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| Status |
Public on Jun 08, 2017 |
| Title |
Identification and Characterization of a Class of MALAT1-like Genomic Loci |
| Organism |
Anolis carolinensis |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
The MALAT1 (Metastasis-Associated Lung Adenocarcinoma Transcript 1) gene encodes a non-coding RNA that is processed into a long nuclear retained transcript (MALAT1) and a small cytoplasmic tRNA-like transcript (mascRNA). Using a RNA sequence- and structure-based covariance model, we identified more than 130 genomic loci in vertebrate genomes containing the MALAT1 3’-end triple helix structure and its immediate downstream tRNA-like structure, including 44 in the green lizard Anolis carolinensis. Structural and computational analyses revealed a coevolution of the 3’-end module. MALAT1-like genes in Anolis carolinensis are highly expressed in adult testis, thus we named them testis-abundant long noncoding RNAs (tancRNAs). TancRNA loci produce multiple small RNA species, including piRNAs, from the antisense strand. The coevolved 3’-end of tancRNAs serve as potential targets for the PIWI-piRNA complex. Thus, we have identified an evolutionarily conserved class of lncRNAs with similar structural constraints, post-transcriptional processing, subcellular localization and a distinct function in spermatocytes.
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| Overall design |
4 RNA-Seq datasets analyzing gene expression in Anolis carolinensis. NSR-Seq of brain and testis, small RNA-Seq of testis (19-33 nt), small RNA-Seq of testis (52-68 nt).
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| Contributor(s) |
Diermeier SD, Zhang B, Spector DL |
| Citation(s) |
28538188 |
| |
| Submission date |
Apr 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Sarah D Diermeier |
| E-mail(s) |
sarah.diermeier@otago.ac.nz
|
| Organization name |
University of Otago
|
| Department |
Biochemistry
|
| Lab |
Diermeier
|
| Street address |
710 Cumberland Street
|
| City |
Dunedin |
| ZIP/Postal code |
9016 |
| Country |
New Zealand |
| |
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| Platforms (1) |
| GPL23260 |
Illumina Genome Analyzer II (Anolis carolinensis) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA381811 |
| SRA |
SRP103128 |
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