scholarly journals The Tritryps Comparative Repeatome: Insights on Repetitive Element Evolution in Trypanosomatid Pathogens

2019 ◽  
Vol 11 (2) ◽  
pp. 546-551 ◽  
Author(s):  
Sebastián Pita ◽  
Florencia Díaz-Viraqué ◽  
Gregorio Iraola ◽  
Carlos Robello
Keyword(s):  
Repetitive Element ◽  
Element Evolution

scholarly journals Tempo and Mode of Ty Element Evolution in Saccharomyces cerevisiae

Genetics ◽  
1999 ◽  
Vol 151 (4) ◽  
pp. 1341-1351 ◽  
Author(s):  
I King Jordan ◽  
John F McDonald
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Negative Selection ◽  
Sequence Variation ◽  
Size Variation ◽  
Sequence Comparisons ◽  
Ty Elements ◽  
Ty Element ◽  
Amino Acid Sequence Variation ◽  
Element Evolution ◽  
High Level

Abstract The Saccharomyces cerevisiae genome contains five families of long terminal repeat (LTR) retrotransposons, Ty1–Ty5. The sequencing of the S. cerevisiae genome provides an unprecedented opportunity to examine the patterns of molecular variation existing among the entire genomic complement of Ty retrotransposons. We report the results of an analysis of the nucleotide and amino acid sequence variation within and between the five Ty element families of the S. cerevisiae genome. Our results indicate that individual Ty element families tend to be highly homogenous in both sequence and size variation. Comparisons of within-element 5′ and 3′ LTR sequences indicate that the vast majority of Ty elements have recently transposed. Furthermore, intrafamily Ty sequence comparisons reveal the action of negative selection on Ty element coding sequences. These results taken together suggest that there is a high level of genomic turnover of S. cerevisiae Ty elements, which is presumably in response to selective pressure to escape host-mediated repression and elimination mechanisms.

scholarly journals First Application of the SINE (Short Interspersed Repetitive Element) Method to Infer Phylogenetic Relationships in Reptiles: An Example from the Turtle Superfamily Testudinoidea

2004 ◽  
Vol 21 (4) ◽  
pp. 705-715 ◽  
Author(s):  
Takeshi Sasaki ◽  
Kazuhiko Takahashi ◽  
Masato Nikaido ◽  
Seiko Miura ◽  
Yuichirou Yasukawa ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Repetitive Element ◽  
Element Method

scholarly journals A separable domain of the p150 subunit of human chromatin assembly factor-1 promotes protein and chromosome associations with nucleoli

2014 ◽  
Vol 25 (18) ◽  
pp. 2866-2881 ◽  
Author(s):  
Corey L. Smith ◽  
Timothy D. Matheson ◽  
Daniel J. Trombly ◽  
Xiaoming Sun ◽  
Eric Campeau ◽  
...  
Keyword(s):  
Repetitive Element ◽  
Chromatin Assembly ◽  
The Other ◽  
Dna Interactions ◽  
Interaction Sites ◽  
Chromatin Assembly Factor ◽  
Nucleolar Proteins ◽  
Nucleolar Chromosome ◽  
Assembly Factor ◽  
Chromosome Associations

Chromatin assembly factor-1 (CAF-1) is a three-subunit protein complex conserved throughout eukaryotes that deposits histones during DNA synthesis. Here we present a novel role for the human p150 subunit in regulating nucleolar macromolecular interactions. Acute depletion of p150 causes redistribution of multiple nucleolar proteins and reduces nucleolar association with several repetitive element–containing loci. Of note, a point mutation in a SUMO-interacting motif (SIM) within p150 abolishes nucleolar associations, whereas PCNA or HP1 interaction sites within p150 are not required for these interactions. In addition, acute depletion of SUMO-2 or the SUMO E2 ligase Ubc9 reduces α-satellite DNA association with nucleoli. The nucleolar functions of p150 are separable from its interactions with the other subunits of the CAF-1 complex because an N-terminal fragment of p150 (p150N) that cannot interact with other CAF-1 subunits is sufficient for maintaining nucleolar chromosome and protein associations. Therefore these data define novel functions for a separable domain of the p150 protein, regulating protein and DNA interactions at the nucleolus.

Internally located and oppositely oriented polymerase II promoters direct convergent transcription of a LINE-like retroelement, the Dictyostelium repetitive element, from Dictyostelium discoideum

1994 ◽  
Vol 14 (5) ◽  
pp. 3074-3084
Author(s):  
G Schumann ◽  
I Zündorf ◽  
J Hofmann ◽  
R Marschalek ◽  
T Dingermann
Keyword(s):  
Dictyostelium Discoideum ◽  
Repetitive Element ◽  
Building Blocks ◽  
Rna Transcripts ◽  
Convergent Transcription ◽  
Sense Strand ◽  
Cloned Cdna ◽  
Dna Strand ◽  
The Right ◽  
Complementary Sense

The Dictyostelium discoideum NC4 genome harbors approximately 150 individual copies of a retrotransposable element called the Dictyostelium repetitive element (DRE). This element contains nonidentical terminal repeats (TRs) consisting of conserved building blocks A and B in the left TR and B and C in the right TR. Seven different-sized classes of RNA transcripts from these elements were resolved by Northern (RNA) blot analysis, but their combined abundance was very low. When D. discoideum cells were grown in the presence of the respiratory chain blocker antimycin A, steady-state concentrations of these RNA species increased 10- to 20-fold. The D. discoideum genome contains two DRE subtypes, the full-length 5.7-kb DREa and the internally deleted 2.4-kb DREb. Both subtypes are transcribed, as confirmed by analysis of cloned cDNA. Primary transcripts from the sense strand originate at nucleotide +1 and terminate at two dominant sites, located 21 or 28 nucleotides upstream from the 3' end of the elements. The activity of a reasonably strong polymerase II promoter in the 5'-terminal A module is slightly upregulated by the tRNA gene located 50 +/- 4 nucleotides upstream and drastically reduced by the adjacent B module of the DRE. Transcripts from the opposite DNA strand (complementary-sense transcripts) were also detected, directed by an internally located polymerase II promoter residing within the C module. This latter transcription was initiated at multiple sites within the oligo(dA12) stretch which terminates DREs.

scholarly journals Comparison and Utilization of Repetitive-Element PCR Techniques for Typing Lactobacillus Isolates from the Chicken Gastrointestinal Tract

2009 ◽  
Vol 75 (21) ◽  
pp. 6764-6776 ◽  
Author(s):  
David P. Stephenson ◽  
Robert J. Moore ◽  
Gwen E. Allison
Keyword(s):  
Gastrointestinal Tract ◽  
Lactobacillus Reuteri ◽  
Repetitive Element ◽  
Necrotic Enteritis ◽  
High Throughput Analysis ◽  
Strain Diversity ◽  
Disease Induction ◽  
First Time ◽  
Pcr Techniques ◽  
Type Strains

ABSTRACT Three repetitive-element PCR techniques were evaluated for the ability to type strains of Lactobacillus species commonly identified in the chicken gastrointestinal tract. Enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) produced species- and strain-specific profiles for Lactobacillus crispatus, Lactobacillus gallinarum, Lactobacillus johnsonii, and Lactobacillus reuteri isolates. The technique typed strains within these species equally as well as pulsed-field gel electrophoresis. DNA concentration and quality did not affect the ERIC-PCR profiles, indicating that this method, unlike other high-resolution methods, can be adapted to high-throughput analysis of isolates. Subsequently, ERIC-PCR was used to type Lactobacillus species diversity of a large collection of isolates derived from chickens grown under commercial and necrotic enteritis disease induction conditions. This study has illustrated, for the first time, that there is great strain diversity within each Lactobacillus species present and has revealed that chickens raised under commercial conditions harbor greater species and strain diversity than chickens raised under necrotic enteritis disease induction conditions.

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