1
|
Poszewiecka B, Gogolewski K, Stankiewicz P, Gambin A. Revised time estimation of the ancestral human chromosome 2 fusion. BMC Genomics 2022; 23:616. [PMID: 36008753 PMCID: PMC9413910 DOI: 10.1186/s12864-022-08828-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 11/24/2022] Open
Abstract
Background The reduction of the chromosome number from 48 in the Great Apes to 46 in modern humans is thought to result from the end-to-end fusion of two ancestral non-human primate chromosomes forming the human chromosome 2 (HSA2). Genomic signatures of this event are the presence of inverted telomeric repeats at the HSA2 fusion site and a block of degenerate satellite sequences that mark the remnants of the ancestral centromere. It has been estimated that this fusion arose up to 4.5 million years ago (Mya). Results We have developed an enhanced algorithm for the detection and efficient counting of the locally over-represented weak-to-strong (AT to GC) substitutions. By analyzing the enrichment of these substitutions around the fusion site of HSA2 we estimated its formation time at 0.9 Mya with a 95% confidence interval of 0.4-1.5 Mya. Additionally, based on the statistics derived from our algorithm, we have reconstructed the evolutionary distances among the Great Apes (Hominoidea). Conclusions Our results shed light on the HSA2 fusion formation and provide a novel computational alternative for the estimation of the speciation chronology.
Collapse
Affiliation(s)
| | | | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, US
| | - Anna Gambin
- Institute of Informatics, Warsaw University, Warsaw, Poland
| |
Collapse
|
2
|
Hirai H, Hirai Y, Udono T, Matsubayashi K, Tosi AJ, Koga A. Structural variations of subterminal satellite blocks and their source mechanisms as inferred from the meiotic configurations of chimpanzee chromosome termini. Chromosome Res 2019; 27:321-332. [PMID: 31418128 DOI: 10.1007/s10577-019-09615-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/09/2019] [Accepted: 07/29/2019] [Indexed: 10/26/2022]
Abstract
African great apes have large constitutive heterochromatin (C-band) blocks in subtelomeric regions of the majority of their chromosomes, but humans lack these. Additionally, the chimpanzee meiotic cell division process demonstrates unique partial terminal associations in the first meiotic prophase (pachytene). These are likely formed as a result of interaction among subtelomeric C-band blocks. We thus conducted an extensive study to define the features in the subtelomeric heterochromatic regions of chimpanzee chromosomes undergoing mitotic metaphase and meiotic cell division. Molecular cytogenetic analyses with probes of both subterminal satellite DNA (a main component of C-band) and rDNA demonstrated principles of interaction among DNA arrays. The results suggest that homologous and ectopic recombination through persistent subtelomeric associations (post-bouquet association observed in 32% of spermatocytes in the pachytene stage) appears to create variability in heterochromatin patterns and simultaneously restrain subtelomeric genome polymorphisms. That is, the meeting of non-homologous chromosome termini sets the stage for ectopic pairing which, in turn, is the mechanism for generating variability and genomic dispersion of subtelomeric C-band blocks through a system of concerted evolution. Comparison between the present study and previous reports indicated that the chromosomal distribution rate of sutelomeric regions seems to have antagonistic correlation with arm numbers holding subterminal satellite blocks in humans, chimpanzees, and gorillas. That is, the increase of subterminal satellite blocks probably reduces genomic diversity in the subtelomeric regions. The acquisition vs. loss of the subtelomeric C-band blocks is postulated as the underlying engine of this chromosomal differentiation yielded by meiotic chromosomal interaction.
Collapse
Affiliation(s)
- Hirohisa Hirai
- Primate Research Institute, Kyoto University, Inuyama, Aichi, 484-8506, Japan. .,The Unit of Human-Nature Interlaced Life Science, Kyoto University Research Coordination Alliance, Kyoto, Japan.
| | - Yuriko Hirai
- Primate Research Institute, Kyoto University, Inuyama, Aichi, 484-8506, Japan
| | - Toshifumi Udono
- Kumamoto Sanctuary, Wildlife Research Center, Kyoto University, Uto, Kumamoto, Japan
| | | | - Anthony J Tosi
- Department of Anthropology and School of Biomedical Science, Kent State University, Kent, OH, 44242, USA
| | - Akihiko Koga
- Primate Research Institute, Kyoto University, Inuyama, Aichi, 484-8506, Japan
| |
Collapse
|
3
|
GARCÍA F, GARCIA M, MORA L, ALARCÓN L, EGOZCUE J, PONSÀ M. Qualitative analysis of constitutive heterochromatin and primate evolution. Biol J Linn Soc Lond 2003. [DOI: 10.1046/j.1095-8312.2003.00223.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
4
|
Vallente-Samonte RU, Conte RA, Verma RS. Syntenic homology of human unique DNA sequences within chromossome regions 5q31, 10q22, 13q32-33 and 19q13.1 in the great apes. Genet Mol Biol 2000. [DOI: 10.1590/s1415-47572000000300004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Homologies between chromosome banding patterns and DNA sequences in the great apes and humans suggest an apparent common origin for these two lineages. The availability of DNA probes for specific regions of human chromosomes (5q31, 10q22, 13q32-33 and 19q13.1) led us to cross-hybridize these to chimpanzee (Pan troglodytes, PTR), gorilla (Gorilla gorilla, GGO) and orangutan (Pongo pygmaeus, PPY) chromosomes in a search for equivalent regions in the great apes. Positive hybridization signals to the chromosome 5q31-specific DNA probe were observed at HSA 5q31, PTR 4q31, GGO 4q31 and PPY 4q31, while fluorescent signals using the chromosome 10q22-specific DNA probe were noted at HSA 10q22, PTR 8q22, GGO 8q22 and PPY 7q22. The chromosome arms showing hybridization signals to the Quint-EssentialTM 13-specific DNA probe were identified as HSA 13q32-33, PTR 14q32-33, GGO 14q32-33 and PPY 14q32-33, while those presenting hybridization signals to the chromosome 19q13.1-specific DNA probe were identified as HSA 19q13.1, PTR 20q13, GGO 20q13 and PPY 20q13. All four probes presumably hybridized to homologous chromosomal locations in the apes, which suggests a homology of certain unique DNA sequences among hominoid species.
Collapse
|
5
|
Watson KR. Man's Closeness to the Apes Argues for a Soul. Linacre Q 1999. [DOI: 10.1080/20508549.1999.11877557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Kathryn R. Watson
- Loyola University of Los Angeles in 1973, with a B.S. degree in biology
| |
Collapse
|
6
|
García F, Nogués C, Garcia M, Egozcue J, Ponsà M. Characterization of constitutive heterochromatin in Cebus apella (Cebidae, Primates) and Pan troglodytes (Hominidae, Primates): comparison to human chromosomes. Am J Primatol 1999; 49:205-21. [PMID: 10512541 DOI: 10.1002/(sici)1098-2345(199911)49:3<205::aid-ajp1>3.0.co;2-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Using G bands, some homologies between the chromosomes of Cebus apella (CAP) and human chromosomes are difficult to establish. To solve this problem, we analyzed these homologies by fluorescence in situ hybridization using human whole chromosome probes (ZOO-FISH). The results indicated that 1) the human probe for chromosome 2 partially hybridizes with CAP chromosomes 13 and 5, 2) the human probe for chromosome 3 partially hybridizes with CAP chromosomes 18 and 20, 3) the human probe for chromosome 9 partially hybridizes with CAP chromosome 19, and 4) the human probe for chromosome 14 hybridizes with the p-terminal and q-terminal regions of CAP chromosome 6. However, none of the human probes employed hybridized with the heterochromatic regions of CAP chromosomes. For this reason, we characterized the heterochromatic regions of CAP chromosomes and of the chromosomes of Pan troglodytes (PTR), to allow comparison between CAP, PTR, and human chromosomes using in situ digestion of fixed chromosomes with the restriction enzymes AluI, HaeIII, and RsaI and by fluorescent staining with DA/DAPI. The results show that 1) centromeric heterochromatin is heterogeneous in the three species studied and 2) noncentromeric heterochromatin is homogeneous within each of the three species, but is different for each species. Thus, centromeric heterochromatin undergoes a higher degree of variability than noncentromeric heterochromatin.
Collapse
Affiliation(s)
- F García
- Departament de Biologia Cellular i Fisiologia, Facultat de Ciències, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | | | | | | | | |
Collapse
|
7
|
|
8
|
Samonte RV, Ramesh KH, Verma RS. Origin of human chromosome 2 revisited. J Genet 1998. [DOI: 10.1007/bf02933040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
9
|
Ramesh KH, Gupta S, Verma RS. Assignment of human MYCN proto-oncogene to chromosome band 12q24 in higher primates. Gene 1996; 177:169-72. [PMID: 8921863 DOI: 10.1016/0378-1119(96)00295-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Controversies concerning the reduction of chromosome number from 48 to 46 in humans by putative fusion of two ape chromosomes still persist. Nevertheless, abundant evidence suggests that human chromosome 2 was derived by fusion. Consequently, the recent availability of the human MYCN gene probe which was localized to 2p24.3 facilitated our search for its location in the human equivalent chromosome(s) of chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla) and orangutan (Pongo pygmaeus). In all three species, the human MYCN gene was localized to the long arm of chromosome 12 band 12q24 which is the corresponding band equivalent of the short arm of human chromosome 2. The conservation of MYCN gene in higher primates at the equivalent chromosome locus that corresponds to that of the human provides additional prevailing view towards tracing the evolutionary pathways concerning the origin of chromosome 2, though we recognize that there are conceptual problems concerning human descent.
Collapse
Affiliation(s)
- K H Ramesh
- Division of Genetics, Long Island College Hospital, SUNY Health Science Center, Brooklyn 11201, USA
| | | | | |
Collapse
|
10
|
Samonte RV, Ramesh KH, Verma RS. Regional localization of human M-BCR gene to chromosome 23 band q11 in the great apes. Genetica 1996; 98:111-3. [PMID: 8765683 DOI: 10.1007/bf00120226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We hybridized a human M-BCR DNA probe to the chromosomes of chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla) and orangutan (Pongo pygmaeus) by FISH-technique. The human M-BCR gene was localized to chromosome 23 band q11 (23q11), which is equivalent to the human chromosome 22 band q11 in all three species. The conservation of M-BCR gene in higher primates at the corresponding human chromosome locus provides phylogenetic clues concerning the evolution of genes.
Collapse
Affiliation(s)
- R V Samonte
- Division of Genetics, Long Island College Hospital, SUNY Health Science Center at Brooklyn, NY 11201, USA
| | | | | |
Collapse
|
11
|
Luke S, Gandhi S, Verma RS. Conservation of the Down syndrome critical region in humans and great apes. Gene X 1995; 161:283-5. [PMID: 7665094 DOI: 10.1016/0378-1119(95)00270-g] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A quarter century ago, a chimpanzee with trisomy 22 was reported to have the clinical manifestation of Down syndrome. The features of Down syndrome in human have been associated with chromosome 21 band q22.3. The recent availability of chromosome and loci specific probes has prompted us to utilize the human cosmid probe (D21S65) for the trisomy 21 region in the chromosomes of the chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla) and orangutan (Pongo pygmeus). Interestingly, the hybridization site for the Down syndrome region was found on the equivalent ape chromosome 22 in all three primates (the human equivalent of chromosome 21). Apparently, these results support the notion that the Down syndrome critical region of human chromosome 21 band q22.3 is conserved in great apes, which has displayed mongolism in a chimpanzee when present in triplicate conditions. Furthermore, other probes can be used as phylogenetic signals to enhance the understanding of human descent.
Collapse
Affiliation(s)
- S Luke
- Division of Genetics, Long Island College Hospital, SUNY Health Science Center, Brooklyn 11201, USA
| | | | | |
Collapse
|
12
|
Luke S, Verma RS. The genomic synteny at DNA level between human and chimpanzee chromosomes. Chromosome Res 1993; 1:215-9. [PMID: 8156160 DOI: 10.1007/bf00710127] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The evolutionary relationship between human (Homo sapiens) and chimpanzee (Pan troglodytes) has been the subject of debate and scrutiny for over two decades. The close relationship established by numerous parameters may or may not reflect homology at the DNA level. The recent advent of a molecular method termed the chromosome in situ suppression hybridization (CISS)-technique has prompted us to explore the phylogenetic relationship at the DNA sequence level. Cross-hybridization data using human-derived whole chromosome paints (WCPs) suggests an apparent genomic synteny with chimpanzee chromosomes at the DNA level, thus providing a better understanding of an evolutionary relationship between humans and chimpanzees.
Collapse
Affiliation(s)
- S Luke
- Division of Genetics, Long Island College Hospital, SUNY Health Science Center, Brooklyn 11201
| | | |
Collapse
|