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
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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
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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
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Conserved presence of G-quadruplex forming sequences in the Long Terminal Repeat Promoter of Lentiviruses [PDF]
Scientific Reports, 2017 G-quadruplexes (G4s) are secondary structures of nucleic acids that epigenetically regulate cellular processes. In the human immunodeficiency lentivirus 1 (HIV-1), dynamic G4s are located in the unique viral LTR promoter.
Rosalba Perrone +3 more
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NFAT5 regulates HIV-1 in primary monocytes via a highly conserved long terminal repeat site. [PDF]
PLoS Pathogens, 2006 To replicate, HIV-1 capitalizes on endogenous cellular activation pathways resulting in recruitment of key host transcription factors to its viral enhancer. RNA interference has been a powerful tool for blocking key checkpoints in HIV-1 entry into cells.
Shahin Ranjbar +7 more
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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
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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
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Human Endogenous Retrovirus-H Long Terminal Repeat-Associating Protein 2 Possesses Prognostic Significance and Promotes Progression of Papillary Thyroid Cancer [PDF]
International Journal of General Medicine, 2022 Yongzhi Niu,1 Yichuan Huang,1 Anbing Dong,2 Yinghe Sun2 1Department of Otolaryngology-Head and Neck Surgery, The Affiliated Hospital of Qingdao University, Qingdao, People’s Republic of China; 2Department of Thyroid Surgery, The Affiliated Hospital of ...
Niu Y, Huang Y, Dong A, Sun Y
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cAMP Signaling Enhances HIV-1 Long Terminal Repeat (LTR)-directed Transcription and Viral Replication in Bone Marrow Progenitor Cells [PDF]
Clinical Medicine Insights: Pathology, 2017 CD34 + hematopoietic progenitor cells have been shown to be susceptible to HIV-1 infection, possibly due to a low-level expression of CXCR4, a coreceptor for HIV-1 entry.
Anupam Banerjee +5 more
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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
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