Using precision nuclear run-on sequencing (PRO-seq) and CpG methylated sites generated from Oxford Nanopore Technologies long-read sequencing data, we assessed RNA polymerase engagement across retroelements genome-wide, revealing correlations between nascent transcription, sequence divergence, CpG density, and methylation. We discovered 43 previously unknown repeats and repeat variants and characterized 19 complex, composite repetitive structures, which often carry genes, across T2T-CHM13. Using this method, we developed an updated catalog of human repetitive sequences and refined previous repeat annotations. We implemented a comprehensive repeat annotation workflow using previously known human repeats and de novo repeat modeling followed by manual curation, including assessing overlaps with gene annotations, segmental duplications, tandem repeats, and annotated repeats. O’Neill +24 authors +22 authors +17 authors fewer Authors Info & Affiliations Gerton, Wojciech Makalowski, Daniel Olson, Jeb Rosen, Arian F. de Lima, Charles Limouse, Reza Halabian, Luke Wojenski, , Matias Rodriguez, Nicolas Altemose, Arang Rhie, Leighton J.
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