Dyads of GGC and GCC form hotspot colonies that coincide with the evolution of human and other great apes
Abstract Background GGC and GCC short tandem repeats (STRs) are of various evolutionary, biological, and pathological implications. However, the fundamental two-repeats (dyads) of these STRs are widely unexplored. Results On a genome-wide scale, we mapped (GGC)2 and (GCC)2 dyads in human, and found...
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| Format: | Article |
| Language: | English |
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BMC
2024-02-01
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| Series: | BMC Genomic Data |
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| Online Access: | https://doi.org/10.1186/s12863-024-01207-z |
| _version_ | 1797273026012643328 |
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| author | M. Arabfard N. Tajeddin S. Alizadeh M. Salesi H. Bayat H. R. Khorram Khorshid S. Khamse A. Delbari M. Ohadi |
| author_facet | M. Arabfard N. Tajeddin S. Alizadeh M. Salesi H. Bayat H. R. Khorram Khorshid S. Khamse A. Delbari M. Ohadi |
| author_sort | M. Arabfard |
| collection | DOAJ |
| description | Abstract Background GGC and GCC short tandem repeats (STRs) are of various evolutionary, biological, and pathological implications. However, the fundamental two-repeats (dyads) of these STRs are widely unexplored. Results On a genome-wide scale, we mapped (GGC)2 and (GCC)2 dyads in human, and found monumental colonies (distance between each dyad < 500 bp) of extraordinary density, and in some instances periodicity. The largest (GCC)2 and (GGC)2 colonies were intergenic, homogeneous, and human-specific, consisting of 219 (GCC)2 on chromosome 2 (probability < 1.545E-219) and 70 (GGC)2 on chromosome 9 (probability = 1.809E-148). We also found that several colonies were shared in other great apes, and directionally increased in density and complexity in human, such as a colony of 99 (GCC)2 on chromosome 20, that specifically expanded in great apes, and reached maximum complexity in human (probability 1.545E-220). Numerous other colonies of evolutionary relevance in human were detected in other largely overlooked regions of the genome, such as chromosome Y and pseudogenes. Several of the genes containing or nearest to those colonies were divergently expressed in human. Conclusion In conclusion, (GCC)2 and (GGC)2 form unprecedented genomic colonies that coincide with the evolution of human and other great apes. The extent of the genomic rearrangements leading to those colonies support overlooked recombination hotspots, shared across great apes. The identified colonies deserve to be studied in mechanistic, evolutionary, and functional platforms. |
| first_indexed | 2024-03-07T14:38:39Z |
| format | Article |
| id | doaj.art-38cf3407de4c4428b8b25ba9550bbb8c |
| institution | Directory Open Access Journal |
| issn | 2730-6844 |
| language | English |
| last_indexed | 2024-03-07T14:38:39Z |
| publishDate | 2024-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomic Data |
| spelling | doaj.art-38cf3407de4c4428b8b25ba9550bbb8c2024-03-05T20:29:43ZengBMCBMC Genomic Data2730-68442024-02-0125111110.1186/s12863-024-01207-zDyads of GGC and GCC form hotspot colonies that coincide with the evolution of human and other great apesM. Arabfard0N. Tajeddin1S. Alizadeh2M. Salesi3H. Bayat4H. R. Khorram Khorshid5S. Khamse6A. Delbari7M. Ohadi8Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical SciencesIranian Research Center on Aging, University of Social Welfare and Rehabilitation SciencesIranian Research Center on Aging, University of Social Welfare and Rehabilitation SciencesChemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical SciencesIranian Research Center on Aging, University of Social Welfare and Rehabilitation SciencesPersonalized Medicine and Genometabolomics Research Center, Hope Generation FoundationIranian Research Center on Aging, University of Social Welfare and Rehabilitation SciencesIranian Research Center on Aging, University of Social Welfare and Rehabilitation SciencesIranian Research Center on Aging, University of Social Welfare and Rehabilitation SciencesAbstract Background GGC and GCC short tandem repeats (STRs) are of various evolutionary, biological, and pathological implications. However, the fundamental two-repeats (dyads) of these STRs are widely unexplored. Results On a genome-wide scale, we mapped (GGC)2 and (GCC)2 dyads in human, and found monumental colonies (distance between each dyad < 500 bp) of extraordinary density, and in some instances periodicity. The largest (GCC)2 and (GGC)2 colonies were intergenic, homogeneous, and human-specific, consisting of 219 (GCC)2 on chromosome 2 (probability < 1.545E-219) and 70 (GGC)2 on chromosome 9 (probability = 1.809E-148). We also found that several colonies were shared in other great apes, and directionally increased in density and complexity in human, such as a colony of 99 (GCC)2 on chromosome 20, that specifically expanded in great apes, and reached maximum complexity in human (probability 1.545E-220). Numerous other colonies of evolutionary relevance in human were detected in other largely overlooked regions of the genome, such as chromosome Y and pseudogenes. Several of the genes containing or nearest to those colonies were divergently expressed in human. Conclusion In conclusion, (GCC)2 and (GGC)2 form unprecedented genomic colonies that coincide with the evolution of human and other great apes. The extent of the genomic rearrangements leading to those colonies support overlooked recombination hotspots, shared across great apes. The identified colonies deserve to be studied in mechanistic, evolutionary, and functional platforms.https://doi.org/10.1186/s12863-024-01207-zHumanGreat ape(GGC)2(GCC)2ColonyRecombination hotspot |
| spellingShingle | M. Arabfard N. Tajeddin S. Alizadeh M. Salesi H. Bayat H. R. Khorram Khorshid S. Khamse A. Delbari M. Ohadi Dyads of GGC and GCC form hotspot colonies that coincide with the evolution of human and other great apes BMC Genomic Data Human Great ape (GGC)2 (GCC)2 Colony Recombination hotspot |
| title | Dyads of GGC and GCC form hotspot colonies that coincide with the evolution of human and other great apes |
| title_full | Dyads of GGC and GCC form hotspot colonies that coincide with the evolution of human and other great apes |
| title_fullStr | Dyads of GGC and GCC form hotspot colonies that coincide with the evolution of human and other great apes |
| title_full_unstemmed | Dyads of GGC and GCC form hotspot colonies that coincide with the evolution of human and other great apes |
| title_short | Dyads of GGC and GCC form hotspot colonies that coincide with the evolution of human and other great apes |
| title_sort | dyads of ggc and gcc form hotspot colonies that coincide with the evolution of human and other great apes |
| topic | Human Great ape (GGC)2 (GCC)2 Colony Recombination hotspot |
| url | https://doi.org/10.1186/s12863-024-01207-z |
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