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PubMed2006

[Epigenetics of specific chromosome regions].

Investigation of protein complexes, various types of protein modifications and the structure of the chromatin of specific chromosome regions, such as centromeres, telomeres, and adjacent heterochromatic regions, considerably complicated the notion on DNA, prevailing five decades ago, as molecules that exclusively control coding and realization of genetic information. Striking plasticity of the primary structure of centromeric and telomeric DNA suggests a variety of molecular mechanisms underlying fundamental and universal functions of these key chromosome regions. The present review is an attempt to consider the current concepts on the structure of the DNA and protein components, as well as the structure of the chromatin of specific chromosome regions in eukaryotes, and the concerted evolution of these components, leading to the formation of a hierarchy of coordinated DNA-protein complexes.

Animals↗
PubMed2000

Molecular structure and evolution of an alpha satellite/non-alpha satellite junction at 16p11.

We have determined the detailed molecular structure and evolution of an alpha satellite junction from human chromosome 16p11. The analysis reveals that the alpha satellite sequence bordering the transition lacks higher-order structure and that the non-alpha satellite portion consists of a mosaic of duplicated segments of complex evolutionary origin. The 16p11 junction was formed recently (5-10 million years ago) by the duplication and transposition of genomic segments from Xq28 and 4q24. Once this mosaic structure was formed, a larger complex was spread among multiple pericentromeric regions. This resulted in the formation of large (>62 kb) paralogous segments that share a high degree ( approximately 97%) of sequence similarity. Both phylogenetic and comparative analyses indicate that these pericentromeric-directed duplications occurred around the time of the divergence of the human, gorilla and chimpanzee lineages, resulting in the subtle restructuring of the primate genome among these species. The available data suggest that such chimeric structures are a general property of several different human chromosomes near their alpha satellite junctions.

Animals↗
PubMed1996

Loss of telomeric sequences in a ring derived from chromosome 8 in refractory anemia with excess of blasts in transformation.

Using the fluorescence in situ hybridization technique, we analyzed a ring chromosome that appeared as a karyotype evolution in a patient affected by refractory anemia with excess of blasts in transformation. Metaphases hybridized with a chromosome-8-specific centromeric probe indicated that the ring retained the centromere of chromosome 8. Successively, utilizing a probe specific for all human telomeres, we observed that the ring lost telomeric sequences. This study demonstrated that the formation of a ring chromosome in hematologic disorders can cause loss of genetic material not revealed by banding techniques and therefore providing further proof of the advantages of molecular cytogenetic techniques.

Aged↗
PubMed2001

Genomic structure and chromosome location of the human gene encoding the zinc finger autoantigen ZNF330.

We have recently described a novel zinc finger cDNA, ZNF330, which was immunologically characterized as a new human autoantigen, highly conserved during evolution from nematodes to humans. The protein was found at the nucleolus and the cytoplasm in interphase and transiently associates with centromeres in mitosis as determined by immunofluorescence analysis. We now describe that the association of ZNF330 with the nucleolus but not with the cytoplasm is RNA-dependent as shown by RNAse treatment of fixed culture cells, since ZNF330 localization was unaffected by DNAse treatment. We also report the cloning, structural organization and chromosome location of the human ZNF330 gene. The gene is comprised of 10 exons and spans approximately 16 kb of genomic DNA. The conserved residues forming nine CXXC motifs are contained in exons 3 to 9. Several major transcription initiation sites were located 126, 124 and 121 bp upstream of the translation initiation codon ATG, as determined by primer extension analysis. The human ZNF330 gene was mapped by FISH to chromosome 4q31.1-->q31.2, the site of the FRA4C locus previously described as a common fragile site for acquired chromosome instability in humans.

Animals↗
PubMed2005

Breakpoint analysis of the pericentric inversion between chimpanzee chromosome 10 and the homologous chromosome 12 in humans.

During this study, we analysed the pericentric inversion that distinguishes human chromosome 12 (HSA12) from the homologous chimpanzee chromosome (PTR10). Two large chimpanzee-specific duplications of 86 and 23 kb were observed in the breakpoint regions, which most probably occurred associated with the inversion. The inversion break in PTR10p caused the disruption of the SLCO1B3 gene in exon 11. However, the 86-kb duplication includes the functional SLCO1B3 locus, which is thus retained in the chimpanzee, although inverted to PTR10q. The second duplication spans 23 kb and does not contain expressed sequences. Eleven genes map to a region of about 1 Mb around the breakpoints. Six of these eleven genes are not among the differentially expressed genes as determined previously by comparing the human and chimpanzee transcriptome of fibroblast cell lines, blood leukocytes, liver and brain samples. These findings imply that the inversion did not cause major expression differences of these genes. Comparative FISH analysis with BACs spanning the inversion breakpoints in PTR on metaphase chromosomes of gorilla (GGO) confirmed that the pericentric inversion of the chromosome 12 homologs in GGO and PTR have distinct breakpoints and that humans retain the ancestral arrangement. These findings coincide with the trend observed in hominoid karyotype evolution that humans have a karyotype close to an ancestral one, while African great apes present with more derived chromosome arrangements.

Animals↗
PubMed1997

Complex evolution of tandem-repetitive DNA in the Chironomus thummi species group.

The subspecies Chironomus thummi thummi and C. t. piger display dramatic differences in the copy number and chromosomal localization of a tandemly repeated DNA family (Cla elements). In order to analyze the evolutionary dynamics of this repeat family, we studied the organization of Cla elements in the related outgroup species C. luridus. We find three different patterns of Cla element organization in C. luridus, showing that Cla elements may be either strictly tandem-repetitive or be an integral part of two higher-order tandem repeats (i.e., Hinf[lur] elements, Sal[lur] elements). All three types of Cla-related repeats are localized in the centromeres of C. luridus chromosomes. This suggests that the dispersed chromosomal localization of Cla elements in C. t. thummi may be the result of an amplification and transposition during evolution of this subspecies.

Animals↗
PubMed1999

Comparative painting reveals strong chromosome homology over 80 million years of bird evolution.

Chickens and the great flightless emu belong to two distantly related orders of birds in the carinate and ratite subclasses that diverged at least 80 million years ago. In the first ZOO-FISH study between bird species, we hybridized single chromosome paints from the chicken (Gallus domesticus) onto the emu chromosomes. We found that the nine macrochromosomes show remarkable homology between the two species, indicating strong conservation of karyotype through evolution. One chicken macrochromosome (4) was represented by a macro- and a microchromosome in the emu, suggesting that microchromosomes and macrochromosomes are interconvertible. The chicken Z chromosome paint hybridized to the emu Z and most of the W, confirming that ratite sex chromosomes are largely homologous; the centromeric region of the W which hybridized weakly may represent the location of the sex determining gene(s).

Animals↗
PubMed1997

A reappraisal of the tandem fusion theory of karyotype evolution in Indian muntjac using chromosome painting.

We have tested the tandem fusion hypothesis of the origin of the Indian muntjac karyotype (2n = 6/7) by using reciprocal chromosome painting between the Indian muntjac, Chinese muntjac (n = 46) and brown brocket deer (2n = 70 + 3B) with chromosome-specific paint probes derived from flow-sorted chromosomes of these three deer species. Our results have shown that the euchromatic blocks of all chromosome arms of the brown brocket deer have been conserved apparently unchanged in number and content in the Indian muntjac. While confirming the conservation in toto of most of Chinese muntjac euchromatin in the karyotype of the Indian muntjac, we demonstrate that the synteny of chromosomes 1, 2, 3, 4 and 5 of the Chinese muntjac has been disrupted by chromosome rearrangements other than fusions. This indicates that the present karyotype of the Indian muntjac cannot be reconstructed from the hypothetical Chinese muntjac-like 2n = 46 ancestral karyotype exclusively by chromosome fusions. Furthermore, we have shown that the breakpoints of these rearrangements appear to have occurred near to the fusion points formed during the origin of the 2n = 46 karyotype of the Chinese muntjac from a 2n = 70 karyotype, which is believed to be ancestral for the family Cervidae. Moreover, we substantiate that on the Indian muntjac chromosomes, the C5 probe, which is derived from the centromeric satellite sequences of the Chinese muntjac, maps to the putative fusion points determined by comparative chromosome painting and presumably represents the remnants of ancestral centromeric sequences.

Animals↗
PubMed1995

Chromosome rearrangements at telomeric level in hematologic disorders.

Following retrospective screening of our karyotype data from 414 consecutive non-childhood, neoplastic, and preneoplastic hematologic diseases, we have isolated 11 cases with alterations involving one or two chromosome termini, including: a) nonclonal telomeric telomeric associations (tas), b) subclonal terminal rearrangements consisting of additional (add) material of unknown origin fused at the end of the chromosome, c) clonal telomere-centromere fusion (t telcen) with pseudodicentric structure. Most of these abnormalities were present in karyotypes with multiple alterations and associated to an evolutive stage of the disease (9 of 94 cases studied in progression, including three of 22 CML studied in blast crisis). The immunophenotype of the cell populations was lymphoid in eight cases, six of which were NHL, and myeloid, erythroid, and undifferentiated in the other three. More data on telomeric abnormalities may clarify whether there is ubiquitous genomic instability of neoplastic cells or an inborn cell lineage predisposition favoring rearrangements involving telomeres.

Adult↗
PubMed2006

Molecular genetic determinants of human brain size.

Cognitive skills such as tool use, syntactical languages, and self-awareness differentiate humans from other primates. The underlying basis for this cognitive difference has been widely associated with a high encephalization quotient and an anatomically distinct, exceptionally large cerebral cortex. Investigations on congenital microcephaly had revealed several genes that affect mammalian brain size when mutated. At least four of these, microcephalin (MCPH1), abnormal spindle-like microcephaly-associated (ASPM), cyclin-dependent kinase 5 regulatory associated protein 2 (CDK5RAP2), and centromere-associated protein J (CENPJ) are known to have undergone significant positive selection in the great apes and human lineages during primate evolution. MCPH1 and ASPM both have very young single nucleotide polymorphism haplotypes associated with modern humans, and these genes are presumably still evolving in Homo sapiens. Microcephalin has a role in DNA damage response and regulation of cell cycle checkpoints. The other known microcephaly-associated genes encode microtubule-associated centrosomal proteins that might regulate neural progenitor cell division and cell number. Recent reports have also unveiled a previously unknown function of ephrins and Eph in the regulation of neural progenitor cell death with a consequential effect on brain size. Understanding the mechanism for developmental control of brain organogenesis by these genes, and others such as FOXP2, shall provide fresh perspectives on the evolution of human intelligence.

Animals↗
PubMed2002

Gene content and function of the ancestral chromosome fusion site in human chromosome 2q13-2q14.1 and paralogous regions.

Various portions of the region surrounding the site where two ancestral chromosomes fused to form human chromosome 2 are duplicated elsewhere in the human genome, primarily in subtelomeric and pericentromeric locations. At least 24 potentially functional genes and 16 pseudogenes reside in the 614-kb of sequence surrounding the fusion site and paralogous segments on other chromosomes. By comparing the sequences of genomic copies and transcripts, we show that at least 18 of the genes in these paralogous regions are transcriptionally active. Among these genes are new members of the cobalamin synthetase W domain (CBWD) and forkhead domain FOXD4 gene families. Copies of RPL23A and SNRPA1 on chromosome 2 are retrotransposed-processed pseudogenes that were included in segmental duplications; we find 53 RPL23A pseudogenes in the human genome and map the functional copy of SNRPA1 to 15qter. The draft sequence of the human genome also provides new information on the location and intron-exon structure of functional copies of other 2q-fusion genes (PGM5, retina-specific F379, helicase CHLR1, and acrosin). This study illustrates that the duplication and rearrangement of subtelomeric and pericentromeric regions have functional relevance to human biology; these processes can change gene dosage and/or generate genes with new functions.

Amino Acid Sequence↗
PubMed2000

pTAR-encoded proteins in plasmid partitioning.

Partition cassettes, essential for the segregational stability of low-copy-number bacterial plasmids, typically encode two autoregulated proteins and an adjacent cis-acting centromere analog to which one or perhaps both proteins bind. The diminutive partition region of pTAR of Agrobacterium spp. was reported to be exceptional, encoding only a single protein, ParA (D. R. Gallie and C. I. Kado, J. Mol. Biol. 193:465-478, 1987). However, resequencing of the region revealed two small downstream genes, parB and orf-84, of which only parB was found to be essential for partitioning in A. tumefaciens. Purified ParA exhibited a weak ATPase activity that was modestly increased by nonspecific DNA. ParB bound in vitro to repeated sequences present in a region, parS, that possesses centromere and operator functions and within which we identified the primary transcription start site by primer extension. In certain respects the Par proteins behave normally in the foreign host Escherichia coli. In E. coli, as in A. tumefaciens, ParB repressed the partition operon; ParA, inactive alone, augmented this repression. Functional similarities between the partition system of pTAR and those of other plasmids and bacteria are prominent, despite differences in size, organization, and amino acid sequence.

Adenosine Triphosphatases↗
PubMed2003

Key-string algorithm--novel approach to computational analysis of repetitive sequences in human centromeric DNA.

AIM: To use a novel computational approach, Key-string Algorithm (KSA), for the identification and analysis of arbitrarily large repetitive sequences and higher-order repeats (HORs) in noncoding DNA. This approach is based on the use of key string that plays a role of an arbitrarily constructed "computer enzyme". METHOD: A cluster of novel KSA-related methods was introduced and developed on the basis of a combination of computations on a very modest scale, by eye inspection and graphical display of results of analysis. Sequence analysis software was developed, containing seven programs for KSA-related analyses. This approach was demonstrated in the case study of alpha satellites and HORs in the human genetic sequence AC017075.8 (193277 bp) from the centromeric region of human chromosome 7. The KSA segmentation method was applied by using DCCGTTT, GTA, and TTTC key strings. RESULTS: Fifty-five copies of 2734-bp 16mer HORs were identified and investigated, and a start-string TTTTTTAAAAA was identified. The HOR-matrix was constructed and employed for graphical display of mutations. KSA identification of HORs in AC017075.8 was compared with that of RepeatMasker and Tandem Repeat Finder, which identified alpha monomers in AC017075.8, but not the HORs. On the basis of KSA study, the centromere folding was described as an effect of HORs and super-HORs (3 x 2734 bp) in AC017075.8. The following novel computational KSA-based methods, easy-to-use and intended for computational "pedestrians", were demonstrated: color-HOR diagram, KSA-divergence method, 171-bp subsequence-convergence diagram, and total frequency distribution of the key-string subsequence lengths. The results were supplemented by Fast Fourier Transform, employing a novel mapping of symbolic genomic sequence into a numerical sequence. CONCLUSION: The KSA approach offers a simple and robust framework for a wide range of investigations of large repetitive sequences and HORs, involving a very modest scope of computations that can be carried out by using a PC. As the KSA method is HOR-oriented, the identification of HORs is even easier than the identification of underlying alpha monomer itself. This approach provides an easy identification of point mutations, insertions, and deletions, with respect to consensus. This may be useful in a wide range of investigations and applied in forensic medicine, medical diagnosis of malignant diseases, biological evolution, and paleontology.

Algorithms↗
PubMed1992

Highly repeated DNA sequences in birds: the structure and evolution of an abundant, tandemly repeated 190-bp DNA fragment in parrots.

Up to 6.8% of the parrot (Psittaciformes) genome consists of a tandemly repeated, 190-bp sequence (P1) located in the centromere of many if not all chromosomes. Monomer repeats from 10 different psittacine species representing four subfamilies were isolated and cloned. The intraspecific sequence variation ranged from 1.5 to 7%. The interspecific sequence variation ranged from less than 3% between two species of cockatoos to approximately 45% between cockatoos and other parrots. The monomer sequences of all 10 parrot species contained several conserved (> 90%) sequence elements at identical locations within the repeat. A comparison with tandemly repeated DNA sequences in other avian species showed that several of these conserved elements were also present at similar locations within the 184-bp repeat of the Chilean flamingo (Phoenicopterus chilensis), suggesting a great antiquity of the repeat. One of the elements was also found in the tandemly repeated sequences of the crane (Gruidae) and falcon (Falconidae) families. The data were used for the construction of a partial most parsimonious relationship that supports a regional subdivision of the Psittaciformes.

Animals↗
PubMed2000

Kinetochore reproduction in animal evolution: cell biological explanation of karyotypic fission theory.

Karyotypic fission theory of Todd offers an explanation for the diverse range of diploid numbers of many mammalian taxa. Theoretically, a full complement of acrocentric chromosomes can be introduced into a population by chromosomal fission. Subsequent inheritance of ancestral chromosomes and paired fission derivatives potentially generates a diploid range from the ancestral condition to double its number of chromosomes. Although it is undisputed that both chromosomal fission and fusion ("Robertsonian rearrangements") have significantly contributed to karyological diversity, it is generally assumed that independent events, the fission of single chromosomes or the fusion of two chromosomes, are the sources of such change. The karyotypic fission idea by contrast posits that all mediocentric chromosomes simultaneously fission. Here I propose a specific cell biological mechanism for Todd's karyotypic fission concept, "kinetochore reproduction theory," where a complete set of dicentric chromatids is synthesized during gametogenesis, and kinetochore protein dephosphorylation regulates dicentric chromatid segregation. Three postulates of kinetochore reproduction theory are: (i) breakage of dicentric chromosomes between centromere pairs forms acrocentric derivatives, (ii) de novo capping of newly synthesized acrocentric ends with telomeric DNA stabilizes these derivatives, and (iii) mitotic checkpoints regulate chromosomal disjunction to generate fissioned karyotypes. Subsequent chromosomal rearrangement, especially pericentric inversion, increases the probability of genetic isolation amongst incipient sympatric species polytypic for fission-generated acrocentric autosomes. This mechanism obviates the requirement for numerous independent Robertsonian rearrangements and neatly accounts for mammalian karyotype evolution as exemplified in analyses of Carnivora, Artiodactyla, and Primates.

Animals↗
PubMed2006

Physical organization of the 1.709 satellite IV DNA family in Bovini and Tragelaphini tribes of the Bovidae: sequence and chromosomal evolution.

Repetitive DNA in the mammalian genome is a valuable record and marker for evolution, providing information about the order and driving forces related to evolutionary events. The evolutionarily young 1.709 satellite IV DNA family is present near the centromeres of many chromosomes in the Bovidae. Here, we isolated 1.709 satellite DNA sequences from five Bovidae species belonging to Bovini: Bos taurus (BTA, cattle), Bos indicus (BIN, zebu), Bubalus bubalis (BBU, water buffalo) and Tragelaphini tribes: Taurotragus oryx (TOR, eland) and Tragelaphus euryceros (TEU, bongo). Its presence in both tribes shows the sequence predates the evolutionary separation of the two tribes (more than 10 million years ago), and primary sequence shows increasing divergence with evolutionary distance. Genome organization (Southern hybridization) and physical distribution (in situ hybridization) revealed differences in the molecular organization of these satellite DNA sequences. The data suggest that the sequences on the sex chromosomes and the autosomes evolve as relatively independent groups, with the repetitive sequences suggesting that Bovini autosomes and the Tragelaphini sex chromosomes represent the more primitive chromosome forms.

Animals↗
PubMed1997

The chromosomal distributions of Ty1-copia group retrotransposable elements in higher plants and their implications for genome evolution.

Retrotransposons make up a major fraction--sometimes more than 40%--of all plant genomes investigated so far. We have isolated the reverse transcriptase domains of the Ty1-copia group elements from several species, ranging in genome size from some 100 Mbp to 23,000 Mbp, and determined the distribution patterns of these retrotransposons on metaphase chromosomes and within interphase nuclei by DNA:DNA in situ hybridization. With some exceptions, the reverse transcriptase domains were distributed over the length of the chromosomes. Exclusion from rDNA sites and some centromeres (e.g., slash pine, 23,000 Mbp, or barley, 5500 Mbp) is frequent, whereas many species exclude retrotransposons from other sites of heterochromatin (e.g., intercalary and centromeric sites in broad bean). In contrast, in the plant Arabidopsis thaliana, widely used for plant molecular genetic studies because of its small genome (c. 100 Mbp), the Ty1-copia group reverse transcriptase gene domains are concentrated in the centromeric regions, colocalizing with the 180 bp satellite sequence pAL1. Unlike the pAL1 sequence, however, the Ty1-copia signal is also detectable as weaker, diffuse hybridization along the lengths of the chromosomes. Possible mechanisms for evolution of the contrasting distributions are discussed. Understanding the physical distribution of retrotransposons and comparisons of the distribution between species is critical to understanding their evolution and the significance for generation of the new patterns of variability and in speciation.

Chromosome Mapping↗
PubMed2001

A population of autoantibodies against a centromere-associated protein A major epitope motif cross-reacts with related cryptic epitopes on other nuclear autoantigens and on the Epstein-Barr nuclear antigen 1.

Autoimmune diseases arise from a host's immune response against self-antigens. The triggering events ultimately resulting in such a break of tolerance are largely unknown. It is also not known why certain molecular structures become autoantigenic. The hypothesis has long been proposed that autoimmune diseases arise from molecular mimicry followed by an epitope spreading mechanism. Recently we have shown that the anti-centromere-associated protein A (CENP-A) immune response is directed against an autoantigenic motif, G/A-P-R/S-R-R, that occurs three times in the N-terminal amino acids of CENP-A. In the present study we used mutational analyses with immobilized oligopeptide arrays to identify the amino acids in this motif that are responsible for antibody binding. In particular, we found that surprisingly mimotopes of this motif are present in a vast number of autoantigens and in the Epstein-Barr nuclear antigen 1. With affinity-purified antibodies we show that the antibodies against this motif are polyclonal and cross-react with several autoantigens. However, in these autoantigens this motif often represents a cryptic epitope explaining the obvious conflict between our results and the known high specificity of autoantibodies. The presence of such an ubiquitous structure on autoantigens suggests a novel peptide-driven mechanism for the evolution of autoantibodies.

Amino Acid Motifs↗