Structural variations of subterminal satellite blocks and their source mechanisms as inferred from the meiotic configurations of chimpanzee chromosome termini

Hirai, Hirohisa; Hirai, Yohei; Udono, Toshifumi; Matsubayashi, Kiyoaki; Tosi, Anthony J.; Koga, Akihiko

doi:10.1007/s10577-019-09615-z

Cited by 5 publications

(8 citation statements)

References 44 publications

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“…Those investigations found that gorillas have only two pairs of loci with rDNA arrays, while the other hominoids have considerably more (eight or five pairs), as mentioned earlier [19,26]. Interestingly, our recent research [25] demonstrated that gorillas have StSat loci at one or both ends of all chromosomes, but none of the StSat loci colocalize with rDNA arrays in somatic metaphase chromosomes. This strongly suggests the following.…”

Section: Relationship Of Rdna and Other Repeat Arrayssupporting

confidence: 60%

“…Cells 2020, 9, x 5 of 13 in studies of somatic chromosomes in humans and apes [16,19,[39][40][41][42][43][44]. The existence of nonassociation (exclusion) systems between specific repeat arrays has also recently been found in studies of meiotic cell division [25]. The RA//StSat exclusion and the RA//URA exclusion, both being demonstrated in Figure 1, are representatives of such systems.…”

Section: Manifestations Of Chromosomal Configuration In Meiotic Prophasementioning

confidence: 79%

“…In one example, we observed the chromosomal configuration of subterminal satellites (StSat)-a repeat array that is specific to African apes-and inferred their evolutionary aspects together with those of rDNA arrays [25]. Other investigations have discovered the variability of rDNA localization and NOR loci in the great apes (orangutans, gorillas, chimpanzees, and bonobo), and humans [25][26][27]. Those investigations found that gorillas have only two pairs of loci with rDNA arrays, while the other hominoids have considerably more (eight or five pairs), as mentioned earlier [19,26].…”

Section: Relationship Of Rdna and Other Repeat Arraysmentioning

confidence: 99%

“…Cells 2020, 9, x 3 of 13 chromosomal configuration of subterminal satellites (StSat)-a repeat array that is specific to African apes-and inferred their evolutionary aspects together with those of rDNA arrays [25]. Other investigations have discovered the variability of rDNA localization and NOR loci in the great apes (orangutans, gorillas, chimpanzees, and bonobo), and humans [25][26][27].…”

Section: Relationship Of Rdna and Other Repeat Arraysmentioning

confidence: 99%

“…The regulation of genomic dispersion by the molecular effect is also implicated in studies of rDNA localization in orangutans, which have eight pairs of NORs when compared to the other great apes, which have locations on only five (chimpanzees & bonobos) and two (gorilla) chromosome pairs [19]. Interestingly, orangutans (Asian great apes) have no StSat blocks, whereas these arrays are extensive in all of the African great apes [25,49]. This situation suggests that the genomic dispersion of rDNA is limited in African apes by molecular effect: in this case, non-affinity with StSat.…”

Section: Conditions Of the "Molecular Effect" System Of Genomic Dispementioning

confidence: 99%

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Chromosome Dynamics Regulating Genomic Dispersion and Alteration of Nucleolus Organizer Regions (NORs)

Hirai

2020

Cells

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The nucleolus organizer regions (NORs) demonstrate differences in genomic dispersion and transcriptional activity among all organisms. I postulate that such differences stem from distinct genomic structures and their interactions from chromosome observations using fluorescence in situ hybridization and silver nitrate staining methods. Examples in primates and Australian bulldog ants indicate that chromosomal features indeed play a significant role in determining the properties of NORs. In primates, rDNA arrays that are located on the short arm of acrocentrics frequently form reciprocal associations ("affinity"), but they lack such associations ("non-affinity") with other repeat arrays-a binary molecular effect. These "rules" of affinity vs. non-affinity are extrapolated from the chromosomal configurations of meiotic prophase. In bulldog ants, genomic dispersions of rDNA loci expand much more widely following an increase in the number of acrocentric chromosomes formed by centric fission. Affinity appears to be a significantly greater force: associations likely form among rDNA and heterochromatin arrays of acrocentrics-thus, more acrocentrics bring about more rDNA loci. The specific interactions among NOR-related genome structures remain unclear and require further investigation. Here, I propose that there are limited and non-limited genomic dispersion systems that result from genomic affinity rules, inducing specific chromosomal configurations that are related to NORs.

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Section: Relationship Of Rdna and Other Repeat Arrayssupporting

confidence: 60%

Section: Manifestations Of Chromosomal Configuration In Meiotic Prophasementioning

confidence: 79%

Section: Relationship Of Rdna and Other Repeat Arraysmentioning

confidence: 99%

Section: Relationship Of Rdna and Other Repeat Arraysmentioning

confidence: 99%

Section: Conditions Of the "Molecular Effect" System Of Genomic Dispementioning

confidence: 99%

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Chromosome Dynamics Regulating Genomic Dispersion and Alteration of Nucleolus Organizer Regions (NORs)

Hirai

2020

Cells

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Complete sequencing of ape genomes

Yoo,

Rhie,

Hebbar

et al. 2024

Preprint

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We present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan, and siamang. We achieve chromosome-level contiguity with unparalleled sequence accuracy (<1 error in 500,000 base pairs), completely sequencing 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, providing more in-depth evolutionary insights. Comparative analyses, including human, allow us to investigate the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference. This includes newly minted gene families within lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes, and subterminal heterochromatin. This resource should serve as a definitive baseline for all future evolutionary studies of humans and our closest living ape relatives.

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Incomplete lineage sorting of segmental duplications defines the human chromosome 2 fusion site early during African great ape speciation

Jiang,

Zhang,

Yang

et al. 2024

Preprint

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All great apes differ karyotypically from humans due to the fusion of chromosomes 2a and 2b, resulting in human chromosome 2. Yet, the structure, function, and evolutionary history of the genomic regions associated with this fusion remain poorly understood. Here, we analyze finished telomere-to-telomere chromosomes in great apes and macaques to show that the fusion was associated with multiple pericentric inversions, segmental duplications (SDs), and the rapid turnover of subterminal repetitive DNA. We characterized the fusion site at single-base-pair resolution and identified three distinct SDs that originated more than 5 million years ago. These three distinct SDs were differentially distributed among African great apes as a result of incomplete lineage sorting (ILS) and lineage-specific duplication. Most conspicuously, one of these SDs shares homology to a hypomethylated SD spacer sequence present in hundreds of copies in the subterminal heterochromatin of chimpanzees and bonobos. The fusion in human was accompanied by a systematic degradation of the three divergent α-satellite arrays representing the ancestral centromere creating five distinct structural haplotypes in humans. CRISPR/Cas9-mediated depletion of the fusion site in human cell lines significantly alters the expression of 108 genes, indicating a potential regulatory consequence to this human-specific karyotypic change.

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Structural variations of subterminal satellite blocks and their source mechanisms as inferred from the meiotic configurations of chimpanzee chromosome termini

Cited by 5 publications

References 44 publications

Chromosome Dynamics Regulating Genomic Dispersion and Alteration of Nucleolus Organizer Regions (NORs)

Chromosome Dynamics Regulating Genomic Dispersion and Alteration of Nucleolus Organizer Regions (NORs)

Complete sequencing of ape genomes

Incomplete lineage sorting of segmental duplications defines the human chromosome 2 fusion site early during African great ape speciation

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