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

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…

• NS
  National Science Foundation

  Awards: 1732253, 1627442, 1643825, 1613806, P20GM103546, DBI-1627442, IOS-1732253, IOS-1758800, 1758800
• CI
  Connecticut Innovations
• SI
  Stowers Institute for Medical Research
• UO
  University of Montana
• WW
  Westfälische Wilhelms-Universität Münster
• NI
  National Institutes of Health

  Awards: R24DK106766, U01HG010971, 1R01HG011274-01, P20GM103546, R01HG009190, R21HG010548-01, R01GM132600, U24HG006620, R01HG010169, U24HG010263, U01CA253481, R01HG002385, R01GM123312
• SR
  Stanford Research Computing Center, Stanford University
• NH
  National Human Genome Research Institute

  Awards: U01HG010971, 1R01HG011274, R01HG009190, U24HG006620, R01HG002385, 1R01HG011274-01, U24HG010263