Ancestry of SINE-R.C2 a human-specific retroposon

Abstract

We have reported previously that a retroposon, containing a variable number of tandemly repeated nucleotide sequences, is present in the third intron of the human C2 gene. This element, termed SINE-R.C2, is a member of a large retroposon family derived from the endogenous retrovirus HERV-K10 and estimated to include a few thousand copies per haploid human genome. In the present study we analyzed genomic DNA from 175 humans from several ethnic groups including Americans of European and African descent, Chinese, Africans, Australians, Pacific Islanders, Japanese, and Koreans. They all contained SINE-R.C2, as indicated by Southern blotting. However, SINE-R.C2 was absent from the genome of nonhuman primates, although SINE-R-type elements were present in chimpanzees and gorillas and the HERV-K10 genome was apparently present in all primates except for New World monkeys. These results indicate that HERV-K10 was inserted into the genome after the divergence of New World monkeys; the prototype SINE-R element, after divergence of orangutans; and SINE-R.C2, after the split between humans and chimpanzees.

The viruses in all of us: characteristics and biological significance of human endogenous retrovirus sequences.

“…Retroelements like solitary LTRs contribute to allelic variation in contemporary populations, as has been shown in the complement and HLA loci (51,53). They can also serve as useful markers to study the evolution of those genes in the primate lineage (62,63).…”

Isolation and phytogeny of SINE‐R retroposons derived from human endogenous retrovirus HERV‐K family in schizophrenia

“…Using the bioinformatic tool, we examined that a schizo-cDNA clone derived from the postmortem tissue of the frontal cortex of an individual suffering from schizophrenia (GenBank, accession no. AA772777) was found to have sequences showing a high degree of homology to the SINE-R.C2 (Zhu et al, 1994). Therefore, we designed PCR primers from the schizophrenic brain cDNA.…”

“…SINE-R retroposons were amplified by the primer pair JS902 (5'-GAGAATGGGCCATGATG-AC-3', bases 4-22) and JS9O3 (5'-GATCATTCTTGG-ATGTTTCT-3', bases 466-485) from schizophrenic brain Sll cDNA clone (GenBank, accession no. AA772777), which has a high level of sequence homology with SINE-R.C2, 11, 14, 19, and HS307/ HS408 elements (Ono et al, 1987;Zhu et al, 1994;Kim et al, 1999b). The PCR conditions were those of Kim et al (1996) with an annealing temperature of 56°C.…”

“…SINE-R.C2 element was discovered within the third intron of the gene for C2, the second component of complement, located in class HI of the major histocompatibility complex on the short arm of human chromosome 6 (Carroll et al, 1984;Zhu et al, 1992). By Southern blot analysis, SINE-R.C2 has been found to be human specific (Zhu et al, 1994). A retroposon (schizo-cDNA) was detected from a cDNA library from postmortem brain in schizophrenia (Yee et al, 1998).…”

Phylogenetic analysis of a retroposon family as represented on the human X chromosome.

“…chromosomal changes in the genome? We have reported that the SINE-R.C2, a human specific retroposon (Zhu et al, 1994) that was derived from the HERV-K sequence, has close homologies with two sequences (HS307 and HS408) within the Xq21.3 block of that transposed to the Y chromosome sometime after the separation of the human and chimpanzee lineages (Kim et al, 1999b), and that a number of similar elements are present on the 7, 17, and Y chromosomes Crow, 1999, 2000) and in the African great apes (Kim et al, 1999c). This retroposon may therefore represent a family that has been active in recent human evolution.…”