Glycosylation of the Tandem Repeat Unit of the MUC2 Polypeptide Leading to the Synthesis of the Tn Antigen

1998 ◽  
Vol 245 (1) ◽  
pp. 23-27 ◽  
Author(s):  
Mizue Inoue ◽  
Ikuo Yamashina ◽  
Hiroshi Nakada
Keyword(s):  
Tandem Repeat ◽  
Repeat Unit ◽  
Tn Antigen

scholarly journals Products of Chemoenzymatic Synthesis Representing MUC1 Tandem Repeat Unit with T-, ST- or STn-antigen Revealed Distinct Specificities of Anti-MUC1 Antibodies

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Yayoi Yoshimura ◽  
Kaori Denda-Nagai ◽  
Yoshie Takahashi ◽  
Izuru Nagashima ◽  
Hiroki Shimizu ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Repeat Unit ◽  
Structural Features ◽  
T Antigen ◽  
Enzyme Linked Immunosorbent Assay ◽  
Serine Residue ◽  
Tn Antigen ◽  
Glycosylation Sites ◽  
Sialyl Tn Antigen ◽  
Cancer Diagnosis And Therapy

Abstract Anti-mucin1 (MUC1) antibodies have long been used clinically in cancer diagnosis and therapy and specific bindings of some of them are known to be dependent on the differential glycosylation of MUC1. However, a systematic comparison of the binding specificities of anti-MUC1 antibodies was not previously conducted. Here, a total of 20 glycopeptides including the tandem repeat unit of MUC1, APPAHGVTSAPDTRPAPGSTAPPAHGV with GalNAc (Tn-antigen), Galβ1-3GalNAc (T-antigen), NeuAcα2-3Galβ1-3GalNAc (sialyl-T-antigen), or NeuAcα2-6GalNAc (sialyl-Tn-antigen) at each threonine or serine residue were prepared by a combination of chemical glycopeptide synthesis and enzymatic extension of carbohydrate chains. These glycopeptides were tested by the enzyme-linked immunosorbent assay (ELISA) for their capacity to bind 13 monoclonal antibodies (mAbs) known to be specific for MUC1. The results indicated that anti-MUC1 mAbs have diverse specificities but can be classified into a few characteristic groups based on their binding pattern toward glycopeptides in some cases having a specific glycan at unique glycosylation sites. Because the clinical significance of some of these antibodies was already established, the structural features identified by these antibodies as revealed in the present study should provide useful information relevant to their further clinical use and the biological understanding of MUC1.

scholarly journals Finding Long Tandem Repeats In Long Noisy Reads

2020 ◽  
Author(s):  
Shinichi Morishita ◽  
Kazuki Ichikawa ◽  
Gene Myers
Keyword(s):  
Tandem Repeat ◽  
Error Rate ◽  
Tandem Repeats ◽  
Repeat Unit ◽  
Error Rates ◽  
De Bruijn Graph ◽  
Frequency Distributions ◽  
Sequencing Technologies ◽  
Long Reads ◽  
Repeat Expansions

Abstract Motivation Long tandem repeat expansions of more than 1000 nt have been suggested to be associated with diseases, but remain largely unexplored in individual human genomes because read lengths have been too short. However, new long-read sequencing technologies can produce single reads of 10,000 nt or more that can span such repeat expansions, although these long reads have high error rates, of 10%-20%, which complicates the detection of repetitive elements. Moreover, most traditional algorithms for finding tandem repeats are designed to find short tandem repeats (< 1000 nt) and cannot effectively handle the high error rate of long reads in a reasonable amount of time. Results Here, we report an efficient algorithm for solving this problem that takes advantage of the length of the repeat. Namely, a long tandem repeat has hundreds or thousands of approximate copies of the repeated unit, so despite the error rate, many short k-mers will be error-free in many copies of the unit. We exploited this characteristic to develop a method for first estimating regions that could contain a tandem repeat, by analyzing the k-mer frequency distributions of fixed-size windows across the target read, followed by an algorithm that assembles the k-mers of a putative region into the consensus repeat unit by greedily traversing a de Bruijn graph. Experimental results indicated that the proposed algorithm largely outperformed Tandem Repeats Finder (TRF), a widely used program for finding tandem repeats, in terms of sensitivity. Software availability https://github.com/morisUtokyo/mTR

scholarly journals Complete nucleotide sequence of the ribosomal RNA tandem repeat unit fromGiardia intestinalis

1990 ◽  
Vol 18 (13) ◽  
pp. 4006-4006 ◽  
Author(s):  
Andrew Healey ◽  
Roger Mitchell ◽  
Jacqueline A. Upcroft ◽  
Peter F. L. Boreham ◽  
Peter Upcroft
Keyword(s):  
Nucleotide Sequence ◽  
Ribosomal Rna ◽  
Tandem Repeat ◽  
Complete Nucleotide Sequence ◽  
Repeat Unit

Mass spectrometric analysis of combinatorial peptide libraries derived from the tandem repeat unit of MUC2 mucin

2003 ◽  
Vol 9 (6) ◽  
pp. 361-374 ◽  
Author(s):  
Gitta Schlosser ◽  
Zoltán Takáts ◽  
Károly Vékey ◽  
Gabriella Pócsfalvi ◽  
Antonio Malorni ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Repeat Unit ◽  
Mass Spectrometric ◽  
Peptide Libraries ◽  
Mass Spectrometric Analysis ◽  
Spectrometric Analysis ◽  
Combinatorial Peptide Libraries

Structure and evolution of the U2 small nuclear RNA multigene family in primates: gene amplification under natural selection?

1990 ◽  
Vol 10 (11) ◽  
pp. 5876-5882
Author(s):  
A G Matera ◽  
A M Weiner ◽  
C W Schmid
Keyword(s):  
Tandem Repeat ◽  
World Monkey ◽  
Repeat Unit ◽  
Intrinsic Property ◽  
Tandem Array ◽  
Old World Monkeys ◽  
Restriction Maps ◽  
Specific Sequence ◽  
Old World ◽  
Old World Monkey

The organization of U2 genes was compared in apes, Old World monkeys, and the prosimian galago. In humans and all apes (gibbon, orangutan, gorilla, and chimpanzee), the U2 genes were organized as a tandem repeat of a 6-kb element; however, the restriction maps of the 6-kb elements in these divergent species differed slightly, demonstrating that mechanisms must exist for maintaining sequence homogeneity within this tandem array. In Old World monkeys, the U2 genes were organized as a tandem repeat of an 11-kb element; the restriction maps of the 11-kb elements in baboon and two closely related macaques, bonnet and rhesus monkeys, also differed slightly, confirming that efficient sequence homogenization is an intrinsic property of the U2 tandem array. Interestingly, the 11-kb monkey repeat unit differed from the 6-kb hominid repeat unit by a 5-kb block of monkey-specific sequence. Finally, we found that the U2 genes of the prosimian galago were dispersed rather than tandemly repeated, suggesting that the hominid and Old World monkey U2 tandem arrays resulted from independent amplifications of a common ancestral U2 gene. Alternatively, the 5-kb monkey-specific sequence could have been inserted into the 6-kb array or deleted from the 11-kb array soon after divergence of the hominid and Old World monkey lineages.

Self-amplification of satellite DNA in vitro

Genome ◽  
1998 ◽  
Vol 41 (3) ◽  
pp. 429-434 ◽  
Author(s):  
J B Buntjer ◽  
J A Lenstra
Keyword(s):  
Tandem Repeat ◽  
Satellite Dna ◽  
Genomic Dna ◽  
Tandem Repeats ◽  
Repeat Unit ◽  
Dna Amplification ◽  
Repeat Units ◽  
Rapid Amplification ◽  
Species Specific

We describe a PCR-like reaction in which genomic DNA acts as a template as well as a primer. Interaction between genomic tandem repeat units leads to self-amplification of satellite DNA. This genomic self-priming PCR (GSP-PCR) allowed the rapid amplification of species-specific tandem repeats of horse, cattle, dolphin, and chicken. A novel specific satellite of ostrich with a repeat unit of 60 bp was isolated using this method.Key words: satellite DNA, amplification, isolation, species-specific probes.

scholarly journals Microhomologies Are Associated with Tandem Duplications and Structural Variation in Plant Mitochondrial Genomes

2020 ◽  
Vol 12 (11) ◽  
pp. 1965-1974
Author(s):  
Hanhan Xia ◽  
Wei Zhao ◽  
Yong Shi ◽  
Xiao-Ru Wang ◽  
Baosheng Wang
Keyword(s):  
Tandem Repeat ◽  
Structural Variation ◽  
Tandem Repeats ◽  
Repeat Unit ◽  
Mitochondrial Genomes ◽  
Repeat Array ◽  
Mitochondrial Genome Evolution ◽  
Tandem Duplications ◽  
Short Tandem

Abstract Short tandem repeats (STRs) contribute to structural variation in plant mitochondrial genomes, but the mechanisms underlying their formation and expansion are unclear. In this study, we detected high polymorphism in the nad7-1 region of the Pinus tabuliformis mitogenome caused by the rapid accumulation of STRs and rearrangements over a few million years ago. The STRs in nad7-1 have a 7-bp microhomology (TAG7) flanking the repeat array. We then scanned the mitogenomes of 136 seed plants to understand the role of microhomology in the formation of STR and mitogenome evolution. A total of 13,170 STRs were identified, and almost half of them were associated with microhomologies. A substantial amount (1,197) of microhomologies was long enough to mediate structural variation, and the length of microhomology is positively correlated with the length of tandem repeat unit. These results suggest that microhomology may be involved in the formation of tandem repeat via microhomology-mediated pathway, and the formation of longer duplicates required greater length of microhomology. We examined the abundance of these 1,197 microhomologies, and found 75% of them were enriched in the plant mitogenomes. Further analyses of the 400 prevalent microhomologies revealed that 175 of them showed differential enrichment between angiosperms and gymnosperms and 186 differed between angiosperms and conifers, indicating lineage-specific usage and expansion of microhomologies. Our study sheds light on the sources of structural variation in plant mitochondrial genomes and highlights the importance of microhomology in mitochondrial genome evolution.

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