Person:
Jordan,
I. King
Jordan,
I. King
Permanent Link
Associated Organization(s)
Organizational Unit
ORCID
ArchiveSpace Name Record
Publication Search Results
Now showing
1 - 3 of 3
-
ItemDual coding of siRNAs and miRNAs by Plant Transposable Elements(Georgia Institute of Technology, 2008-03) Piriyapongsa, Jittima ; Jordan, I. KingWe recently proposed a specific model whereby miRNAs encoded from short nonautonomous DNA-type TEs known as MITEs evolved from corresponding ancestral full-length (autonomous) elements that originally encoded short interfering (siRNAs). Our miRNA-origins model predicts that evolutionary intermediates may exist as TEs that encode both siRNAs and miRNAs, and we analyzed Arabidopsis thaliana and Oryza sativa (rice) genomic sequence and expression data to test this prediction. We found a number of examples of individual plant TE insertions that encode both siRNAs and miRNAs. We show evidence that these dual coding TEs can be expressed as readthrough transcripts from the intronic regions of spliced RNA messages. These TE transcripts can fold to form the hairpin (stem–loop) structures characteristic of miRNA genes along with longer doublestranded RNA regions that typically are processed as siRNAs. Taken together with a recent study showing Drosha independent processing of miRNAs from Drosophila introns, our results indicate that ancestral miRNAs could have evolved from TEs prior to the full elaboration of the miRNA biogenesis pathway. Later, as the specific miRNA biogenesis pathway evolved, and numerous other expressed inverted repeat regions came to be recognized by the miRNA processing endonucleases, the host gene-related regulatory functions of miRNAs emerged. In this way, host genomes were afforded an additional level of regulatory complexity as a by-product of TE defense mechanisms. The siRNA-to-miRNA evolutionary transition is representative of a number of other regulatory mechanisms that evolved to silence TEs and were later co-opted to serve as regulators of host gene expression.
-
ItemEvaluating the protein coding potential of exonized transposable element sequences(Georgia Institute of Technology, 2007-11-26) Piriyapongsa, Jittima ; Rutledge, Mark T. ; Patel, Sanil ; Borodovsky, Mark ; Jordan, I. KingBackground: Transposable element (TE) sequences, once thought to be merely selfish or parasitic members of the genomic community, have been shown to contribute a wide variety of functional sequences to their host genomes. Analysis of complete genome sequences have turned up numerous cases where TE sequences have been incorporated as exons into mRNAs, and it is widely assumed that such 'exonized' TEs encode protein sequences. However, the extent to which TE-derived sequences actually encode proteins is unknown and a matter of some controversy. We have tried to address this outstanding issue from two perspectives: i-by evaluating ascertainment biases related to the search methods used to uncover TE-derived protein coding sequences (CDS) and ii-through a probabilistic codon-frequency based analysis of the protein coding potential of TE-derived exons. Results: We compared the ability of three classes of sequence similarity search methods to detect TE-derived sequences among data sets of experimentally characterized proteins: 1-a profile-based hidden Markov model (HMM) approach, 2-BLAST methods and 3-RepeatMasker. Profile based methods are more sensitive and more selective than the other methods evaluated. However, the application of profile-based search methods to the detection of TE-derived sequences among well-curated experimentally characterized protein data sets did not turn up many more cases than had been previously detected and nowhere near as many cases as recent genome-wide searches have. We observed that the different search methods used were complementary in the sense that they yielded largely non-overlapping sets of hits and differed in their ability to recover known cases of TE-derived CDS. The probabilistic analysis of TE-derived exon sequences indicates that these sequences have low protein coding potential on average. In particular, non-autonomous TEs that do not encode protein sequences, such as Alu elements, are frequently exonized but unlikely to encode protein sequences. Conclusion: The exaptation of the numerous TE sequences found in exons as bona fide protein coding sequences may prove to be far less common than has been suggested by the analysis of complete genomes. We hypothesize that many exonized TE sequences actually function as post-transcriptional regulators of gene expression, rather than coding sequences, which may act through a variety of double stranded RNA related regulatory pathways. Indeed, their relatively high copy numbers and similarity to sequences dispersed throughout the genome suggests that exonized TE sequences could serve as master regulators with a wide scope of regulatory influence.
-
ItemA family of human microRNA genes from miniature-inverted repeat transposable elements(Georgia Institute of Technology, 2007-02-14) Piriyapongsa, Jittima ; Jordan, I. KingWhile hundreds of novel microRNA (miRNA) genes have been discovered in the last few years alone, the origin and evolution of these non-coding regulatory sequences remain largely obscure. In this report, we demonstrate that members of a recently discovered family of human miRNA genes, hsa-mir-548, are derived from Made1 transposable elements. Made1 elements are short miniature inverted-repeat transposable elements (MITEs), which consist of two 37 base pair (bp) terminal inverted repeats that flank 6 bp of internal sequence. Thus, Made1 elements are nearly perfect palindromes, and when expressed as RNA they form highly stable hairpin loops. Apparently, these Made1-related structures are recognized by the RNA interference enzymatic machinery and processed to form 22 bp mature miRNA sequences. Consistent with their origin from MITEs, hsa-mir- 548 genes are primate-specific and have many potential paralogs in the human genome. There are more than 3,500 putative hsa-mir-548 target genes; analysis of their expression profiles and functional affinities suggests cancer-related regulatory roles for hsa-mir-548. Taken together, the characteristics of Made1 elements, and MITEs in general, point to a specific mechanism for the generation of numerous small regulatory RNAs and target sites throughout the genome. The evolutionary lineage-specific nature of MITEs could also provide for the generation of novel regulatory phenotypes related to species diversification. Finally, we propose that MITEs may represent an evolutionary link between siRNAs and miRNAs.