scholarly journals Consideration of the haplotype diversity at nonallelic homologous recombination hotspots improves the precision of rearrangement breakpoint identification

2017 ◽  
Vol 38 (12) ◽  
pp. 1711-1722 ◽  
Author(s):  
Morten Hillmer ◽  
Anna Summerer ◽  
Victor-Felix Mautner ◽  
Josef Högel ◽  
David N. Cooper ◽  
...  
Keyword(s):  
Homologous Recombination ◽  
Haplotype Diversity ◽  
Recombination Hotspots ◽  
Nonallelic Homologous Recombination ◽  
Rearrangement Breakpoint

scholarly journals The M26 Hotspot of Schizosaccharomyces pombe Stimulates Meiotic Ectopic Recombination and Chromosomal Rearrangements

Genetics ◽  
1998 ◽  
Vol 149 (3) ◽  
pp. 1191-1204 ◽  
Author(s):  
Jeffrey B Virgin ◽  
Jeffrey P Bailey
Keyword(s):  
Homologous Recombination ◽  
Schizosaccharomyces Pombe ◽  
Dna Sequences ◽  
Chromosomal Rearrangements ◽  
Low Frequency ◽  
Repeated Sequences ◽  
Crossing Over ◽  
Ectopic Recombination ◽  
Recombination Hotspots ◽  
Integration Sites

Abstract Homologous recombination is increased during meiosis between DNA sequences at the same chromosomal position (allelic recombination) and at different chromosomal positions (ectopic recombination). Recombination hotspots are important elements in controlling meiotic allelic recombination. We have used artificially dispersed copies of the ade6 gene in Schizosaccharomyces pombe to study hotspot activity in meiotic ectopic recombination. Ectopic recombination was reduced 10–1000-fold relative to allelic recombination, and was similar to the low frequency of ectopic recombination between naturally repeated sequences in S. pombe. The M26 hotspot was active in ectopic recombination in some, but not all, integration sites, with the same pattern of activity and inactivity in ectopic and allelic recombination. Crossing over in ectopic recombination, resulting in chromosomal rearrangements, was associated with 35–60% of recombination events and was stimulated 12-fold by M26. These results suggest overlap in the mechanisms of ectopic and allelic recombination and indicate that hotspots can stimulate chromosomal rearrangements.

scholarly journals Homoeologous exchanges occur through intragenic recombination generating novel transcripts and proteins in wheat and other polyploids

2020 ◽  
pp. 202003505 ◽  
Author(s):  
Zhibin Zhang ◽  
Xiaowan Gou ◽  
Hongwei Xun ◽  
Yao Bian ◽  
Xintong Ma ◽  
...  
Keyword(s):  
Homologous Recombination ◽  
Molecular Mechanisms ◽  
Genome Structure ◽  
Whole Genome Sequence ◽  
Intragenic Recombination ◽  
Protein Fusion ◽  
Coding Regions ◽  
Recombination Hotspots ◽  
Widespread Phenomenon ◽  
Arabidopsis Suecica

Recombination between homeologous chromosomes, also known as homeologous exchange (HE), plays a significant role in shaping genome structure and gene expression in interspecific hybrids and allopolyploids of several plant species. However, the molecular mechanisms that govern HEs are not well understood. Here, we studied HE events in the progeny of a nascent allotetraploid (genome AADD) derived from two diploid progenitors of hexaploid bread wheat using cytological and whole-genome sequence analyses. In total, 37 HEs were identified and HE junctions were mapped precisely. HEs exhibit typical patterns of homologous recombination hotspots, being biased toward low-copy, subtelomeric regions of chromosome arms and showing association with known recombination hotspot motifs. But, strikingly, while homologous recombination preferentially takes place upstream and downstream of coding regions, HEs are highly enriched within gene bodies, giving rise to novel recombinant transcripts, which in turn are predicted to generate new protein fusion variants. To test whether this is a widespread phenomenon, a dataset of high-resolution HE junctions was analyzed for allopolyploid Brassica, rice, Arabidopsis suecica, banana, and peanut. Intragenic recombination and formation of chimeric genes was detected in HEs of all species and was prominent in most of them. HE thus provides a mechanism for evolutionary novelty in transcript and protein sequences in nascent allopolyploids.

scholarly journals A Case of 17q21.31 Microduplication and 7q31.33 Microdeletion, Associated with Developmental Delay, Microcephaly, and Mild Dysmorphic Features

2014 ◽  
Vol 2014 ◽  
pp. 1-6 ◽  
Author(s):  
Adrian Mc Cormack ◽  
Juliet Taylor ◽  
Leah Te Weehi ◽  
Donald R. Love ◽  
Alice M. George
Keyword(s):  
Homologous Recombination ◽  
Developmental Delay ◽  
Microarray Analysis ◽  
Lower Incidence ◽  
Clinical Phenotype ◽  
Microarray Technology ◽  
Dysmorphic Features ◽  
Low Copy Repeats ◽  
Nonallelic Homologous Recombination ◽  
Chromosome Regions

Concurrent cryptic microdeletion and microduplication syndromes have recently started to reveal themselves with the advent of microarray technology. Analysis has shown that low-copy repeats (LCRs) have allowed chromosome regions throughout the genome to become hotspots for nonallelic homologous recombination to take place. Here, we report a case of a 7.5-year-old girl who manifests microcephaly, developmental delay, and mild dysmorphic features. Microarray analysis identified a microduplication in chromosome 17q21.31, which encompasses theCRHR1, MAPT,andKANSL1genes, as well as a microdeletion in chromosome 7q31.33 that is localised within theGRM8gene. To our knowledge this is one of only a few cases of 17q21.31 microduplication. The clinical phenotype of patients with this microduplication is milder than of those carrying the reciprocal microdeletions, and suggests that the lower incidence of the former compared to the latter may be due to underascertainment.

scholarly journals Globozoospermia is mainly due to DPY19L2 deletion via non-allelic homologous recombination involving two recombination hotspots

2012 ◽  
Vol 21 (16) ◽  
pp. 3695-3702 ◽  
Author(s):  
Elias ElInati ◽  
Paul Kuentz ◽  
Claire Redin ◽  
Sara Jaber ◽  
Frauke Vanden Meerschaut ◽  
...  
Keyword(s):  
Homologous Recombination ◽  
Recombination Hotspots

scholarly journals Intrachromosomal mitotic nonallelic homologous recombination is the major molecular mechanism underlying type-2 NF1 deletions

2010 ◽  
Vol 31 (10) ◽  
pp. 1163-1173 ◽  
Author(s):  
Angelika C. Roehl ◽  
Julia Vogt ◽  
Tanja Mussotter ◽  
Antje N. Zickler ◽  
Helene Spöti ◽  
...  
Keyword(s):  
Homologous Recombination ◽  
Molecular Mechanism ◽  
Nonallelic Homologous Recombination

scholarly journals Identification of meiotic recombination through gamete genome reconstruction using whole genome linked-reads

2018 ◽  
Author(s):  
Peng Xu ◽  
Zechen Chong ◽  
Keyword(s):  
Meiotic Recombination ◽  
Haplotype Diversity ◽  
Genomic Analysis ◽  
Genomic Diversity ◽  
Pedigree Information ◽  
Human Populations ◽  
Whole Genome ◽  
Homologous Chromosomes ◽  
Template Strand ◽  
Recombination Hotspots

AbstractMeiotic recombination (MR), which transmits exchanged genetic materials between homologous chromosomes to offspring, plays a crucial role in shaping genomic diversity in eukaryotic organisms. In humans, thousands of meiotic recombination hotspots have been mapped by population genetics approaches. However, direct identification of MR events for individuals is still challenging due to the difficulty in resolving the haplotypes of homologous chromosomes and reconstructing the gamete genome. Whole genome linked-read sequencing (lrWGS) can generate haplotype sequences of mega-base pairs (N50 ~2.5Mb) after computational phasing. However, the haplotype information is still isolated in a large number of fragmented genomic regions and limited by switch errors, impeding its further application in the chromosome-scale analysis. In this study, we developed a tool MRLR (Meiotic Recombination identification by Linked-Read sequencing) for the analysis of individual MR events. By leveraging trio pedigree information with lrWGS haplotypes, our pipeline is sufficient to reconstruct the whole human gamete genome with 99.8% haplotyping accuracy. By analyzing the haplotype exchange between homologous chromosomes, MRLR identified 462 high-resolution MR events in 6 human trio samples from the Genome In A Bottle (GIAB) and the Human Genome Structural Variation Consortium (HGSVC). In three datasets of the HGSVC, our results recapitulated 149 (92%) previously identified high-confident MR events and discovered 85 novel events. About half (40) of the new events are supported by single-cell template strand sequencing (Strand-seq) results. We found that 332 (71.9%) MR events co-localize with recombination hotspots (>10 cM/Mb) in human populations, and MR breakpoint regions are enriched in PRDM9 and DMC1 binding sites. In addition, 48% (221) breakpoint regions were detected inside a gene, indicating these MRs can directly affect the haplotype diversity of genic regions. Taken together, our approach provides new opportunities in the haplotype-based genomic analysis of individual meiotic recombination. The MRLR software is implemented in Perl and is freely available at https://github.com/ChongLab/MRLR.

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