PstI repeat: a family of short interspersed nucleotide element (SINE)-like sequences in the genomes of cattle, goat, and buffalo

Genome ◽  
2002 ◽  
Vol 45 (1) ◽  
pp. 44-50 ◽  
Author(s):  
Faruk G Sheikh ◽  
Sudit S Mukhopadhyay ◽  
Prabhakar Gupta
Keyword(s):  
Nucleotide Sequence ◽  
Dna Sequences ◽  
Sequence Homology ◽  
Copy Number ◽  
Southern Hybridization ◽  
Repetitive Dna Sequences ◽  
Type I ◽  
Type Ii ◽  
Repeat Type ◽  
Highly Repetitive Dna

The PstI family of elements are short, highly repetitive DNA sequences interspersed throughout the genome of the Bovidae. We have cloned and sequenced some members of the PstI family from cattle, goat, and buffalo. These elements are approximately 500 bp, have a copy number of 2 × 105 – 4 × 105, and comprise about 4% of the haploid genome. Studies of nucleotide sequence homology indicate that the buffalo and goat PstI repeats (type II) are similar types of short interspersed nucleotide element (SINE) sequences, but the cattle PstI repeat (type I) is considerably more divergent. Additionally, the goat PstI sequence showed significant sequence homology with bovine serine tRNA, and is therefore likely derived from serine tRNA. Interestingly, Southern hybridization suggests that both types of SINEs (I and II) are present in all the species of Bovidae. Dendrogram analysis indicates that cattle PstI SINE is similar to bovine Alu-like SINEs. Goat and buffalo SINEs formed a separate cluster, suggesting that these two types of SINEs evolved separately in the genome of the Bovidae.Key words: repeat, SINE, Bovidae, genome.

scholarly journals Repetitive DNA sequences accelerate molecular cytogenetic research in plants with small chromosomes

2019 ◽  
Vol 24 (2) ◽  
pp. 82
Author(s):  
Agus Budi Setiawan ◽  
Ari Wibowo ◽  
Chee How Teo ◽  
Shinji Kikuchi ◽  
Takato Koba
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
5S Rdna ◽  
Repetitive Dna Sequences ◽  
Type I ◽  
Chromosome Identification ◽  
Metaphase Chromosomes ◽  
Homologous Chromosomes ◽  
Centromeric Sequence ◽  
Subtelomeric Sequence

Repetitive DNA sequences are highly abundant in plant genomes and are favorable probes for chromosome identification in plants. However, it is difficult to conduct studies on the details of metaphase chromosome structures in plants with small chromosomes due to their highly condensed status. Therefore, identification of homologous chromosomes for karyotyping and analyzing chromosome structures is a challenging issue for cytogeneticists without specific probes and precise chromosome stages. In this study, five repetitive DNA probes, i.e., 5S and 45S ribosomal DNAs (rDNAs), melon centromeric sequence (Cmcent), cucumber subtelomeric sequence (Type I), and microsatellite (CT)10 repeats, were used to identify primary constrictions and homologous chromosomes for karyotyping. Four and two loci of 45S rDNA were respectively observed on metaphase and pachytene chromosomes of Abelia × grandiflora. Cmcent was detected on both primary constrictions of melon pachytene and metaphase chromosomes. Furthermore, one pair of 5S rDNA signals were hybridized on melon metaphase chromosomes. Eight and two loci of 45S and 5S rDNA were respectively detected on cucumber chromosomes. Type I and (CT)10 probes were specifically hybridized on subtelomeric and interstitial regions on the chromosomes, respectively. These results suggest that repetitive DNA sequences are versatile probes for chromosome identification in plants with small chromosomes, particularly for karyotyping analyses.

Genes for intermediate filament proteins and the draft sequence of the human genome

2001 ◽  
Vol 114 (14) ◽  
pp. 2569-2575 ◽  
Author(s):  
Michael Hesse ◽  
Thomas M. Magin ◽  
Klaus Weber
Keyword(s):  
Human Genome ◽  
Dna Sequences ◽  
Intermediate Filament ◽  
Muscle Protein ◽  
Gene Families ◽  
Type I ◽  
Type Ii ◽  
Draft Sequence ◽  
Intermediate Filament Proteins ◽  
Processed Pseudogenes

We screened the draft sequence of the human genome for genes that encode intermediate filament (IF) proteins in general, and keratins in particular. The draft covers nearly all previously established IF genes including the recent cDNA and gene additions, such as pancreatic keratin 23, synemin and the novel muscle protein syncoilin. In the draft, seven novel type II keratins were identified, presumably expressed in the hair follicle/epidermal appendages. In summary, 65 IF genes were detected, placing IF among the 100 largest gene families in humans. All functional keratin genes map to the two known keratin clusters on chromosomes 12 (type II plus keratin 18) and 17 (type I), whereas other IF genes are not clustered. Of the 208 keratin-related DNA sequences, only 49 reflect true keratin genes, whereas the majority describe inactive gene fragments and processed pseudogenes. Surprisingly, nearly 90% of these inactive genes relate specifically to the genes of keratins 8 and 18. Other keratin genes, as well as those that encode non-keratin IF proteins, lack either gene fragments/pseudogenes or have only a few derivatives. As parasitic derivatives of mature mRNAs, the processed pseudogenes of keratins 8 and 18 have invaded most chromosomes, often at several positions. We describe the limits of our analysis and discuss the striking unevenness of pseudogene derivation in the IF multigene family. Finally, we propose to extend the nomenclature of Moll and colleagues to any novel keratin.

Palindromic unit highly repetitive DNA sequences exhibit species specificity within Enterobacteriacea

1990 ◽  
Vol 141 (9) ◽  
pp. 1103-1116 ◽  
Author(s):  
E. Gilson ◽  
S. Bachellier ◽  
S. Perrin ◽  
D. Perrin ◽  
P.A.D. Grimont ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Species Specificity ◽  
Repetitive Dna Sequences ◽  
Highly Repetitive Dna

Localization and characterization of recombinant DNA clones derived from the highly repetitive DNA sequences in the Indian muntjac cells: their presence in the Chinese muntjac

Chromosoma ◽  
1986 ◽  
Vol 93 (6) ◽  
pp. 521-528 ◽  
Author(s):  
Loh-Chung Yu ◽  
Daniel Lowensteiner ◽  
Elsie F. -K. Wong ◽  
Ikuhisa Sawada ◽  
Joe Mazrimas ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Recombinant Dna ◽  
Repetitive Dna Sequences ◽  
Indian Muntjac ◽  
Highly Repetitive Dna

scholarly journals Directed PCR-free engineering of highly repetitive DNA sequences

2011 ◽  
Vol 11 (1) ◽  
pp. 87 ◽  
Author(s):  
Annika Scior ◽  
Steffen Preissler ◽  
Miriam Koch ◽  
Elke Deuerling
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Repetitive Dna Sequences ◽  
Highly Repetitive Dna

Differentiation of triticale cultivars through FISH karyotyping of their rye chromosomes

Genome ◽  
2013 ◽  
Vol 56 (5) ◽  
pp. 267-272 ◽  
Author(s):  
Maia Fradkin ◽  
María Rosa Ferrari ◽  
Shirley Mary Espert ◽  
Víctor Ferreira ◽  
Ezequiel Grassi ◽  
...  
Keyword(s):  
Cluster Analysis ◽  
In Situ Hybridization ◽  
Dna Sequences ◽  
Fish Analysis ◽  
Repetitive Dna Sequences ◽  
Agronomic Characters ◽  
Breeding Programs ◽  
Specific Localization ◽  
Highly Repetitive Dna

The aim of this work was to cytogenetically characterize triticale cultivars through fluorescence in situ hybridization (FISH) analysis of their rye chromosomes. In the present work, we studied six cultivars of triticale (‘Cayú-UNRC’, ‘Cumé-UNRC’, ‘Genú-UNRC’, ‘Ñinca-UNRC’, ‘Quiñé-UNRC’, and ‘Tizné-UNRC’), released by the Universidad Nacional de Río Cuarto (UNRC), Córdoba, Argentina. The cultivars were obtained from the International Center for the Improvement of Maize and Wheat (CIMMYT) and improved for fresh forage, haymaking, and feed grain at UNRC. The distribution and organization of highly repetitive DNA sequences of Secale cereale (pSc74, pSc200, pSc250, and pSc119.2) using FISH analyses revealed a specific localization of the signals for several rye chromosomes, which allowed us to distinguish the cultivars. Cluster analysis showed a great cytogenetic similarity among the rye cultivars used to originate these hybrids. The knowledge of the variability among triticale cultivars is necessary to propose future crosses in breeding programs. This study will also be valuable to identify commercial seeds and to analyze the possible association between agronomic characters and the presence of certain rye chromosomes or specific regions in these chromosomes.

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