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Mini-Review: The chromatin tapestry as a framework for neurodevelopment
- Ben Nolan,
- Timothy E. Reznicek,
- Christopher T. Cummings,
- and M. Jordan Rowley
Genome Res. October 2024 34: 1477-1486; doi:10.1101/gr.278408.123
...et al. 2019). Altogether, CTCF loops are one part of a complex chromatin ecosystem and cell type specificities likely correspond to multiple impacted chromatin features within a complex mechanism (Segueni and Noordermeer 2022).Intergenic and intragenic interactionsHi-C maps display bright “foci...
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Method: A scalable computational framework for predicting gene expression from candidate cis-regulatory elements
- Qinhu Zhang,
- Siguo Wang,
- Zhipeng Li,
- Wenzheng Bao,
- Wenjian Liu,
- and De-Shuang Huang
Genome Res. February 2026 36: 361-374; Published in Advance January 16, 2026, doi:10.1101/gr.281219.125
...extra data. For example, GraphReg (Karbalayghareh et al. 2022) introduced a graph attention network that integrates chromatin contact data (Hi-C) to predict gene expression. CREaTor (Li et al. 2023) presented a hierarchical deep learning model based on the self-attention mechanism, which utilizes c...
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Research: Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution
- Chang Liu,
- Congmao Wang,
- George Wang,
- Claude Becker,
- Maricris Zaidem,
- and Detlef Weigel
Genome Res. August 2016 26: 1057-1068; Published in Advance May 25, 2016, doi:10.1101/gr.204032.116
...310029, China Corresponding authors: chang.liu@zmbp.uni-tuebingen.de , weigel@weigelworld.org Abstract The three-dimensional packing of the genome plays an important role in regulating gene expression. We have used Hi-C, a genome-wide chromatin conformation capture (3C) method...
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Research: Genome-wide analysis of local chromatin packing in Arabidopsis thaliana
- Congmao Wang,
- Chang Liu,
- Damian Roqueiro,
- Dominik Grimm,
- Rebecca Schwab,
- Claude Becker,
- Christa Lanz,
- and Detlef Weigel
Genome Res. February 2015 25: 246-256; Published in Advance November 3, 2014, doi:10.1101/gr.170332.113
..., Schwab Weigel, Detlef Grimm, Dominik Grimm, D genome;gr.170332.113 1549-5469 10.1101/gr.170332.113 1088-9051 Genome-wide analysis of local chromatin packing in Arabidopsis thaliana Wang et al. Hi-C map Research Genome-wide analysis of local chromatin packing in Arabidopsis thaliana Congmao Wang,1...
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Method: NicE-C efficiently reveals open chromatin–associated chromosome interactions at high resolution
- Zhengyu Luo,
- Ran Zhang,
- Tengfei Hu,
- Yuting Zhu,
- Yueming Wu,
- Wenfei Li,
- Zhi Zhang,
- Xuebiao Yao,
- Haiyi Liang,
- and Xiaoyuan Song
Genome Res. March 2022 32: 534-544; Published in Advance February 1, 2022, doi:10.1101/gr.275986.121
...informative open chromatin interactions at 1-kb resolution, whereas OCEAN-C provide very weak interactions, if any, with the same cis valid pairs (Fig. 2A–D). Genome-wide analyses showed that all three methods could enrich P-P loops and stripes compared to Hi-C, with NicE-C and Trac-looping showing much...
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Method: A universal framework for detecting cis-regulatory diversity in DNA regions
- Anushua Biswas and
- Leelavati Narlikar
Genome Res. September 2021 31: 1646-1662; Published in Advance July 19, 2021, doi:10.1101/gr.274563.120
...with few binding sites have a significantly lower tag density.CTCF-bound regions display remarkable sequence-level diversityWe next investigated ChIP-seq data sets. CTCF is a highly conserved TF, known to play different critical roles in regulation from binding insulators to forming chromatin loops...
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Research: Chromatin activation as a unifying principle underlying pathogenic mechanisms in multiple myeloma
- Raquel Ordoñez,
- Marta Kulis,
- Nuria Russiñol,
- Vicente Chapaprieta,
- Arantxa Carrasco-Leon,
- Beatriz García-Torre,
- Stella Charalampopoulou,
- Guillem Clot,
- Renée Beekman,
- Cem Meydan,
- Martí Duran-Ferrer,
- Núria Verdaguer-Dot,
- Roser Vilarrasa-Blasi,
- Paula Soler-Vila,
- Leire Garate,
- Estíbaliz Miranda,
- Edurne San José-Enériz,
- Juan R. Rodriguez-Madoz,
- Teresa Ezponda,
- Rebeca Martínez-Turrilas,
- Amaia Vilas-Zornoza,
- David Lara-Astiaso,
- Daphné Dupéré-Richer,
- Joost H.A. Martens,
- Halima El-Omri,
- Ruba Y. Taha,
- Maria J. Calasanz,
- Bruno Paiva,
- Jesus San Miguel,
- Paul Flicek,
- Ivo Gut,
- Ari Melnick,
- Constantine S. Mitsiades,
- Jonathan D. Licht,
- Elias Campo,
- Hendrik G. Stunnenberg,
- Xabier Agirre,
- Felipe Prosper,
- and Jose I. Martin-Subero
Genome Res. September 2020 30: 1217-1227; Published in Advance August 20, 2020, doi:10.1101/gr.265520.120
...start site (TSS) (Fig. 3A). Using GM12878 as a cellular model, Hi-C data (GSE63525) (Rao et al. 2014) revealed that the active enhancer elements showed significant 3D interactions to the TXN promoter region. The presence of this loop and the fact that TXN is the only overexpressed gene within the TAD...
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Research: Rapid reversible changes in compartments and local chromatin organization revealed by hyperosmotic shock
- Ramon Amat,
- René Böttcher,
- François Le Dily,
- Enrique Vidal,
- Javier Quilez,
- Yasmina Cuartero,
- Miguel Beato,
- Eulàlia de Nadal,
- and Francesc Posas
Genome Res. January 2019 29: 18-28; Published in Advance December 6, 2018, doi:10.1101/gr.238527.118
...strong effect on chromatin organization. To assess chromosome organization, we harvested T47D cells that were maintained in isotonic medium or were exposed to mild hyperosmotic stress (110 mM NaCl) for 1 h, and performed in situ Hi-C. We used arrested T47D cells to eliminate possible effects of stress...
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Research: YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment
- Jonathan A. Beagan,
- Michael T. Duong,
- Katelyn R. Titus,
- Linda Zhou,
- Zhendong Cao,
- Jingjing Ma,
- Caroline V. Lachanski,
- Daniel R. Gillis,
- and Jennifer E. Phillips-Cremins
Genome Res. July 2017 27: 1139-1152; Published in Advance May 23, 2017, doi:10.1101/gr.215160.116
...between biological replicates (Fig. 3A; Supplemental Table 1; Supplemental Fig. 3A). Additionally, our 5C data showed strong biological concordance with published Hi-C data from the murine cortex (Dixon et al. 2012) across a 1-Mb region surrounding the Sox2 gene in NPCs (Supplemental Fig. 3B). Looping...
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Research: Nucleosome remodeling at origins of global genome–nucleotide excision repair occurs at the boundaries of higher-order chromatin structure
- Patrick van Eijk,
- Shuvro Prokash Nandi,
- Shirong Yu,
- Mark Bennett,
- Matthew Leadbitter,
- Yumin Teng,
- and Simon H. Reed
Genome Res. January 2019 29: 74-84; Published in Advance December 14, 2018, doi:10.1101/gr.237198.118
...observed no global change in nucleosome occupancy levels throughout the yeast in cells treated with UV radiation (Fig. 1B). We do detect a small increase in the frequency of low-occupancy nucleosomes (fewer than 350 normalized reads) immediately after UV irradiation (Fig. 1B, red line). Genome-wide...
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