1
|
Mary L, Loget P, Odent S, Aussel D, Le Bouar G, Launay E, Henry C, Belaud-Rotureau MA, Jaillard S. Multicolor-FISH Characterization of a Prenatal Mosaicism for a Chromosomal Rearrangement Undetected by Molecular Cytogenetics. Cytogenet Genome Res 2021; 161:143-152. [PMID: 33827072 DOI: 10.1159/000514592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/19/2021] [Indexed: 11/19/2022] Open
Abstract
Fetal mosaicism for chromosomal rearrangements remains a challenge to diagnose, even in the era of whole-genome sequencing. We present here a case of fetal mosaicism for a chromosomal rearrangement explored in amniocytes and fetal muscle, consisting of a major cell population (95%) with partial monosomy 4q and a minor population (5%) with additional material replacing the 4qter deleted segment. Molecular techniques (MLPA, array-CGH) failed to assess the origin of this material. Only multicolor-FISH identified the additional segment on chromosome 4 as derived from chromosome 17. Due to the poor prognosis, the couple chose to terminate the pregnancy. Because of low-level mosaicism, chromosomal microarray analysis (CMA), now considered as first-tier prenatal genetic analysis, did not allow the identification of the minor cell line. In case of large CNVs (>5 Mb) detected by CMA, karyotyping may be considered to elucidate the mechanism of the underlying rearrangement and eliminate mosaicism.
Collapse
Affiliation(s)
- Laura Mary
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France.,INSERM, EHESP, IRSET - UMR_S 1085, Université Rennes 1, Rennes, France
| | - Philippe Loget
- Service d'Anatomie et Cytologie Pathologiques, CHU Rennes, Rennes, France
| | - Sylvie Odent
- Service de Génétique Clinique, CHU Rennes, CLAD Ouest, Rennes, France
| | - Dominique Aussel
- Service de Gynécologie-Obstétrique, Clinique de La Sagesse, Rennes, France
| | - Gwenaelle Le Bouar
- Unité de Médecine fœtale, Service de Gynécologie-Obstétrique, CHU Rennes, Rennes, France
| | - Erika Launay
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
| | - Catherine Henry
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
| | - Marc-Antoine Belaud-Rotureau
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France.,INSERM, EHESP, IRSET - UMR_S 1085, Université Rennes 1, Rennes, France
| | - Sylvie Jaillard
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France.,INSERM, EHESP, IRSET - UMR_S 1085, Université Rennes 1, Rennes, France
| |
Collapse
|
2
|
Puntieri F, Andrioli NB, Nieves M. Association between Genomic Instability and Evolutionary Chromosomal Rearrangements in Neotropical Primates. Genome Biol Evol 2018; 10:1647-1656. [PMID: 29905781 PMCID: PMC6366543 DOI: 10.1093/gbe/evy119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2018] [Indexed: 11/17/2022] Open
Abstract
During the last decades, the mammalian genome has been proposed to have regions prone to
breakage and reorganization concentrated in certain chromosomal bands that seem to
correspond to evolutionary breakpoints. These bands are likely to be involved in
chromosome fragility or instability. In Primates, some biomarkers of genetic damage may be
associated with various degrees of genomic instability. Here, we investigated the
usefulness of Sister Chromatid Exchange as a biomarker of potential sites of frequent
chromosome breakage and rearrangement in Alouatta caraya, Ateles
chamek, Ateles paniscus, and Cebus cay. These Neotropical
species have particular genomic and chromosomal features allowing the analysis of genomic
instability for comparative purposes. We determined the frequency of spontaneous induction
of Sister Chromatid Exchanges and assessed the relationship between these and structural
rearrangements implicated in the evolution of the primates of interest. Overall,
A. caraya and C. cay presented a low proportion of
statistically significant unstable bands, suggesting fairly stable genomes and the
existence of some kind of protection against endogenous damage. In contrast,
Ateles showed a highly significant proportion of unstable bands; these
were mainly found in the rearranged regions, which is consistent with the numerous genomic
reorganizations that might have occurred during the evolution of this genus.
Collapse
Affiliation(s)
- Fiona Puntieri
- GIBE (Grupo de Investigación en Biología Evolutiva), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Ciudad Universitaria Pab. 2, 4° piso, Labs. 43-46, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Nancy B Andrioli
- GIBE (Grupo de Investigación en Biología Evolutiva), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Ciudad Universitaria Pab. 2, 4° piso, Labs. 43-46, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Mariela Nieves
- GIBE (Grupo de Investigación en Biología Evolutiva), Departamento de Ecología, Genética y Evolución, Facultad de Ciencias Exactas y Naturales, Ciudad Universitaria Pab. 2, 4° piso, Labs. 43-46, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.,Instituto de Ecología, Genética y Evolución de Buenos Aires, CONICET-Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| |
Collapse
|
3
|
Capilla L, Sánchez-Guillén RA, Farré M, Paytuví-Gallart A, Malinverni R, Ventura J, Larkin DM, Ruiz-Herrera A. Mammalian Comparative Genomics Reveals Genetic and Epigenetic Features Associated with Genome Reshuffling in Rodentia. Genome Biol Evol 2018; 8:3703-3717. [PMID: 28175287 PMCID: PMC5521730 DOI: 10.1093/gbe/evw276] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2016] [Indexed: 12/16/2022] Open
Abstract
Understanding how mammalian genomes have been reshuffled through structural changes is fundamental to the dynamics of its composition, evolutionary relationships between species and, in the long run, speciation. In this work, we reveal the evolutionary genomic landscape in Rodentia, the most diverse and speciose mammalian order, by whole-genome comparisons of six rodent species and six representative outgroup mammalian species. The reconstruction of the evolutionary breakpoint regions across rodent phylogeny shows an increased rate of genome reshuffling that is approximately two orders of magnitude greater than in other mammalian species here considered. We identified novel lineage and clade-specific breakpoint regions within Rodentia and analyzed their gene content, recombination rates and their relationship with constitutive lamina genomic associated domains, DNase I hypersensitivity sites and chromatin modifications. We detected an accumulation of protein-coding genes in evolutionary breakpoint regions, especially genes implicated in reproduction and pheromone detection and mating. Moreover, we found an association of the evolutionary breakpoint regions with active chromatin state landscapes, most probably related to gene enrichment. Our results have two important implications for understanding the mechanisms that govern and constrain mammalian genome evolution. The first is that the presence of genes related to species-specific phenotypes in evolutionary breakpoint regions reinforces the adaptive value of genome reshuffling. Second, that chromatin conformation, an aspect that has been often overlooked in comparative genomic studies, might play a role in modeling the genomic distribution of evolutionary breakpoints.
Collapse
Affiliation(s)
- Laia Capilla
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Rosa Ana Sánchez-Guillén
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Biología Evolutiva, Instituto de Ecología A.C, Xalapa, Veracruz, Apartado, Mexico
| | - Marta Farré
- Biología Evolutiva, Instituto de Ecología A.C, Xalapa, Veracruz, Apartado, Mexico
| | - Andreu Paytuví-Gallart
- Department of Comparative Biomedical Sciences, The Royal Veterinary College, London, UK.,Sequentia Biotech S.L. Calle Comte d'Urgell, Barcelona, Spain
| | - Roberto Malinverni
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Jacint Ventura
- Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Denis M Larkin
- Biología Evolutiva, Instituto de Ecología A.C, Xalapa, Veracruz, Apartado, Mexico
| | - Aurora Ruiz-Herrera
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain.,Sequentia Biotech S.L. Calle Comte d'Urgell, Barcelona, Spain
| |
Collapse
|
4
|
Farré M, Robinson TJ, Ruiz-Herrera A. An Integrative Breakage Model of genome architecture, reshuffling and evolution: The Integrative Breakage Model of genome evolution, a novel multidisciplinary hypothesis for the study of genome plasticity. Bioessays 2015; 37:479-88. [PMID: 25739389 DOI: 10.1002/bies.201400174] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 12/23/2022]
Abstract
Our understanding of genomic reorganization, the mechanics of genomic transmission to offspring during germ line formation, and how these structural changes contribute to the speciation process, and genetic disease is far from complete. Earlier attempts to understand the mechanism(s) and constraints that govern genome remodeling suffered from being too narrowly focused, and failed to provide a unified and encompassing view of how genomes are organized and regulated inside cells. Here, we propose a new multidisciplinary Integrative Breakage Model for the study of genome evolution. The analysis of the high-level structural organization of genomes (nucleome), together with the functional constrains that accompany genome reshuffling, provide insights into the origin and plasticity of genome organization that may assist with the detection and isolation of therapeutic targets for the treatment of complex human disorders.
Collapse
Affiliation(s)
- Marta Farré
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Campus UAB, Barcelona, Spain
| | | | | |
Collapse
|
5
|
Pokorná M, Rens W, Rovatsos M, Kratochvíl L. A ZZ/ZW Sex Chromosome System in the Thick-Tailed Gecko ( Underwoodisaurus milii; Squamata: Gekkota: Carphodactylidae), a Member of the Ancient Gecko Lineage. Cytogenet Genome Res 2014; 142:190-6. [DOI: 10.1159/000358847] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2013] [Indexed: 11/19/2022] Open
|
6
|
Brown JD, Mitchell SE, O'Neill RJ. Making a long story short: noncoding RNAs and chromosome change. Heredity (Edinb) 2011; 108:42-9. [PMID: 22072070 DOI: 10.1038/hdy.2011.104] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
As important as the events that influence selection for specific chromosome types in the derivation of novel karyotypes, are the events that initiate the changes in chromosome number and structure between species, and likewise polymorphisms, variants and disease states within species. Although once thought of as transcriptional 'noise', noncoding RNAs (ncRNAs) are now recognized as important mediators of epigenetic regulation and chromosome stability. Here we highlight recent work that illustrates the influence short and long ncRNAs have as participants in the function and stability of chromosome regions such as centromeres, telomeres, evolutionary breakpoints and fragile sites. We summarize recent evidence that ncRNAs can facilitate chromosome change and present mechanisms by which ncRNAs create DNA breaks. Finally, we present hypotheses on how they may create novel karyotypes and thus affect chromosome evolution.
Collapse
Affiliation(s)
- J D Brown
- Allied Health Sciences Department, University of Connecticut, Storrs, CT, USA
| | | | | |
Collapse
|
7
|
Farré M, Bosch M, López-Giráldez F, Ponsà M, Ruiz-Herrera A. Assessing the role of tandem repeats in shaping the genomic architecture of great apes. PLoS One 2011; 6:e27239. [PMID: 22076140 PMCID: PMC3208591 DOI: 10.1371/journal.pone.0027239] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 10/12/2011] [Indexed: 11/18/2022] Open
Abstract
Background Ancestral reconstructions of mammalian genomes have revealed that evolutionary breakpoint regions are clustered in regions that are more prone to break and reorganize. What is still unclear to evolutionary biologists is whether these regions are physically unstable due solely to sequence composition and/or genome organization, or do they represent genomic areas where the selection against breakpoints is minimal. Methodology and Principal Findings Here we present a comprehensive study of the distribution of tandem repeats in great apes. We analyzed the distribution of tandem repeats in relation to the localization of evolutionary breakpoint regions in the human, chimpanzee, orangutan and macaque genomes. We observed an accumulation of tandem repeats in the genomic regions implicated in chromosomal reorganizations. In the case of the human genome our analyses revealed that evolutionary breakpoint regions contained more base pairs implicated in tandem repeats compared to synteny blocks, being the AAAT motif the most frequently involved in evolutionary regions. We found that those AAAT repeats located in evolutionary regions were preferentially associated with Alu elements. Significance Our observations provide evidence for the role of tandem repeats in shaping mammalian genome architecture. We hypothesize that an accumulation of specific tandem repeats in evolutionary regions can promote genome instability by altering the state of the chromatin conformation or by promoting the insertion of transposable elements.
Collapse
Affiliation(s)
- Marta Farré
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | | | - Francesc López-Giráldez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
| | - Montserrat Ponsà
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Aurora Ruiz-Herrera
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- * E-mail:
| |
Collapse
|
8
|
Rovatsos MT, Marchal JA, Romero-Fernández I, Fernández FJ, Giagia-Athanosopoulou EB, Sánchez A. Rapid, independent, and extensive amplification of telomeric repeats in pericentromeric regions in karyotypes of arvicoline rodents. Chromosome Res 2011; 19:869-82. [PMID: 21979796 DOI: 10.1007/s10577-011-9242-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 09/09/2011] [Accepted: 09/09/2011] [Indexed: 11/26/2022]
Abstract
The distribution of telomeric repeats was analyzed by fluorescence in situ hybridization in 15 species of arvicoline rodents, included in three different genera: Chionomys, Arvicola, and Microtus. The results demonstrated that in most or the analyzed species, telomeric sequences are present, in addition to normal telomeres localization, as large blocks in pericentromeric regions. The number, localization, and degree of amplification of telomeric sequences blocks varied with the karyotype and the morphology of the chromosomes. Also, in some cases telomeric amplification at non-pericentromeric regions is described. The interstitial telomeric sequences are evolutionary modern and have rapidly colonized and spread in pericentromeric regions of chromosomes by different mechanisms and probably independently in each species. Additionally, we colocalized telomeric repeats and the satellite DNA Msat-160 (also located in pericentromeric regions) in three species and cloned telomeric repeats in one of them. Finally, we discuss about the possible origin and implication of telomeric repeats in the high rate of karyotypic evolution reported for this rodent group.
Collapse
Affiliation(s)
- M Th Rovatsos
- Section of Animal Biology, Department of Biology, University of Patras, GR-26500, Patras, Greece
| | | | | | | | | | | |
Collapse
|
9
|
Anchoring the dog to its relatives reveals new evolutionary breakpoints across 11 species of the Canidae and provides new clues for the role of B chromosomes. Chromosome Res 2011; 19:685-708. [DOI: 10.1007/s10577-011-9233-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 08/15/2011] [Accepted: 08/16/2011] [Indexed: 12/27/2022]
|
10
|
Brown JD, O'Neill RJ. Chromosomes, conflict, and epigenetics: chromosomal speciation revisited. Annu Rev Genomics Hum Genet 2010; 11:291-316. [PMID: 20438362 DOI: 10.1146/annurev-genom-082509-141554] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Since Darwin first noted that the process of speciation was indeed the "mystery of mysteries," scientists have tried to develop testable models for the development of reproductive incompatibilities-the first step in the formation of a new species. Early theorists proposed that chromosome rearrangements were implicated in the process of reproductive isolation; however, the chromosomal speciation model has recently been questioned. In addition, recent data from hybrid model systems indicates that simple epistatic interactions, the Dobzhansky-Muller incompatibilities, are more complex. In fact, incompatibilities are quite broad, including interactions among heterochromatin, small RNAs, and distinct, epigenetically defined genomic regions such as the centromere. In this review, we will examine both classical and current models of chromosomal speciation and describe the "evolving" theory of genetic conflict, epigenetics, and chromosomal speciation.
Collapse
Affiliation(s)
- Judith D Brown
- Department of Allied Health Sciences, University of Connecticut, Storrs, CT 06269, USA
| | | |
Collapse
|
11
|
Gifalli-Iughetti C, Koiffmann CP. Synteny of human chromosomes 14 and 15 in the platyrrhines (Primates, Platyrrhini). Genet Mol Biol 2009; 32:786-91. [PMID: 21637455 PMCID: PMC3036896 DOI: 10.1590/s1415-47572009005000069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Accepted: 03/11/2009] [Indexed: 11/22/2022] Open
Abstract
In order to study the intra- and interspecific variability of the 14/15 association in Platyrrhini, we analyzed 15 species from 13 genera, including species that had not been described yet. The DNA libraries of human chromosomes 14 and 15 were hybridized to metaphases of Alouatta guariba clamitans, A. caraya, A. sara, Ateles paniscus chamek, Lagothrix lagothricha, Brachyteles arachnoides, Saguinus midas midas, Leontopithecus chrysomelas, Callimico goeldii, Callithrix sp., Cebus apella, Aotus nigriceps, Cacajao melanocephalus,Chiropotes satanas and Callicebus caligatus. The 14/15 hybridization pattern was present in 13 species, but not in Alouatta sara that showed a 14/15/14 pattern and Aotus nigriceps that showed a 15/14/15/14 pattern. In the majority of the species, the HSA 14 homologue retained synteny for the entire chromosome, whereas the HSA 15 homologue displayed fragmented segments. Within primates, the New World monkeys represent the taxon with the highest variability in chromosome number (2n = 16 to 62). The presence of the HSA 14/15 association in all species and subspecies studied herein confirms that this association is the ancestral condition for platyrrhines and that this association has been retained in most platyrrhines, despite the occurrence of extensive inter- and intrachromosomal rearrangements in this infraorder of Primates.
Collapse
Affiliation(s)
- Cristiani Gifalli-Iughetti
- Centro de Estudos do Genoma Humano, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP Brazil
| | | |
Collapse
|
12
|
Robinson TJ, Ruiz-Herrera A. Defining the ancestral eutherian karyotype: a cladistic interpretation of chromosome painting and genome sequence assembly data. Chromosome Res 2008; 16:1133-41. [PMID: 19067196 DOI: 10.1007/s10577-008-1264-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 08/28/2008] [Accepted: 08/28/2008] [Indexed: 11/28/2022]
Abstract
A cladistic analysis of genome assemblies (syntenic associations) for eutherian mammals against two distant outgroup species--opossum and chicken--permitted a refinement of the 46-chromosome karyotype formerly inferred in the ancestral eutherian. We show that two intact chromosome pairs (corresponding to human chromosomes 13 and 18) and three conserved chromosome segments (10q, 19p and 8q in the human karyotype) are probably symplesiomorphic for Eutheria because they are also present as unaltered orthologues in one or both outgroups. Seven additional syntenies (4q/8p/4pq, 3p/21, 14/15, 10p/12pq/22qt, 19q/16q, 16p/7a and 12qt/22q), each involving human chromosomal segments that in various combinations correspond to complete chromosomes in the ancestral eutherian karyotype, are also present in one or both outgroup taxa and thus are probable symplesiomorphies for Eutheria. Interestingly, several of the symplesiomorphic characters identified in chicken and/or opossum are present in more distant outgroups such as pufferfish and zebrafish (for example 3p/21, 14/15, 19q/16q and 16p/7a), suggesting their retention since vertebrate common ancestry approximately 450 million years ago. However, eight intact pairs (corresponding to human chromosomes 1, 5, 6, 9, 11, 17, 20 and the X) and three chromosome segments (7b, 2p-q13 and 2q13-qter) are derived characters potentially consistent with eutherian monophyly. Our analyses clarify the distinction between shared-ancestral and shared-derived homology in the eutherian ancestral karyotype.
Collapse
Affiliation(s)
- Terence J Robinson
- Evolutionary Genomics Group, Department of Botany and Zoology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa.
| | | |
Collapse
|
13
|
Ruiz-Herrera A, Robinson TJ. Evolutionary plasticity and cancer breakpoints in human chromosome 3. Bioessays 2008; 30:1126-37. [DOI: 10.1002/bies.20829] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
14
|
Abstract
Phylogenetic reconstructions are often plagued by difficulties in distinguishing phylogenetic signal (due to shared ancestry) from phylogenetic noise or homoplasy (due to character-state convergences or reversals). We use a new interpretive hypothesis, termed hemiplasy, to show how random lineage sorting might account for specific instances of seeming "phylogenetic discordance" among different chromosomal traits, or between karyotypic features and probable species phylogenies. We posit that hemiplasy is generally less likely for underdominant chromosomal polymorphisms (i.e., those with heterozygous disadvantage) than for neutral polymorphisms or especially for overdominant rearrangements (which should tend to be longer-lived), and we illustrate this concept by using examples from chiropterans and afrotherians. Chromosomal states are especially powerful in phylogenetic reconstructions because they offer strong signatures of common ancestry, but their evolutionary interpretations remain fully subject to the principles of cladistics and the potential complications of hemiplasy.
Collapse
|
15
|
An integrative view of dynamic genomic elements influencing human brain evolution and individual neurodevelopment. Med Hypotheses 2008; 71:360-73. [DOI: 10.1016/j.mehy.2008.03.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2008] [Revised: 03/01/2008] [Accepted: 03/06/2008] [Indexed: 11/23/2022]
|
16
|
Kehrer-Sawatzki H, Cooper DN. Molecular mechanisms of chromosomal rearrangement during primate evolution. Chromosome Res 2008; 16:41-56. [PMID: 18293104 DOI: 10.1007/s10577-007-1207-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Breakpoint analysis of the large chromosomal rearrangements which have occurred during primate evolution promises to yield new insights into the underlying mechanisms of mutagenesis. Comparison of these evolutionary breakpoints with those that are disease-associated in humans, and which occur during either meiotic or mitotic cell division, should help to identify basic mechanistic similarities as well as differences. It has recently become clear that segmental duplications (SDs) have had a very significant impact on genome plasticity during primate evolution. In comparisons of the human and chimpanzee genomes, SDs have been found in flanking regions of 70-80% of inversions and approximately 40% of deletions/duplications. A strong spatial association between primate-specific breakpoints and SDs has also become evident from comparisons of human with other mammalian genomes. The lineage-specific hyperexpansion of certain SDs observed in the genomes of human, chimpanzee, gorilla and gibbon is indicative of the intrinsic instability of some SDs in primates. However, since many primate-specific breakpoints map to regions lacking SDs, but containing interspersed high-copy repetitive sequence elements such as SINEs, LINEs, LTRs, alpha-satellites and (AT)( n ) repeats, we may infer that a range of different molecular mechanisms have probably been involved in promoting chromosomal breakage during the evolution of primate genomes.
Collapse
|
17
|
Horvath JE, Willard HF. Primate comparative genomics: lemur biology and evolution. Trends Genet 2007; 23:173-82. [PMID: 17331617 DOI: 10.1016/j.tig.2007.02.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2006] [Revised: 01/08/2007] [Accepted: 02/12/2007] [Indexed: 12/23/2022]
Abstract
Comparative genome sequencing projects are providing insight into aspects of genome biology that raise new questions and challenge existing paradigms. Placement in the phylogenetic tree can often be a major determinant of which organism to choose for study. Lemurs hold a key position at the base of the primate evolutionary tree and will be highly informative for the genomics community by offering comparisons of primate-specific characteristics and processes. Combining research in chromosome evolution, genome evolution and behavior with lemur comparative genomic sequencing will offer insights into many levels of primate evolution. We discuss the current state of lemur cytogenetic and phylogenetic analyses, and suggest how focusing more genomic efforts on lemurs will be beneficial to understanding human and primate evolution, as well as disease, and will contribute to conservation efforts.
Collapse
Affiliation(s)
- Julie E Horvath
- Duke Institute for Genome Sciences & Policy, Duke University, Durham, NC 27708, USA.
| | | |
Collapse
|
18
|
Yan J, Bouchard EF, Samassekou O, Chen BZ. Identification of a human chromosome-specific interstitial telomere-like sequence (ITS) at 22q11.2 using double-strand PRINS. Cytogenet Genome Res 2007; 116:29-37. [PMID: 17268175 DOI: 10.1159/000097415] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2006] [Accepted: 07/25/2006] [Indexed: 12/28/2022] Open
Abstract
Interstitial telomeric sequences (ITSs), telomere-like repeats at intrachromosomal sites, are common in mammals and consist of tandem repeats of the canonical telomeric repeat, TTAGGG, or a repeat similar to this. We report that the ITS in human chromosome region 22q11.2 is, in the sequenced genome database, 101 tandem repeats of the sequence TTAGGGAGG. Using the primed in situ labeling (PRINS) technique and primers against the canonical telomeric repeat (TTAGGG), we illuminated telomeric sites for all chromosomes and an ITS locus at 22q11.2. Using the TTAGGGAGG sequence, we designed PRINS primers that efficiently and specifically illuminate the 22q11.2 ITS locus without illuminating telomeric and other ITS loci. The 22q11.2 locus has more repeat units than other ITSs loci enabling an unprecedented high detection frequency for this interstitial telomere locus. The 22q11.2 is associated with hot spots for disease-related chromosome breaks for multiple disorders, such as DiGeorge syndrome and chronic myeloid leukemia. We describe our findings that the ITS at 22q11.2 is in the same area of, and proximal to the common rearrangement region of multiple disorders. We suggest that the ITS might be involved in DNA repair processes in this area to protect the chromosome from more serious damage.
Collapse
Affiliation(s)
- J Yan
- Service of Genetics, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada.
| | | | | | | |
Collapse
|
19
|
Rylands AB. Primate Genetics — Is Taxonomy a Trivial Pursuit? Review ofPrimate Cytogenetics, edited by Stefan Müller, Ludwig Maximilian University, Munich, Germany. S. Karger, Basel, Switzerland. 268pp. ISSN: 1424–8581. 111 Figures, 56 Tables. Hardcover: 122.00 Swiss francs, Eur87.00, US$ 111.00. 2005. A reprint ofCytogenetic and Genome Research, Volume 108(1–3). ACTA ACUST UNITED AC 2007. [DOI: 10.1896/052.022.0117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
20
|
Froenicke L, Caldés MG, Graphodatsky A, Müller S, Lyons LA, Robinson TJ, Volleth M, Yang F, Wienberg J. Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes? Genome Res 2006; 16:306-10. [PMID: 16510895 PMCID: PMC1415215 DOI: 10.1101/gr.3955206] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Lutz Froenicke
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California 95616, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Mora L, Sánchez I, Garcia M, Ponsà M. Chromosome territory positioning of conserved homologous chromosomes in different primate species. Chromosoma 2006; 115:367-75. [PMID: 16607509 DOI: 10.1007/s00412-006-0064-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2006] [Revised: 02/24/2006] [Accepted: 03/09/2006] [Indexed: 12/17/2022]
Abstract
Interphase chromosomes form distinct spatial domains called chromosome territories (CTs). The position of CTs is known not to be at random and is related to chromosome size and gene density. To elucidate how CTs are arranged in primate proliferating fibroblasts and whether the radial position of CTs has been conserved during primate evolution, several specific CTs corresponding to conserved chromosomes since the Simiiformes (human 6, 12, 13, and 17 homologous CTs) have been studied in 3D preserved interphase nuclei from proliferant cells of two New World monkey species (Lagothrix lagothricha, Saimiri sciureus) and in human by three-dimensional fluorescent in situ hybridization (3D-FISH). Our results indicate that both gene-density and chromosome size influence chromosome territory arrangement in the nucleus. This influence is greater for chromosome-size than for gene-density in the three species studied. A comparison of the radial position of a given CT and its homolog in the species analyzed suggests similar CT distributions for homologous chromosomes. Our statistical analysis using the logit model shows that such homologous positionings cannot, however, be considered identical.
Collapse
Affiliation(s)
- Laia Mora
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallés, Spain
| | | | | | | |
Collapse
|
22
|
Ruiz-Herrera A, Castresana J, Robinson TJ. Is mammalian chromosomal evolution driven by regions of genome fragility? Genome Biol 2006; 7:R115. [PMID: 17156441 PMCID: PMC1794428 DOI: 10.1186/gb-2006-7-12-r115] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2006] [Revised: 11/06/2006] [Accepted: 12/08/2006] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND A fundamental question in comparative genomics concerns the identification of mechanisms that underpin chromosomal change. In an attempt to shed light on the dynamics of mammalian genome evolution, we analyzed the distribution of syntenic blocks, evolutionary breakpoint regions, and evolutionary breakpoints taken from public databases available for seven eutherian species (mouse, rat, cattle, dog, pig, cat, and horse) and the chicken, and examined these for correspondence with human fragile sites and tandem repeats. RESULTS Our results confirm previous investigations that showed the presence of chromosomal regions in the human genome that have been repeatedly used as illustrated by a high breakpoint accumulation in certain chromosomes and chromosomal bands. We show, however, that there is a striking correspondence between fragile site location, the positions of evolutionary breakpoints, and the distribution of tandem repeats throughout the human genome, which similarly reflect a non-uniform pattern of occurrence. CONCLUSION These observations provide further evidence that certain chromosomal regions in the human genome have been repeatedly used in the evolutionary process. As a consequence, the genome is a composite of fragile regions prone to reorganization that have been conserved in different lineages, and genomic tracts that do not exhibit the same levels of evolutionary plasticity.
Collapse
Affiliation(s)
- Aurora Ruiz-Herrera
- Evolutionary Genomics Group, Department of Botany & Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| | - Jose Castresana
- Institut de Biologia Molecular de Barcelona, CSIC, Department of Physiology and Molecular Biodiversity, Jordi Girona 18, 08034 Barcelona, Spain
| | - Terence J Robinson
- Evolutionary Genomics Group, Department of Botany & Zoology, University of Stellenbosch, Private Bag X1, Matieland 7602, South Africa
| |
Collapse
|
23
|
Gericke GS. Chromosomal fragility, structural rearrangements and mobile element activity may reflect dynamic epigenetic mechanisms of importance in neurobehavioural genetics. Med Hypotheses 2006; 66:276-85. [PMID: 16183210 DOI: 10.1016/j.mehy.2005.06.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2005] [Revised: 06/22/2005] [Accepted: 06/27/2005] [Indexed: 01/07/2023]
Abstract
Advances in human genome analyses have not yet allowed identification of specific genetic mechanisms underlying the expression of human neurobehavioural disorders. There is an increasing awareness that several genes may contribute to behavioural phenotypes and these genes appear to interact in as yet undetermined ways. It has been suggested that the problem needs elucidation from an epigenetic, gene expression perspective. Cytogenetic instability manifesting as chromosomal fragile sites, translocations, duplications, deletions and inversions, when co-occurring with neurobehavioural disorders, may offer a doorway to the investigation of such chromatin level, regulatory region, epigenetic processes. Due to earlier indications of non-specificity of chromosomal aberrations, poor phenotype:genotype correlations and a shift to analysing candidate coding regions on high resolution map level, the only utility of chromosomal breakpoints came to be seen as harbouring possible candidate genes of interest when segregating together with particular neurobehavioural disorders. More recent findings of the expression of highly specific subsets of fragile sites in association with Tourette and Rett syndromes need to be extended to other neurobehavioural disorders to ascertain whether observed patterns can be considered representative of 'chromatin endophenotypes' correlating with discrete sets of neurobehavioural symptoms. Environmental/epigenetic factors could affect the chromatin characteristics of the genome arising through DNA strand breakage, mobile element activity and retroinsertion, establishing new architectural features of regulatory control networks very rapidly in comparison to coding region evolution rates. Microarray-based techniques for the genome-wide mapping of in vivo protein-DNA interactions offer increasingly comprehensive views of genetic and epigenetic regulatory networks. It may be informative to include functionally significant chromatin structural variation analyses when considering candidate genes for neurobehavioural disorders.
Collapse
Affiliation(s)
- G S Gericke
- Genetics Division, Ampath National Pathology Laboratories, P.O. Box 2040, Brooklyn Square, 0075 Pretoria, Gauteng, South Africa.
| |
Collapse
|
24
|
Szamalek JM, Goidts V, Chuzhanova N, Hameister H, Cooper DN, Kehrer-Sawatzki H. Molecular characterisation of the pericentric inversion that distinguishes human chromosome 5 from the homologous chimpanzee chromosome. Hum Genet 2005; 117:168-76. [PMID: 15883840 DOI: 10.1007/s00439-005-1287-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2004] [Accepted: 01/25/2005] [Indexed: 11/30/2022]
Abstract
Human and chimpanzee karyotypes differ by virtue of nine pericentric inversions that serve to distinguish human chromosomes 1, 4, 5, 9, 12, 15, 16, 17, and 18 from their chimpanzee orthologues. In this study, we have analysed the breakpoints of the pericentric inversion characteristic of chimpanzee chromosome 4, the homologue of human chromosome 5. Breakpoint-spanning BAC clones were identified from both the human and chimpanzee genomes by fluorescence in situ hybridisation, and the precise locations of the breakpoints were determined by sequence comparisons. In stark contrast to some other characterised evolutionary rearrangements in primates, this chimpanzee-specific inversion appears not to have been mediated by either gross segmental duplications or low-copy repeats, although micro-duplications were found adjacent to the breakpoints. However, alternating purine-pyrimidine (RY) tracts were detected at the breakpoints, and such sequences are known to adopt non-B DNA conformations that are capable of triggering DNA breakage and genomic rearrangements. Comparison of the breakpoint region of human chromosome 5q15 with the orthologous regions of the chicken, mouse, and rat genomes, revealed similar but non-identical syntenic disruptions in all three species. The clustering of evolutionary breakpoints within this chromosomal region, together with the presence of multiple pathological breakpoints in the vicinity of both 5p15 and 5q15, is consistent with the non-random model of chromosomal evolution and suggests that these regions may well possess intrinsic features that have served to mediate a variety of genomic rearrangements, including the pericentric inversion in chimpanzee chromosome 4.
Collapse
Affiliation(s)
- Justyna M Szamalek
- Department of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | | | | | | | | | | |
Collapse
|
25
|
Ruiz-Herrera A, García F, Aguilera M, Garcia M, Ponsà Fontanals M. Comparative chromosome painting in Aotus reveals a highly derived evolution. Am J Primatol 2005; 65:73-85. [PMID: 15645457 DOI: 10.1002/ajp.20098] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The genus Aotus represents a highly diverse group with an especially intricate taxonomy. No standard cytogenetic nomenclature for the genus has yet been established. So far, cytogenetic studies have characterized 18 different karyotypes with diploid numbers ranging from 46 to 58 chromosomes. By combining G-banding comparisons and molecular cytogenetic techniques, we were able to describe the most likely pattern of chromosome evolution and phylogenetic position of two Aotus karyomorphs (KMs) from Venezuela: Aotus nancymai (KM3, 2n=54) and Aotus sp. (KM9, 2n=50). All of the proposed Platyrrhini ancestral associations (2/16, 3/21, 5/7, 8/18, 10/16, 14/15) were found in the Aotus KMs studied, except 2/16 and 10/16. In addition, some derived chromosomal associations were also detected in both KMs (1/3, 1/16, 2/12, 2/20, 3/14, 4/15, 5/15, 7/11, 9/15, 9/17, 10/11, and 10/22). Although some of these associations have been found in other New World monkeys, our results suggest that Aotus species have undergone a highly derived chromosomal evolution. The homologies between these two Aotus KMs and human chromosomes were established, indicating that KM3 has a more derived karyotype than KM9 with respect to the ancestral Platyrrhini karyotype.
Collapse
Affiliation(s)
- Aurora Ruiz-Herrera
- Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | | | | | | |
Collapse
|