Global repeat map algorithm (GRM) reveals differences in alpha satellite number of tandem and higher order repeats (HORs) in human, Neanderthal and chimpanzee genomes – novel tandem repeat database

Vlahović, Ines; Glunčić, Matko; Dekanić, Krešimir; Mršić, Leo; Jerković, Hrvoje; Martinjak, Ivica; Paar, V.

doi:10.23919/mipro48935.2020.9245278

Cited by 6 publications

(4 citation statements)

References 12 publications

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“…NBPF HORs were identi ed in the NCBI assembly (2023) of human, pan troglodytes and Neanderthal genomes using the GRM algorithm [53][54][55] . The GRM algorithm is an e cient and robust method speci cally designed to detect and analyze very large repeat units, such as HORs, within genomic sequences.…”

Section: Methodsmentioning

confidence: 99%

Tandemly repeated NBPF 3mer HOR copies (Olduvai triplets) in Neanderthal AltaiNea.hg19 assembly and two novel tandem arrays of NBPF 3mer HOR repeats in complete T2T-CHM13 assembly of human chromosome 1

Glunčić

Vlahović

Rosandić

et al. 2023

Preprint

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It is known that the ~ 1.6 kb NBPF repeats are human specific and contributing to cognitive capabilities, with increasing frequency in higher order repeat 3mer HORs (Olduvai triplets). From chimpanzee to modern human there is a discontinuous jump from 0 to ~ 50 tandemly organized 3mer HORs. Here we investigate the structure of NBPF 3mer HORs in the Neanderthal genome assembly of Pääbo and collaborators, comparing it to the results obtained for human hg38.p14 chromosome 1. Our findings reveal corresponding NBPF 3mer HOR arrays in Neanderthals with slightly different monomer structures and numbers of HOR copies compared to humans. Additionally, we compute the NBPF 3mer HOR pattern for the complete telomere-to-telomere human genome assembly (T2T-CHM13) by Miga and collaborators, identifying two novel tandem arrays of NBPF 3mer HOR repeats with 5 and 9 NBPF 3mer HOR copies. We hypothesize that these arrays correspond to novel NBPF genes (here referred to as NBPFA1 and NBPFA2). Further improving the quality of the Neanderthal genome using T2T-CHM13 as a reference would be of great interest in determining the presence of such distant novel NBPF genes in the Neanderthal genome and enhancing our understanding of human evolution.

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Section: Methodsmentioning

confidence: 99%

Tandemly repeated NBPF 3mer HOR copies (Olduvai triplets) in Neanderthal AltaiNea.hg19 assembly and two novel tandem arrays of NBPF 3mer HOR repeats in complete T2T-CHM13 assembly of human chromosome 1

Glunčić

Vlahović

Rosandić

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…The NBPF HORs were identified in the NCBI assembly (2023) of human, pan troglodytes and Neanderthal genomes using the GRM algorithm (Gluncic M & Paar V, 2013, Gluncic M et al, 2019, Vlahović I et al, 2020. The GRM algorithm is an efficient and robust method specifically designed to detect and analyze very large repeat units, such as HORs, within genomic sequences.…”

Section: Methodsmentioning

confidence: 99%

Tandemly repeated NBPF 3mer HOR copies (Olduvai triplets) in Neanderthal AltaiNea.hg19 assembly and two novel tandem arrays of NBPF 3mer HOR repeats in complete T2T-CHM13 assembly of human chromosome 1

Glunčić

Vlahović

Rosandić

et al. 2023

Preprint

View full text Add to dashboard Cite

It is known that the ~1.6 kb NBPF repeats are human specific and contributing to cognitive capabilities, with increasing frequency in higher order repeat 3mer HORs (Olduvai triplets). From chimpanzee to modern human there is a discontinuous jump from 0 to ~50 tandemly organized 3mer HORs. Here we investigate the structure of NBPF 3mer HORs in the Neanderthal genome assembly, comparing it to the results obtained for human hg38 chromosome 1. Our findings reveal corresponding NBPF 3mer HOR arrays in Neanderthals with slightly different monomer structures and numbers of HOR copies compared to humans. Additionally, we compute the NBPF 3mer HOR pattern for the human genome assembly T2T-CHM13, identifying two novel tandem arrays of NBPF 3mer HOR repeats with 5 and 9 NBPF 3mer HOR copies. We hypothesize that these arrays correspond to novel NBPF genes (here referred to as NBPFA1 and NBPFA2). Further improving the quality of the Neanderthal genome using T2T-CHM13 as a reference would be of great interest in determining the presence of such distant novel NBPF genes in the Neanderthal genome and enhancing our understanding of human evolution.

show abstract

“…NBPF HORs are identified in NCBI assembly (2022) of human and nonhuman primate genomes ( https://www.ncbi.nlm.nih.gov/genome/ ), using GRM algorithm. GRM algorithm is efficient and robust method convenient to identify and study in a given genomic sequence very large repeat units, like HORs ( Paar et al, 2011 ; Gluncic & Paar, 2013 ; Gluncic et al, 2019 ; Vlahović et al, 2020 ). The computational noise in detecting repeats increases with increased length and/or complexity of HOR repeat unit, which can mask some peaks corresponding to HOR copies.…”

Section: Methodsmentioning

confidence: 99%

“…An efficient and robust computational tool to identify large HOR copies, as for example, α satellite HORs, is the global repeat map (GRM) algorithm ( Paar et al, 2011 ; Gluncic & Paar, 2013 ; Gluncic et al, 2019 ; Vlahović et al, 2020 ). HOR method to determine α satellite repeat structure is based on identifying α satellite HOR copies in a given sequence in the first step, and in the second step deducing α satellite monomers from the HOR structure.…”

Section: Introductionmentioning

confidence: 99%

Tandemly repeated NBPF HOR copies (Olduvai triplets): Possible impact on human brain evolution

et al. 2022

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Previously it was found that the neuroblastoma breakpoint family (NBPF) gene repeat units of ∼1.6 kb have an important role in human brain evolution and function. The higher order organization of these repeat units has been discovered by both methods, the higher order repeat (HOR)-searching method and the HLS searching method. Using the HOR searching method with global repeat map algorithm, here we identified the tandemly organized NBPF HORs in the human and nonhuman primate NCBI reference genomes. We identified 50 tandemly organized canonical 3mer NBPF HOR copies (Olduvai triplets), but none in nonhuman primates chimpanzee, gorilla, orangutan, and Rhesus macaque. This discontinuous jump in tandemly organized HOR copy number is in sharp contrast to the known gradual increase in the number of Olduvai domains (NBPF monomers) from nonhuman primates to human, especially from ∼138 in chimpanzee to ∼300 in human genome. Using the same global repeat map algorithm method we have also determined the 3mer tandems of canonical 3mer HOR copies in 20 randomly chosen human genomes (10 male and 10 female). In all cases, we found the same 3mer HOR copy numbers as in the case of the reference human genome, with no mutation. On the other hand, some point mutations with respect to reference genome are found for some NBPF monomers which are not tandemly organized in canonical HORs.

show abstract

Global repeat map algorithm (GRM) reveals differences in alpha satellite number of tandem and higher order repeats (HORs) in human, Neanderthal and chimpanzee genomes – novel tandem repeat database

Cited by 6 publications

References 12 publications

Tandemly repeated NBPF 3mer HOR copies (Olduvai triplets) in Neanderthal AltaiNea.hg19 assembly and two novel tandem arrays of NBPF 3mer HOR repeats in complete T2T-CHM13 assembly of human chromosome 1

Tandemly repeated NBPF 3mer HOR copies (Olduvai triplets) in Neanderthal AltaiNea.hg19 assembly and two novel tandem arrays of NBPF 3mer HOR repeats in complete T2T-CHM13 assembly of human chromosome 1

Tandemly repeated NBPF 3mer HOR copies (Olduvai triplets) in Neanderthal AltaiNea.hg19 assembly and two novel tandem arrays of NBPF 3mer HOR repeats in complete T2T-CHM13 assembly of human chromosome 1

Tandemly repeated NBPF HOR copies (Olduvai triplets): Possible impact on human brain evolution

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