Minimal repeats are ubiquitous sites of crossover and recombination across the human genome
Bibliographic record
Abstract
BACKGROUND: Crossover and recombination create genetic diversity that reflects differences in the DNA sequences of different organisms. We previously reported that trinucleotide 2-repeat units (T2Us) are sites of crossover and consequent colonization, which are massively spread and shared across the genomes of human and several other primates. These sites underscore the preference for AT- over CG-rich sequences as recombination sites. METHODS: We extended our study to simpler repeat cores, consisting of AT/TA and CG/GC dinucleotides. An algorithm was designed to extract the genomic regions with a higher probability of recombination. To this end, we hypothesized that dinucleotide 3-repeat units (D3Us) are, at least in part, the basic overlapping units resulting from unequal crossover between dinucleotide 2-repeat units (D2Us). We mapped TATATA, ATATAT, CGCGCG, and GCGCGC across the human genome and analyzed their colonization (the distance between consecutive D3Us < 500 bp). We also studied several randomly selected colonies of diverse sizes in up to 100 vertebrate species using the UCSC and Ensembl Genome Browsers. RESULTS: We found approximately four million AT/TA D3Us and one hundred thousand CG/GC D3Us across the human genome. The majority of these D3Us resided in colonies and spread ubiquitously along all chromosomes. AT/TA colonies were significantly larger and more intricate than CG/GC colonies. D2Us and D3Us were the primary sites of unequal crossover in these colonies, resulting in the emergence of primary recombinants (overlapping recombinants of D2Us/D3Us) and a vast repertoire of secondary recombinants (non-overlapping recombinants of D2Us/D3Us) and eventually, colonies of enormous intricacy and significance based on Poisson distribution. Intricacy was consistently detected across diverse colony sizes, from the smallest to the largest. The randomly selected colonies that were studied in other species were specific to or of their largest size in human. CONCLUSION: We report ubiquitous and intricate colonies, in which D2Us and D3Us were the primary sites of crossover and recombination. It is plausible that minimal repeats such as D2Us, D3Us, and T2Us mark recombination as a ubiquitous rule across the human genome. This phenomenon is likely to transform our understanding of the magnitude, biological, and evolutionary outcomes of crossover and recombination.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.004 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".