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Topological Data Analysis Generates High-Resolution, Genome-wide Maps of Human Recombination
- Source :
- Cell Systems. 3:83-94
- Publication Year :
- 2016
- Publisher :
- Elsevier BV, 2016.
-
Abstract
- SummaryMeiotic recombination is a fundamental evolutionary process driving diversity in eukaryotes. In mammals, recombination is known to occur preferentially at specific genomic regions. Using topological data analysis (TDA), a branch of applied topology that extracts global features from large data sets, we developed an efficient method for mapping recombination at fine scales. When compared to standard linkage-based methods, TDA can deal with a larger number of SNPs and genomes without incurring prohibitive computational costs. We applied TDA to 1,000 Genomes Project data and constructed high-resolution whole-genome recombination maps of seven human populations. Our analysis shows that recombination is generally under-represented within transcription start sites. However, the binding sites of specific transcription factors are enriched for sites of recombination. These include transcription factors that regulate the expression of meiosis- and gametogenesis-specific genes, cell cycle progression, and differentiation blockage. Additionally, our analysis identifies an enrichment for sites of recombination at repeat-derived loci matched by piwi-interacting RNAs.
- Subjects :
- 0301 basic medicine
Histology
Genetic Linkage
Computational biology
Biology
Polymorphism, Single Nucleotide
Genome
Article
Pathology and Forensic Medicine
03 medical and health sciences
Meiosis
Genetic linkage
Humans
Homologous Recombination
Gene
Genetics
Genome, Human
Chromosome Mapping
Cell Biology
030104 developmental biology
Topological data analysis
Human genome
Homologous recombination
Recombination
Genome-Wide Association Study
Subjects
Details
- ISSN :
- 24054712
- Volume :
- 3
- Database :
- OpenAIRE
- Journal :
- Cell Systems
- Accession number :
- edsair.doi.dedup.....bc2701b92fad14b53d8f609d3974c004