: https://doaj.org/toc/1744-4292

Access URL: https://doaj.org/article/c65102c402d24f72a3ba53873d6608ca

Comparative 3D genome architecture in vertebrates

Authors: Diyan Li, Mengnan He, Qianzi Tang, Shilin Tian, Jiaman Zhang, Yan Li, Danyang Wang, Long Jin, Chunyou Ning, Wei Zhu, Silu Hu, Keren Long, Jideng Ma, Jing Liu, Zhihua Zhang, Mingzhou Li

Source: BMC Biology, Vol 20, Iss 1, Pp 1-21 (2022)

Subject Terms: Chromatin architecture, Gene expression, Evolution, Vertebrates, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1741-7007

Access URL: https://doaj.org/article/372a9070fd3e427db3c2248c5c11ef27

3D chromatin architecture and transcription regulation in cancer

Authors: Siwei Deng, Yuliang Feng, Siim Pauklin

Source: Journal of Hematology & Oncology, Vol 15, Iss 1, Pp 1-23 (2022)

Subject Terms: Chromatin architecture, Chromatin 3D topology, Epigenetics, Transcription regulation, Tumorigenesis, Diseases of the blood and blood-forming organs, RC633-647.5, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: https://doaj.org/toc/1756-8722

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Chromosome conformation capture technologies as tools to detect structural variations and their repercussion in chromatin 3D configuration

Authors: Aura Stephenson-Gussinye, Mayra Furlan-Magaril

Source: Frontiers in Cell and Developmental Biology, Vol 11 (2023)

Subject Terms: chromatin, chromosome conformation capture (3C), structural variation (SV), chromatin architecture, topologically associated domains, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fcell.2023.1219968/full; https://doaj.org/toc/2296-634X

Access URL: https://doaj.org/article/9e49679857b54972a69fef62a9f567bf