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Research: Epigenetic modification and inheritance in sexual reversal of fish
- Changwei Shao,
- Qiye Li,
- Songlin Chen,
- Pei Zhang,
- Jinmin Lian,
- Qiaomu Hu,
- Bing Sun,
- Lijun Jin,
- Shanshan Liu,
- Zongji Wang,
- Hongmei Zhao,
- Zonghui Jin,
- Zhuo Liang,
- Yangzhen Li,
- Qiumei Zheng,
- Yong Zhang,
- Jun Wang,
- and Guojie Zhang
Genome Res. April 2014 24: 604-615; Published in Advance February 2, 2014, doi:10.1101/gr.162172.113
...in the offspring of a pseudomale family and the transgenerational epigenetic inheritance of sexual reversal in tongue sole fish. Footnotes ↵ 9 Corresponding authors E-mail zhanggj@genomics.cn E-mail chensl@ysfri.ac.cn [Supplemental material is available for this article...
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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
...sperm nucleus and raise new questions about the potential role for sperm chromatin as a carrier of epigenetic information from fathers to offspring.Sperm chromatin assays are contaminated by cell-free chromatinWe previously identified cell-free chromatin as a major (∼20%–30%) contaminant of immature...
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Research: Widespread and frequent horizontal transfers of transposable elements in plants
- Moaine El Baidouri,
- Marie-Christine Carpentier,
- Richard Cooke,
- Dongying Gao,
- Eric Lasserre,
- Christel Llauro,
- Marie Mirouze,
- Nathalie Picault,
- Scott A. Jackson,
- and Olivier Panaud
Genome Res. May 2014 24: 831-838; Published in Advance February 11, 2014, doi:10.1101/gr.164400.113
...demonstrated their putative functional impact as epigenetic mediators (Kobayashi et al. 2004). TEs achieve their transposition cycle within their host and are thus considered to be lineage specific because, like genes, they are inherited vertically from one generation to another. However, unlike genes, they do...
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Research: DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity
- Steven R. Eichten,
- Tim Stuart,
- Akanksha Srivastava,
- Ryan Lister,
- and Justin O. Borevitz
Genome Res. November 2016 26: 1520-1531; Published in Advance September 9, 2016, doi:10.1101/gr.205468.116
...(Fig. 3F). Depending on the questions to answer, one may prefer to have a larger number of DMRs as possible candidate variants (combined with a larger chance of false positives). This is in contrast to the conservative approach of multiple filters required for the tile-based DMRs. The two DMR...
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Research: Environmentally induced plasticity of programmed DNA elimination boosts somatic variability in Paramecium tetraurelia
- Valerio Vitali,
- Rebecca Hagen,
- and Francesco Catania
Genome Res. October 2019 29: 1693-1704; Published in Advance September 23, 2019, doi:10.1101/gr.245332.118
...transgenerational inheritance.To gain insight into this question, we assessed how many IESs are retained simultaneously in the four independently rearranged F0 and F1 somatic nuclei. Leveraging 1000 simulated data sets based on random draws from the set of PGM-IESs, we estimated that the expected maximum number...
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Review: Contrasting genetic architectures in different mouse reference populations used for studying complex traits
- David A. Buchner and
- Joseph H. Nadeau
Genome Res. June 2015 25: 775-791; Published in Advance May 7, 2015, doi:10.1101/gr.187450.114
.... Planned crosses and pedigree information can be used to investigate parental and inherited epigenetic effects. Detailed phenotyping can be undertaken in time-course studies. Cells, tissues, and organs can be accessed that are not available in humans. Results of these studies can then be used to guide...
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Research: Global profiling of DNA methylation erasure in mouse primordial germ cells
- Sylvain Guibert,
- Thierry Forné,
- and Michael Weber
Genome Res. April 2012 22: 633-641; Published in Advance February 22, 2012, doi:10.1101/gr.130997.111
...and preimplantation embryos. Nat Genet 43: 811–814. Smyth GK, Speed T. 2003. Normalization of cDNAmicroarray data.Methods 31: 265–273. Whitelaw NC, Whitelaw E. 2008. Transgenerational epigenetic inheritance in health and disease. Curr Opin Genet Dev 18: 273–279. Wu SC, Zhang Y. 2010. Active DNA demethylation: many...
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Methods: Genome-wide prediction of imprinted murine genes
- Philippe P. Luedi,
- Alexander J. Hartemink,
- and Randy L. Jirtle
Genome Res. June 2005 15: 875-884; doi:10.1101/gr.3303505
...upstream of the gene and occasionally it overlaps the first exon ( Onyango et al. 2000 ). To incorporate these findings in a systematic manner, we encoded the answers to the following questions by means of indicator variables. First, does the first exon at least partially contain a CpG island? Second, does...

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