SSNIP-seq: A simple and rapid method for isolation of single-sperm nucleic acid for high-throughput sequencing

Meiotic crossovers promote correct chromosome segregation and the shuffling of genetic diversity. However, the measurement of crossovers remains challenging, impeding our ability to decipher the molecular mechanisms that are necessary for their formation and regulation. Here we demonstrate a novel repurposing of the single-nucleus Assay for Transposase Accessible Chromatin with sequencing (snATAC-seq) as a simple and high-throughput method to identify and characterise meiotic crossovers from sperm nuclei. We first validate the feasibility of obtaining genome-wide coverage from snATAC-seq by using ATAC-seq on bulk haploid mouse sperm, ensuring adequate variant detection for haplotyping. Subsequently, we adapt droplet-based snATAC-seq for crossover detection, revealing over 25,000 crossovers in F1 hybrid mice. Comparison between wildtype and a hyper-recombinogenicFancm-deficient mutant mouse model confirmed an increase in crossover rates in this genotype, however a distribution which was unchanged. We also find that regions with the highest rate of crossover formation are enriched for DMC1 and PRDM9, with a subset that is further enriched for DMC1 inFancm-deficient mice. Our findings demonstrate the utility of snATAC-seq as a robust and scalable tool for high-throughput crossover detection, offering insights into meiotic crossover dynamics and elucidating the underlying molecular mechanisms. It is possible that the research presented here with snATAC-seq of haploid sperm could be extended into fertility-related diagnostics.

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High throughput sequencing technology and its clinical application in circulating tumor DNA detection in patients with tumors.

Xu,

Zhou,

Zhu

2024

Investigación Clínica

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The high-throughput sequencing (HTS) is now a highly favoured technology in the field of genome research. A distinctive feature of this sequenc-ing method is its data-yielding capability, which is capable of generating more than 100 times than the first-generation Sanger sequencing platform. HTS technology has been widely adopted for its advantages, including high through-put, sensitivity, automaticity, information density and cost-effectiveness. Not only does it help in the treatment and diagnosis of multiple diseases, but it also provides new insights into the research in molecular biology of tumors. Moreover, circulating tumor DNA (ctDNA) tests based on HTS technology are increasingly extensively implemented for clinical purposes. In this review, we will focus on the significant achievements and performances of the HTS, and first-hand data from extensive experience will be summarized and analyzed to discuss the advantages and specifics associated with each sequencing system and further summarize the characteristics of their clinical applications.

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SSNIP-seq: A simple and rapid method for isolation of single-sperm nucleic acid for high-throughput sequencing

Cited by 3 publications

References 16 publications

Fancm has dual roles in the limiting of meiotic crossovers and germ cell maintenance in mammals

Fancm has dual roles in the limiting of meiotic crossovers and germ cell maintenance in mammals

A high-resolution meiotic crossover map from single-nucleus ATAC-seq reveals insights into the recombination landscape in mammalian sperm

High throughput sequencing technology and its clinical application in circulating tumor DNA detection in patients with tumors.

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