Predominance of constitutional chromosomal rearrangements in human chromosomal fragile sites

Chromosomal fragile sites (CFSs) are loci or regions susceptible to spontaneous or induced occurrence of gaps, breaks and rearrangements. In this work, we studied the data of 4535 patients stored at DECIPHER (Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources). We mapped fragile sites to chromosomal bands and divided the 23 chromosomes into fragile and non-fragile sites. The frequency of rearrangements at the chromosomal location of clones found to be deleted or duplicated in the array/CGH analysis, provided by DECIPHER, was compared in Chromosomal Fragile Sites vs. non-Fragile Sites of the human genome. The POSSUM Web was used to complement this study. The results indicated 1) a predominance of rearrangements in CFSs, 2) the absence of statistically significant difference between the frequency of rearrangements in common CFSs vs. rare CFSs, 3) a predominance of deletions over duplications in CFSs. These results on constitutional chromosomal rearrangements are evocative of the findings previously reported by others relatively to cancer supporting the current line of evidence and suggesting that a common mechanism can underlie the generation of constitutional and somatic rearrangements. The combination of insights obtained from our results and their interrelationships can indicate strategies by which the mechanisms can be targeted with preventive medical interventions.

Knowledge-embedded spatio-temporal analysis for euploidy embryos identification in couples with chromosomal rearrangements

Background:The goal of the assisted reproductive treatment is to transfer one euploid blastocyst and to help infertile women giving birth one healthy neonate.Some algorithms have been used to assess the ploidy status of embryos derived from couples with normal chromosome,who subjected to preimplantation genetic testing for aneuploidy(PGT-A)treatment.However,it is currently unknown whether artificial intelligence model can be used to assess the euploidy status of blastocyst derived from populations with chromosomal rearrangement.Methods:From February 2020 to May 2021,we collected the whole raw time-lapse videos at multiple focal planes from in vitro cultured embryos,the clinical information of couples,and the comprehensive chromosome screening results of those blastocysts that had received PGT treatment.Initially,we developed a novel deep learning model called the Attentive Multi-Focus Selection Network(AMSNet)to analyze time-lapse videos in real time and predict blastocyst formation.Building upon AMSNet,we integrated additional clinically predictive variables and created a second deep learning model,the Attentive Multi-Focus Video and Clinical Information Fusion Network(AMCFNet),to assess the euploidy status of embryos.The efficacy of the AMCFNet was further tested in embryos with parental chromosomal rearrangements.The receiver operating characteristic curve(ROC)was used to evaluate the superiority of the model.Results:A total of 4112 embryos with complete time-lapse videos were enrolled for the blastocyst formation prediction task,and 1422 qualified blastocysts received PGT-A(n=589)or PGT for chromosomal structural rearrangement(PGT-SR,n=833)were enrolled for the euploidy assessment task in this study.The AMSNet model using seven focal raw time-lapse videos has the best real-time accuracy.The real-time accuracy for AMSNet to predict blastocyst formation reached above 70%on the day 2 of embryo culture,and then increased to 80%on the day 4 of embryo culture.Combing with 4 clinical features of couples,the AUC of AMCFNet with 7 focal points increased to 0.729 in blastocysts derived from couples with chromosomal rearrangement.Conclusion:Integrating seven focal raw time-lapse images of embryos and parental clinical information,AMCFNet model have the capability of assessing euploidy status in blastocysts derived from couples with chromosomal rearrangement.

THE DNase-1 SENSITIVE REGIONS IN GENOMES OF BURKITT' S LYMPHOMA CELLS

This article reported the distribution of DNase-1 sensitive regions in genomes of three Burkitt's lymphoma cell lines, P3HR-1, Raji and Ramos cell lines using a new method of in situ nick translation of chromosomes substituted completely by BrdU. The results showed that the Blym locus on chromosomes In three cell lines and the c-myc locus on chromosomes in P3HR-1 were the DNase-1 sensitive regions and found that the rearrangemental sites of chromosomes present in three Burkltt' s lymphoma cell lines were sensitive to DNase-1 digestion, Indicating that c-myc, bcl-1 genes located at the rearrangemental sites and the Blym gene in Burkltt' s lymphoma are the active genes having the capability of expression.

Current Status and Recent Advances in Preimplantation Genetic Testing for Structural Rearrangements

Preimplantation genetic testing(PGT)is an early form of prenatal genetic diagnosis,which can identify the abnormal embryos cultured in vitro,allow only transfer of genetically normal embryos,and improve the pregnancy rate.In recent years,the rapid development of microarrays and next-generation sequencing(NGS)technologies has remarkably accelerated the clinical application of PGT.In particular,a variety of detection methods have emerged and achieved significant progress in PGT for structural rearrangements(PGT-SR).The detection-related abilities of these methods range from the detection of limited chromosome aneuploidy to comprehensive chromosome screening of the whole genome to differentiation of embryos with normal or balanced translocation/inversion karyotypes.In this study,we reviewed PGT-SR-related detection techniques to provide a better reference for clinical application and research.We have also discussed the potential development of novel techniques in the future.

The genomes of seven economic Caesalpinioideae trees provide insights into polyploidization history and secondary metabolite biosynthesis

The Caesalpinioideae subfamily contains many well-known trees that are important for economic sustainability and human health,but a lack of genomic resources has hindered their breeding and utilization.Here,we present chromosome-level reference genomes for the two food and industrial trees Gleditsia sinensis(921 Mb)and Biancaea sappan(872 Mb),the three shade and ornamental trees Albizia julibrissin(705 Mb),Delonix regia(580 Mb),and Acacia confusa(566 Mb),and the two pioneer and hedgerow trees Leucaena leucocephala(1338 Mb)and Mimosa bimucronata(641 Mb).Phylogenetic inference shows that the mimosoid clade has a much higher evolutionary rate than the other clades of Caesalpinioideae.Macrosynteny comparison suggests that the fusion and breakage of an unstable chromosome are responsible for the difference in basic chromosome number(13 or 14)for Caesalpinioideae.After an ancient whole-genome duplication(WGD)shared by all Caesalpinioideae species(CWGD,~72.0 million years ago[MYA]),there were two recent successive WGD events,LWGD-1(16.2-19.5 MYA)and LWGD-2(7.1-9.5 MYA),in L.leucocephala.Thereafter,~40%gene loss and genome-size contraction have occurred during the diploidization process in L.leucocephala.To investigate secondary metabolites,we identified all gene copies involved in mimosine metabolism in these species and found that the abundance of mimosine biosynthesis genes in L.leucocephala largely explains its high mimosine production.We also identified the set of all potential genes involved in triterpenoid saponin biosynthesis in G.sinensis,which is more complete than that based on previous transcriptome-derived unigenes.Our results and genomic resources will facilitate biological studies of Caesalpinioideae and promote the utilization of valuable secondary metabolites.

Haplotype-resolved chromosome-level genome of hexaploid Jerusalem artichoke provides insights into its origin,evolution,and inulin metabolism

Jerusalem artichoke(Helianthus tuberosus)is a global multifunctional crop.It has wide applications in the food,health,feed,and biofuel industries and in ecological protection;it also serves as a germplasm pool for breeding of the global oil crop common sunflower(Helianthus annuus).However,biological studies of Je-rusalem artichoke have been hindered by a lack of genome sequences,and its high polyploidy and large genome size have posed challenges to genome assembly.Here,we report a 21-Gb chromosome-level as-sembly of the hexaploid Jerusalem artichoke genome,which comprises 17 homologous groups,each with 6 pseudochromosomes.We found multiple large-scale chromosome rearrangements between Jerusalem artichoke and common sunflower,and our results show that the hexaploid genome of Jerusalem artichoke was formed by a hybridization event between a tetraploid and a diploid Helianthus species,followed by chromosome doubling of the hybrid,which occurred approximately 2 million years ago.Moreover,we iden-tied more copies of actively expressed genes involved in inulin metabolism and showed that these genes may still be undergoing loss of function or sub-or neofunctionalization.These genomic resources will pro-mote further biological studies,breeding improvement,and industrial utilization of Helianthus crops.

Alteration of Terminal Heterochromatin and Chromosome Rearrangements in Derivatives of Wheat-Rye Hybrids

Wheat-rye addition and substitution lines and their self progenies revealed variations in telomeric heterochromatin and centromeres, Furthermore, a mitotically unstable dicentric chromosome and stable multicentric chromosomes were observed in the progeny of a Chinese Spring-lmperial rye 3R addition line. An unstable multicentric chromosome was found in the progeny of a 6R/6D substitution line. Drastic variation of terminal heterochromatin including movement and disappearance of terminal heterochromatin occurred in the progeny of wheat- rye addition line 3R, and the 5RS ditelosomic addition line. Highly stable minichromosomes were observed in the progeny ofa monosomic 4R addition line, a ditelosomic 5RS addition line and a 6R/6D substitution line. Minichromosomes, with and without the FISH signals for telomeric DNA （TTTAGGG）n, derived from a monosomic 4R addition line are stable and transmissible to the next generation. The results indicated that centromeres and terminal heterochromatin can be profoundly altered in wheat-rye hybrid derivatives.

Chromosomal changes detected by fluorescence in situ hybridization in patients with acute lymphoblastic leukemia

Objectives To investigate patients with acute lymphoblastic leukemia (ALL) for TEL/AML1 fusion, BCR/ABL fusion, MLL gene rearrangements, and numerical changes of chromosomes 4, 10, 17 and 21 by fluorescence in situ hybridization (FISH) and to determine the relationship and the significance of those findings.Methods Fifty-one American patients (34 men and 17 women) were included in this study. Of them there were 41 patients with pro-B cell type ALL, 9 with B cell type ALL and 1 with T cell type ALL. Chromosome metaphases of each sample were prepared according to standard protocols. Fluorescence in situ hybridization was performed using commercially available DNA probes, including whole chromosome painting probes, locus specific probes, specific chromosome centromere probes and dual color/multiple color translocation fusion probes. The digital image analysis was carried out using Cytovision and Quips FISH programs.Results An overall incidence of chromosomal anomalies, including t (9; 22), MLL gene rearrangements, t (12;21), and numerical chromosomal anomalies of chromosomes 4, 10, 17 and 21 was found in 33 patients (65%). Thirty-one of them were pediatric patients and two adults. The t (12;21) was the commonest chromosomal anomaly detected in this population; 14 out of the 45 pediatric patients (31%) were positive for TEL/AML1 fusion, among which three had an additional derivative 21 [t (12;21) ], four had a deletion of 12p and two had an extra copy of chromosome 21. All 14 patients with positive TEL/AML1 fusion had ALL pre-B cell or B-cell lineage according to standard immunotyping. The percentage of cells with fusion signals ranged from 20% to 80%. All fourteen patients positive for TEL/AML1 gene fusion were mosaic. Three out of the 14 patients positive for the TEL/AML1 gene fusion were originally reported to be culture failures and none of the remaining eleven samples had been found to have chromosome 12 abnormalities by conventional cytogenetic techniques. All pediatric patients with pre-T or T cell lineage and the six adults were negative for TEL/AML1 fusion. One patient had double Philadelphia chromosomes, three had a rearrangement or a deletion of the MLL gene, one had t (4;11) and two had a deletion of the MLL. One of the patients with an MLL deletion also had a large ring of chromosome 21, and r (21) was caused by AML1 gene tandemly duplicated at least five times. The second case with the MLL deletion was also unique, the patient had at (12;21) as well. A total of 20 patients had numerical changes (gain or loss) of chromosomes 4,10,17 and 21. Eight patients were found to have trisomies of three or four different chromosomes. Interestingly, seven of these patients did not have TEL/AML1, BCR/ ABL or the MLL gene rearrangement; one did have the TEL/AML1 gene fusion. Eleven patients with pro-B cell or 8 cell type ALL (9 children with ALL, 2 adults with ALL) had numerical changes of chromosome 21 (gain 1 or 2 chromosome 21), among them, 10 patients had no structural alteration of chromosome 21, and one was combined by t (12; 21). Four patients had a monosomy of chromosome 17 and three out of these patients with monosomy 17 also had a fusion signal of TEL/AML1. Conclusions FISH plays an important role in detecting chromosome changes, especially in some cryptic chromosome translocations and patients with culture failures. This study found a trend towards a division between patients who had structural changes such as t (12;21) or a ring chromosome 21 and those who had numerical changes of chromosome 21 as well as the patients with TEL/AML1 fusion and patients with the coexistence of numerical chromosomal changes of chromosomes 4, 10 and 17. In our opinion there are two separate mechanisms which lead to the development or progression of leukemia.

Global methylation status of sperm DNA in carriers of chromosome structural aberrations

Male infertility might be clearly associated with aberrant DNA methylation patterns in human spermatozoa. An association between oxidative stress and the global methylation status of the sperm genome has also been suggested. The aim of the present study was to determine whether the global sperm DNA methylation status was affected in the spermatozoa of carriers of chromosome structural aberrations. The relationships between the 5-methylcytosine （msC） levels in spermatozoa and chromatin integrity status were evaluated. The study patients comprised male carriers of chromosome structural aberrations with reproductive failure （n = 24）, and the controls comprised normozoospermic sperm volunteers （n = 23）. The global msC level was measured using thin-layer chromatography （TLC） and immunofluorescence （IF） techniques. The sperm chromatin integrity was assessed using aniline blue （AB） staining and TUNEL assay. The mean msC levels were similar between the investigated chromosome structural aberrations carriers （P） and controls （K）. However, sperm chromatin integrity tests revealed significantly higher values in chromosomal rearrangement carriers than in controls （P 〈 0.05）. Although the potential relationship between sperm chromatin integrity status and sperm DNA fragmentation and the msC level juxtaposed in both analyzed groups （P vs K） was represented in a clearly opposite manner, the low chromatin integrity might be associated with the high hypomethylation status of the sperm DNA observed in carriers of chromosome structural aberrations.

Gene fusions and chimeric RNAs,and their implications in cancer

Gene fusions are appreciated as ideal cancer biomarkers and therapeutic targets.Chimeric RNAs are traditionally thought to be products of gene fusions,and thus,also cancerspecific.Recent research has demonstrated that chimeric RNAs can be generated by intergenic splicing in the absence of gene fusion,and such chimeric RNAs are also found in normal physiology.These new findings challenge the traditional theory of chimeric RNAs exclusivity to cancer,and complicates use of chimeric RNAs in cancer detection.Here,we provide an overview of gene fusions and chimeric RNAs,and emphasize their differences.We note that gene fusions are able to generate chimeric RNAs in accordance with the central dogma of biology,and that chimeric RNAs may also be able to influence the generation of the gene fusions per the“horse before the cart”hypothesis.We further expand upon the“horse before the cart”hypothesis,summarizing current evidence in support of the theory and exploring its potential impact on the field.

From gene editing to genome engineering: restructuring plant chromosomes via CRISPR/Cas

In the last years,tremendous progress has been achieved in the field of gene editing in plants.By the induction of single site-specific double-strand breaks(DSBs),the knockout of genes by non-homologous end joining has become routine in many plant species.Recently,the efficiency of inducing pre-planned mutations by homologous recombination has also been improved considerably.However,very little effort has been undertaken until now to achieve more complex changes in plant genomes by the simultaneous induction of several DSBs.Several reports have been published on the efficient induction of deletions.However,the induction of intrachromosomal inversions and interchromosomal recombination by the use of CRISPR/Cas has only recently been reported.In this review,we want to sum up these results and put them into context with regards to what is known about natural chromosome rearrangements in plants.Moreover,we review the recent progress in CRISPR/Cas-based mammalian chromosomal rearrangements,which might be inspiring for plant biologists.In the long run,the controlled restructuring of plant genomes should enable us to link or break linkage of traits at will,thus defining a new area of plant breeding.

Issues in the Reconstruction of Gene Order Evolution

As genomes evolve over hundreds of millions years, the chromosomes become rearranged, with segments of some chromosomes inverted, while other chromosomes reciprocally exchange chunks from their ends. These rearrangements lead to the scrambling of the elements of one genome with respect to another descended from a common ancestor. Multidisciplinary work undertakes to mathematically model these processes and to develop statistical analyses and mathematical algorithms to understand the scrambling in the chromosomes of two or more related genomes. A major focus is the reconstruction of the gene order of the ancestral genomes.