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Series GSE97451 Query DataSets for GSE97451
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.
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).
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
Organization name University of Otago
Department Biochemistry
Lab Diermeier
Street address 710 Cumberland Street
City Dunedin
ZIP/Postal code 9016
Country New Zealand
Platforms (1)
GPL23260 Illumina Genome Analyzer II (Anolis carolinensis)
Samples (4)
GSM2564798 NSR_Brain
GSM2564799 NSR_Testis
GSM2564800 Testis_36
BioProject PRJNA381811
SRA SRP103128

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Supplementary file Size Download File type/resource
GSE97451_RAW.tar 224.2 Mb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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