Short Arms Of Acrocentric Chromosomes Research Articles

Non-canonical DNA in human and other ape telomere-to-telomere genomes.

Non-canonical (non-B) DNA structures-e.g., bent DNA, hairpins, G-quadruplexes, Z-DNA, etc.-which form at certain sequence motifs (e.g., A-phased repeats, inverted repeats, etc.), have emerged as important regulators of cellular processes and drivers of genome evolution. Yet, they have been understudied due to their repetitive nature and potentially inaccurate sequences generated with short-read technologies. Here we comprehensively characterize such motifs in the long-read telomere-to-telomere (T2T) genomes of human, bonobo, chimpanzee, gorilla, Bornean orangutan, Sumatran orangutan, and siamang. Non-B DNA motifs are enriched at the genomic regions added to T2T assemblies, and occupy 9-15%, 9-11%, and 12-38% of autosomes, and chromosomes X and Y, respectively. Functional regions (e.g., promoters and enhancers) and repetitive sequences are enriched in non-B DNA motifs. Non-B DNA motifs concentrate at short arms of acrocentric chromosomes in a pattern reflecting their satellite repeat content and might contribute to satellite dynamics in these regions. Most centromeres and/or their flanking regions are enriched in at least one non-B DNA motif type, consistent with a potential role of non-B structures in determining centromeres. Our results highlight the uneven distribution of predicted non-B DNA structures across ape genomes and suggest their novel functions in previously inaccessible genomic regions.

Whole-genome analysis of a putative rare and complex interchromosomal reciprocal insertion: thorough investigations for a straightforward interpretation

Research questionShould whole-genome investigations be considered systematically before a complex chromosomal abnormality preimplantation genetic testing for structural chromosomal rearrangements (PGT-SR) management is carried out using conventional cytogenetic techniques? DesignA male carrying a putative rare interchromosomal reciprocal insertion (IRI) 46,XY,ins(14;?)(q11;?).ish der(14)ins(14;22)(q11.2;q11.2q11.2)(xcp14+,xcp22+,N25+,3’TRA/D+),der(22)ins(22;14)(q11.2;q11.2q11.2)(xcp22+,xcp14+,N25-,5’TRA/D+), and his partner were referred to our centre for preimplantation genetic testing analysis after three spontaneous miscarriages. Whole-genome sequencing was used to distinguish between the proposed IRI and an alternative explanation of reciprocal translocation. Fluorescence in-situ hybridization was used to detect all chromosome segments involved in this chromosomal rearrangement, to identify transferable normal and balanced embryos. ResultsWhole-genome sequencing allowed the determination of the number of chromosomal breakpoints involved in chromosomal rearrangement between chromosomes 14 and 22. Finally, only two breakpoints were identified instead of four in IRI rearrangements, which suggests a reciprocal translocation rearrangement. A probe strategy was established to highlight all chromosomal imbalances, whether IRI or reciprocal translocation, and preimplantation genetic testing cycles were achieved. ConclusionConventional cytogenetic techniques are not capable of identifying all complex chromosomal rearrangements, especially those involving centromeric regions and short arms of acrocentric chromosomes. The advent of new sequencing technologies has allowed for a better appreciation of genome complexity. In this study, whole-genome analysis provided additional information to explain the occurrence of genomic events and confirmed that the initial diagnosis of IRI identified by conventional cytogenetic techniques was, in fact, a simple reciprocal translocation. A reliable PGT-SR strategy was proposed for this couple to achieve their parental project.

Instability of Short Arm of Acrocentric Chromosomes: Lesson from Non-Acrocentric Satellited Chromosomes. Report of 24 Unrelated Cases

Satellited non-acrocentric autosomal chromosomes (ps–qs-chromosomes) are the result of an interchange between sub- or telomeric regions of autosomes and the p arm of acrocentrics. The sequence homology at the rearrangement breakpoints appears to be, among others, the most frequent mechanism generating these variant chromosomes. The unbalanced carriers of this type of translocation may or may not display phenotypic abnormalities. With the aim to understand the causative mechanism, we revised all the ps–qs-chromosomes identified in five medical genetics laboratories, which used the same procedures for karyotype analysis, reporting 24 unrelated cases involving eight chromosomes. In conclusion, we observed three different scenarios: true translocation, benign variant and complex rearrangement. The detection of translocation partners is essential to evaluate possible euchromatic unbalances and to infer their effect on phenotype. Moreover, we emphasize the importance to perform both, molecular and conventional cytogenetics methods, to better understand the behavior of our genome.

Jumping translocations of chromosome 1q occurring by a multi-stage process in an acute myeloid leukemia progressed from myelodysplastic syndrome with a TET2 mutation

BackgroundJumping translocations (JTs) are rare chromosome rearrangements characterized by re-localization of one donor chromosome to multiple recipient chromosomes. Here, we describe an acute myeloid leukemia (AML) that progressed from myelodysplastic syndrome (MDS) in association with acquisition of 1q JTs. The sequence of molecular and cytogenetic changes in our patient may provide a mechanistic model for the generation of JTs in leukemia.Case presentationA 68-year-old man presented with pancytopenia. Bone marrow aspirate and biopsy showed a hypercellular marrow with multilineage dysplasia, consistent with MDS, with no increase in blasts. Karyotype and MDS fluorescence in situ hybridization (FISH) panel were normal. Repeat bone marrow aspirate and biopsy after 8 cycles of azacitidine, with persistent pancytopenia, showed no changes in morphology, and karyotype was again normal. Myeloid mutation panel showed mutations in RUNX1, SRSF2, ASXL1, and TET2. Three years after diagnosis, he developed AML with myelodysplasia-related changes. Karyotype was abnormal, with unbalanced 1q JTs to the short arms of acrocentric chromosomes 14 and 21, leading to gain of 1q.ConclusionsOur patient had MDS with pathogenic mutations of the RUNX1, SRSF2, ASXL1, and TET2 genes and developed 1q JTs at the time of progression from MDS to AML. Our data suggest that the formation of 1q JTs involves multiple stages and may provide a mechanistic model for the generation of JTs in leukemia.

Presence of 15p Marker D15Z1 on the Short Arm of Acrocentric Chromosomes is Associated with Aneuploid Offspring in Mexican Couples.

Variation in the location of the 15p region D15Z1 is recognized as a polymorphism in several human populations. We used high-stringency Fluorescence In Situ Hybridization (FISH) to detect D15Z1 in a Mexican cohort. Here, we report the presence of extra D15Z1 sequences on the p-arm of acrocentric chromosomes other than 15 in two groups of Mexican couples, one with healthy offspring (n = 75) and the other with aneuploid offspring (n = 87), mainly trisomy 21. The additional D15Z1 polymorphism was significantly increased in individuals with aneuploid offspring (26.4%), in comparison to individuals with healthy offspring (14%). The most frequent acceptor chromosome of D15Z1 was chromosome 13p, followed by 14p, and finally, 21p. Our results show an overall frequency of 21.6% of this polymorphism in the Mexican population and suggest that its presence might be associated with the mis-segregation of other acrocentric chromosomes and aneuploid offspring. The high frequency of the polymorphism of the D15Z1 sequence on acrocentric chromosomes other than 15 suggests a sequence homogenization of the acrocentric p arms, related to the important function of the centromere and the nucleolar organization region, which flank satellite III DNA.

70. PREIMPLANTATION GENETIC TESTING FOR YQH-AUTOSOME TRANSLOCATION CARRIERS: ANALYSIS OF GAMETE SEGREGATION

Introduction Y-autosome translocations occur in approximately 1:2000 in population and represent special group of reciprocal exchanges. Due to a balanced nature they do not influence on phenotype in general. However, Y-autosome translocation can dislocate sex bivalent formation and chromosome synapsis in the first meiotic division prophase that led to gamete aneuploidy or pachytene arrest. More often Y-derived DNA, predominantly Yq12 band, is translocated onto the short arm of acrocentric chromosomes, mainly chromosomes 15 and 22 due to a strong correlation in their satellite DNA sequences. In women inheritance of such derivative acrocentric chromosomes could be associated with the risk of ovarian malignancy, but the particular mechanism of this pathological effect is not entirely clear since the Yq12 band consists of tandemly organized satellite DNA sequences. It can be associated with the transcription of satellite DNAwhich occurs during carcinogenesis. Material & methods Two families with Yq12/15p and one – with Yq12/22p translocations were analyzed during IVF cycle with PGT in International Centre for Reproductive Medicine. The mean age of men and women was 36±2.8 and 34.25±1.4 years respectively. Karyotyping analysis was performed using GTG banding technique on metaphase chromosomes from peripheral blood lymphocytes. Fluorescence in situ hybridization (FISH) was used to clarify the breakpoint on chromosomes and confirm the chromosomes-specificity of the probes. Additionally, seven chromosomes (13, 14, 15 or 22, 16, 18, 21, X), which are not involved in rearrangement, were analyzed. Results FISH with chromosome specific probes was performed on blastomere from cleavage-stage embryo. A total of 42 blastomeres were analyzed. In 43% of the blastomeres «adjacent-1» segregationwith derivate autosome and X or Y chromosomes was revealed. Segregation 3:1 was observed in 10% of the cells, with no predominant inheritance of the derivative autosome. In 21% of cells the type of chromosome segregation could not be determined due to mosaicismor polyploidy. 45% of the cells were aneuploid for autosomes, which are not involved in the translocation, which may be connected with interchromosomal effect. Conclusions Carriers of Yq12/15p or Yq12/22p translocations have a predominant inheritance of the derivative autosome, which can be associated with the disruption ofsex bivalent segregation. This research was supported by Russian Foundation for Basic Research (grant # 18-34-00279 ).

Features of the state of the chromosomal apparatus of spouses with disorders of reproductive function

Chromosomal anomalies are the most frequent reason of infertility in the world. This is one of the reasons for abortion in the early stages, stillbirth or the birth of a child with multiple malformations. The general level of chromosomal aberrations in the population is 0.5-3.0 %, while among people with impaired fertility this level ranges from 2.9 to 14%. The results of karyotyping of 1024 patients with problems of reproduction function, which appealed to the Center of Human Reproduction «Clinic of Professor Feskov O.» in the period from 2009 to 2014, were presented in the article. For the cytogenetic research of patients, metaphase chromosomes were used. Samples were obtained from culture of peripheral blood according to standard technique. For staining of chromosomes slides GTG-method and CBG-method were used. Analysis of slides was carried out in accordance with the International system of the cytogenetic nomenclature. Different types of chromosomal aberrations have been detected in the karyotypes of the patients in 6.05% cases, in population this value is 0.5–3.0 %. This increase in the number of changes in karyotype in patients with infertility in comparison with the population level is statistically significant (р˂0.05). There are numerical chromosome abnormalities, structural chromosome rearrangements and chromosomes polymorphisms in the patients. Among identified changes the chromosomes polymorphisms are more frequent, it total 2.4% in our group. Among them 1.25% cases of increase in length of satellite on the short arm of acrocentric chromosomes, 0.67% – increase in length of centromeric heterochromatin, 0.38% – increase in length of heterochromatin on the long arm of chromosomes 9, 16, Y. Structural chromosome rearrangements were found in 2.11% patients, among them inversions – 0.86%, Robertsonian translocations and reciprocal translocations – 0.58% і 0.1% respectively, insertions – 0.1%, additional material of unknown origin – 0.1% and marker chromosomes – 0.1%. Numerical chromosomes abnormalities have been detected in 1.63% cases (17 patients out of 1042) – among them Klinefelter syndrome – 0.67% patients, and cases with different mosaic karyotype for sex chromosomes – 0.96%. So it is recommended to carry out karyotyping of couples with infertility.

The Case of X and Y Localization of Nucleolus Organizer Regions (NORs) in Tragulus javanicus (Cetartiodactyla, Mammalia).

There are differences in number and localization of nucleolus organizer regions (NORs) in genomes. In mammalian genomes, NORs are located on autosomes, which are often situated on short arms of acrocentric chromosomes and more rarely in telomeric, pericentromeric, or interstitial regions. In this work, we report the unique case of active NORs located on gonоsomes of a eutherian mammal, the Javan mouse-deer (Tragulus javanicus). We have investigated the position of NORs by FISH experiments with ribosomal DNA (rDNA) sequences (18S, 5.8S, and 28S) and show the presence of a single NOR site on the X and Y chromosomes. The NOR is localized interstitially on the p-arm of the X chromosome in close proximity with prominent C-positive heterochromatin blocks and in the pericentromeric area of mostly heterochromatic Y. The NOR sites are active on both the X and Y chromosomes in the studied individual and surrounded by GC enriched heterochromatin. We hypothesize that the surrounding heterochromatin might have played a role in the transfer of NORs from autosomes to sex chromosomes during the karyotype evolution of the Javan mouse-deer.

Editorial: Marching Toward 100% Whole Genome Sequencing.

Editorial: Marching Toward 100% Whole Genome Sequencing.

Karyological, morphological, and phylogenetic diversification in Leucocoryne Lindl (Allioideae, Amaryllidaceae)

The genus Leucocoryne (Amaryllidaceae) comprises approximately 15 species and is the only genus of the tribe Ipheieae endemic to the western region of Chile in sclerophyll and arid winter-rainfall biomes in the Andes. To better understand the karyotype diversification of this genus, nine species of Leucocoryne were analyzed in terms of their chromosome number and morphology, CMA and DAPI heterochromatic bands, distribution of rDNA sites, and their molecular phylogenetic relationships. Based on phylogenetic analyses Leucocoryne was divided in four clades: I (L. alliacea and L. conferta); II (L. dimorphopetala and L. narcisoides); III (L. coquimbensis, L. macropetala, L. appendiculata, L. talinensis, L. angustipetala, L. purpurea, and L. violacescens); and IV (L. vittata, L. ixioides, L. foetida, and L. pauciflora). The species were diploids with 2n = 10 (6M + 4A) or tetraploids with 2n = 18 (14M + 4A)/2n = 19 (13M + 6A). 45S rDNA sites were co-localized with CMA+/DAPI− bands on the short arms of acrocentric chromosomes in all species. 5S rDNA sites were observed on one, two, or four pairs of metacentric chromosomes per species. Estimations of the ancestral karyotype suggest that 2n = 10 (6M + 2A) with one 5S rDNA site per monoploid complement was the plesiomorphic condition of the genus Leucocoryne. Increases in number of 5S rDNA sites in the same species associated with biome shifts from sclerophyll to arid winter-rainfall region occurred independently in clade II and clade III. The two species of clade II retained the six fertile stamens (plesiomorphic condition) in contrast to the other Leucocoryne species that reduced to only three functional stamens. Based on these findings, we discuss the role of environmental change on the diversification of this group.

Recombinogenic telomeres in diploid Sorex granarius (Soricidae, Eulipotyphla) fibroblast cells.

The telomere structure in the Iberian shrew Sorex granarius is characterized by unique, striking features, with short arms of acrocentric chromosomes carrying extremely long telomeres (up to 300 kb) with interspersed ribosomal DNA (rDNA) repeat blocks. In this work, we investigated the telomere physiology of S. granarius fibroblast cells and found that telomere repeats are transcribed on both strands and that there is no telomere-dependent senescence mechanism. Although telomerase activity is detectable throughout cell culture and appears to act on both short and long telomeres, we also discovered that signatures of a recombinogenic activity are omnipresent, including telomere-sister chromatid exchanges, formation of alternative lengthening of telomeres (ALT)-associated PML-like bodies, production of telomere circles, and a high frequency of telomeres carrying marks of a DNA damage response. Our results suggest that recombination participates in the maintenance of the very long telomeres in normal S. granarius fibroblasts. We discuss the possible interplay between the interspersed telomere and rDNA repeats in the stabilization of the very long telomeres in this organism.

Ag-NORs Analysis in Three Species of Red-Backed Voles, with a Consideration of Generic Allocation of Anderson's Red-Backed Vole

To further make karyotaxonomic characterization of Anderson's red-backed vole (Eothenomys andersoni) certain, Ag-NOR-carrying chromosomes were identified by sequential G-band/silver staining in the red-backed voles Myodes (formerly Clethrionomys) rufocanus (Mru), E. andersoni (Ean), and E. smithii (Esm). These voles had the same diploid number (2n = 56), and their karyotypes scarcely differed from each other in chromosome constitution and G-banding pattern. Ag-NORs from these voles were all centromere-cap (cmc) type, being located at the tip of minute short arms of acrocentric chromosomes. Ten pairs of autosomes carried Ag-NORs in Mru, while Ean and Esm carried those on nineteen pairs of autosomes. Ean shared Ag-NORs with Esm on nos. 2, 5, 7, 10, and 13, but not with Mru at all, although nos. 3, 6, 8, 12, 19, 20, 22, 23, and 26 had Ag-NORs in common among three species. These Ag-NORs varied extensively in number from cell to cell with a range of 9–14 in Mru, 14–22 in Ean and 8–22 in Esm. No evidence of Ag-NORs was obtained on the sex chromosomes XY or on nos. 11, 14, and 27 in either species. These findings may be cytological evidence supporting the view of Aimi (1980) who ranked Anderson's red-backed vole as Eothenomys.

Mosaicism for an unbalanced Y;21 translocation in an infertile man: a case report

Approximately 30 % of male infertility cases are considered ‘idiopathic’ and an additional 40 % have only insufficient/uncertain causes (e.g. varicocele, infections) [1]. It is also estimated that about 30 % of azoo-/oligozoospermia are caused by chromosomal abnormalities (such as 47,XXY or balanced translocations), Y-chromosomal deletions or mutations in genes involved in germ cell production and function [2]. Compared to newborns, infertile males have a higher prevalence of autosomal reciprocal translocations [3], but translocations involving the sex chromosomes are rare [4]. The frequency of Y;autosome translocations in the general population was estimated to be 1 in 2000 [5]. In the more common forms, the heterochromatic region of the long arm of the Y chromosome is translocated onto the short arm of acrocentric chromosomes and fertility is usually not affected in carriers [6]. In contrast, the rare translocations of the euchromatic part of the Y chromosome are frequently associated with azoospermia [7]. Whenever one of the Azoospermia Factor (AZF) regions on Yq is affected by the translocation, this can be considered the cause for azoo- or severe oligozoospermia [8]. Incorrect or incomplete X/Y pairing during meiosis leading to defective sex vesical formation and consequently to spermatogenetic arrest may be another explanation for infertility of Y;autosome translocation carriers [9, 10]. Translocation carriers have an increased risk for offspring with unbalanced chromosomal aberrations and patients with unbalanced Y;autosome translocations are frequently mentally retarded, depending on the affected autosomal region [11]. The frequency of unbalanced spermatozoa may vary considerably depending on the translocation and utilising fluorescence in situ hybridisation (FISH) may help in assessing the individual risk.

Heterochromatin Blocks Constituting the Entire Short Arms of Acrocentric Chromosomes of Azara's Owl Monkey: Formation Processes Inferred From Chromosomal Locations

Centromeres and telomeres of higher eukaryotes generally contain repetitive sequences, which often form pericentric or subtelomeric heterochromatin blocks. C-banding analysis of chromosomes of Azara's owl monkey, a primate species, showed that the short arms of acrocentric chromosomes consist mostly or solely of constitutive heterochromatin. The purpose of the present study was to determine which category, pericentric, or subtelomeric is most appropriate for this heterochromatin, and to infer its formation processes. We cloned and sequenced its DNA component, finding it to be a tandem repeat sequence comprising 187-bp repeat units, which we named OwlRep. Subsequent hybridization analyses revealed that OwlRep resides in the pericentric regions of a small number of metacentric chromosomes, in addition to the short arms of acrocentric chromosomes. Further, in the pericentric regions of the acrocentric chromosomes, OwlRep was observed on the short-arm side only. This distribution pattern of OwlRep among chromosomes can be simply and sufficiently explained by assuming (i) OwlRep was transferred from chromosome to chromosome by the interaction of pericentric heterochromatin, and (ii) it was amplified there as subtelomeric heterochromatin. OwlRep carries several direct and inverted repeats within its repeat units. This complex structure may lead to a higher frequency of chromosome scission and may thus be a factor in the unique distribution pattern among chromosomes. Neither OwlRep nor similar sequences were found in the genomes of the other New World monkey species we examined, suggesting that OwlRep underwent rapid amplification after the divergence of the owl monkey lineage from lineages of the other species.

Targeting of the Human Coagulation Factor IX Gene at rDNA Locus of Human Embryonic Stem Cells

BackgroundGenetic modification is a prerequisite to realizing the full potential of human embryonic stem cells (hESCs) in human genetic research and regenerative medicine. Unfortunately, the random integration methods that have been the primary techniques used keep creating problems, and the primary alternative method, gene targeting, has been effective in manipulating mouse embryonic stem cells (mESCs) but poorly in hESCs.Methodology/Principal FindingsHuman ribosomal DNA (rDNA) repeats are clustered on the short arm of acrocentric chromosomes. They consist of approximately 400 copies of the 45S pre-RNA (rRNA) gene per haploid. In the present study, we targeted a physiological gene, human coagulation factor IX, into the rDNA locus of hESCs via homologous recombination. The relative gene targeting efficiency (>50%) and homologous recombination frequency (>10−5) were more than 10-fold higher than those of loci targeted in previous reports. Meanwhile, the targeted clones retained both a normal karyotype and the main characteristics of ES cells. The transgene was found to be stably and ectopically expressed in targeted hESCs.Conclusion/SignificanceThis is the first targeting of a human physiological gene at a defined locus on the hESC genome. Our findings indicate that the rDNA locus may serve as an ideal harbor for transgenes in hESCs.

Distribution of 45S rDNA sites in chromosomes of plants: Structural and evolutionary implications

Background45S rDNA sites are the most widely documented chromosomal regions in eukaryotes. The analysis of the distribution of these sites along the chromosome in several genera has suggested some bias in their distribution. In order to evaluate if these loci are in fact non-randomly distributed and what is the influence of some chromosomal and karyotypic features on the distribution of these sites, a database was built with the position and number of 45S rDNA sites obtained by FISH together with other karyotypic data from 846 plant species.ResultsIn angiosperms the most frequent numbers of sites per diploid karyotype were two and four, suggesting that in spite of the wide dispersion capacity of these sequences the number of rDNA sites tends to be restricted. The sites showed a preferential distribution on the short arms, mainly in the terminal regions. Curiously, these sites were frequently found on the short arms of acrocentric chromosomes where they usually occupy the whole arm. The trend to occupy the terminal region is especially evident in holokinetic chromosomes, where all of them were terminally located. In polyploids there is a trend towards reduction in the number of sites per monoploid complement. In gymnosperms, however, the distribution of rDNA sites varied strongly among the sampled families.ConclusionsThe location of 45S rDNA sites do not vary randomly, occurring preferentially on the short arm and in the terminal region of chromosomes in angiosperms. The meaning of this preferential location is not known, but some hypotheses are considered and the observed trends are discussed.

Cytogenetic and phylogenetic studies of diploid and polyploid members of Tribe Anemoninae (Ranunculaceae)

The ancestry, phylogenetic differentiation and systematic classification of the worldwide-distributed genus Anemone have been debated for many years. In this paper 11 Anemone, three Pulsatilla species and Hepatica nobilis were subjected to detailed karyotype analysis with the aim of obtaining new cytogenetic data that will contribute to karyotype evolutionary studies of the tribe Anemoninae. The results are interpreted in a phylogenetic context, established from the intergenic nontranscribed spacer (NTS) of 5S rDNA and internal transcribed spacer (ITS) of 35S rDNA. One to three 35S and one to three 5S rDNA loci are present in diploid and polyploid taxa. The 35S rDNA loci are located terminally on the short arm of acrocentric chromosomes, while for 5S rDNA there is no preferential chromosomal position as it exhibits terminal, subterminal, interstitial or pericentromeric positions, and is located either on acrocentric or metacentric chromosomes. The karyotype of hexaploid A. baldensis (2n = 6x = 48) is presented for the first time, and A. sylvestris is proposed as one of its putative parental species. Chromosome fusion/translocation is proposed as the key mechanism involved in reduction of the basic chromosome number from 8 in the Anemone subgenus to 7 in the Anemonidium subgenus. The cytogenetic data obtained are mainly supported by ITS and NTS phylogeny. Diversification of the genus Anemone was accompanied by a large reduction of heterochromatin, from the Mediterranean anemones that have large amounts of heterochromatin to the New World anemones without any detectable heterochromatic blocks.

Complex distal 10q rearrangement in a girl with mild intellectual disability: Follow up of the patient and review of the literature of non‐acrocentric satellited chromosomes

We report on an intellectually disabled girl with a de novo satellited chromosome 10 (10qs) and performed a review of the literature of the non-acrocentric satellited chromosomes (NASC). Satellites and stalks normally occur on the short arms of acrocentric chromosomes; however, the literature cites several reports of satellited non-acrocentric chromosomes, which presumably result from a translocation with an acrocentric chromosome. This is, to our knowledge, the third report of a 10qs chromosome. The phenotype observed in the proband prompted a search for a structural rearrangement of chromosome 10q. By microsatellite analysis we observed a 4 Mb deletion on the long arm of chromosome 10, approximately 145 kb from the telomere. FISH and array CGH analyses revealed a complex rearrangement involving in range from the centromere to the telomere: A 9.64 Mb 10q26.11-q26.2 duplication, a 1.3 Mb region with no copy number change, followed by a 5.62 Mb 10q26.2-q26.3 deletion and a translocation of satellite material. The homology between the repeat sequences at 10q subtelomere region and the sequences on the acrocentric short arms may explain the origin of the rearrangement and it is likely that the submicroscopic microdeletion and microduplication are responsible for the abnormal phenotype in our patient. The patient presented here, with a 15-year follow-up, manifests a distinct phenotype different from the 10q26 pure distal monosomy and trisomy syndromes.

DNA Methylation Patterns of Metaphase Chromosomes in Human Preimplantation Embryos

We performed a stage-by-stage study of DNA methylation patterns in metaphase chromosomes from blastomeres of triploid and abnormal diploid human embryos. QFH-banded homologous parental chromosomes differ in their DNA methylation patterns at the metaphase of the 1st cleavage division. Chromosomes of both parental genomes are gradually demethylated at subsequent cleavages, undergoing hemimethylation in 2-cell embryos. At the 4-cell stage hypomethylated chromosomes initially appear and are further registered until the blastocyst stage. The proportion of hemimethylated and hypomethylated chromosomes varies between the blastomeres since the 4-cell stage with no preference for certain chromosomes to be hemi- or hypomethylated demonstrates random segregation of hypomethylated, undermethylated and methylated chromatids during cell cleavage. By the blastocyst stage the chromosomes acquire band- and, thus, chromosome-specific methylation patterns, with 5-methylcytosine-rich DNA preferentially accumulated in R- and T-bands and in the short arms of acrocentric chromosomes. Thus, demethylaton and remethylation of parental genomes of human embryos proceeds in the same manner from the 1st metaphase stage up to the blastocyst. These processes involve all chromosomes and all bands from each chromosome and lead to establishment of chromosome-specific DNA methylation patterns by the blastocyst stage with no differences between homologous chromosomes.

Laser confocal microscopy analysis of human interphase nuclei by three-dimensional FISH reveals dynamic perinucleolar clustering of telomeres

Nuclear functions are strongly dependent on the three-dimensional organization of the interphase nucleus. Given the importance of telomeres in the behaviour and stability of chromosomes, we have investigated the architecture of the human nucleus from the telomere perspective by 3D-FISH and laser confocal microscopy. We observed a randomly scattered telomere distribution in all confocal sections of the interphase nuclear volume with various levels of telomere clustering in different cell types. This distribution is independent of H2AX presence or phosphorylation status. We also observed that telomeres usually cluster at the periphery of the nucleolus following its cell cycle dependent dynamic formation but are never present in the interior of the nucleolus. These perinucleolar telomeric clusters contain the telomeres of the short arms of acrocentric chromosomes, explaining the p-arm association of acrocentric chromosomes frequently found in metaphase. Thus, chromosome positioning in metaphase spreads is tightly connected to the three-dimensional architecture of the interphase nucleus.