Terminal Regions Of Chromosomes Research Articles

Molecular and cytogenetic characterization of Crassostrea angulata chromosomes

We have conducted a molecular cytogenetic study of Crassostrea angulata, by treating its mitotic chromosomes with C-banding, fluorochrome and oligopeptide staining, restriction enzyme banding and fluorescent in situ hybridization, using three repetitive or multicopy DNAs (the GATA sequence, the TTAGGG telomeric repeat and the 5S rDNA). Results on C-banding indicate the presence of heterochromatin in several chromosomes occupying telomeric positions. The staining with DAPI, DA/DAPI and AMD/DAPI allow concluding that large regions rich in AT in the chromosomes of C. angulata do not exist. Restriction banding has shown few restriction sites for AluI (AGTC site) and a relative abundance of G-C in terminal and interstitial chromosome regions, inferred by the digestion with HaeIII (GGCC site) and BamHI (GGATCC site). In situ hybridization with GATA indicated that these repeated sequences are widely dispersed in the genome of this species, whereas hybridization with the telomeric repeat revealed small bright hybridization signals, uniform in size and intensity, on each telomere of all chromosomes but not in interstitial positions. Location of 5S rDNA displayed the presence of two 5S-bearing chromosome pairs, of large size, on the subterminal position of the karyotype of C. angulata, this location being different from the ones encoding the major ribosomal genes in chromosome pair 10 (described in a previous paper).

Use of Subtelomeric FISH in the Work-Up of Children with Developmental Delay

Small rearrangements in the telomeric region (the terminal regions of chromosomes) are responsible for many cases of developmental delay with minor

Epigenetic assembly of centromeric chromatin at ectopic alpha-satellite sites on human chromosomes.

To investigate the mechanism of chromatin assembly at human centromeres, we isolated cultured human cell lines in which a transfected alpha-satellite (alphoid) YAC was integrated ectopically into the terminal region of host chromosome 16, where it was stably maintained. Centromere activity of the alphoid YAC was suppressed at ectopic locations on the host chromosome, as indicated by the absent or reduced assembly of CENP-A and -C. However, long-term culture in selective medium, or short-term treatment with the histone deacetylase inhibitor Trichostatin A (TSA), promoted the re-assembly of CENPA, -B and -C at the YAC site and the release of minichromosomes containing the YAC integration site. Chromatin immunoprecipitation analyses of the re-formed minichromosome and the alphoid YAC-based stable human artificial chromosome both indicated that CENP-A and CENP-B assembled only on the inserted alphoid array but not on the YAC arms. On the YAC arms at the alphoid YAC integration sites, TSA treatment increased both the acetylation level of histone H3 and the transcriptional level of a marker gene. An increase in the level of transcription was also observed after long-term culture in selective medium. These activities, which are associated with changes in chromatin structure, might reverse the suppressed chromatin state of the YAC at ectopic loci, and thus might be involved in the epigenetic change of silent centromeres on ectopic alphoid loci.

Telomeric repeat-length alterations in colorectal carcinoma are associated with loss of heterozygosity and point mutation in p53 gene

The telomere, the terminal region of eukaryotic chromosomes, plays an important role in the stability of DNA replication and in the protection of chromosomal ends. To investigate whether the two-stage mechanism of cellular aging and immortalization in vitro is involved in the carcinogenesis and immortalization of human colorectal carcinomas, we examined for genetic alterations in the telomeres and in the p53, Rb, and K-ras genes. Based on our results, we discuss the effects that these genetic changes might have on mechanisms, such as the mortality stage 1 (M1), that normally prevent immortalization in carcinoma cells. Telomeric repeat-lengths (TRL) were measured by Southern blot analysis, and p53 Rb and K-ras gene variants were detected by PCR based assays. Thirty-six primary colorectal carcinomas were examined. Telomere alterations were found in 19 of 36 (52.8%) cases, while mutations of the p53 gene were observed in 15 of 36 (41.7%) cases and LOH involving p53 observed in 14 of 36 (38.9%) cases. Twelve of 15 (80%) cases with p53 mutations also showed altered TRL, so that p53 mutations were positively associated with TRL alterations (p=0.008). Ten of 14 (71.4%) cases with LOH of p53 also showed alteration in TRL, also revealing a positive association with TRL (p=0.09). The six cases with both p53 mutation and LOH all showed altered TRL. K-ras gene mutations and LOH involving the Rb gene were not associated with alterations in TRL. These results suggest that inactivation of p53 is one of the factors that promotes immortalization and overcomes M1 in colorectal carcinoma.

2배체 담배 Nicotiana plumbaginifolia의 핵형 분석과 rDNAs의 Physical Mapping

2배체 담배인 Nicotiana plumbaginifolia를 대상으로 상염색법과 FISH 기법을 통한 염색체 분석을 수행하여 다음과 같은 결과를 얻었다. N. plumbaginifolia의 체세포 염색체 수는 2n=20이며, arm ratio 비교를 통한 핵형 분석에서 중기 염색체 조성은 3쌍의 중부 염색체 (염색체 1,2 및 7)와 7쌍의 차중부 염색체 (염색체 3, 4, 5, 6, 7, 9 및 10)로 관찰되었다. 염색체의 길이는 2.29~4.50 <TEX>$\mu\textrm{m}$</TEX>로 나타났으며, 염색체 1번과 2번은 부수체 염색체로 관찰되었다. 5S와 45S rDNA를 탐침으로 FISH를 수행한 결과 2번 염색체의 동원체 부위에서 한 쌍의 5S signal이 확인되었고, 1번 염색체의 부수체에서 한 쌍의 45S signal이 관찰되었다. Karyotype analysis and chromosomal localization of 5S and 45S rDNAs using FISH (fluorescence in situ hybridization) technique were carried out in Nicotiana plumbaginifolia. Somatic chromosome number of N. plumbaginifolia was 2n=20 and kyarotype was composed of three pairs of metacentric chromosomes (1,2 and 7) and seven pairs of submetacentric chromosomes (3, 4, 5, 6, 8, 9 and 10). Length of chromosomes was ranged from 2.29 to 4.50 <TEX>${\mu}{\textrm}{m}$</TEX>. Chromosome 1 and 2 were identified as satellite chromosomes. In FISH experiment, one pair of 5S rDNA signals was detected on the centromeric region of chromosome 2 and one pair of 45S rDNA signals was detected on the terminal region of chromosome 1.

Origin and differentiation of a sex chromosome system in Parodon hilarii (Pisces, Parodontidae). Satellite DNA, G- and C-banding.

A satellite DNA sequence of Parodon hilarii (named pPh2004) was isolated, cloned and sequenced. This satellite DNA is composed of 200bp, 60% AT rich. In situ hybridization (FISH) results revealed that the satellite DNA pPh2004 is located in the terminal regions of several chromosomes, forming highly evident blocks in some and punctual marks in others. The comparison between the FISH and C-banding results showed that the location of this satellite DNA coincides with that of most terminal heterochromatins. However, some regions are only marked by FISH whereas other regions are only marked by C-banding. The possible existence of more than one satellite DNA family could explain these partial differences. The in situ hybridization with the satellite DNA and the G- and C-bandings confirmed the presence of a sex chromosome system of the ZZ/ZW type in P. hilarii, as well as the correct identification of the Z chromosome in the karyotype. This chromosome displays a segment of terminal heterochromatin in the long arm, similar to the segment observed in the short arm of the W chromosome, also showing a G-banding pattern similar to that of the short arm and part of the long arm of the W chromosome. A hypothesis on the origin of the W chromosome from an ancestral chromosome similar to the Z chromosome is presented.

Hodgkin's lymphoma cell lines are characterized by frequent aberrations on chromosomes 2p and 9p including REL and JAK2.

Four Hodgkin's lymphoma cell lines (KM-H2, HDLM-2, L428, L1236) were analyzed for cytogenetic aberrations, applying multiplex fluorescence in situ hybridization, chromosome banding and comparative genomic hybridization. Each line was characterized by a highly heterogeneous pattern of karyotypic changes with a large spectrum of different translocated chromosomes (range 22-57). A recurrent finding in all cell lines was the presence of chromosomal rearrangements of the short arm of chromosome 2 involving the REL oncogene locus. Furthermore, multiple translocated copies of telomeric chromosomal segments were frequently detected. This resulted in a copy number increase of putative oncogenes, e.g., JAK2 (9p24) in 3 cell lines, FGFR3 (4p16) and CCND2 (12p13) in 2 cell lines as well as MYC (8q24) in 1 cell line. Our data confirm previous cytogenetic results from primary Hodgkin's tumors suggesting an important pathogenic role of REL and JAK2 in this disease. In addition, they provide evidence for a novel cytogenetic pathomechanism leading to increased copy numbers of putative oncogenes from terminal chromosomal regions, most probably in the course of chromosomal stabilization by telomeric capture.

Molecular characterization of a set of wheat deletion stocks for use in chromosome bin mapping of ESTs.

The objective of this study was molecular characterization of a set of deletion stocks and other aneuploids for use in chromosome bin mapping of ESTs in wheat. Wheat aneuploid stocks including 21 nullisomic-tetrasomic (NT), 24 ditelosomic (Dt), and 101 deletion (del) lines were screened with 526 EST clones. A total of 1,951 loci were detected by 493 informative EST clones and tagged 150 of the 159 deletion intervals or chromosome bins. Previously described deletion lines del1AS-4, del6AL-2, del6BS-6, and del7DS-6 were found to have normal chromosome constitution. The short arm deletion in del3AS-3 may be translocated from an unknown chromosome as this stock is nullisomic for the 3AS arm. Thirty-five new deletions were detected in 26 lines. Most of the new deletions occurred in terminal regions of chromosomes and probably resulted from the loss of very small terminal fragments that were difficult to detect cytologically. Eleven chromosome aberrations were also detected in two NT and five Dt lines. Overall, the chromosome bin map provides a resolution of around 28 Mb for an anchor map of a basic set of seven chromosomes of the Triticeae. Any target gene can be allocated to a specific 28-Mb bin and associated ESTs, anchored to the other Triticeae/grass maps including rice and, therefore, amenable to molecular cloning by comparative and wheat-based positional cloning methods.

Cell cycle-dependent localization of two novel prokaryotic chromosome segregation and condensation proteins in Bacillus subtilis that interact with SMC protein

Disruption of ypuG and ypuH open reading frames in Bacillus subtilis leads to temperature-sensitive slow growth, a defect in chromosome structure and formation of anucleate cells. The genes, which were named scpA and scpB, were found to be epistatic to the smc gene. Fusions of ScpA and ScpB to the fluorescent proteins YFP or CFP showed that both proteins co-localize to two or four discrete foci that were present at mid-cell in young cells, and within both cell halves, generally adjacent to chromosomal origin regions, in older cells. ScpA and ScpB foci are associated with DNA and depend on the presence of SMC and both Scps. ScpA and ScpB are associated with each other and with SMC in vivo, as determined using the FRET technique and immunoprecipitation assays. Genes similar to scpA and scpB are present in many bacteria and archaea, which suggests that their gene products form a condensation complex with SMC in most prokaryotes. The observed foci could constitute condensation factories that pull DNA away from mid-cell into both cell halves.

Multi-color Genomic In Situ Hybridization Identifies Parental Chromosomes in Somatic Hybrids of Diospyros kaki and D. glandulosa

Multi-color genomic in situ hybridization (MCGISH) was performed for mitotic cells of the somatic hybrids of Diospyros kaki (2n = 6x = 90) and D. glandulosa (2n = 2x = 30). Total DNA of D. kaki and D. glandulosa were isolated and labeled with biotin-16-UTP and digoxigenin (DIG)-11-UTP, respectively. The labeled DNAs were used as probes to differentiate parental chromosomes. The biotin-labeled probe was detected with avidin-rhodamine, and the DIG-labeled probe was detected with anti-DIG-FITC (fluorescein isothiocyanate). Ninety chromosomes from D. kaki that showed reddish-orange and 30 chromosomes from D. glandulosa that showed greenish-yellow were observed under a fluorescence microscope. Some chromosomes showed cross-hybridization with both probes at their terminal or other chromosome regions. These results indicated that MCGISH could be used to analyze genomes of Diospyros species whose chromosomes are small and numerous.

Organization of the 378 bp satellite repeat in terminal heterochromatin of Allium fistulosum

Telomeres, DNA-protein structures, are important elements of the eukaryotic chromosome. Telomeric regions of the majority of higher plants contain heptanucleotides TTTAGGG arranged into a tandem repeat. However, some taxa have no such repeats. These are some species of lilies (Lilium) and onions (Allium). For example, terminal regions of chromosomes of Spanish onion (Allium fistulosum) contain satellite DNA whose unit repeats are 380 bp in length, and the short arm of its chromosome 8 contains rDNA repeats. This study deals with the terminal heterochromatin and organization of the satellite repeat in A. fistulosum. Fluorescent in situ hybridization (FISH) was used to locate the satellite DNA on chromosomes and on extended DNA of A. fistulosum. Nonsatellite DNA was found in the structure of telomeric repeat. Polymerase chain reaction (PCR) and Southern hybridization were used for analysis of terminal heterochromatin. Various rearrangements were found in the satellite repeat. The roles of retrotransposones and microsatellites in the formation of terminal heterochromatin are discussed.

Multiplex FISH telomere integrity assay identifies an unbalanced cryptic translocation der(5)t(3;5)(q27;p15.3) in a family with three mentally retarded individuals.

Cryptic rearrangements involving the terminal regions of chromosomes are suspected to be the cause of idiopathic mental retardation in a significant number of cases. This finding highlights the necessity of a primary screening test for such chromosome aberrations. Here we present a multiplex fluorescence in situ hybridization telomere integrity assay which allows the detection of submicroscopic aberrations in the telomeric regions of all chromosomes. This novel approach identified an unbalanced cryptic translocation der(5)t(3;5)(q27;p15.3) in a family with three cases of unexplained mental retardation and dysmorphic features. The symptoms of the patients represent neither the classical dup(3q)- nor cri du chat syndrome, although all affected individuals demonstrate several features of both syndromes. The identification of two balanced translocation carriers emphasizes the significance of the telomere integrity assay for genetic counseling and prenatal diagnosis.

Heterochromatin differentiation in holocentric chromosomes of Rhynchospora (Cyperaceae)

Holocentric chromosomes of six species of Rhynchospora, R. ciliata, R. pubera, R. riparia and R. barbata (2n = 10), R. nervosa (2n = 30) and R. globosa (2n = 36), were stained with CMA3/DAPI fluorochromes or treated with C-banding and sequentially stained with Giemsa or CMA3/DAPI. Variability in banding pattern was found among the species studied. Heterochromatin was observed on terminal and interstitial chromosome regions, indicating that the holocentric chromosomes of Rhynchospora show a heterochromatin distribution pattern similar to those plant monocentric chromosomes.

Chromosome N-banding polymorphism in Aegilops geniculata Roth.

The chromosome morphology and the variation in the N-band distribution along the chromosomes were studied in 13 accessions of the wild wheat Aegilops geniculata Roth (2n=28, genome formula UUM°M°). The karyotype consisted of four metacentric, five submetacentric, three subtelocentric, and two satellited pairs of chromosomes. The N-banding technique stained differentially all 14 chromosome pairs. The most prominent bands were observed near the centromeres and in the intercalary regions of both arms. Telomeric bands were found in only seven chromosomes. All chromosomes produced a specific banding pattern, permitting their identification. Polymorphism for presence or absence of particular bands was observed among the different accessions. The variable bands were located predominantly at the terminal and subterminal chromosome regions, and were also unevenly distributed over chromosomes. This polymorphism resulted in up to eight distinct banding pattern variants for each of the Ae. geniculata chromosomes. Each accession in this study showed a unique overall karyotype, sharing 0 to 8 chromosomes of identical banding pattern with the other accessions. A generalized idiogram of Aegilops geniculata is presented.

Genomic organization, chromosomal localization, and transcriptional variants of the murine Pactolus gene.

The Pactolus gene encodes a cell surface protein similar to that of the beta integrin subunit family. The murine Pactolus gene is comprised of 16 exons that encompass 24 kb of the genome. The genomic organization of the Pactolus gene is very similar to that described for the human beta2 integrin gene (and deduced for murine beta2 integrin), including a separate exon containing only 5' untranslated sequences. The Pactolus gene was mapped to a terminal region of murine Chromosome (Chr) 16, distinct from the previously mapped site of the beta2 integrin gene on murine Chr 10. The Pactolus gene encodes three distinct transcripts via alternative splicing. The Pactolus A transcript encodes the full-length protein including transmembrane and cytoplasmic domains, while the Pactolus B transcript truncates translation before reaching these membrane-anchoring sequences. A newly discovered form, Pactolus C, is found in neonatal samples (along with Pactolus A) and would also encode a prematurely terminated protein. This form is derived from an alternative splicing event that skips part of exon 11, deletes exon 12, and uses an alternative acceptor site upstream of exon 13. The formation of the Pactolus B and C forms is thus governed by a complex alternative splicing mechanism that is affected by the developmental status of the animal.

Acute myeloid leukemia possessing jumping translocation is related to highly elevated levels of EAT/mcl-1, a Bcl-2 related gene with anti-apoptotic functions

Jumping translocations (JTs) are unbalanced chromosomal translocations in which an identical chromosomal region is translocated to the telomeric region of different chromosomes. JTs are rare in hematological malignancies where they are second translocations and may be an indicator of poor prognosis. We report a case of acute myeloid leukemia with t(16;21) and a JT in which the long arm of chromosome 1 distal to q21 is translocated to the terminal region of chromosome 10. The leukemic cells exhibit high expression of EAT/mcl1, an anti-apoptotic Bcl-2 related gene. Since EAT/mcl1 is mapped to 1q21 near the breakpoint in the JTs, high level expression of EAT/mcl1 may be associated with the poor prognosis of leukemia with JTs.

Subtle overlapping deletions in the terminal region of chromosome 6q24.2‐q26: Three cases studied using FISH

Interstitial deletions in the terminal region of chromosome 6 are rare. We describe three new cases with subtle interstitial deletions in the q24-q26 region of the long arm of chromosome 6. The karyotypes were analyzed at a 550 band level. Patient1 is a 9-month-old boy with an interstitial deletion, del(6)(q24.2q25.1), developmental delay, low birth weight, hypotonia, heart murmur, respiratory distress, craniofacial and genital anomalies. This is the first report of a case with deletion del(6)(q24.2q25.1). Patient 2 is a 17-year-old young man with an interstitial deletion del(6)(q25.1q25.3), developmental delay, short stature, mental retardation, autism, head, face, chest, hand and feet anomalies and a history of seizures. For the first time autism was described as a manifestation in 6q deletions. Patient 3 is baby boy with a de novo interstitial deletion, del(6)(q25.1q26), anomalies of the brain, genital organs, limbs and feet. This is the first report of a case with deletion, del(6)(q25.1q26). In all three patients, fluorescence in situ hybridization (FISH) using chromosome 6 painting probe ruled out an insertion. The ESR (6q25.1) and TBP (6q27) probes were used to confirm the breakpoints. Since TBP signal is present in all cases, it confirmed an interstitial deletion proximal to this probe. Patient 1 has a deletion of the ESR locus; Patient 2 and 3 have signals for the ESR locus on both chromosomes 6. Therefore the deletion in Patients 2 and 3 are between ESR and TBP loci distal to that of Patient 1. FISH validated the deletion breakpoints assessed by conventional cytogenetics. Am. J. Med. Genet. 87:17–22, 1999. © 1999 Wiley-Liss, Inc.

Densely methylated sequences that are preferentially localized at telomere-proximal regions of human chromosomes.

We have constructed a library of densely methylated DNA sequences from human blood DNA by selecting fragments with a high affinity for a methyl-CpG binding domain (MBD) column. PCR analysis of the library confirmed the presence of known densely methylated CpG island sequences. Analysis of random clones, however, showed that the library was dominated by sequences whose G+C content and CpG frequency were intermediate between those of bulk genomic DNA and bona fide CpG islands. When human chromosomes were probed with the library by fluorescent in situ hybridisation (FISH), the predominant sites of labelling were at terminal regions of many chromosomes, approximately corresponding to T-bands. Analysis of the methylation status of random clones indicated that all were heavily methylated at CpGs in blood DNA, but many were under-methylated in sperm DNA. Lack of methylation in germ cells may reduce CpG depletion at some sub-terminal sequences and result in a high density of methyl-CpG when these regions become methylated in somatic cells.

Subtle overlapping deletions in the terminal region of chromosome 6q24.2-q26: Three cases studied using FISH

Interstitial deletions in the terminal region of chromosome 6 are rare. We describe three new cases with subtle interstitial deletions in the q24-q26 region of the long arm of chromosome 6. The karyotypes were analyzed at a 550 band level. Patient1 is a 9-month-old boy with an interstitial deletion, del(6)(q24.2q25.1), developmental delay, low birth weight, hypotonia, heart murmur, respiratory distress, craniofacial and genital anomalies. This is the first report of a case with deletion del(6)(q24.2q25.1). Patient 2 is a 17-year-old young man with an interstitial deletion del(6)(q25.1q25.3), developmental delay, short stature, mental retardation, autism, head, face, chest, hand and feet anomalies and a history of seizures. For the first time autism was described as a manifestation in 6q deletions. Patient 3 is baby boy with a de novo interstitial deletion, del(6)(q25.1q26), anomalies of the brain, genital organs, limbs and feet. This is the first report of a case with deletion, del(6)(q25.1q26). In all three patients, fluorescence in situ hybridization (FISH) using chromosome 6 painting probe ruled out an insertion. The ESR (6q25.1) and TBP (6q27) probes were used to confirm the breakpoints. Since TBP signal is present in all cases, it confirmed an interstitial deletion proximal to this probe. Patient 1 has a deletion of the ESR locus; Patient 2 and 3 have signals for the ESR locus on both chromosomes 6. Therefore the deletion in Patients 2 and 3 are between ESR and TBP loci distal to that of Patient 1. FISH validated the deletion breakpoints assessed by conventional cytogenetics.

Clarification of the order of acrosin and aconitase 2 genes on the physical and linkage maps of porcine chromosome 5.

Introduction: The acrosin gene (ACR) has been assigned to the terminal region of swine chromosome 5 p-arm, p15, by fluorescence in situ hybridization1. The aconitase gene (ACO2) was assumed to map to the p telomeric region of chromosome 5, on the basis of its position in linkage map1,2. In order to explore the arrangement of ACO2 and ACR on the chromosome and in the linkage map, we have molecularly cloned porcine genomic fragments containing at least a part of the ACO2 and ACR genes.