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Thakur J, Packiaraj J, Henikoff S. Sequence, Chromatin and Evolution of Satellite DNA. Int J Mol Sci 2021; 22:ijms22094309. [PMID: 33919233 PMCID: PMC8122249 DOI: 10.3390/ijms22094309] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 12/15/2022] Open
Abstract
Satellite DNA consists of abundant tandem repeats that play important roles in cellular processes, including chromosome segregation, genome organization and chromosome end protection. Most satellite DNA repeat units are either of nucleosomal length or 5–10 bp long and occupy centromeric, pericentromeric or telomeric regions. Due to high repetitiveness, satellite DNA sequences have largely been absent from genome assemblies. Although few conserved satellite-specific sequence motifs have been identified, DNA curvature, dyad symmetries and inverted repeats are features of various satellite DNAs in several organisms. Satellite DNA sequences are either embedded in highly compact gene-poor heterochromatin or specialized chromatin that is distinct from euchromatin. Nevertheless, some satellite DNAs are transcribed into non-coding RNAs that may play important roles in satellite DNA function. Intriguingly, satellite DNAs are among the most rapidly evolving genomic elements, such that a large fraction is species-specific in most organisms. Here we describe the different classes of satellite DNA sequences, their satellite-specific chromatin features, and how these features may contribute to satellite DNA biology and evolution. We also discuss how the evolution of functional satellite DNA classes may contribute to speciation in plants and animals.
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Affiliation(s)
- Jitendra Thakur
- Department of Biology, Emory University, Atlanta, GA 30322, USA;
- Correspondence:
| | - Jenika Packiaraj
- Department of Biology, Emory University, Atlanta, GA 30322, USA;
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
- Fred Hutchinson Cancer Research Center, Howard Hughes Medical Institute, Seattle, WA 98109, USA
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Marshall OJ, Chueh AC, Wong LH, Choo KA. Neocentromeres: new insights into centromere structure, disease development, and karyotype evolution. Am J Hum Genet 2008; 82:261-82. [PMID: 18252209 PMCID: PMC2427194 DOI: 10.1016/j.ajhg.2007.11.009] [Citation(s) in RCA: 287] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2007] [Revised: 10/26/2007] [Accepted: 11/05/2007] [Indexed: 11/30/2022] Open
Abstract
Since the discovery of the first human neocentromere in 1993, these spontaneous, ectopic centromeres have been shown to be an astonishing example of epigenetic change within the genome. Recent research has focused on the role of neocentromeres in evolution and speciation, as well as in disease development and the understanding of the organization and epigenetic maintenance of the centromere. Here, we review recent progress in these areas of research and the significant insights gained.
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Affiliation(s)
- Owen J. Marshall
- Chromosome and Chromatin Research, Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
| | - Anderly C. Chueh
- Chromosome and Chromatin Research, Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
| | - Lee H. Wong
- Chromosome and Chromatin Research, Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
| | - K.H. Andy Choo
- Chromosome and Chromatin Research, Murdoch Children's Research Institute, Parkville, VIC 3052, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC 3052, Australia
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3
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Amor DJ, Choo KHA. Neocentromeres: role in human disease, evolution, and centromere study. Am J Hum Genet 2002; 71:695-714. [PMID: 12196915 PMCID: PMC378529 DOI: 10.1086/342730] [Citation(s) in RCA: 194] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2002] [Accepted: 07/03/2002] [Indexed: 01/03/2023] Open
Abstract
The centromere is essential for the proper segregation and inheritance of genetic information. Neocentromeres are ectopic centromeres that originate occasionally from noncentromeric regions of chromosomes. Despite the complete absence of normal centromeric alpha-satellite DNA, human neocentromeres are able to form a primary constriction and assemble a functional kinetochore. Since the discovery and characterization of the first case of a human neocentromere in our laboratory a decade ago, 60 examples of constitutional human neocentromeres distributed widely across the genome have been described. Typically, these are located on marker chromosomes that have been detected in children with developmental delay or congenital abnormalities. Neocentromeres have also been detected in at least two types of human cancer and have been experimentally induced in Drosophila. Current evidence from human and fly studies indicates that neocentromere activity is acquired epigenetically rather than by any alteration to the DNA sequence. Since human neocentromere formation is generally detrimental to the individual, its biological value must lie beyond the individual level, such as in karyotype evolution and speciation.
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Affiliation(s)
- David J Amor
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
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Mackie Ogilvie C, Harrison RH, Horsley SW, Hodgson SV, Kearney L. A mitotically stable marker chromosome negative for whole chromosome libraries, centromere probes and chromosome specific telomere regions: a novel class of supernumerary marker chromosome? CYTOGENETICS AND CELL GENETICS 2001; 92:69-73. [PMID: 11306799 DOI: 10.1159/000056871] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A two year-old child presented with mild developmental delay. On karyotype analysis, a supernumerary small marker chromosome (SMC) was found in all cells examined. This SMC was approximately the size of an isochromosome 18p, being symmetrical with a central constriction. C-banding and silver staining were negative and FISH with all chromosome-specific paints, centromere probes and telomere probes showed no hybridization to the SMC; telomere repeat sequences were however present on both arms. Comparative genomic hybridization showed no amplification of any chromosome region. Flow sorting of the SMC and reverse painting onto normal metaphase spreads showed no hybridization to any chromosome, whereas reverse painting onto the patient's own metaphases showed hybridization to the SMC only. This SMC may thus represent either a complex amplicon of different genomic regions, or a multifold amplification of a very small region, with a neocentromere comprising an active kinetochore but no alphoid DNA. Prognostic implications for the proband were difficult to assess due to the absence of reports of similar marker chromosomes in the literature.
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Affiliation(s)
- C Mackie Ogilvie
- Division of Medical and Molecular Genetics, King's, Guy's and St. Thomas' Medical School, London, UK.
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Morrissette JD, Celle L, Owens NL, Shields CL, Zackai EH, Spinner NB. Boy with bilateral retinoblastoma due to an unusual ring chromosome 13 with activation of a latent centromere. AMERICAN JOURNAL OF MEDICAL GENETICS 2001; 99:21-8. [PMID: 11170089 DOI: 10.1002/1096-8628(20010215)99:1<21::aid-ajmg1122>3.0.co;2-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We present a patient with bilateral retinoblastoma and developmental delay who has an abnormal male karyotype containing 47 chromosomes, including an acentric derivative chromosome 13. We postulate that the derivative 13 occurred after a break at 13q14, with the proximal portion of the chromosome forming a ring and the distal portion undergoing duplication. Thus, this patient is trisomic for 13q14-->qter. The derivative chromosome with duplicated distal portion (13q14-->qter) lacked the 13 centromere and was negative for chromosome 13 alpha-satellite DNA by low stringency FISH. Nevertheless, this chromosome is stably transmitted in lymphocytes and fibroblasts. A single primary constriction was observed at band 13q21, consistent with activation of a latent centromere (neocentromere) at this band. The neocentromere on der(13) was positive for multiple centromeric proteins, suggesting that it acts as the functional centromere. By FISH, the Rb gene was present on the normal 13, the proximally derived ring chromosome, but not on the derivative chromosome. Although there was no evidence for disruption of the Rb gene, this chromosome rearrangement most likely results in abnormal expression of the Rb gene product.
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Affiliation(s)
- J D Morrissette
- Division of Human Genetics and Molecular Biology, Children's Hospital of Philadelphia, 34th Street and Civic Center Boulevard, Philadelphia, PA 19104, USA
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Abstract
Two cases of marker chromosomes derived from a non-centromeric location were studied to determine the characteristics of these markers with respect to the presence of functional centromeres and whether an associated phenotype could be described. The markers were characterized by fluorescence in situ hybridization and centromeric protein studies. Assessments were done to identify clinical features. Case 1 is a girl referred at age 1.5 years with swirly areas of hyperpigmentation, bilateral preauricular pits, hypotonia, developmental delay, and seizures. Case 2 is a male first evaluated as a newborn and then later during the first year of life. He had streaky hypopigmentation, right preauricular pit, accessory nipples, postaxial polydactyly, asymmetric cerebral ventricles, duplicated right kidney, a right pulmonary artery stenosis, and seizures. Mosaicism for an extra marker from the 3qter region was present in both cases. Both markers had a constriction near one end and were C-band negative. Centromeric protein studies indicated absence of CENP-B, presence of CENP-C (data for case 1 only), and presence of CENP-E. Marker chromosomes were thus identified with a chromosomal origin far from their usual centromeric region and yet appeared to have functional centromeres. These two cases did not permit a specific clinical phenotype to be ascribed to the presence of tetrasomy for 3q26.2 approximately 3q27.2-->3qter.
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Affiliation(s)
- I Teshima
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children and University of Toronto, Toronto, Canada
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Warburton PE, Dolled M, Mahmood R, Alonso A, Li S, Naritomi K, Tohma T, Nagai T, Hasegawa T, Ohashi H, Govaerts LC, Eussen BH, Van Hemel JO, Lozzio C, Schwartz S, Dowhanick-Morrissette JJ, Spinner NB, Rivera H, Crolla JA, Yu C, Warburton D. Molecular cytogenetic analysis of eight inversion duplications of human chromosome 13q that each contain a neocentromere. Am J Hum Genet 2000; 66:1794-806. [PMID: 10777715 PMCID: PMC1378043 DOI: 10.1086/302924] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2000] [Accepted: 03/13/2000] [Indexed: 11/03/2022] Open
Abstract
Neocentromeres are fully functional centromeres that have arisen in previously noncentromeric chromosomal locations on rearranged chromosomes. The formation of neocentromeres results in the mitotic stability of chromosomal fragments that do not contain endogenous centromeres and that would normally be lost. Here we describe a unique collection of eight independent patient-derived cell lines, each of which contains a neocentromere on a supernumerary inversion duplication of a portion of human chromosome 13q. Findings in these patients reveal insight into the clinical manifestations associated with polysomy for portions of chromosome 13q. The results of FISH and immunofluorescent analysis of the neocentromeres in these chromosomes confirm the lack of alpha-satellite DNA and the presence of CENtromere proteins (CENP)-C, -E, and hMAD2. The positions of the inversion breakpoints in these chromosomes have been placed onto the physical map of chromosome 13, by means of FISH mapping with cosmid probes. These cell lines define, within chromosome 13q, at least three distinct locations where neocentromeres have formed, with five independent neocentromeres in band 13q32, two in band 13q21, and one in band 13q31. The results of examination of the set of 40 neocentromere-containing chromosomes that have thus far been described, including the 8 neocentromere-containing chromosomes from chromosome 13q that are described in the present study, suggest that chromosome 13q has an increased propensity for neocentromere formation, relative to some other human chromosomes. These neocentromeres will provide the means for testing hypotheses about sequence requirements for human centromere formation.
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Affiliation(s)
- P E Warburton
- Department of Human Genetics, Mount Sinai School of Medicine, New York, NY, 10029, USA.
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Reddy KS, Sulcova V, Schwartz S, Noble JE, Phillips J, Brasel JA, Huff K, Lin HJ. Mosaic tetrasomy 8q: Inverted duplication of 8q23.3qter in an analphoid marker. ACTA ACUST UNITED AC 2000. [DOI: 10.1002/(sici)1096-8628(20000501)92:1<69::aid-ajmg12>3.0.co;2-o] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Barbi G, Kennerknecht I, Wöhr G, Avramopoulos D, Karadima G, Petersen MB. Mirror-symmetric duplicated chromosome 21q with minor proximal deletion, and with neocentromere in a child without the classical Down syndrome phenotype. AMERICAN JOURNAL OF MEDICAL GENETICS 2000; 91:116-22. [PMID: 10748409 DOI: 10.1002/(sici)1096-8628(20000313)91:2<116::aid-ajmg7>3.0.co;2-q] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We report on a mentally retarded child with multiple minor anomalies and an unusually rearranged chromosome 21. This der(21) chromosome has a deletion of 21p and of proximal 21q, whereas the main portion of 21q is duplicated leading to a mirror-symmetric appearance with the mirror axis at the breakpoint. The centromere is only characterized by a secondary constriction (with a centromeric index of a G chromosome) at an unexpected distal position, but fluorescence in situ hybridization (FISH) with either chromosome specific or with all human centromeres alpha satellite DNA shows no cross hybridization. Thus, the marker chromosome represents a further example of an "analphoid marker with neocentromere." Molecular analysis using polymorphic markers on chromosome 21 verified a very small monosomic segment of the proximal long arm of chromosome 21, and additionally trisomy of the remaining distal segment. Although trisomic for almost the entire 21q arm, our patient shows no classical Down syndrome phenotype, but only a few minor anomalies found in trisomy 21 and in monosomy of proximal 21q, respectively.
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Affiliation(s)
- G Barbi
- Abteilung Medizinische Genetik der Universität, Ulm, Germany.
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Rowe AG, Abrams L, Qu Y, Chen E, Cotter PD. Tetrasomy 15q25?qter: Cytogenetic and molecular characterization of an analphoid supernumerary marker chromosome. ACTA ACUST UNITED AC 2000. [DOI: 10.1002/1096-8628(20000828)93:5<393::aid-ajmg9>3.0.co;2-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Rivera H, Vasquez AI, García-Cruz D, Crolla JA. Neocentromere at 13q32 in one of two stable markers derived from a 13q21 break. AMERICAN JOURNAL OF MEDICAL GENETICS 1999; 85:385-8. [PMID: 10398265 DOI: 10.1002/(sici)1096-8628(19990806)85:4<385::aid-ajmg15>3.0.co;2-p] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A 10-month-old girl with psychomotor retardation, microcephaly, bilateral microphthalmia, and postaxial polydactyly of the feet was karyotyped using banding techniques and (single or dual color) fluorescent in situ hybridization (FISH) with four probes: D13Z1/D21Z1, pancentromeric, pantelomeric, and a mix of 13q subtelomeric and 13/21 alphoid repeats. She was found to have a 47-chromosome karyotype in which a normal 13 was replaced by two stable markers derived from a breakpoint at 13q21.1, namely a del(13)(q21.1) and an isofragment(13) (qter-->q21.1::q21.1-->qter). The latter had a single C-negative but Cd-positive primary constriction at 13q32 which, however, was not obvious in about 12% of the cells. FISH studies showed that the small 13q- had the 13-centromere and a 13q telomere (as shown for a specific 13q subtelomeric signal) onto the broken end whereas the isofragment lacked alphoid signals but had 13q subtelomeric sequences on both ends. Parental karyotypes were normal. The patient's rearrangement represents the eighth chromosome-13-derived marker with a nonalphoid neocentromere located at 13q. All in all, such neocentromeres have been described in 29 markers derived from chromosomes 2, 3, 8-11, 13-15, 20, and Y, and plausibly result from the epigenetic activation of a latent centromere, which may even be a telomere with neocentric activity. The 13q telomere found in the del(13q) was probably captured from the homologous chromosome.
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Affiliation(s)
- H Rivera
- División de Genética, Instituto Mexicano del Seguro Social, Guadalajara, Jalisco, Mexico.
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Abstract
Large blocks of tandemly repeated sequences, or satellites, surround the centromeres of complex eukaryotes. During mitosis in Drosophila, satellite DNA binds proteins that, during interphase, bind other sites. The requirement for a repeat to borrow a partner protein from those available at mitosis might limit the spectrum of repeat units that can be expanded into large blocks. To account for the ubiquity and pericentric localization of satellites, we propose that they are utilized to maintain regions of late replication, thus ensuring that the centromere is the last region to replicate on a chromosome.
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Affiliation(s)
- A K Csink
- Fred Hutchinson, Cancer Research Center, Seattle, WA 98109-1024, USA
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Choo KH. Centromere DNA dynamics: latent centromeres and neocentromere formation. Am J Hum Genet 1997; 61:1225-33. [PMID: 9399915 PMCID: PMC1716064 DOI: 10.1086/301657] [Citation(s) in RCA: 138] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
MESH Headings
- Animals
- Autoantigens
- Centromere/metabolism
- Centromere/ultrastructure
- Centromere Protein A
- Chromatin/genetics
- Chromosomal Proteins, Non-Histone/physiology
- Chromosome Mapping
- Chromosomes, Artificial, Yeast
- Chromosomes, Fungal/genetics
- Chromosomes, Fungal/ultrastructure
- Chromosomes, Human/genetics
- Chromosomes, Human/ultrastructure
- DNA/genetics
- DNA/metabolism
- DNA, Fungal/genetics
- DNA, Fungal/metabolism
- DNA, Satellite/physiology
- Fungal Proteins/physiology
- Humans
- Repetitive Sequences, Nucleic Acid
- Saccharomyces cerevisiae/genetics
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Affiliation(s)
- K H Choo
- Murdoch Institute for Research into Birth Defects, Royal Children's Hospital, Parkville, Australia.
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