Epigenetic patterns in a complete human genome

Ariel Gershman; Michael E.G. Sauria; Xavi Guitart; Mitchell R. Vollger; Paul W. Hook; Savannah J. Hoyt; Miten Jain; Alaina Shumate; Roham Razaghi; Sergey Koren; Nicolas Altemose; Gina V. Caldas; Glennis A. Logsdon; Arang Rhie; Evan E. Eichler; Michael C. Schatz; Rachel J. O'Neill; Adam M. Phillippy; Karen H. Miga; Winston Timp

doi:10.1126/science.abj5089

Epigenetic patterns in a complete human genome

Ariel Gershman, Michael E.G. Sauria, Xavi Guitart, Mitchell R. Vollger, Paul W. Hook, Savannah J. Hoyt, Miten Jain, Alaina Shumate, Roham Razaghi, Sergey Koren, Nicolas Altemose, Gina V. Caldas, Glennis A. Logsdon, Arang Rhie, Evan E. Eichler, Michael C. Schatz, Rachel J. O'Neill, Adam M. Phillippy, Karen H. Miga, Winston Timp

Whiting School of Engineering

Research output: Contribution to journal › Article › peer-review

Abstract

The completion of a telomere-to-telomere human reference genome, T2T-CHM13, has resolved complex regions of the genome, including repetitive and homologous regions. Here, we present a high-resolution epigenetic study of previously unresolved sequences, representing entire acrocentric chromosome short arms, gene family expansions, and a diverse collection of repeat classes. This resource precisely maps CpG methylation (32.28 million CpGs), DNA accessibility, and short-read datasets (166,058 previously unresolved chromatin immunoprecipitation sequencing peaks) to provide evidence of activity across previously unidentified or corrected genes and reveals clinically relevant paralog-specific regulation. Probing CpG methylation across human centromeres from six diverse individuals generated an estimate of variability in kinetochore localization. This analysis provides a framework with which to investigate the most elusive regions of the human genome, granting insights into epigenetic regulation.

Original language	English (US)
Article number	eabj5089
Journal	Science
Volume	376
Issue number	6588
DOIs	https://doi.org/10.1126/science.abj5089
State	Published - Apr 1 2022

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Gershman, A., Sauria, M. E. G., Guitart, X., Vollger, M. R., Hook, P. W., Hoyt, S. J., Jain, M., Shumate, A., Razaghi, R., Koren, S., Altemose, N., Caldas, G. V., Logsdon, G. A., Rhie, A., Eichler, E. E., Schatz, M. C., O'Neill, R. J., Phillippy, A. M., Miga, K. H., & Timp, W. (2022). Epigenetic patterns in a complete human genome. Science, 376(6588), Article eabj5089. https://doi.org/10.1126/science.abj5089

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abstract = "The completion of a telomere-to-telomere human reference genome, T2T-CHM13, has resolved complex regions of the genome, including repetitive and homologous regions. Here, we present a high-resolution epigenetic study of previously unresolved sequences, representing entire acrocentric chromosome short arms, gene family expansions, and a diverse collection of repeat classes. This resource precisely maps CpG methylation (32.28 million CpGs), DNA accessibility, and short-read datasets (166,058 previously unresolved chromatin immunoprecipitation sequencing peaks) to provide evidence of activity across previously unidentified or corrected genes and reveals clinically relevant paralog-specific regulation. Probing CpG methylation across human centromeres from six diverse individuals generated an estimate of variability in kinetochore localization. This analysis provides a framework with which to investigate the most elusive regions of the human genome, granting insights into epigenetic regulation.",

author = "Ariel Gershman and Sauria, {Michael E.G.} and Xavi Guitart and Vollger, {Mitchell R.} and Hook, {Paul W.} and Hoyt, {Savannah J.} and Miten Jain and Alaina Shumate and Roham Razaghi and Sergey Koren and Nicolas Altemose and Caldas, {Gina V.} and Logsdon, {Glennis A.} and Arang Rhie and Eichler, {Evan E.} and Schatz, {Michael C.} and O'Neill, {Rachel J.} and Phillippy, {Adam M.} and Miga, {Karen H.} and Winston Timp",

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year = "2022",

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doi = "10.1126/science.abj5089",

language = "English (US)",

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AU - Sauria, Michael E.G.

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AU - Hook, Paul W.

AU - Hoyt, Savannah J.

AU - Jain, Miten

AU - Shumate, Alaina

AU - Razaghi, Roham

AU - Koren, Sergey

AU - Altemose, Nicolas

AU - Caldas, Gina V.

AU - Logsdon, Glennis A.

AU - Rhie, Arang

AU - Eichler, Evan E.

AU - Schatz, Michael C.

AU - O'Neill, Rachel J.

AU - Phillippy, Adam M.

AU - Miga, Karen H.

AU - Timp, Winston

PY - 2022/4/1

Y1 - 2022/4/1

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AB - The completion of a telomere-to-telomere human reference genome, T2T-CHM13, has resolved complex regions of the genome, including repetitive and homologous regions. Here, we present a high-resolution epigenetic study of previously unresolved sequences, representing entire acrocentric chromosome short arms, gene family expansions, and a diverse collection of repeat classes. This resource precisely maps CpG methylation (32.28 million CpGs), DNA accessibility, and short-read datasets (166,058 previously unresolved chromatin immunoprecipitation sequencing peaks) to provide evidence of activity across previously unidentified or corrected genes and reveals clinically relevant paralog-specific regulation. Probing CpG methylation across human centromeres from six diverse individuals generated an estimate of variability in kinetochore localization. This analysis provides a framework with which to investigate the most elusive regions of the human genome, granting insights into epigenetic regulation.

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Epigenetic patterns in a complete human genome

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