scholarly journals Recurrence of Chromosome Rearrangements and Reuse of DNA Breakpoints in the Evolution of the Triticeae Genomes

2016 ◽  
Vol 6 (12) ◽  
pp. 3837-3847 ◽  
Author(s):  
Wanlong Li ◽  
Ghana S Challa ◽  
Huilan Zhu ◽  
Wenjie Wei
Keyword(s):  
Chromosomal Rearrangements ◽  
Draft Genome ◽  
Transcription Factor Gene ◽  
Sequence Organization ◽  
Helix Loop Helix ◽  
Translocation Breakpoints ◽  
Recurrent Translocation ◽  
Model Grass ◽  
Breakpoint Reuse ◽  
Grass Genomes

Abstract Chromosomal rearrangements (CRs) play important roles in karyotype diversity and speciation. While many CR breakpoints have been characterized at the sequence level in yeast, insects, and primates, little is known about the structure of evolutionary CR breakpoints in plant genomes, which are much more dynamic in genome size and sequence organization. Here, we report identification of breakpoints of a translocation between chromosome arms 4L and 5L of Triticeae, which is fixed in several species, including diploid wheat and rye, by comparative mapping and analysis of the draft genome and chromosome survey sequences of the Triticeae species. The wheat translocation joined the ends of breakpoints downstream of a WD40 gene on 4AL and a gene of the PMEI family on 5AL. A basic helix-loop-helix transcription factor gene in 5AL junction was significantly restructured. Rye and wheat share the same position for the 4L breakpoint, but the 5L breakpoint positions are not identical, although very close in these two species, indicating the recurrence of 4L/5L translocations in the Triticeae. Although barley does not carry the translocation, collinearity across the breakpoints was violated by putative inversions and/or transpositions. Alignment with model grass genomes indicated that the translocation breakpoints coincided with ancient inversion junctions in the Triticeae ancestor. Our results show that the 4L/5L translocation breakpoints represent two CR hotspots reused during Triticeae evolution, and support breakpoint reuse as a widespread mechanism in all eukaryotes. The mechanisms of the recurrent translocation and its role in Triticeae evolution are also discussed.

scholarly journals The SCL/TAL-1 gene is expressed in progenitors of both the hematopoietic and vascular systems during embryogenesis

Blood ◽  
1994 ◽  
Vol 83 (5) ◽  
pp. 1200-1208 ◽  
Author(s):  
AR Kallianpur ◽  
JE Jordan ◽  
SJ Brandt
Keyword(s):  
T Cell ◽  
Neural Development ◽  
Fetal Liver ◽  
Chromosomal Rearrangements ◽  
Chromosomal Translocation ◽  
Cell Types ◽  
Hematopoietic Differentiation ◽  
Helix Loop Helix ◽  
Adult Mice ◽  
Rare Cells

Activation of the SCL (or TAL-1) gene as a result of chromosomal translocation or deletion is a frequent molecular lesion in acute T- cell leukemia. By virtue of its membership in the basic helix-loop- helix family of transcription factors, the SCL gene is a candidate to regulate events in hematopoietic differentiation. We have used polyclonal antibody raised against a bacterial expressed malE-SCL fusion protein to characterize SCL protein expression in postimplantation embryos and in neonatal and adult mice. SCL protein was detected at day 7.5 post coitum at both embryonic and extraembryonic sites, approximately 24 hours before the formation of recognizable hematopoietic elements. Expression then localized to blood islands of the yolk sac followed by localization to fetal liver and spleen, paralleling the hematopoietic activity of these tissues during development. SCL protein was detected in erythroblasts in fetal and adult spleen, myeloid cells and megakaryocytes in spleen and bone marrow, mast cells in skin, and in rare cells in fetal and adult thymus. In addition, SCL protein was noted in endothelial progenitors in blood islands and in endothelial cells and angioblasts in a number of organs at times coincident with their vascularization. SCL expression was also observed in other nonhematopoietic cell types in the developing skeletal and nervous systems. These results show that SCL expression is one of the earliest markers of mammalian hematopoietic development and are compatible with a role for this transcription factor in terminal differentiation of the erythroid and megakaryocytic lineages. SCL expression by cells in the thymus suggests that the gene may be active at some stage of T-cell differentiation and may be relevant to its involvement by chromosomal rearrangements in T- lymphoid leukemias. Finally, expression of the gene in developing brain, cartilage, and vascular endothelium indicates SCL may have actions in neural development, osteogenesis, and vasculogenesis, as well as in hematopoietic differentiation.

scholarly journals Molecular detection of chromosomal translocations that disrupt the putative retinoblastoma susceptibility locus.

1989 ◽  
Vol 9 (1) ◽  
pp. 1-5 ◽  
Author(s):  
M J Higgins ◽  
M F Hansen ◽  
W K Cavenee ◽  
M Lalande
Keyword(s):  
Molecular Detection ◽  
Chromosomal Rearrangements ◽  
Restriction Enzymes ◽  
Chromosomal Translocations ◽  
Candidate Sequence ◽  
Rb1 Gene ◽  
Large Size ◽  
Screening Strategies ◽  
Translocation Breakpoints ◽  
Presymptomatic Diagnosis

A candidate DNA sequence with many of the properties predicted for the retinoblastoma susceptibility (RB1) locus has been cloned (S. H. Friend, R. Bernards, S. Rogelj, R. A. Weinberg, J. M. Rapaport, D. M. Albert, and T. P. Dryja, Nature [London] 323:643-645, 1986). The large size of this gene (ca. 200 kilobases [kb]) and its multiple dispersed exons (Wiggs et al., N. Engl. J. Med. 318:151-157, 1988) complicate molecular screening strategies important in prenatal and presymptomatic diagnosis and in carrier detection. Here we used field inversion gel electrophoresis (FIGE) to construct a restriction map of approximately 1,000 kb of DNA surrounding the RB1 locus and to detect the translocation breakpoints in three retinoblastoma patients. DNA probes from either the 5' or 3' end of the gene were used to detect a 250-kb EagI restriction fragment in DNA from unaffected individuals. Both probes identified an additional hybridizing fragment in the DNA from each patient, permitting the breakpoints in all three to be mapped within the cloned RB1 gene. Analysis of the breakpoint in one translocation cell line allowed the RB1 gene to be oriented with its 5' end toward the centromere. The 5' end of the gene also appeared to be associated with a clustering of sites for several infrequently cleaving restriction enzymes, indicating the presence of an HpaII tiny fragment island. The detection and mapping of the translocation breakpoints of all three retinoblastoma patients to within the putative RB1 gene substantiated the authenticity of this candidate sequence and demonstrated the utility of FIGE in detecting chromosomal rearrangements affecting this locus.

scholarly journals TECHNIQUES FOR MANIPULATING CHROMOSOMAL REARRANGEMENTS AND THEIR APPLICATION TO DROSOPHILA MELANOGASTER. II. TRANSLOCATIONS

Genetics ◽  
1984 ◽  
Vol 108 (3) ◽  
pp. 573-587
Author(s):  
Loring Craymer
Keyword(s):  
Tandem Duplication ◽  
Gene Dosage ◽  
Chromosomal Rearrangements ◽  
Region Of Interest ◽  
Reciprocal Translocations ◽  
The Third ◽  
Translocation Breakpoints ◽  
Inversion Breakpoints ◽  
Derivatives Of ◽  
Tandem Duplications

ABSTRACT Translocations have long been valued for their segregational properties. This paper extends the utility of translocations by considering recombinational derivatives of pairs of simple reciprocal translocations. Three major derivative structures are noted. One of these derivatives is suitable for use in half-tetrad experiments. A second should find use in recombining markers with translocation breakpoints. The third is an insertional-tandem duplication: it has a section of one chromosome inserted into a heterologue with a section of the latter chromosome tandemly repeated about the breaks of the insert. All of these structures are contained in "constellations" of chromosomes that regularly segregate aneuploid-1 products (informationally equivalent to nonrecombinant adjacent-1 segregants) for one of the parental translocations but do not segregate euploid products. This is in contrast to the parental T  1/T  2 constellations which segregate euploid products but not aneuploid-1 products. Methods are described for selecting translocation recombinants on the basis of this dichotomy. Several examples of translocation recombinants have been recovered with these techniques, and the recombination frequencies seem to be consistent with those observed for crossovers between inversion breakpoints. Recombinant chromosomes tend to disjoin, but it is observed that the tendency may vary according to the region involved in the recombination, and it is suggested that this difference reflects a difference in chiasmata terminalization times. Special consideration is given to insertional-tandem duplications. Large insertional-tandem duplications are useful in cytogenetic screens. Small insertional-tandem duplications are useful in gene dosage studies and other experiments that require an insert from one chromosome to another. Large duplications can be deleted to form small duplications. To generate a small insert for a specified region, it is only necessary to have one translocation with a breakpoint flanking the region of interest. The second translocation can have a breakpoint quite far from the region: an insertional-tandem duplication containing the region that has one closely flanking breakpoint can be deleted to create a smaller duplication that has two closely flanking breakpoints.

Molecular detection of chromosomal translocations that disrupt the putative retinoblastoma susceptibility locus

1989 ◽  
Vol 9 (1) ◽  
pp. 1-5
Author(s):  
M J Higgins ◽  
M F Hansen ◽  
W K Cavenee ◽  
M Lalande
Keyword(s):  
Molecular Detection ◽  
Chromosomal Rearrangements ◽  
Restriction Enzymes ◽  
Chromosomal Translocations ◽  
Candidate Sequence ◽  
Rb1 Gene ◽  
Large Size ◽  
Screening Strategies ◽  
Translocation Breakpoints ◽  
Presymptomatic Diagnosis

A candidate DNA sequence with many of the properties predicted for the retinoblastoma susceptibility (RB1) locus has been cloned (S. H. Friend, R. Bernards, S. Rogelj, R. A. Weinberg, J. M. Rapaport, D. M. Albert, and T. P. Dryja, Nature [London] 323:643-645, 1986). The large size of this gene (ca. 200 kilobases [kb]) and its multiple dispersed exons (Wiggs et al., N. Engl. J. Med. 318:151-157, 1988) complicate molecular screening strategies important in prenatal and presymptomatic diagnosis and in carrier detection. Here we used field inversion gel electrophoresis (FIGE) to construct a restriction map of approximately 1,000 kb of DNA surrounding the RB1 locus and to detect the translocation breakpoints in three retinoblastoma patients. DNA probes from either the 5' or 3' end of the gene were used to detect a 250-kb EagI restriction fragment in DNA from unaffected individuals. Both probes identified an additional hybridizing fragment in the DNA from each patient, permitting the breakpoints in all three to be mapped within the cloned RB1 gene. Analysis of the breakpoint in one translocation cell line allowed the RB1 gene to be oriented with its 5' end toward the centromere. The 5' end of the gene also appeared to be associated with a clustering of sites for several infrequently cleaving restriction enzymes, indicating the presence of an HpaII tiny fragment island. The detection and mapping of the translocation breakpoints of all three retinoblastoma patients to within the putative RB1 gene substantiated the authenticity of this candidate sequence and demonstrated the utility of FIGE in detecting chromosomal rearrangements affecting this locus.

Balanced Rearrangements of Chromosome 6 in Acute Leukaemia: Clustered Breakpoints in 6q22-q23 and Possible Involvement of c-MYB/AHI1 in a New Recurrent Translocation, t(6;7)(q23;q31).

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 2893-2893
Author(s):  
Paul B. Sinclair ◽  
Christine J. Harrison ◽  
Marie Jarosova ◽  
Letizia Foroni
Keyword(s):  
Target Genes ◽  
Fragile Site ◽  
Single Case ◽  
Chromosomal Rearrangements ◽  
Position Effect ◽  
In Situ Hybridisation ◽  
Fragile Sites ◽  
Chromosome 6 ◽  
Fluorescence In Situ Hybridisation ◽  
Recurrent Translocation

Abstract While deletions of the long arm of chromosome 6 (6q) are common in patients with ALL, translocations are rare, most are considered sporadic and none have been cloned. Among myeloid malignancies, the recurrent translocations: t(6;11)(q27;q23), t(6;11)(q21;q23) and t(6;8)(q27;p11) give rise to known fusion oncogenes. Other uncharacterised balanced or unbalanced 6q abnormalities have occasionally been reported. Using fluorescence in-situ hybridisation (FISH) with HGMP mapped PAC and BAC clones, we investigated chromosomal rearrangements of 6q in acute leukemia. Previously we reported 24 cases with deletions of 6q (Sinclair et al 2004, Can Res 64; 4089), here we describe the analysis of 11 patients with novel balanced rearrangements. Six of seven breakpoints in ALL and two in a single case of AML were localised to a 10.5 Mb ‘hotspot’ within 6q22–q23. Of these, five were analysed down to the level of a single clone. In two cases of childhood T ALL, both carrying a t(6;7)(q23;q31~36), split FISH signals were produced by adjacent PACs, RP1–32B1 and RP3–388E23, mapping the breakpoints to within a ~150Kb region. A search of published karyotypes identified five similar rearrangements, four also in pediatric T ALL, all present as a sole abnormality or represented in the major clone. Of genes in the region, two (c-MYB and AHI1) are tightly regulated during normal hemopoietic development and over-expression of both has been reported to occur in hemopoietic malignancies. Moreover, clusters of retroviral insertion sites occur within both genes and immediately proximal to c-MYB in murine and feline leukemias and lymphomas. Thus we have defined a new primary recurrent translocation in T ALL that is likely to target either c-MYB and/or AHI1.Three other non recurrent rearrangements of 6q22–q23, mapped in detail, interrupted regions without known genes.. Therefore, these abnormalities were unlikely to have promoted leukemia through classical oncogene activation, but may have influenced expression of one or more common target genes through a long-range position effect. Alternatively these clustered rearrangements may mark the position of a new fragile site on 6q. Additional 6q breakpoints in three cases of AML and one of ALL mapped to 6q15, 6q21, 6q25 and 6q26–q27, and were coincident with the positions of a known oncogene partner AF6q21, the haemopoietic transcription factor BACH2 and two cloned fragile sites FRA6E and FRA6F. Putative partner genes of four translocations were investigated by FISH and the involvement of MLL was demonstrated in one case with t(6;11)(q15;q23).

scholarly journals The cold-induced basic helix-loop-helix transcription factor gene MdCIbHLH1 encodes an ICE-like protein in apple

2012 ◽  
Vol 12 (1) ◽  
pp. 22 ◽  
Author(s):  
Xiao-Ming Feng ◽  
Qiang Zhao ◽  
Ling-Ling Zhao ◽  
Yu Qiao ◽  
Xing-Bin Xie ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factor Gene ◽  
Factor Gene ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix

scholarly journals Basic helix-loop-helix transcription factor gene family phylogenetics and nomenclature

2010 ◽  
Vol 80 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Michael K. Skinner ◽  
Alan Rawls ◽  
Jeanne Wilson-Rawls ◽  
Eric H. Roalson
Keyword(s):  
Transcription Factor ◽  
Gene Family ◽  
Transcription Factor Gene ◽  
Factor Gene ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Transcription Factor Gene Family

Deciphering balanced translocations in infertile males by Next Generation Sequencing to identify candidate genes for spermatogenesis disorders

2021 ◽  
Author(s):  
T Yammine ◽  
N Reynaud ◽  
H Lejeune ◽  
F Diguet ◽  
Pa Rollat-Farnier ◽  
...  
Keyword(s):  
Male Infertility ◽  
Candidate Genes ◽  
Gene Disruption ◽  
Chromosomal Rearrangements ◽  
Position Effect ◽  
Copy Number Variations ◽  
Molecular Techniques ◽  
Male Population ◽  
Translocation Breakpoints ◽  
Balanced Translocations

Abstract Male infertility affects about 7% of the general male population. Balanced structural chromosomal rearrangements are observed in 0.4 to 1.4% of infertile males and are considered as a well-established cause of infertility. However, underlying pathophysiological mechanisms still need to be clarified. A strategy combining standard and high throughput cytogenetic and molecular technologies was applied in order to identify the candidate genes that might be implicated in the spermatogenesis defect in three male carriers of different balanced translocations. Fluorescence in situ hybridization (FISH) and whole genome paired-end sequencing were used to characterize translocation breakpoints at the molecular level while exome sequencing was performed in order to exclude the presence of any molecular event independent from the chromosomal rearrangement in the patients. All translocation breakpoints were characterized in the three patients. We identified four variants: a position effect on LACTB2 gene in Patient 1, a heterozygous CTDP1 gene disruption in Patient 2, two single nucleotide variations (SNVs) in DNAH5 gene and a heterozygous 17q12 deletion in Patient 3. The variants identified in this study need further validation to assess their roles in male infertility. This study shows that beside the mechanical effect of structural rearrangement on meiosis, breakpoints could result in additional alterations such as gene disruption or position effect. Moreover, additional SNVs or copy number variations may be fortuitously present and could explain the variable impact of chromosomal rearrangements on spermatogenesis. In conclusion, this study confirms the relevance of combining different cytogenetic and molecular techniques to investigate patients with spermatogenesis disorders and structural rearrangements on genomic scale.

scholarly journals Exceptional Complex Chromosomal Rearrangements in Three Generations

2015 ◽  
Vol 2015 ◽  
pp. 1-5
Author(s):  
Hannie Kartapradja ◽  
Nanis Sacharina Marzuki ◽  
Mark D. Pertile ◽  
David Francis ◽  
Lita Putri Suciati ◽  
...  
Keyword(s):  
Chromosomal Rearrangements ◽  
Partial Trisomy ◽  
Structural Rearrangement ◽  
Derivative Chromosome ◽  
Chromosome 4 ◽  
Partial Monosomy ◽  
Three Generations ◽  
Complex Chromosomal Rearrangements ◽  
Whole Genome Microarray ◽  
Translocation Breakpoints

We report an exceptional complex chromosomal rearrangement (CCR) found in three individuals in a family that involves 4 chromosomes with 5 breakpoints. The CCR was ascertained in a phenotypically abnormal newborn with additional chromosomal material on the short arm of chromosome 4. Maternal karyotyping indicated that the mother carried an apparently balanced CCR involving chromosomes 4, 6, 11, and 18. Maternal transmission of the derivative chromosome 4 resulted in partial trisomy for chromosomes 6q and 18q and a partial monosomy of chromosome 4p in the proband. Further family studies found that the maternal grandmother carried the same apparently balanced CCR as the proband’s mother, which was confirmed using the whole chromosome painting (WCP) FISH. High resolution whole genome microarray analysis of DNA from the proband’s mother found no evidence for copy number imbalance in the vicinity of the CCR translocation breakpoints, or elsewhere in the genome, providing evidence that the mother’s and grandmother’s CCRs were balanced at a molecular level. This structural rearrangement can be categorized as an exceptional CCR due to its complexity and is a rare example of an exceptional CCR being transmitted in balanced and/or unbalanced form across three generations.

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