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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
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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 |
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Submission date |
Apr 05, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Sarah D Diermeier |
E-mail(s) |
sarah.diermeier@otago.ac.nz
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Organization name |
University of Otago
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Department |
Biochemistry
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Lab |
Diermeier
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Street address |
710 Cumberland Street
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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 |