The IGBB is a member of the NIH-funded Mississippi IDeA Network of Biomedical Research Excellence (Mississippi INBRE or MS-INBRE), a program designed to build biomedical infrastructure throughout the state. Through MS-INBRE, Mississippi students and faculty at Mississippi's undergraduate institutions are (1) trained in biomedical research techniques, (2) given the opportunity to work with top researchers at Mississippi's major research universities, (3) afforded access to state-of-the-art bioscience equipment, and (4) provided with assistance in preparing grant proposals. The IGBB serves as the MS-INBRE proteomics/computational biology core. For more information about MS-INBRE, click here.
Dr. Chuan-Yu Hsu (Sue)Senior Research Associate
GENOMICS LEAD
email(662) 325-9511
Pace 121
Biography:
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Large Numbers of Novel miRNAs Originate from DNA Transposons and Are Coincident with a Large Species Radiation in Bats
IGBB Authors:
Roy N. Platt, Michael W. Vandewege, Federico G. Hoffmann, David A. RayPUBLICATION YEAR:
2014IMPACT FACTOR:
14.308TIMES CITED (as of August 10, 2017):
CITATION PERCENTILE:
93Platt RN, Vandewege MW, Kern C, Schmidt CJ, Hoffmann FG, Ray DA (2014) Large Numbers of Novel miRNAs Originate from DNA Transposons and Are Coincident with a Large Species Radiation in Bats.
Molecular Biology & Evolution 31(6): 1536-1545.
DOI:
EID:
DOWNLOAD PDFABSTRACTVesper bats (family Vespertilionidae) experienced a rapid adaptive radiation beginning around 36 Ma that resulted in the second most species-rich mammalian family (>400 species). Coincident with that radiation was an initial burst of DNA transposon activity that has continued into the present in some species. Such extensive and recent DNA transposon activity has not been seen in any other extant mammal. Indeed, retrotransposon activity is much more common in all other sequenced mammal genomes. Deep sequencing of the small RNA fraction from a vespertilionid bat, Eptesicus fuscus, as well as a dog and horse revealed large numbers of 17-24 bp putative miRNAs (p/miRNAs). Although the origination rate of p/miRNAs is similar in all three taxa, 61.1% of postdivergence p/miRNAs in Eptesicus are derived from transposable elements (TEs) compared with only 23.9% and 16.5% in the dog and horse, respectively. Not surprisingly, given the retrotransposon bias of dog and horse, the majority of TE-derived p/miRNAs are associated with retrotransposons. In Eptesicus, however, 58.7% of the TE-derived and 35.9% of the total p/miRNAs arose not from retrotransposons but from bat-specific DNA transposons. Notably, we observe that the timing of the DNA transposon expansion and the resulting introduction of novel p/miRNAs coincide with the rapid diversification of the family Vespertilionidae. Furthermore, potential targets of the DNA transposon-derived p/miRNAs are identifiable and enriched for genes that are important for regulation of transcription. We propose that lineage-specific DNA transposon activity lead to the rapid and repeated introduction of novel p/miRNAs. Some of these p/miRNAs are likely functional miRNAs and potentially influenced the diversification of Vespertilionidae. Our observations suggest a mechanism for introducing functional genomic variation rapidly through the expansion of DNA transposons that fits within the TE-thrust hypothesis.
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The IGBB is an HPC² member center.
