High-throughput mapping of meiotic crossover and chromosome mis-segregation events in interspecific hybrid mice

Abstract

We developed "sci-LIANTI", a high-throughput, high-coverage single-cell DNA sequencing method that combines single-cell combinatorial indexing ("sci") and linear amplification via transposon insertion ("LIANTI"). To characterize rare chromosome missegregation events in male meiosis and their relationship to the landscape of meiotic crossovers, we applied sci-LIANTI to profile the genomes of 6,928 sperm and sperm precursors from 20 infertile, interspecific F1 male mice. From 1,663 haploid and 292 diploid cells, we mapped 24,672 crossover events and identified genomic and epigenomic contexts that influence crossover hotness. Surprisingly, we observed frequent mitotic chromosome segregation during meiosis. Moreover, segregation during meiosis in individual cells was highly biased towards either mitotic or meiotic events. We anticipate that sci-LIANTI can be applied to fully 25 characterize various recombination landscapes, as well as to other fields requiring highthroughput, high-coverage single-cell genome sequencing.One Sentence Summary: Single-cell genome sequencing maps crossover and non-meiotic chromosome segregation during spermatogenesis in interspecific hybrid mice. 30

Characterizing the temporal dynamics of gene expression in single cells with sci-fate

“…Finally, trajectory 3 corresponds to cells that transition from G1 to either S phase or G1 arrest 23 over the course of the experiment. The inference of G1 arrest subsequent to DEX treatment is consistent 24 with the dynamics of cell state proportions in this experiment as well as with previous research 56,57 . Inferred single cell state transition links recapitulate expected dynamics 1 2 We next sought to evaluate whether the distribution of cell state transitions inferred by sci-fate are 3 consistent with the expected dynamics.…”

“…Joint profiling of the total and newly synthesized transcriptome in cortisol response 24 Cortisol influences the activity of almost every cell in the body, regulating genes involved in diverse 25 processes including development, metabolism and immune response 26 . To investigate the dynamics of 26 cortisol response, we applied sci-fate to an in vitro model wherein dexamethasone (DEX), a synthetic 27 mimic of cortisol, activates glucocorticoid receptor (GR), which binds to thousands of locations across 28 the genome and significantly alters cell state within a rapid timeframe [27][28][29][30] .…”

“…23 1e, right). Interestingly, with this joint approach, the cells corresponding to two clusters defined by 24 analysis of whole transcriptomes (clusters 1 & 4 in Fig. 1f) each split into two groups (Fig.…”

“…Each sci-fate transcriptome in this dataset consists of two components --the newly 22 synthesized transcriptome, whose detection rate we are hoping to estimate, and the 'leftover' 23 transcriptome, i.e. transcripts that were present at the onset of 4SU labeling, minus any degradation over 24 the course of the two hours. Comparing the 0 hr (untreated) and 2 hr DEX treatment groups, we expect 25 that their leftover transcriptomes should be identical, as should sci-fate's detection rate for newly 26 synthesized transcripts.…”

Inverted meiosis and the evolution of sex by loss of complementation

“…Suppression of the second division requires further analysis because, in inverted meiosis, there is evidence for a bias in favour of z segregation (because chromatids pair with each other more likely than with the sister chromatid with which there was no chiasma, perhaps because they are in close proximity and remain linked at their termini by chromatin threads (Cabral et al, , Marques, Schubert, Houben, & Pedrosa‐Harand, )). A recent study (Yin et al, ) shows that in inverted meiosis in mouse the z type is much more likely (up to two orders of magnitude) than the x type.…”