Characterizing meiotic chromosomes' structure and pairing using a designer sequence optimized for Hi‐C

Abstract

In chromosome conformation capture experiments (Hi‐C), the accuracy with which contacts are detected varies due to the uneven distribution of restriction sites along genomes. In addition, repeated sequences or homologous regions remain indistinguishable because of the ambiguities they introduce during the alignment of the sequencing reads. We addressed both limitations by designing and engineering 144 kb of a yeast chromosome with regularly spaced restriction sites (Syn‐HiC design). In the Syn‐HiC region, Hi‐C signal‐to‐noise ratio is enhanced and can be used to measure the shape of an unbiased distribution of contact frequencies, allowing to propose a robust definition of a Hi‐C experiment resolution. The redesigned region is also distinguishable from its native homologous counterpart in an otherwise isogenic diploid strain. As a proof of principle, we tracked homologous chromosomes during meiotic prophase in synchronized and pachytene‐arrested cells and captured important features of their spatial reorganization, such as chromatin restructuration into arrays of Rec8‐delimited loops, centromere declustering, individualization, and pairing. Overall, we illustrate the promises held by redesigning genomic regions to explore complex biological questions.

PDS5 proteins regulate the length of axial elements and telomere integrity during male mouse meiosis

“…Since SC length is restored in Smc1β -/-Sycp3 -/double mutant spermatocytes, cohesin might in fact counteract chromosome axis compaction promoted by the SC (Novak et al, 2008). Whether cohesin complexes mediating cohesion and those driving loop extrusion are the same or the coordination between them remains an open question (Muller et al, 2018;Holzmann 2019). In any case, PDS5 regulates both activities of cohesin, and it is therefore not surprising that its deletion results in defects similar to those reported for meiotic cohesin mutants.…”

Detecting chromatin interactions along and between sister chromatids with SisterC

“…Cohesin mediated interactions along chromosome arms have been identified by Hi-C before 7,23,24 , however prior to SisterC it has not been possible to differentiate between interactions between and along sister chromatids. When we plot all inter-sister interactions (figure 4a) and intra-sister interactions (figure 4b) at and around individual cohesin sites (far left panels), we see that cohesin sites preferentially interact with sites located at least 5kb away on either side.…”

A major role for Eco1 in regulating cohesin-mediated mitotic chromosome folding

“…1b). Second, we computed the average contact signal of 80kb windows centred on contact between each possible pair of Scc1 enrichment sites 14 , separated by increasing distances (5kb to 165kb; 20kb steps) and divided it by the average contact map between random regions separated by similar distances (Methods, 15,16 ).…”

“…Contact probability as a function of genomic distance P(s) was determined as described 16 . Intra-chromosomal pairs of reads were selected and partitioned by chromosome arms.…”