Organizational Variation of DYZ1 Repeat Sequences on the Human Y Chromosome and Its Diagnostic Potentials

Rahman, Mohammed Mahidur; Bashamboo, Anu; Prasad, Aparna; Pathak, Deepali; Ali, Sher

doi:10.1089/dna.2004.23.561

Cited by 19 publications

(10 citation statements)

References 25 publications

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“…Therefore, to illustrate the utility of our HSat2,3 reference database for studying satellite array size variation using short-read sequencing data, we investigated the total size of the Y-chromosome heterochromatic locus classically known as DYZ1 (corresponding to subfamily HSat3A6) using genomic sequence data from 396 male individuals from the 1000 Genomes Project [64], [65]. Predicted DYZ1 array sizes (see Methods, Table 2, Dataset S4) varied over an order of magnitude (7-98 Mb, with mean 24 Mb), consistent with previous experimental observations of Y-chromosome length variability [27], [70], [71].…”

Section: Resultssupporting

confidence: 72%

“…Satellite arrays have been shown previously to vary in size within the human population [31]–[34], [69]–[71]. Therefore, to illustrate the utility of our HSat2,3 reference database for studying satellite array size variation using short-read sequencing data, we investigated the total size of the Y-chromosome heterochromatic locus classically known as DYZ1 (corresponding to subfamily HSat3A6) using genomic sequence data from 396 male individuals from the 1000 Genomes Project [64], [65].…”

Section: Resultsmentioning

confidence: 99%

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Genomic Characterization of Large Heterochromatic Gaps in the Human Genome Assembly

et al. 2014

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The largest gaps in the human genome assembly correspond to multi-megabase heterochromatic regions composed primarily of two related families of tandem repeats, Human Satellites 2 and 3 (HSat2,3). The abundance of repetitive DNA in these regions challenges standard mapping and assembly algorithms, and as a result, the sequence composition and potential biological functions of these regions remain largely unexplored. Furthermore, existing genomic tools designed to predict consensus-based descriptions of repeat families cannot be readily applied to complex satellite repeats such as HSat2,3, which lack a consistent repeat unit reference sequence. Here we present an alignment-free method to characterize complex satellites using whole-genome shotgun read datasets. Utilizing this approach, we classify HSat2,3 sequences into fourteen subfamilies and predict their chromosomal distributions, resulting in a comprehensive satellite reference database to further enable genomic studies of heterochromatic regions. We also identify 1.3 Mb of non-repetitive sequence interspersed with HSat2,3 across 17 unmapped assembly scaffolds, including eight annotated gene predictions. Finally, we apply our satellite reference database to high-throughput sequence data from 396 males to estimate array size variation of the predominant HSat3 array on the Y chromosome, confirming that satellite array sizes can vary between individuals over an order of magnitude (7 to 98 Mb) and further demonstrating that array sizes are distributed differently within distinct Y haplogroups. In summary, we present a novel framework for generating initial reference databases for unassembled genomic regions enriched with complex satellite DNA, and we further demonstrate the utility of these reference databases for studying patterns of sequence variation within human populations.

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Section: Resultssupporting

confidence: 72%

Section: Resultsmentioning

confidence: 99%

Genomic Characterization of Large Heterochromatic Gaps in the Human Genome Assembly

et al. 2014

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“…Labelling was done with biotin-dUTP using a Nick translation kit from Vysis (Illinois, USA). Hybridization, washing, counterstaining and mounting of the slides were conducted following standard protocols [25]. The slides were screened under the Olympus fluorescence microscope (BX 51) fitted with vertical fluorescence illuminator U-LH100HG UV, excitation and barrier filters and images were captured with a charge-coupled device (CCD) camera.…”

Section: Methodsmentioning

confidence: 99%

DYZ1 arrays show sequence variation between the monozygotic males

et al. 2014

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BackgroundMonozygotic twins (MZT) are an important resource for genetical studies in the context of normal and diseased genomes. In the present study we used DYZ1, a satellite fraction present in the form of tandem arrays on the long arm of the human Y chromosome, as a tool to uncover sequence variations between the monozygotic males.ResultsWe detected copy number variation, frequent insertions and deletions within the sequences of DYZ1 arrays amongst all the three sets of twins used in the present study. MZT1b showed loss of 35 bp compared to that in 1a, whereas 2a showed loss of 31 bp compared to that in 2b. Similarly, 3b showed 10 bp insertion compared to that in 3a. MZT1a germline DNA showed loss of 5 bp and 1b blood DNA showed loss of 26 bp compared to that of 1a blood and 1b germline DNA, respectively. Of the 69 restriction sites detected in DYZ1 arrays, MboII, BsrI, TspEI and TaqI enzymes showed frequent loss and or gain amongst all the 3 pairs studied. MZT1 pair showed loss/gain of VspI, BsrDI, AgsI, PleI, TspDTI, TspEI, TfiI and TaqI restriction sites in both blood and germline DNA. All the three sets of MZT showed differences in the number of DYZ1 copies. FISH signals reflected somatic mosaicism of the DYZ1 copies across the cells.ConclusionsDYZ1 showed both sequence and copy number variation between the MZT males. Sequence variation was also noticed between germline and blood DNA samples of the same individual as we observed at least in one set of sample. The result suggests that DYZ1 faithfully records all the genetical changes occurring after the twining which may be ascribed to the environmental factors.

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“…The BAC DNA was labeled with Fluorescein tagged dUTP (Invitrogen) using the Nick Translation Kit from Abott Molecular Inc. (IL, USA). FISH was subsequently conducted following established protocols [38]. The slides were screened under an Olympus fluorescence microscope (BX 51) fitted with a vertical fluorescence illuminator U-LH100HG UV, excitation and barrier filters.…”

Section: Methodsmentioning

confidence: 99%

Molecular Mining of Alleles in Water Buffalo Bubalus bubalis and Characterization of the TSPY1 and COL6A1 Genes

et al. 2011

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BackgroundMinisatellites are an integral part of eukaryotic genomes and show variation in the complexity of their organization. Besides their presence in non-coding regions, a small fraction of them are part of the transcriptome, possibly participating in gene regulation, expression and silencing. We studied the minisatellite (TGG)n tagged transcriptome in the water buffalo Bubalus bubalis across various tissues and the spermatozoa, and characterized the genes TSPY1 and COL6A1 discovered in the process.ResultsMinisatellite associated sequence amplification (MASA) conducted using cDNA and oligonucleotide primer (TGG)5 uncovered 38 different mRNA transcripts from somatic tissues and gonads and 15 from spermatozoa. These mRNA transcripts corresponded to several known and novel genes. The majority of the transcripts showed the highest level of expression either in the testes or spermatozoa with exception of a few showing higher expression levels in the lungs and liver. Transcript SR1, which is expressed in all the somatic tissues and gonads, was found to be similar to the Bos taurus collagen type VI alpha 1 gene (COL6A1). Similarly, SR29, a testis-specific transcript, was found to be similar to the Bos taurus testis-specific Y-encoded protein-1 representing cancer/testis antigen 78 (CT78). Subsequently, full length coding sequences (cds) of these two transcripts were obtained. Quantitative PCR (q-PCR) revealed 182-202 copies of theTSPY1 gene in water buffalo, which localized to the Y chromosome.ConclusionsThe MASA approach enabled us to identify several genes, including two of clinical significance, without screening an entire cDNA library. Genes identified with TGG repeats are not part of a specific family of proteins and instead are distributed randomly throughout the genome. Genes showing elevated expression in the testes and spermatozoa may prove to be potential candidates for in-depth characterization. Furthermore, their possible involvement in fertility or lack thereof would augment animal biotechnology.

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Organizational Variation of DYZ1 Repeat Sequences on the Human Y Chromosome and Its Diagnostic Potentials

Cited by 19 publications

References 25 publications

Genomic Characterization of Large Heterochromatic Gaps in the Human Genome Assembly

Genomic Characterization of Large Heterochromatic Gaps in the Human Genome Assembly

DYZ1 arrays show sequence variation between the monozygotic males

Molecular Mining of Alleles in Water Buffalo Bubalus bubalis and Characterization of the TSPY1 and COL6A1 Genes

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