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LINC00507 Is Specifically Expressed in the Primate Cortex and Has Age-Dependent Expression Patterns

Abstract

Over the past decade, there has been an increase in the appreciation of the role of non-coding RNA in the development of organism phenotype. It is possible to divide the non-coding elements of the transcriptome into three categories: short non-coding RNAs, circular RNAs and long non-coding RNAs. Long non-coding RNAs are those transcripts that are greater than 200 nts in length and lack any significant open reading frames that produce proteins greater then 100 amino acids. Long intervening non-coding RNAs (lincRNAs) are a subclass of long non-coding RNAs. In contrast to protein coding RNAs, lincRNAs are expressed in a more tissue- and species-specific manner. In particular, many lincRNAs are only conserved amongst higher primates. This coupled with the propensity of many lincRNAs to be expressed in the brain, suggests that they are in fact one of the major drivers of organism complexity. We analysed 39 lincRNAs that are expressed in the frontal cortex and identified LINC00507 as being expressed in a cortex-specific manner in non-human primates and humans. The expression patterns of LINC00507 appear to be age-dependent, suggesting it may be involved in brain development of higher primates. Moreover, the analysis of LINC00507 potential to bind ribosomes revealed that this previously identified non-coding transcript may harbour a micropeptide.

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Acknowledgments

The Genotype-Tissue Expression (GTEx) Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health. Additional funds were provided by the NCI, NHGRI, NHLBI, NIDA, NIMH and NINDS. Donors were enrolled at Biospecimen Source Sites funded by NCI\SAIC-Frederick, Inc. (SAIC-F) subcontracts to the National Disease Research Interchange (10XS170), Roswell Park Cancer Institute (10XS171) and Science Care, Inc. (X10S172). The Laboratory, Data Analysis, and Coordinating Center (LDACC) was funded through a contract (HHSN268201000029C) to The Broad Institute, Inc. Biorepository operations were funded through an SAIC-F subcontract to Van Andel Institute (10ST1035). Additional data repository and project management were provided by SAIC-F (HHSN261200800001E). The Brain Bank was supported by supplements to University of Miami grants DA006227 and DA033684 and to contract N01MH000028. Statistical Methods development grants were made to the University of Geneva (MH090941 and MH101814), the University of Chicago (MH090951, MH090937, MH101820, MH101825), the University of North Carolina–Chapel Hill (MH090936 and MH101819), Harvard University (MH090948), Stanford University (MH101782), Washington University St Louis (MH101810), and the University of Pennsylvania (MH101822). This research was supported by the Framework Programme FP7/2007-2013 under the project EPISTOP (grant agreement no: 602391 to EA) and (NeuroGeM grant 733051052 to EA and JDM).

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Correspondence to Michael Janitz.

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Supplementary Figure 1

Tissue-specific expression patterns of LINC00507. Out of 53 different tissue types LINC00507 only appears to be expressed in the brain. More specifically, expression was only detected in the anterior cingulate cortex, cortex and frontal cortex. Only basal levels of expression were seen in other tissue types. Expression (y-axis) is in reads per kilobase of transcript per million mapped reads (RPKM). The figure was produced using the GTEx database. (PNG 98 kb)

Supplementary Figure 2

Splice variants of LINC00507. LINC00507 is alternatively spliced, producing three splice variants, LINC00507-001, LINC00507-002, LINC00507-003 (Ensembl IDs). Exons are indicated by open rectangles, introns are indicated by lines. Figure adapted from Ensembl (http://asia.ensembl.org/index.html). (PNG 17 kb)

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Mills, J.D., Ward, M., Chen, B.J. et al. LINC00507 Is Specifically Expressed in the Primate Cortex and Has Age-Dependent Expression Patterns. J Mol Neurosci 59, 431–439 (2016). https://doi.org/10.1007/s12031-016-0745-4

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  • DOI: https://doi.org/10.1007/s12031-016-0745-4

Keywords

  • LINC00507
  • Micropeptide
  • lincRNAs
  • RNA-Seq
  • Non-coding RNA
  • Cerebral cortex
  • Brain