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Research: Topologically associating domains and their role in the evolution of genome structure and function in Drosophila
- Yi Liao,
- Xinwen Zhang,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. March 2021 31: 397-410; Published in Advance February 9, 2021, doi:10.1101/gr.266130.120
...Topologically associating domains and their role in the evolution of structure and function in Drosophila Yi Liao1, Xinwen Zhang1, Mahul Chakraborty1 and J.J. Emerson1,2 1Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA; 2Center for Complex...
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Research: Allele-specific control of replication timing and genome organization during development
- Juan Carlos Rivera-Mulia,
- Andrew Dimond,
- Daniel Vera,
- Claudia Trevilla-Garcia,
- Takayo Sasaki,
- Jared Zimmerman,
- Catherine Dupont,
- Joost Gribnau,
- Peter Fraser,
- and David M. Gilbert
Genome Res. June 2018 28: 800-811; Published in Advance May 7, 2018, doi:10.1101/gr.232561.117
...to parental imprinting, confirming that the RT differences observed in hybrid mouse ESCs are not associated with imprinting.Long-range interactions in RT asynchronous domains are restricted to the early replicating alleleRT and Hi-C eigenvectors correlated strongly and RT asynchrony was associated...
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Research: Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains
- Sergey V. Ulianov,
- Ekaterina E. Khrameeva,
- Alexey A. Gavrilov,
- Ilya M. Flyamer,
- Pavel Kos,
- Elena A. Mikhaleva,
- Aleksey A. Penin,
- Maria D. Logacheva,
- Maxim V. Imakaev,
- Alexander Chertovich,
- Mikhail S. Gelfand,
- Yuri Y. Shevelyov,
- and Sergey V. Razin
Genome Res. January 2016 26: 70-84; Published in Advance October 30, 2015, doi:10.1101/gr.196006.115
...appear to evolve primarily as constant and unsplit units. Previous studies in Drosophila embryonic nuclei and embryoderived Kc167 cells (Hou et al. 2012; Sexton et al. 2012) detected TADs of various sizes roughly corresponding to epigenetic domains. Additionally, long-range genomic contacts...
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Research: Orc4 spatiotemporally stabilizes centromeric chromatin
- Lakshmi Sreekumar,
- Kiran Kumari,
- Krishnendu Guin,
- Asif Bakshi,
- Neha Varshney,
- Bhagya C. Thimmappa,
- Leelavati Narlikar,
- Ranjith Padinhateeri,
- Rahul Siddharthan,
- and Kaustuv Sanyal
Genome Res. April 2021 31: 607-621; Published in Advance January 29, 2021, doi:10.1101/gr.265900.120
..., the establishment of centromeric chromatin and its subsequent propagation through many generations depends on a variety of factors that are often species specific. These include centromere-specific DNA sequence elements, replication timing, and transcriptional status of centromere DNA, as well as the influence...
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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
.... Moreover, polycomb-group proteins play an important role in this reorganization by establishing new long-range interactions that propagate transcription silencing upon heat-stress (Li et al. 2015). However, the dynamics of these changes in chromatin structure in mammals in response stimuli and its...
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Research: The nuclear matrix protein HNRNPU maintains 3D genome architecture globally in mouse hepatocytes
- Hui Fan,
- Pin Lv,
- Xiangru Huo,
- Jicheng Wu,
- Qianfeng Wang,
- Lu Cheng,
- Yun Liu,
- Qi-Qun Tang,
- Ling Zhang,
- Feng Zhang,
- Xiaoqi Zheng,
- Hao Wu,
- and Bo Wen
Genome Res. February 2018 28: 192-202; Published in Advance December 22, 2017, doi:10.1101/gr.224576.117
..., and reduces chromatin loop intensities. Long-range chromatin interactions between and within compartments or TADs are also significantly remodeled upon HNRNPU depletion. Intriguingly, HNRNPU mainly associates with active chromatin, and 80% of HNRNPU peaks coincide with the binding of CTCF or RAD21...
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Research: H3S10ph broadly marks early-replicating domains in interphase ESCs and shows reciprocal antagonism with H3K9me2
- Carol C.L. Chen,
- Preeti Goyal,
- Mohammad M. Karimi,
- Marie H. Abildgaard,
- Hiroshi Kimura,
- and Matthew C. Lorincz
Genome Res. January 2018 28: 37-51; Published in Advance December 11, 2017, doi:10.1101/gr.224717.117
...with H3S10ph. H3S10ph broadly demarcates gene-rich regions in G1 and is positively correlated with domains of early DNA replication timing (RT) but negatively correlated with H3K9me2 and lamin-associated domains (LADs). Consistent with mitosis-independent kinase activity, this pattern was preserved...
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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
...revolutionized our understanding of 3D organization; for review, see Kempfer and Pombo (2020). These methods, which measure long-range chromatin interactions, reveal intricate features of chromatin organization at fine-scale resolutions, commonly visualized by 2D contact maps (Lieberman-Aiden et al. 2009; Hsieh...
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Research: Somatic structural variant formation is guided by and influences genome architecture
- Nikos Sidiropoulos,
- Balca R. Mardin,
- F. Germán Rodríguez-González,
- Ivan D. Bochkov,
- Shilpa Garg,
- Adrian M. Stütz,
- Jan O. Korbel,
- Erez Lieberman Aiden,
- and Joachim Weischenfeldt
Genome Res. April 2022 32: 643-655; Published in Advance February 17, 2022, doi:10.1101/gr.275790.121
...and replication timing switch was linked with up-regulation of both genes within this locus (WDR72, fold-change = 7.5, and UNC13C, fold-change = 7.8) (Fig. 4B) and the emergence of new loop domains (upper right square, shown as open boxes on the Hi-C map) (Fig. 4B). Most of these new looping contacts coincided...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
...). Nonetheless, there are also instances in which large duplications spanning >100 kb in length are observed (Naish et al. 2021; Wlodzimierz et al. 2023b). In both Arabidopsis and Erianthus, higher-order duplications are often separated by megabase distances, consistent with long-range recombination (Naish et al...
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