LTR_FINDER_parallel: parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons [PDF]
Mobile DNA, 2019 Annotation of plant genomes is still a challenging task due to the abundance of repetitive sequences, especially long terminal repeat (LTR) retrotransposons.
Shujun Ou, Ning Jiang
doaj +3 more sources
LtrDetector: A tool-suite for detecting long terminal repeat retrotransposons de-novo [PDF]
BMC Genomics, 2019 Background Long terminal repeat retrotransposons are the most abundant transposons in plants. They play important roles in alternative splicing, recombination, gene regulation, and defense mechanisms. Large-scale sequencing projects for plant genomes are
Joseph D. Valencia, Hani Z. Girgis
doaj +3 more sources
Tat inhibition by didehydro-Cortistatin A promotes heterochromatin formation at the HIV-1 long terminal repeat [PDF]
Epigenetics & Chromatin, 2019 Background Transcription from the integrated HIV-1 promoter is directly governed by its chromatin environment, and the nucleosome-1 downstream from the transcription start site directly impedes transcription from the HIV-1 promoter. The HIV-1 Tat protein
Chuan Li +2 more
doaj +5 more sources
Comparative analysis of miniature inverted–repeat transposable elements (MITEs) and long terminal repeat (LTR) retrotransposons in six Citrus species [PDF]
BMC Plant Biology, 2019 Background Miniature inverted-repeat transposable elements (MITEs) and long terminal repeat (LTR) retrotransposons are ubiquitous in plants genomes, and highly important in their evolution and diversity.
Yan Liu +8 more
doaj +3 more sources
Stable and Conserved G-Quadruplexes in the Long Terminal Repeat Promoter of Retroviruses. [PDF]
ACS Infect Dis, 2019 Retroviruses infect almost all vertebrates, from humans to domestic and farm animals, from primates to wild animals, where they cause severe diseases, including immunodeficiencies, neurological disorders, and cancer.
Ruggiero E +4 more
europepmc +6 more sources
Cell Compartment-Specific Folding of Ty1 Long Terminal Repeat Retrotransposon RNA Genome [PDF]
Viruses, 2022 The structural transitions RNAs undergo during trafficking are not well understood. Here, we used the well-developed yeast Ty1 retrotransposon to provide the first structural model of genome (g) RNA in the nucleus from a retrovirus-like transposon ...
Małgorzata Zawadzka +4 more
doaj +2 more sources
A machine learning based framework to identify and classify long terminal repeat retrotransposons. [PDF]
PLoS Computational Biology, 2018 Transposable elements (TEs) are repetitive nucleotide sequences that make up a large portion of eukaryotic genomes. They can move and duplicate within a genome, increasing genome size and contributing to genetic diversity within and across species ...
Leander Schietgat +7 more
doaj +2 more sources
Detection of long terminal repeat loci derived from endogenous retrovirus in junglefowl using whole-genome sequencing [PDF]
Scientific Reports, 2023 Endogenous retroviruses (ERVs) are genetic elements present in the genome that retain traces of past viral infections. Characterization of ERVs can provide crucial insights into avian evolution.
Shinya Ishihara
doaj +2 more sources
Species-Specific Transcription Factors Associated with Long Terminal Repeat Promoters of Endogenous Retroviruses: A Comprehensive Review [PDF]
BiomoleculesEndogenous retroviruses (ERVs) became a part of the eukaryotic genome through endogenization millions of years ago. Moreover, they have lost their innate capability of virulence or replication.
Md Jakir Hossain +2 more
doaj +2 more sources
Identification of high-copy number long terminal repeat retrotransposons and their expansion in Phalaenopsis orchids [PDF]
BMC Genomics, 2020 Background Transposable elements (TEs) are fragments of DNA that can insert into new chromosomal locations. They represent a great proportion of eukaryotic genomes.
Chia-Chi Hsu +8 more
doaj +2 more sources