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Long interspersed element-1 (LINE-1 or L1) is one of the most abundant retrotransposons in the primate genomes and has contributed to their genome diversity and variations during the primate evolution. Among primate L1 subfamilies, L1Pt subfamilies include Pan troglodytes-specific L1s. L1Pt elements have been successfully expanded in the chimpanzee genome since the divergence of human and chimpanzee lineages. However, only a few full-length L1Pt copies were previously detected in the chimpanzee genome due to incomplete chimpanzee reference genome sequences at the time. In the present study, we aimed to identify chimpanzee-specific L1s using the most recent version of the chimpanzee reference genome (May 2016, panTro5). We identified a total of 3731 chimpanzee-specific L1s. This is much more than previously reported chimpanzee-specific L1 copies. Among these, 223 are full-length (>6 kb), and we annotated their subfamilies and examined their retrotransposition-competency. The result showed that there are two L1Pt subfamilies in the chimpanzee genome, and the nine structurally intact elements belong to L1Pt-1, L1Pt-2, and L1PA2 subfamilies. In addition, we found that the intact full-length L1 group showed significantly higher L1 expression level than the non-intact full-length L1 group using limited RNA-seq data. It is interesting to notice that the number of retrotransposition-competent elements is much less in the chimpanzee genome than that in the human genome. In conclusion, there is increasing evidence to indicate that chimpanzee-specific L1s have changed the chimpanzee genome, causing genomic difference from other primate genomes.
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The pygmy chimpanzee, a species of the genus Pan, family HOMINIDAE. Its common name is Bonobo, which was once considered a separate genus by some; others considered it a subspecies of PAN TROGLODYTES. Its range is confined to the forests of the central Zaire basin. Despite its name, it is often of equal size to P. troglodytes.
The common chimpanzee, a species of the genus Pan, family HOMINIDAE. It lives in Africa, primarily in the tropical rainforests. There are a number of recognized subspecies.
Comprehensive, methodical analysis of complex biological systems by monitoring responses to perturbations of biological processes. Large scale, computerized collection and analysis of the data are used to develop and test models of biological systems.
This line KB is now known to be a subline of the ubiquitous KERATIN-forming tumor cell line HeLa. It was originally thought to be derived from an epidermal carcinoma of the mouth, but was subsequently found, based on isoenzyme analysis, HeLa marker chromosomes, and DNA fingerprinting, to have been established via contamination by HELA CELLS. The cells are positive for keratin by immunoperoxidase staining. KB cells have been reported to contain human papillomavirus18 (HPV-18) sequences.
MOLECULAR BIOLOGY techniques used in the diagnosis of disease. Included are such techniques as IN SITU HYBRIDIZATION of chromosomes for CYTOGENETIC ANALYSIS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS of gene expression patterns in disease states; identification of pathogenic organisms by analysis of species specific DNA sequences; and detection of mutations with POLYMERASE CHAIN REACTION.
Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...