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ARS Home » Southeast Area » Poplarville, Mississippi » Southern Horticultural Research Unit » Research » Publications at this Location » Publication #162277
Title: SINE EXTINCTION PRECEEDED LINE EXTINCTION IN SIGMODONTINE RODENTS: IMPLICATIONS RETROTRANSPOSITIONAL DYNAMICS AND MECHANISMS

Author
item Rinehart, Timothy - Tim
item GRAHN, ROBERT - UNIV OF CALIFORNIA
item WICHMAN, HOLLY - UNIV OF IDAHO

Submitted to: Cytogenetics and Genome Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/8/2004
Publication Date: 6/30/2005
Citation: Rinehart, T.A., Grahn, R.A., Wichman, H.A. 2005. Sine extinction preceeded line extinction in sigmodontine rodents: implications retrotranspositional dynamics and mechanisms. Cytogenetics and Genome Research vol. 110, No. 1-4, pp 416-425.

Interpretive Summary: In general, transposons have been labeled 'junk' DNA because they do not appear to contain directions for organismal or cellular development. However, transposons make up the bulk of DNA found in human and rodent genomes. It is perplexing that such a large part of the genome is made up of useless information and there is ongoing research to explore why and how this came to be. One of the proposed reasons there are so many copies of transposons in our genome is that they selfishly make copies of themselves generation after generation. If this is the case then we would expect that the loss of selfish behavior, or the inability to make copies, would have no effect or a positive effect on the host. This paper explores recent evolutionary history of LINE and SINE transposons that may lack the ability to copy themselves. Our results suggest that there are several, related rodent species that lack recent transposon copies. Several theories are discussed as to why and how these transposons lost their selfish behavior. Interestingly, the rodents without recent LINE and SINE duplication appear healthy but their genomes may be prone to rearrangement suggesting transposons could help 'glue' the useful genes together even though they do not encode for useful proteins themselves.

Technical Abstract: Short Interspersed Nuclear Elements, or SINEs, retrotranspose despite lacking protein-coding capability. It has been proposed that SINEs utilize enzymes produced in trans by Long Interspersed Nuclear Elements, or LINEs. Strong support for this hypothesis is found in LINE and SINE pairs that share sequence homology; however, LINEs and SINEs in primates and rodents are only linked by an insertion site motif. We have now profiled L1 LINE and B1 SINE activity in twenty-four rodent species including candidate taxa for the first documented L1 extinction. As expected, there was no evidence for recent activity of B1s in species that also lack L1 activity. However, B1 silencing appears to have preceded L1 extinction, since B1 activity is also lacking in the genus most closely related to those lacking active L1s despite the presence of active L1s in this genus. A second genus with active L1s but inactive B1s was also identified.