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Alamro H, Alzamel M, Iliopoulos CS, Pissis SP, Watts S. IUPACpal: efficient identification of inverted repeats in IUPAC-encoded DNA sequences. BMC Bioinformatics 2021; 22:51. [PMID: 33549041 PMCID: PMC7866733 DOI: 10.1186/s12859-021-03983-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 01/27/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND An inverted repeat is a DNA sequence followed downstream by its reverse complement, potentially with a gap in the centre. Inverted repeats are found in both prokaryotic and eukaryotic genomes and they have been linked with countless possible functions. Many international consortia provide a comprehensive description of common genetic variation making alternative sequence representations, such as IUPAC encoding, necessary for leveraging the full potential of such broad variation datasets. RESULTS We present IUPACPAL, an exact tool for efficient identification of inverted repeats in IUPAC-encoded DNA sequences allowing also for potential mismatches and gaps in the inverted repeats. CONCLUSION Within the parameters that were tested, our experimental results show that IUPACPAL compares favourably to a similar application packaged with EMBOSS. We show that IUPACPAL identifies many previously unidentified inverted repeats when compared with EMBOSS, and that this is also performed with orders of magnitude improved speed.
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Affiliation(s)
- Hayam Alamro
- Department of Informatics, King’s College London, 30 Aldwych, London, UK
- Department of Information Systems, Princess Nourah bint Abdulrahman University, Riyadh, Kingdom of Saudi Arabia
| | - Mai Alzamel
- Department of Informatics, King’s College London, 30 Aldwych, London, UK
- Computer Science Department, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | | | - Solon P. Pissis
- Centrum Wiskunde & Informatica, Amsterdam, The Netherlands
- Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Steven Watts
- Department of Informatics, King’s College London, 30 Aldwych, London, UK
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Halahleh K, Gale RP, Nagler A. Isochromosome X in Myelodysplastic Syndrome. Acta Haematol 2015; 135:37-8. [PMID: 26303412 DOI: 10.1159/000435829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 06/09/2015] [Indexed: 01/12/2023]
Affiliation(s)
- Khalid Halahleh
- Department of Hematology and Bone Marrow Transplantation, Chaim Sheba Medical Center, Tel Hashomer, Israel
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Scott SA, Cohen N, Brandt T, Warburton PE, Edelmann L. Large inverted repeats within Xp11.2 are present at the breakpoints of isodicentric X chromosomes in Turner syndrome. Hum Mol Genet 2010; 19:3383-93. [PMID: 20570968 PMCID: PMC2916707 DOI: 10.1093/hmg/ddq250] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Revised: 06/03/2010] [Accepted: 06/14/2010] [Indexed: 02/01/2023] Open
Abstract
Turner syndrome (TS) results from whole or partial monosomy X and is mediated by haploinsufficiency of genes that normally escape X-inactivation. Although a 45,X karyotype is observed in half of all TS cases, the most frequent variant TS karyotype includes the isodicentric X chromosome alone [46,X,idic(X)(p11)] or as a mosaic [46,X,idic(X)(p11)/45,X]. Given the mechanism of idic(X)(p11) rearrangement is poorly understood and breakpoint sequence information is unknown, this study sought to investigate the molecular mechanism of idic(X)(p11) formation by determining their precise breakpoint intervals. Karyotype analysis and fluorescence in situ hybridization mapping of eight idic(X)(p11) cell lines and three unbalanced Xp11.2 translocation lines identified the majority of breakpoints within a 5 Mb region, from approximately 53 to 58 Mb, in Xp11.1-p11.22, clustering into four regions. To further refine the breakpoints, a high-resolution oligonucleotide microarray (average of approximately 350 bp) was designed and array-based comparative genomic hybridization (aCGH) was performed on all 11 idic(X)(p11) and Xp11.2 translocation lines. aCGH analyses identified all breakpoint regions, including an idic(X)(p11) line with two potential breakpoints, one breakpoint shared between two idic(X)(p11) lines and two Xp translocations that shared breakpoints with idic(X)(p11) lines. Four of the breakpoint regions included large inverted repeats composed of repetitive gene clusters and segmental duplications, which corresponded to regions of copy-number variation. These data indicate that the rearrangement sites on Xp11.2 that lead to isodicentric chromosome formation and translocations are probably not random and suggest that the complex repetitive architecture of this region predisposes it to rearrangements, some of which are recurrent.
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Affiliation(s)
| | | | | | | | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine of New York University, New York 10029, USA
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Paulsson K, Haferlach C, Fonatsch C, Hagemeijer A, Andersen MK, Slovak ML, Johansson B. The idic(X)(q13) in myeloid malignancies: breakpoint clustering in segmental duplications and association with TET2 mutations. Hum Mol Genet 2010; 19:1507-14. [DOI: 10.1093/hmg/ddq024] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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Manola KN, Stavropoulou C, Georgakakos VN, Zoi K, Fisfis M, Evmorfiadis I, Zoi C, Pantelias GE, Stefanoudaki K, Sambani C. Switch in X-inactivation in a JAK2 V617F-negative case of polycythemia vera with two acquired X-autosome translocations. Leuk Res 2007; 31:1009-14. [PMID: 17204324 DOI: 10.1016/j.leukres.2006.11.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2006] [Revised: 10/27/2006] [Accepted: 11/12/2006] [Indexed: 11/23/2022]
Abstract
We report a JAK2 V617F-negative case of polycythemia vera with two acquired balanced X-autosome translocations and no history of previous exposure to chemo/radiotherapy. The patient's first clone carried a novel translocation t(X;15)(q24;q13) as a sole abnormality. The second clone exhibited an additional translocation, t(X;20)(q13;q13.3), which is a rare recurrent abnormality in myeloid malignancies. This is the first report of a hematological disorder with both X chromosomes being translocated. Late replication studies revealed a switch in X-inactivation from the X chromosome involved in t(X;15) (first clone) to the X chromosome involved in the t(X;20)(q13;q13.3) (second clone). The inactivation of the translocated X chromosomes could provide potential for the inactivation of the adjacent autosomal regions, resulting in epigenetic gene silencing.
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Affiliation(s)
- Kalliopi N Manola
- Laboratory of Cytogenetics, National Center for Scientific Research (NCSR) "Demokritos", 15310 Aghia Paraskevi, Athens, Greece
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Prakash S, Sarran L, Socci N, DeMatteo RP, Eisenstat J, Greco AM, Maki RG, Wexler LH, LaQuaglia MP, Besmer P, Antonescu CR. Gastrointestinal stromal tumors in children and young adults: a clinicopathologic, molecular, and genomic study of 15 cases and review of the literature. J Pediatr Hematol Oncol 2005; 27:179-87. [PMID: 15838387 DOI: 10.1097/01.mph.0000157790.81329.47] [Citation(s) in RCA: 214] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Gastrointestinal stromal tumors (GISTs) are mesenchymal tumors of the intestinal tract that typically occur in adults over the age of 40 years. GISTs in younger patients are rare and not well characterized. The objective was to define the characteristics of GISTs in children and young adults (<30 years old). Clinicopathologic and molecular features, including KIT/PDGFRA genotype, in GISTs from 5 children and 10 young adults were analyzed. Gene expression analysis was performed on 5 gastric tumor samples from 2 children, 2 gastric tumors from young adults, and 10 gastric GISTs from older adults using an U133A Affymetrix platform (22,000 genes). All five pediatric GISTs occurred in girls, involved the stomach as multiple nodules, showed predominantly an epithelioid morphology, often involved lymph nodes, and lacked KIT or PDGFRA mutations. Although all five patients developed recurrence (four in the liver, three in the peritoneum, and two in both sites), four are still alive with disease. Of the 10 GISTs in young adults, half occurred in the small bowel and had spindle cell morphology, and one case had lymph node metastasis. KIT mutations were identified in seven cases, four in exon 11 and three in exon 9. Seven patients developed recurrence, and at last follow-up two patients had died of disease. Gene expression analysis showed high expression of PHKA1, FZD2, NLGN4, IGF1R, and ANK3 in the pediatric and young adult versus older adult cases. GISTs that occur in children are a separate clinicopathologic and molecular subset with predilection for girls, multifocal gastric tumors, and wild-type KIT/PDGFRA genotype. In contrast, GISTs in young adults are a more heterogeneous group, including cases that resemble either the pediatric or the older adult-type tumors. The distinct gene expression profile suggests avenues for investigation of pathogenesis and potential therapeutic strategies.
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Affiliation(s)
- Sonam Prakash
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
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Reddy KS, Richkind K, Ross M, Seirra R. Translocation (X;20)(q13;q13.3): a nonrandom abnormality in four patients with myeloid disorders. ACTA ACUST UNITED AC 2005; 157:70-3. [PMID: 15676151 DOI: 10.1016/j.cancergencyto.2004.05.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2004] [Revised: 05/19/2004] [Accepted: 05/24/2004] [Indexed: 11/15/2022]
Abstract
A recurring translocation (X;20)(q13;q13) was found in four women ranging in age from 57 to 77 years. They had myelodysplasia, myelodysplasia with thrombocytopenia and pancytopenia, transforming to myelofibrosis, and myelodysplasia with sideroblastic anemia, respectively. The t(X;20) was the sole abnormality in three cases; one case also had a der(1;7)(q10;p10). Added to three previously reported cases, our four cases bring the total to seven; thus, t(X;20)(q13;q13) is a nonrandom translocation associated with myeloid disorders. Previous FISH studies showed that the breakpoint on the X is proximal to XIST. In one of our cases, the breakpoint on the X was shown to be proximal to Xq12, by FISH using a probe for the androgen receptor gene locus.
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Warburton PE, Giordano J, Cheung F, Gelfand Y, Benson G. Inverted repeat structure of the human genome: the X-chromosome contains a preponderance of large, highly homologous inverted repeats that contain testes genes. Genome Res 2004; 14:1861-9. [PMID: 15466286 PMCID: PMC524409 DOI: 10.1101/gr.2542904] [Citation(s) in RCA: 193] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We have performed the first genome-wide analysis of the Inverted Repeat (IR) structure in the human genome, using a novel and efficient software package called Inverted Repeats Finder (IRF). After masking of known repetitive elements, IRF detected 22,624 human IRs characterized by arm size from 25 bp to >100 kb with at least 75% identity, and spacer length up to 100 kb. This analysis required 6 h on a desktop PC. In all, 166 IRs had arm lengths >8 kb. From this set, IRs were excluded if they were in unfinished/unassembled regions of the genome, or clustered with other closely related IRs, yielding a set of 96 large IRs. Of these, 24 (25%) occurred on the X-chromosome, although it represents only approximately 5% of the genome. Of the X-chromosome IRs, 83.3% were >/=99% identical, compared with 28.8% of autosomal IRs. Eleven IRs from Chromosome X, one from Chromosome 11, and seven already described from Chromosome Y contain genes predominantly expressed in testis. PCR analysis of eight of these IRs correctly amplified the corresponding region in the human genome, and six were also confirmed in gorilla or chimpanzee genomes. Similarity dot-plots revealed that 22 IRs contained further secondary homologous structures partially categorized into three distinct patterns. The prevalence of large highly homologous IRs containing testes genes on the X- and Y-chromosomes suggests a possible role in male germ-line gene expression and/or maintaining sequence integrity by gene conversion.
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Affiliation(s)
- Peter E Warburton
- Department of Human Genetics, Mount Sinai School of Medicine, New York, New York 10029, USA.
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Liao DJ, Du QQ, Yu BW, Grignon D, Sarkar FH. Novel perspective: focusing on the X chromosome in reproductive cancers. Cancer Invest 2003; 21:641-58. [PMID: 14533452 DOI: 10.1081/cnv-120022385] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In an XX female, one of the two X chromosomes has been inactivated during early embryonic life to achieve a compensation of X-linked gene products between males and females, leaving only one allele of X-linked genes functional. There are some X-linked genes escaping the X-inactivation, i.e., being expressed from both alleles. Escape from X-inactivation varies at different levels; some genes have both alleles active in some women but only one allele active in others, whereas some other genes have both alleles active in neoplastic tissue but only one allele active normally. The X-inactivation may be considered functionally equivalent to a loss of heterozygosity (LOH) for some genes, whereas escape from X-inactivation may be equivalent to functional gene amplification for others. The physiological LOH may make X-linked tumor suppressor genes lose their function more easily, compared with autosomal tumor suppressor genes, thus predisposing women to cancer formation more easily. Moreover, the human X chromosome contains many genes related to cancer or to sex and reproduction. All these properties of the X chromosome suggest that it may play more important roles than any autosomal chromosome in the development and progression of reproductive and urologic cancers.
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Affiliation(s)
- Dezhong Joshua Liao
- Department of Pathology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan, USA.
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Gray BA, Cornfield D, Bent-Williams A, Zori RT. Translocation (X;20)(q13.1;q13.3) as a primary chromosomal finding in two patients with myelocytic disorders. CANCER GENETICS AND CYTOGENETICS 2003; 141:169-74. [PMID: 12606138 DOI: 10.1016/s0165-4608(02)00764-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Reports of X chromosome translocations, as primary chromosomal changes associated with hematologic disorders, remain relatively uncommon. Herein, we report the detection, by conventional cytogenetic methods, of a cytogenetically identical t(X;20) in two different patients with hematologic disorders (probable myelodysplasia and polycythemia vera/acute myelocytic leukemia). In both cases, this translocation appeared as the primary clonal chromosome abnormality, with breakpoints occurring in the long arms of both the X chromosome and chromosome 20 (Xq13.1 and 20q13.3, respectively). Further characterization and comparison of the translocation chromosome products of these two cases by use of fluorescence in situ hybridization techniques is also described. Similar previously reported cytogenetically cases and the potential that this specific rearrangement may represent a nonrandom chromosomal finding are discussed.
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Affiliation(s)
- Brian A Gray
- Department of Pediatrics, College of Medicine, University of Florida, Gainesville, FL, USA
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Van den Wyngaert I, de Vries W, Kremer A, Neefs J, Verhasselt P, Luyten WH, Kass SU. Cloning and characterization of human histone deacetylase 8. FEBS Lett 2000; 478:77-83. [PMID: 10922473 DOI: 10.1016/s0014-5793(00)01813-5] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
To date, seven different human histone deacetylases (HDACs) have been identified, which fall into two distinct classes. We have isolated and characterized a cDNA encoding a novel human HDAC, which we name HDAC8. HDAC8 shows a high degree of sequence similarity to HDAC1 and HDAC2 and thus belongs to the class I of HDACs. HDAC8 is expressed in a variety of tissues. Human cells overexpressing HDAC8 localize the protein in sub-nuclear compartments whereas HDAC1 shows an even nuclear distribution. In addition, the HDAC8 gene is localized on the X chromosome at position q13, which is close to the XIST gene and chromosomal breakpoints associated with preleukemia.
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Affiliation(s)
- I Van den Wyngaert
- Department of Advanced Bio-Technologies, Jansen Research Foundation, Turnhoutseweg 30, 2340 Beerse, Belgium
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