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Series GSE14681 Query DataSets for GSE14681
Status Public on Jul 30, 2009
Title Long intronic non-coding RNA from the KLHL29 locus regulates proliferation of human tumorigenic cell lines
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Many classes of noncoding RNAs (ncRNAs) are known to be involved in gene expression regulation; however, long intronic ncRNAs have received little attention. In previous works, our group has provided evidence that intronic regions, transcribed from 80% of all RefSeq gene loci, are key sources of potentially regulatory ncRNAs. Intronic transcripts were shown to be correlated to the degree of prostate cancer differentiation, regulated by physiological stimuli, and highly expressed in genomic loci related to transcriptional regulation. In the present work we aimed at functional characterization of KLHL29 intronic transcript, one of the most highly expressed in human tissues. Although the protein-coding KLHL29 transcripts are still poorly studied, genes from this family are involved in a wide variety of biological processes, including cell cycle regulation mechanisms. We have observed that the long intronic ncRNA is predominantly transcribed from the opposite strand at the KLHL29 locus, and that the ncRNA overexpression does not affect the levels of protein-coding mRNAs from the same locus. Intriguingly, we found 2,002 genes with significant (q< 5.3%) differential expression between HEK293 cells overexpressing KLHL29 sense (S) or antisense (AS) intronic transcript. Within these genes, GO categories such as ‘Regulation of cell cycle’ and ‘Transcription’ were significantly enriched. Furthermore, human tumorigenic cell lines overexpressing KLHL29 AS intronic transcript showed increased proliferation rates in vitro and increased tumorigenic capacity in nude mice. In conclusion, we suggest that KLHL29 long intronic ncRNA controls the cell cycle mechanisms, probably through a fine-tuning regulation of gene expression.
Overall design Genes were defined as expressed when their intensity signals were above the average negative control value plus three standard deviations; a set of 153 negative controls (Agilent Technologies) was present on the array. Only genes that were detected as expressed in all four replicates of the same HEK293 transfection (or not expressed in the four replicates) were used in further analysis. The intensity values between experiments were normalized by the 40% trimmed mean intensity. For each transfection, one entire replicate experiment was excluded from the analyses, based on evaluating the coefficient of variance among the samples (for S KLHL29 intronic transcript, exclusion of the outlier replicate decreased the coefficient of variance from 0.21-0.24 (obtained by excluding any other replicate) to 0.19; for AS transcript, the coefficient of variance decreased from 0.17-0.18 to 0.12). Differentially expressed genes were identified using three transfection replicates for each construction, employing the Significance Analysis of Microarrays (SAM) tool (Tusher et al., 2001) with the following parameters: two-class response, 100 permutations and K-Nearest Neighbors Imputer. We applied 5.4 or 10.3% FDR (False Discovery Rate) cutoffs, as described in the results. A fold-change filter (1.4-fold cutoff) was applied after identification of significant differentially expressed genes.
Contributor(s) Smirnova AS, Louro R, Loturco DS, Orsini-Palma EI, Brito-Leite C, Soares-Andrade N, Dufner-Almeida LG, Verjovski-Almeida S
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Submission date Feb 02, 2009
Last update date Feb 22, 2018
Contact name Eduardo M Reis
Organization name Instituto de Química da Universidade de São Paulo
Department Departamento de Bioquímica
Street address Av. professor Lineu Prestes, 748
City São Paulo
ZIP/Postal code 05508-900
Country Brazil
Platforms (1)
GPL4133 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature Number version)
Samples (8)
GSM366550 HEK293 cells overexpressing KLHL29 intronic transcript (sense orientation), replicate number 4.
GSM366603 HEK293 cells overexpressing KLHL29 intronic transcript (sense orientation), replicate number 3.
GSM366604 HEK293 cells overexpressing KLHL29 intronic transcript (sense orientation), replicate number 2.
BioProject PRJNA112265

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GSE14681_RAW.tar 6.9 Mb (http)(custom) TAR
Processed data included within Sample table

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