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Letter: Epigenetic profiling at mouse imprinted gene clusters reveals novel epigenetic and genetic features at differentially methylated regions
- Scott V. Dindot,
- Richard Person,
- Mark Strivens,
- Rejinaldo Garcia,
- and Arthur L. Beaudet
Genome Res. August 2009 19: 1374-1383; Published in Advance June 19, 2009, doi:10.1101/gr.089185.108
...-specific modifications include DNA methylation and post-translational modifications to histones, which create allele-specific active and repressive domains at imprinted regions. Through the use of a high-density genomic tiling array, we generated DNA and histone methylation profiles at 11 imprinted gene clusters...
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Method: Methylation profiling in individuals with uniparental disomy identifies novel differentially methylated regions on chromosome 15
- Andrew J. Sharp,
- Eugenia Migliavacca,
- Yann Dupre,
- Elisavet Stathaki,
- Mohammad Reza Sailani,
- Alessandra Baumer,
- Albert Schinzel,
- Deborah J. Mackay,
- David O. Robinson,
- Gilda Cobellis,
- Luigi Cobellis,
- Han G. Brunner,
- Bernhard Steiner,
- and Stylianos E. Antonarakis
Genome Res. September 2010 20: 1271-1278; Published in Advance July 14, 2010, doi:10.1101/gr.108597.110
...expression-based methods, in that these differentialmethylationmarks are generally conserved, even in tissues that lack imprinted expression (Dockery et al. 2009). The presence of overlapping euchromatin and heterochromatin marks has been used to highlight imprinted domains in human (Wen et al. 2008...
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Research: Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer
- Gary C. Hon,
- R. David Hawkins,
- Otavia L. Caballero,
- Christine Lo,
- Ryan Lister,
- Mattia Pelizzola,
- Armand Valsesia,
- Zhen Ye,
- Samantha Kuan,
- Lee E. Edsall,
- Anamaria Aranha Camargo,
- Brian J. Stevenson,
- Joseph R. Ecker,
- Vineet Bafna,
- Robert L. Strausberg,
- Andrew J. Simpson,
- and Bing Ren
Genome Res. February 2012 22: 246-258; Published in Advance December 7, 2011, doi:10.1101/gr.125872.111
...regions of the , our analyses are restricted to regions of facultative heterochromatin and euchromatin. Thus, at least in HCC1954 and IMR90, H3K9me3 appears to be exclusive of DNA methylation outside of constitutive heterochromatin.Our observations suggest that DNA methylation changes in breast cancer...
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Research: The roles of cis- and trans-regulation in the evolution of regulatory incompatibilities and sexually dimorphic gene expression
- Colin D. Meiklejohn,
- Joseph D. Coolon,
- Daniel L. Hartl,
- and Patricia J. Wittkopp
Genome Res. January 2014 24: 84-95; Published in Advance September 16, 2013, doi:10.1101/gr.156414.113
...expression associated with cis-regulation could conceivably result from either molecular mechanisms of gene regulation or evolutionary processes. InDrosophila, global differences betweenmales and females in the balance of euchromatin and heterochromatin (Deng et al. Gene expression evolution in cis and trans...
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Research: Revisiting chromatin packaging in mouse sperm
- Qiangzong Yin,
- Chih-Hsiang Yang,
- Olga S. Strelkova,
- Jingyi Wu,
- Yu Sun,
- Sneha Gopalan,
- Liyan Yang,
- Job Dekker,
- Thomas G. Fazzio,
- Xin Zhiguo Li,
- Johan Gibcus,
- and Oliver J. Rando
Genome Res. December 2023 33: 2079-2093; Published in Advance December 21, 2023, doi:10.1101/gr.277845.123
...of somatic cells: A and B compartments corresponding to euchromatin and heterochromatin, and TADs with flares and loop anchors characteristic of loop extrusion processes. These maps are quite surprising given the compaction required to fit the into the small sperm nucleus, as well as the unusual...
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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...heterochromatin marks from spreading into euchromatin like in other species, such as JmjC-domain proteins DMM-1 in Neurospora crassa and Epe1 in Schizosaccharomyces pombe (Tamaru 2010).Like MBD5/6, MBD2 binds mCG in gene bodies (∼50% of MBD2-binding sites), but unlike MBD5/6, MBD2 rarely binds TEs (∼15% of MBD2...
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LETTER: Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas
- Neerja Karnani,
- Christopher Taylor,
- Ankit Malhotra,
- and Anindya Dutta
Genome Res. June 2007 17: 865-876; doi:10.1101/gr.5427007
...express all their genes monoallelically. The interallelic asynchrony in replication in the pan-S segments suggests that one allele is in euchromatin and the other in heterochromatin. Consistent with this, pan-S areas are unique in being enriched in both activating and repressive marks ( Fig. 7...
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Research: Resetting of the 24-nt siRNA landscape in rice zygotes
- Chenxin Li,
- Jonathan I. Gent,
- Hengping Xu,
- Hong Fu,
- Scott D. Russell,
- and Venkatesan Sundaresan
Genome Res. February 2022 32: 309-323; Published in Advance December 23, 2021, doi:10.1101/gr.275981.121
...inheritance of siRNAs, or the lack thereof, has yet to be rigorously demonstrated in plants.In vegetative tissues such as seedlings, 24-nt siRNAs coincide with mCHH islands—short regions with high CHH methylation—that are enriched around genes and mark the ends of TEs and euchromatin-heterochromatin...
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Research: Genome-wide redistribution of 24-nt siRNAs in rice gametes
- Chenxin Li,
- Hengping Xu,
- Fang-Fang Fu,
- Scott D. Russell,
- Venkatesan Sundaresan,
- and Jonathan I. Gent
Genome Res. February 2020 30: 173-184; Published in Advance January 2, 2020, doi:10.1101/gr.253674.119
...DM) in plants, were depleted from heterochromatin boundaries in both gametes relative to vegetative tissues, reminiscent of siRNA patterns in DDM1-type nucleosome remodeler mutants. In sperm cells, 24-nt siRNAs were spread across heterochromatic regions, while in egg cells, 24-nt siRNAs were concentrated...
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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
.... Spatial organization of chromatin domains and compartments in single chromosomes. Science 353: 598–602. ↵Wen B, Wu H, Bjornsson H, Green RD, Irizarry R, Feinberg AP. 2008. Overlapping euchromatin/heterochromatin-associated marks are enriched in imprinted gene regions and predict allele-specific...

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