Topic
Interspersed repeat
About: Interspersed repeat is a research topic. Over the lifetime, 522 publications have been published within this topic receiving 33821 citations. The topic is also known as: interspersed repetitive sequences & interspersed repetitive sequence.
Papers published on a yearly basis
Papers
Journal Article•
TL;DR: Using the polymerase chain reaction to amplify a (TG)n microsatellite in the human cardiac actin gene, 12 different allelic fragments in 37 unrelated individuals were detected, 32 of whom were heterozygous and Codominant Mendelian inheritance of fragments was observed in three families with a total of 24 children.
Abstract: The human genome contains approximately 50,000 copies of an interspersed repeat with the sequence (dT-dG)n, where n = approximately 10-60. In humans, (TG)n repeats have been found in several sequenced regions. Since minisatellite regions with larger repeat elements often display extensive length polymorphisms, we suspected that (TG)n repeats ("microsatellites") might also be polymorphic. Using the polymerase chain reaction to amplify a (TG)n microsatellite in the human cardiac actin gene, we detected 12 different allelic fragments in 37 unrelated individuals, 32 of whom were heterozygous. Codominant Mendelian inheritance of fragments was observed in three families with a total of 24 children. Because of the widespread distribution of (TG)n microsatellites, polymorphisms of this type may be generally abundant and present in regions where minisatellites are rare, making such microsatellite loci very useful for linkage studies in humans.
2,259 citations
TL;DR: The longest run of uninterrupted CA or GT repeats was found to be the best predictor of informativeness of (dC-dA)n.(dG-dT)n polymorphisms regardless of the repeat sequence category.
1,450 citations
TL;DR: The nucleotide sequences of 15 clones constructed from these 300 nucleotide S 1 -resistant repeats are determined and ten of these cloned sequences are members of the Alu family of interspersed repeats, a dimeric structure that was evidently formed from a head to tail duplication of an ancestral monomeric sequence.
601 citations
TL;DR: A reference-free genome metric called LTR Assembly Index (LAI) that evaluates assembly continuity using LTR-RTs is proposed that can facilitate iterative assembly improvement with assembler selection and identify low-quality genomic regions.
Abstract: Assembling a plant genome is challenging due to the abundance of repetitive sequences, yet no standard is available to evaluate the assembly of repeat space. LTR retrotransposons (LTR-RTs) are the predominant interspersed repeat that is poorly assembled in draft genomes. Here, we propose a reference-free genome metric called LTR Assembly Index (LAI) that evaluates assembly continuity using LTR-RTs. After correcting for LTR-RT amplification dynamics, we show that LAI is independent of genome size, genomic LTR-RT content, and gene space evaluation metrics (i.e., BUSCO and CEGMA). By comparing genomic sequences produced by various sequencing techniques, we reveal the significant gain of assembly continuity by using long-read-based techniques over short-read-based methods. Moreover, LAI can facilitate iterative assembly improvement with assembler selection and identify low-quality genomic regions. To apply LAI, intact LTR-RTs and total LTR-RTs should contribute at least 0.1% and 5% to the genome size, respectively. The LAI program is freely available on GitHub: https://github.com/oushujun/LTR_retriever.
596 citations
TL;DR: The types of transposable elements present in the human genome and their mechanisms of mobility are reviewed and advances in DNA sequencing and genomic technologies have enabled the discovery of novel retrotransposons in individual genomes.
Abstract: The completion of the human genome reference sequence ushered in a new era for the study and discovery of human transposable elements. It now is undeniable that transposable elements, historically dismissed as junk DNA, have had an instrumental role in sculpting the structure and function of our genomes. In particular, long interspersed element-1 (LINE-1 or L1) and short interspersed elements (SINEs) continue to affect our genome, and their movement can lead to sporadic cases of disease. Here, we briefly review the types of transposable elements present in the human genome and their mechanisms of mobility. We next highlight how advances in DNA sequencing and genomic technologies have enabled the discovery of novel retrotransposons in individual genomes. Finally, we discuss how L1-mediated retrotransposition events impact human genomes.
564 citations
Related Topics (5)
Performance Metrics
| Year | Papers |
|---|---|
| 2025 | 3 |
| 2024 | 3 |
| 2023 | 8 |
| 2022 | 12 |
| 2021 | 6 |
| 2020 | 7 |