Biophysical Society Thematic Meeting| Santa Cruz 2018

Genome Biophysics: Integrating Genomics and Biophysics to Understand Structural and Functional Aspects of Genomes

Tuesday Speaker Abstracts

Understanding Tandem Repeats and Methylation with Long-read Sequencing Shinichi Morishita 1 University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba, Japan We address the problem of understanding previously uncharacterized genomic regions such as centromeres, long gaps, short tandem repeat expansions, diploid methylomes/transcriptomes, and plasmids/phages in metagenomes. With our collaborators, integrating the merits of long read sequencing technologies (PacBio Sequel, ONT nanopore, 10X Chromium, and Hi-C), we found: • We sequenced VC2010, a single uniform strain and a non-mutagenized clonal derivative of N2 populations. We used four state-of-the-art genome assemblers to generate independent assemblies. We found that these assemblers were complementary each other to fill gaps in others, producing a nearly complete genome with two gaps. Most of filled gaps were tandem repeat expansions of length 10K-100Kb that could be closed by nanopore reads. • We compared genome assemblies (~800Mb in size) of three medaka (Japanese killifish) inbred strains that diverged ~18 million years ago. In medaka, centromeric monomers in non-acrocentric chromosomes evolved significantly faster than those in acrocentric chromosomes. • Abnormal expansions of TTTCA and TTTTA repeats in intron 4 of SAMD12 were associated with benign adult familial myoclonic epilepsy (BAFME). Transcriptional abortion was observed at the repeat expansions. • Gene expression is regulated by DNA methylation in two homologous chromosomes separately in personal diploid human genomes. Despite its importance, however, observing DNA methylation in individual homologous chromosomes independently (diploid methylomes) has been technically challenging because homologous chromosomes are extremely highly similar (identity of ~99.9%). We developed a statistical method for uncovering complex diploid methylomes by integrating PacBio and 10X methods. • We processed fecal DNA samples from 12 individuals using PacBio’s single- molecule real-time (SMRT) sequencing, and identified 71 plasmids and 11 phages including crAssphases, half of which were unknown but actually prevalent in several different countries. With SMRT sequencing, we also observed DNA methylation motifs shared between plasmids/phages and their hosts, allowing us to assign plasmids/phages to their hosts.

15