From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

Savannah J. Hoyt; Jessica M. Storer; Gabrielle A. Hartley; Patrick G.S. Grady; Ariel Gershman; Leonardo G. de Lima; Charles Limouse; Reza Halabian; Luke Wojenski; Matias Rodriguez; Nicolas Altemose; Arang Rhie; Leighton J. Core; Jennifer L. Gerton; Wojciech Makalowski; Daniel Olson; Jeb Rosen; Arian F.A. Smit; Aaron F. Straight; Mitchell R. Vollger; Travis J. Wheeler; Michael C. Schatz; Evan E. Eichler; Adam M. Phillippy; Winston Timp; Karen H. Miga; Rachel J. O'Neill

doi:10.1126/science.abk3112

From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

Savannah J. Hoyt, Jessica M. Storer, Gabrielle A. Hartley, Patrick G.S. Grady, Ariel Gershman, Leonardo G. de Lima, Charles Limouse, Reza Halabian, Luke Wojenski, Matias Rodriguez, Nicolas Altemose, Arang Rhie, Leighton J. Core, Jennifer L. Gerton, Wojciech Makalowski, Daniel Olson, Jeb Rosen, Arian F.A. Smit, Aaron F. Straight, Mitchell R. VollgerTravis J. Wheeler, Michael C. Schatz, Evan E. Eichler, Adam M. Phillippy, Winston Timp, Karen H. Miga, Rachel J. O'Neill

Whiting School of Engineering

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

Abstract

Mobile elements and repetitive genomic regions are sources of lineage-specific genomic innovation and uniquely fingerprint individual genomes. Comprehensive analyses of such repeat elements, including those found in more complex regions of the genome, require a complete, linear genome assembly. We present a de novo repeat discovery and annotation of the T2T-CHM13 human reference genome. We identified previously unknown satellite arrays, expanded the catalog of variants and families for repeats and mobile elements, characterized classes of complex composite repeats, and located retroelement transduction events. We detected nascent transcription and delineated CpG methylation profiles to define the structure of transcriptionally active retroelements in humans, including those in centromeres. These data expand our insight into the diversity, distribution, and evolution of repetitive regions that have shaped the human genome.

Original language	English (US)
Article number	eabk3112
Journal	Science
Volume	376
Issue number	6588
DOIs	https://doi.org/10.1126/science.abk3112
State	Published - Apr 1 2022

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Hoyt, S. J., Storer, J. M., Hartley, G. A., Grady, P. G. S., Gershman, A., de Lima, L. G., Limouse, C., Halabian, R., Wojenski, L., Rodriguez, M., Altemose, N., Rhie, A., Core, L. J., Gerton, J. L., Makalowski, W., Olson, D., Rosen, J., Smit, A. F. A., Straight, A. F., ... O'Neill, R. J. (2022). From telomere to telomere: The transcriptional and epigenetic state of human repeat elements. Science, 376(6588), Article eabk3112. https://doi.org/10.1126/science.abk3112

Hoyt, SJ, Storer, JM, Hartley, GA, Grady, PGS, Gershman, A, de Lima, LG, Limouse, C, Halabian, R, Wojenski, L, Rodriguez, M, Altemose, N, Rhie, A, Core, LJ, Gerton, JL, Makalowski, W, Olson, D, Rosen, J, Smit, AFA, Straight, AF, Vollger, MR, Wheeler, TJ, Schatz, MC, Eichler, EE, Phillippy, AM, Timp, W, Miga, KH & O'Neill, RJ 2022, 'From telomere to telomere: The transcriptional and epigenetic state of human repeat elements', Science, vol. 376, no. 6588, eabk3112. https://doi.org/10.1126/science.abk3112

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title = "From telomere to telomere: The transcriptional and epigenetic state of human repeat elements",

abstract = "Mobile elements and repetitive genomic regions are sources of lineage-specific genomic innovation and uniquely fingerprint individual genomes. Comprehensive analyses of such repeat elements, including those found in more complex regions of the genome, require a complete, linear genome assembly. We present a de novo repeat discovery and annotation of the T2T-CHM13 human reference genome. We identified previously unknown satellite arrays, expanded the catalog of variants and families for repeats and mobile elements, characterized classes of complex composite repeats, and located retroelement transduction events. We detected nascent transcription and delineated CpG methylation profiles to define the structure of transcriptionally active retroelements in humans, including those in centromeres. These data expand our insight into the diversity, distribution, and evolution of repetitive regions that have shaped the human genome.",

author = "Hoyt, {Savannah J.} and Storer, {Jessica M.} and Hartley, {Gabrielle A.} and Grady, {Patrick G.S.} and Ariel Gershman and {de Lima}, {Leonardo G.} and Charles Limouse and Reza Halabian and Luke Wojenski and Matias Rodriguez and Nicolas Altemose and Arang Rhie and Core, {Leighton J.} and Gerton, {Jennifer L.} and Wojciech Makalowski and Daniel Olson and Jeb Rosen and Smit, {Arian F.A.} and Straight, {Aaron F.} and Vollger, {Mitchell R.} and Wheeler, {Travis J.} and Schatz, {Michael C.} and Eichler, {Evan E.} and Phillippy, {Adam M.} and Winston Timp and Miga, {Karen H.} and O'Neill, {Rachel J.}",

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doi = "10.1126/science.abk3112",

language = "English (US)",

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T2 - The transcriptional and epigenetic state of human repeat elements

AU - Hoyt, Savannah J.

AU - Storer, Jessica M.

AU - Hartley, Gabrielle A.

AU - Grady, Patrick G.S.

AU - Gershman, Ariel

AU - de Lima, Leonardo G.

AU - Limouse, Charles

AU - Halabian, Reza

AU - Wojenski, Luke

AU - Rodriguez, Matias

AU - Altemose, Nicolas

AU - Rhie, Arang

AU - Core, Leighton J.

AU - Gerton, Jennifer L.

AU - Makalowski, Wojciech

AU - Olson, Daniel

AU - Rosen, Jeb

AU - Smit, Arian F.A.

AU - Straight, Aaron F.

AU - Vollger, Mitchell R.

AU - Wheeler, Travis J.

AU - Schatz, Michael C.

AU - Eichler, Evan E.

AU - Phillippy, Adam M.

AU - Timp, Winston

AU - Miga, Karen H.

AU - O'Neill, Rachel J.

PY - 2022/4/1

Y1 - 2022/4/1

N2 - Mobile elements and repetitive genomic regions are sources of lineage-specific genomic innovation and uniquely fingerprint individual genomes. Comprehensive analyses of such repeat elements, including those found in more complex regions of the genome, require a complete, linear genome assembly. We present a de novo repeat discovery and annotation of the T2T-CHM13 human reference genome. We identified previously unknown satellite arrays, expanded the catalog of variants and families for repeats and mobile elements, characterized classes of complex composite repeats, and located retroelement transduction events. We detected nascent transcription and delineated CpG methylation profiles to define the structure of transcriptionally active retroelements in humans, including those in centromeres. These data expand our insight into the diversity, distribution, and evolution of repetitive regions that have shaped the human genome.

AB - Mobile elements and repetitive genomic regions are sources of lineage-specific genomic innovation and uniquely fingerprint individual genomes. Comprehensive analyses of such repeat elements, including those found in more complex regions of the genome, require a complete, linear genome assembly. We present a de novo repeat discovery and annotation of the T2T-CHM13 human reference genome. We identified previously unknown satellite arrays, expanded the catalog of variants and families for repeats and mobile elements, characterized classes of complex composite repeats, and located retroelement transduction events. We detected nascent transcription and delineated CpG methylation profiles to define the structure of transcriptionally active retroelements in humans, including those in centromeres. These data expand our insight into the diversity, distribution, and evolution of repetitive regions that have shaped the human genome.

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From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

Abstract

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