"Mirror reads" in Hi-C data

Abstract

The detailed analysis of chromatin structure has been enabled due to rapid development of chromosome conformation capture techniques. One of the most popular and widespread variations is high throughput conformation capture, or Hi-C, based on paired-end sequencing. Although a standard data analysis protocol exists to process Hi-C output, some results are still controversially interpreted, for example pairs of reads that are mapped to the same strand of the same restriction fragment. Here we propose the name "mirror reads" for these cases and investigate possible biological and methodological context of their emergence. We test multiple hypotheses of mirror reads origin, such as genome duplications, replication fork, cohesion of sister chromatids, and homologous chromosome pairing. The current work demonstrates the association of mirror reads with the presence of homologous chromosomes in the nuclei, and homologous pairing. The results support biological relevance of mirror reads.

Sub-nucleosomal Genome Structure Reveals Distinct Nucleosome Folding Motifs

“…For conventional Hi-C data, it was proposed that ''mirror reads'' (Galitsyna et al, 2017), which represented pairs of reads mapped to the same strand of the same fragment, was considered to suggest the presence of homologous chromosomes in the same nuclei at S and M phase. But in Hi-CO, such mirror reads, which were analyzed as the N/N tandem reads, can also be caused by self-ligation between different DNA fragments within the same nucleosome caused by the MNase endonuclease activity.…”

Pairtools: From sequencing data to chromosome contacts

“…Pairtools scaling calculates strand-oriented scalings that can be used for by-product quality control and filtration (Fig 2e). After the ligation step, some fragments can form a valid pair or produce unwanted 3C+ by-products, such as self-circles, dangling ends (unligated DNA) (S2c Fig) , and mirror reads (potential PCR artifacts) [43]. A short-range peak in divergent orientation is a sign of self-circled DNA, while a short-range peak in convergent orientation is a sign of dangling ends (Figs 2e and S2d) [41,42].…”

Pairtools: from sequencing data to chromosome contacts

“…Pairs in self-circles and dangling ends are located on the same restriction site, either in divergent (self-circles) or convergent (dangling ends) orientation. c. Counts of pairs are categorized into four groups: regular pairs, dangling ends, self circles, and mirror pairs 47 for a test sample of 11 million pairs, by restriction enzyme annotation (columns) and convergence distance (rows). For restriction enzyme annotation, we considered dangling ends to be mapped to the same restriction fragment in the convergent orientation, self circles in the divergent orientation, and mirror pairs in the same orientation.…”

“…Pairtools scaling calculates strand-oriented scalings that can be used for by-product quality control and filtration (Figure 3e). After the ligation step, some fragments can form a valid pair or produce unwanted 3C+ by-products, such as self-circles, dangling ends (unligated DNA) (Supplementary Figure 2c), and mirror reads (potential PCR artifacts) 47 . A short-range peak in divergent orientation is a sign of self-circled DNA, while a short-range peak in convergent orientation is a sign of dangling ends (Figure 3e, Supplementary Figure 2d) 45 46 .…”