Searching journal content for articles similar to Laurent et al. 20 (3): 320.

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  1. Research: Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA
    • Cristian Groza,
    • Bing Ge,
    • Warren A. Cheung,
    • Tomi Pastinen,
    • and Guillaume Bourque
    Genome Res. April 2025 35: 644-652; Published in Advance March 20, 2025, doi:10.1101/gr.279240.124
    ..., saturation analysis suggests that expanding this panmethylome with more assemblies and methylomes would continue to add thousands of new SV-CpGs and SV-5mCpGs per sample.A minority of CpGs are known to be variable, or dynamic, in tissues (Ziller et al. 2013). Similarly, we found that most CpGs in personal...
  2. Research: Dynamic metabolic and molecular changes during seasonal shrinking in Sorex araneus
    • William R. Thomas,
    • Cecilia Baldoni,
    • Yuanyuan Zeng,
    • David Carlson,
    • Julie Holm-Jacobsen,
    • Marion Muturi,
    • Dominik von Elverfeldt,
    • Tue B. Bennike,
    • Dina K.N. Dechmann,
    • John Nieland,
    • Angelique P. Corthals,
    • and Liliana M. Dávalos
    Genome Res. January 2026 36: 61-70; Published in Advance November 4, 2025, doi:10.1101/gr.280639.125
    ...budget with glucose to maintain their active winter lifestyle.To examine metabolic dynamics and regulatory changes throughout Dehnel's phenomenon, and its potential parallels to other wintering strategies, we conducted a multiomic analysis of S. araneus across seasonal time points that match...
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  3. Research: Parental methylome reprogramming in human uniparental blastocysts reveals germline memory transition
    • Jiawei Xu,
    • Yimin Shu,
    • Guidong Yao,
    • Yu Zhang,
    • Wenbin Niu,
    • Yile Zhang,
    • Xueshan Ma,
    • Haixia Jin,
    • Fuli Zhang,
    • Senlin Shi,
    • Yang Wang,
    • Wenyan Song,
    • Shanjun Dai,
    • Luyao Cheng,
    • Xiangyang Zhang,
    • Wei Xie,
    • Aaron J. Hsueh,
    • and Yingpu Sun
    Genome Res. September 2021 31: 1519-1530; Published in Advance July 30, 2021, doi:10.1101/gr.273318.120
    ...methylome analysis showed that the GG blastocysts partially retain the oocyte transcription-dependent methylation pattern, whereas the AG blastocyst methylome showed more extensive demethylation. The methylation states of most known imprinted differentially methylated regions (DMRs) were recapitulated...
  4. Method: Predictive modeling of single-cell DNA methylome data enhances integration with transcriptome data
    • Yasin Uzun,
    • Hao Wu,
    • and Kai Tan
    Genome Res. January 2021 31: 101-109; Published in Advance November 20, 2020, doi:10.1101/gr.267047.120
    ...@email.chop.eduAbstractSingle-cell DNA methylation data has become increasingly abundant and has uncovered many genes with a positive correlation between expression and promoter methylation, challenging the common dogma based on bulk data. However, computational tools for analyzing single-cell methylome...
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  5. Method: Long-read single-molecule maps of the functional methylome
    • Hila Sharim,
    • Assaf Grunwald,
    • Tslil Gabrieli,
    • Yael Michaeli,
    • Sapir Margalit,
    • Dmitry Torchinsky,
    • Rani Arielly,
    • Gil Nifker,
    • Matyas Juhasz,
    • Felix Gularek,
    • Miguel Almalvez,
    • Brandon Dufault,
    • Sreetama Sen Chandra,
    • Alexander Liu,
    • Surajit Bhattacharya,
    • Yi-Wen Chen,
    • Eric Vilain,
    • Kathryn R. Wagner,
    • Jonathan Pevsner,
    • Jeff Reifenberger,
    • Ernest T. Lam,
    • Alex R. Hastie,
    • Han Cao,
    • Hayk Barseghyan,
    • Elmar Weinhold,
    • and Yuval Ebenstein
    Genome Res. April 2019 29: 646-656; Published in Advance March 7, 2019, doi:10.1101/gr.240739.118
    ...is repetitive arrays. These variable copy number elements are homologous DNA sequences that are identical or highly similar (Schmid and Deininger 1975; Batzer and Deininger 2002). Many repetitive elements are mobile and can transpose across the , perform homologous recombination events, and promote dynamic...
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  6. Research: The strand-biased mitochondrial DNA methylome and its regulation by DNMT3A
    • Xiaoyang Dou,
    • Jerome D. Boyd-Kirkup,
    • Joseph McDermott,
    • Xiaoli Zhang,
    • Fang Li,
    • Bowen Rong,
    • Rui Zhang,
    • Bisi Miao,
    • Peilin Chen,
    • Hao Cheng,
    • Jianhuang Xue,
    • David Bennett,
    • Jiemin Wong,
    • Fei Lan,
    • and Jing-Dong J. Han
    Genome Res. October 2019 29: 1622-1634; Published in Advance September 19, 2019, doi:10.1101/gr.234021.117
    ...biased to light (L)-strand non-CpG methylation with conserved peak loci preferentially located at gene–gene boundaries, which was also independently validated by MeDIP and FspEI digestion. Such mtDNA methylation patterns are conserved across different species and developmental stages but display dynamic...
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  7. Research: New guidelines for DNA methylome studies regarding 5-hydroxymethylcytosine for understanding transcriptional regulation
    • Le Li,
    • Yuwei Gao,
    • Qiong Wu,
    • Alfred S.L. Cheng,
    • and Kevin Y. Yip
    Genome Res. April 2019 29: 543-553; Published in Advance February 19, 2019, doi:10.1101/gr.240036.118
    ...@cse.cuhk.edu.hkAbstractMany DNA methylome profiling methods cannot distinguish between 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Because 5mC typically acts as a repressive mark whereas 5hmC is an intermediate form during active demethylation, the inability to separate their signals could lead to incorrect...
  8. Resource: Whole-genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver
    • Xin Li,
    • Yun Liu,
    • Tal Salz,
    • Kasper D. Hansen,
    • and Andrew Feinberg
    Genome Res. December 2016 26: 1730-1741; Published in Advance October 13, 2016, doi:10.1101/gr.211854.116
    ...Whole-genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver Xin Li 1 , Yun Liu 1 , 2 , 3 , Tal Salz 1 , Kasper D. Hansen 1 , 4 , 5 and Andrew Feinberg 1 , 6 , 7 , 8 1Center...
  9. Method: Identification and dynamic quantification of regulatory elements using total RNA
    • Sascha H. Duttke,
    • Max W. Chang,
    • Sven Heinz,
    • and Christopher Benner
    Genome Res. November 2019 29: 1836-1846; Published in Advance October 24, 2019, doi:10.1101/gr.253492.119
    ...for posttranslational histone modifications in transcription. Our findings show that total RNA is sufficient to identify transcribed regulatory elements and capture the dynamics of initiated stable and unstable transcripts at single-nucleotide resolution in eukaryotes.Transcription decodes the regulatory signals...
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  10. Research: Dynamic RNA–protein interactions underlie the zebrafish maternal-to-zygotic transition
    • Vladimir Despic,
    • Mario Dejung,
    • Mengting Gu,
    • Jayanth Krishnan,
    • Jing Zhang,
    • Lydia Herzel,
    • Korinna Straube,
    • Mark B. Gerstein,
    • Falk Butter,
    • and Karla M. Neugebauer
    Genome Res. July 2017 27: 1184-1194; Published in Advance April 5, 2017, doi:10.1101/gr.215954.116
    ...ZGA, hereby named the zebrafishMZTmRNA-bound proteome. This protein constellation consists of many conserved RBPs, some of which are potential stage-specific mRNA interactors that likely reflect the dynamics of RNA–protein interactions during MZT. The enrichment of numerous splicing factors like hn...
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