Molecular and evolutionary characteristics of the fraction of human alpha satellite DNA associated with CENP-A at the centromeres of chromosomes 1, 5, 19, and 21

<p>Abstract</p> <p>Background</p> <p>The mode of evolution of the highly homogeneous Higher-Order-Repeat-containing alpha satellite arrays is still subject to discussion. This is also true of the CENP-A associated repeats where the centromere is formed.</p> <p>Results</p> <p>In this paper, we show that the molecular mechanisms by which these arrays evolve are identical in multiple chromosomes: i) accumulation of crossovers that homogenise and expand the arrays into different domains and subdomains that are mostly unshared between homologues and ii) sporadic mutations and conversion events that simultaneously differentiate them from one another. Individual arrays are affected by these mechanisms to different extents that presumably increase with time. Repeats associated with CENP-A, where the centromere is formed, are subjected to the same evolutionary mechanisms, but constitute minor subsets that exhibit subtle sequence differences from those of the bulk repeats. While the DNA sequence <it>per se </it>is not essential for centromere localisation along an array, it appears that certain sequences can be selected against. On chromosomes 1 and 19, which are more affected by the above evolutionary mechanisms than are chromosomes 21 and 5, CENP-A associated repeats were also recovered from a second homogeneous array present on each chromosome. This could be a way for chromosomes to sustain mitosis and meiosis when the normal centromere locus is ineluctably undermined by the above mechanisms.</p> <p>Conclusion</p> <p>We discuss, in light of these observations, possible scenarios for the normal evolutionary fates of human centromeric regions.</p

Compared genomics of the strand switch region of Leishmania chromosome 1 reveal a novel genus-specific gene and conserved structural features and sequence motifs

BACKGROUND: Trypanosomatids exhibit a unique gene organization into large directional gene clusters (DGCs) in opposite directions. The transcription "strand switch region" (SSR) separating the two large DGCs that constitute chromosome 1 of Leishmania major has been the subject of several studies and speculations. Thus, it has been suspected of being the single replication origin of the chromosome, the transcription initiation site for both DGCs or even a centromere. Here, we have used an inter-species compared genomics approach on this locus in order to try to identify conserved features or motifs indicative of a putative function. RESULTS: We isolated, and compared the structure and nucleotide sequence of, this SSR in 15 widely divergent species of Leishmania and Sauroleishmania. As regards its intrachromosomal position, size and AT content, the general structure of this SSR appears extremely stable among species, which is another demonstration of the remarkable structural stability of these genomes at the evolutionary level. Sequence alignments showed several interesting features. Overall, only 30% of nucleotide positions were conserved in the SSR among the 15 species, versus 74% and 62% in the 5' parts of the adjacent XPP and PAXP genes, respectively. However, nucleotide divergences were not distributed homogeneously along this sequence. Thus, a central fragment of approximately 440 bp exhibited 54% of identity among the 15 species. This fragment actually represents a new Leishmania-specific CDS of unknown function which had been overlooked since the annotation of this chromosome. The encoded protein comprises two trans-membrane domains and is classified in the "structural protein" GO category. We cloned this novel gene and expressed it as a recombinant green fluorescent protein-fused version, which showed its localisation to the endoplasmic reticulum. The whole of these data shorten the actual SSR to an 887-bp segment as compared with the original 1.6 kb. In the rest of the SSR, the percentage of identity was much lower, around 22%. Interestingly, the 72-bp fragment where the putatively single transcription initiation site of chromosome 1 was identified is located in a low-conservation portion of the SSR and is itself highly polymorphic amongst species. Nevertheless, it is highly C-rich and presents a unique poly(C) tract in the same position in all species. CONCLUSION: This inter-specific comparative study, the first of its kind, (a) allowed to reveal a novel genus-specific gene and (b) identified a conserved poly(C) tract in the otherwise highly polymorphic region containing the putative transcription initiation site. This allows hypothesising an intervention of poly(C)-binding proteins known elsewhere to be involved in transcriptional control

Congenital Linear Streaks on the Face and Neck and Microphthalmia in an Infant Girl

Peer reviewe

Les réarrangements chromosomiques complexes (du chromosome à la molécule: développement de deux approches méthodologiques pour la caractérisation des points de cassure)

MONTPELLIER-BU Pharmacie (341722105) / SudocSudocFranceF

Le

La découverte récente, dans différents cancers, d’un nouveau type de remaniements chromosomiques massifs, baptisés chromothripsis (du grec chromo pour chromosome, et thripsis pour briser en éclat), bouleverse les modèles établis de développement progressif des tumeurs. En effet, ce phénomène se caractérise par la pulvérisation d’un (ou de quelques) segment(s) chromosomique(s) et le réassemblage aléatoire des fragments chromosomiques générés, et se produit au cours d’un seul événement cellulaire. Le même phénomène a été identifié en génétique constitutionnelle chez des patients atteints de diverses pathologies du développement, indiquant que le chromothripsis survient aussi au niveau germinal. Les causes du chromothripsis sont variées : radiations, érosion télomérique, apoptose abortive, etc. Deux voies de réparation « express » du génome sont utilisées par la cellule pour restructurer de manière chaotique les régions chromosomiques concernées : les mécanismes de jonction des extrémités non homologues et la réparation par stress réplicatif. L’étude approfondie des séquences d’ADN des zones de chromothripsis permet désormais de mieux cerner la signature moléculaire de ce processus et de mieux appréhender son rôle, jusqu’alors insoupçonné, dans le développement de pathologies congénitales et la progression des cancers

Chromothripsis: potential origin in gametogenesis and preimplantation cell divisions. A review

International audienceObjective: To review the discovery of chromothripsis and analyze its impact on human reproduction.Design: Database and literature analysis.Setting: University hospital.Patient(s): Carriers of massive and complex chromosomal rearrangements.Intervention(s): Cytogenetic analysis and molecular testing (fluorescence in situ hybridization, microarray, whole-genome sequencing).Main outcome measure(s): Chromothripsis occurrence in human gametes and preimplantation embryos, with regard to the potential causative mechanisms described in literature.Result(s): Databases were searched for the literature published up to March 2014. Chromothripsis is characterized by the shattering of one (or a few) chromosome segments followed by a haphazard reassembly of the fragments generated, arising through a single initial catastrophic event. Several mechanisms involving abortive apoptosis, telomere erosion, mitotic errors, micronuclei formation, and p53 inactivation might cause chromothripsis. The remarkable point is that all these plausible mechanisms have been identified in the field of human reproduction as causal factors for reproductive failures and the genesis of chromosomal abnormalities. Specific features of gametogenesis and early embryonic development such as the weakness of cell cycle and mitosis checkpoints and the rapid kinetics of division in germ cells and early cleavage embryos may contribute to the emergence of chromothripsis.Conclusion(s): The discovery of this new class of massive chromosomal rearrangement has deeply modified our understanding on the genesis of complex genomic rearrangements. Data presented in this review support the assumption that chromothripsis could operate in human germlines and during early embryonic development. Chromothripsis might arise more frequently than previously thought in both gametogenesis and early human embryogenesis

Les remaniements chromosomiques complexes

Les remaniements chromosomiques complexes (CCR) regroupent différents types de réarrangements de la structure des chromosomes, dont la juxtaposition peut aboutir à des formules chromosomiques très complexes. Si la réalisation de caryotypes a permis d’identifier un grand nombre de ces remaniements et de distinguer les cas familiaux des cas de novo, on doit à la cytogénétique moléculaire et aux techniques de séquençage la description des mécanismes moléculaires de formation des CCR. La complexité et la diversité des CCR posent les questions de l’origine de ces réarrangements, de leur lien avec l’instabilité chromosomique et de leur impact en pathologie. S’il est désormais possible de caractériser avec précision les CCR et de proposer aux patients porteurs le recours à des techniques de diagnostic sophistiquées, comme le diagnostic préimplantatoire, la ségrégation méiotique de ces remaniements reste très complexe

Characterizing PALB2 intragenic duplication breakpoints in a triple-negative breast cancer case using long-read sequencing

IntroductionAccurate identification and characterization of Large Genomic Rearrangements (LGR), especially duplications, are crucial for precise diagnosis and risk assessment. In this report, we characterized an intragenic duplication breakpoint of PALB2 to determine its pathogenicity significance.MethodsA 52-year-old female with triple-negative breast cancer was diagnosed with a novel PALB2 LGR. An efficient and accurate methodology was applied, combining long-read sequencing and transcript analysis for the rapid characterization of the duplication.ResultsDuplication of exons 5 and 6 of PALB2 was validated by transcript analysis. Long-read sequencing enabled the localization of breakpoints within Alu elements, providing insights into the mechanism of duplication via non-allelic homologous recombination.ConclusionUsing our combined methodology, we reclassified the PALB2 duplication as a pathogenic variant. This reclassification suggests a possible causative link between this specific genetic alteration and the aggressive phenotype of the patient