Characterizing cytosine methylation of polymorphic transposable element insertions using the human pangenome resources.
Xiaoyu Zhuo, Chad Tomlinson, Edward A Belter, Prashant Kumar Kuntala, Wesley N Saintilnord, Juan Jiang, Tina Lindsay, Juan F. Macias-Velasco, Robert S Fulton, Ting Wang and 1 more
Article in Genome research, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 2 papers.
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2citing papers in PubMed
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Xiaoyu ZhuoDepartment of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.ORCID 0000-0002-1400-5609
Chad TomlinsonMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA.
Edward A BelterMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA.
Prashant Kumar KuntalaDepartment of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.
Wesley N SaintilnordDepartment of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.
Juan JiangDepartment of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.
Tina LindsayDepartment of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.
Juan F. Macias-VelascoDepartment of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.
Robert S FultonDepartment of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.
Ting WangDepartment of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110, USA; twang@genetics.wustl.edu.ORCID 0000-0002-6800-242X
Human Pangenome Reference Consortium
Funding
Center for Multiomic Human Brain Cell AtlasUM1MH130994 · NIMH · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI MARIA MARGARITA BEHRENS, Joseph R Ecker · 2022 to 2026
$92.4M
WashU-VAI Somatic Mosaicism across Human Tissues (SMaHT) Program Genome Characterization CenterUM1DA058219 · NIDA · WASHINGTON UNIVERSITY · PI Robert Scott Fulton, Hui Shen · 2023 to 2026
$29.1M
The WashU-UCSC-EBI Human Genome Reference Center."U41HG010972 · NHGRI · WASHINGTON UNIVERSITY · PI Ting Wang · 2019 to 2026
$24.9M
WashU-Northwestern Genomic Variation and Function Data and Administrative Coordinating CenterU24HG012070 · NHGRI · WASHINGTON UNIVERSITY · PI Ting Wang, Feng Yue · 2021 to 2026
$9.7M
Center for Integrated Multi-modal and Multi-scale Nucleome ResearchUM1HG011585 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI DULAC, CATHERINE, LEIN, ED · 2020 to 2024
$6.7M
WashU Somatic Mosaicism across Human Tissues (SMaHT) Program Organizational CenterU24NS132103 · NINDS · WASHINGTON UNIVERSITY · PI FULTON, LUCINDA, LAWSON, HEATHER A. · 2023 to 2025
$4.5M
DECODING THE IMPACT OF TRANSPOSABLE ELEMENTS ON GENE REGULATIONR01HG007175 · NHGRI · WASHINGTON UNIVERSITY · PI WANG, TING · 2014 to 2021
$2.7M
Connecting transposable elements and regulatory innovation using ENCODE dataU01HG009391 · NHGRI · WASHINGTON UNIVERSITY · PI COHEN, BARAK A, FESCHOTTE, CEDRIC · 2017 to 2021
$2.4M
The WashU 4DN Network Data Coordination and Integration CenterU01CA200060 · NCI · WASHINGTON UNIVERSITY · PI WANG, TING · 2015 to 2019
Cytosine methylation, a crucial epigenetic modification, plays a vital role in genomic regulation. Leveraging the advancements in long-read sequencing, we investigate the methylation patterns of polymorphic transposable element (TE) insertions of human lymphoblastoid cell lines (LCLs). We validate the high concordance between long-read methylation calls and the conventional whole-genome bisulfite sequencing (WGBS) method. We then aim to establish general rules of TE methylation with our data by addressing three key questions: (1) what is the methylation profile of each insertion; (2) do newly inserted TEs adopt the methylation pattern of their genomic context; and (3) do new TE insertions affect the methylation of their flanking regions. Although most non-TE insertions exhibit DNA methylation patterns consistent with their genomic context, TE insertions are generally highly methylated, exhibiting distinct, class-specific patterns with some variation within TE bodies. A small percentage of
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.
Characterizing cytosine methylation of polymorphic transposable element insertions using the human pangenome resources. · full record | OpenQuestion