Variation in novel exons (RACEfrags) of theMECP2gene in Rett syndrome patients and controls

Abstract

The study of transcription using genomic tiling arrays has lead to the identification of numerous additional exons. One example is the MECP2 gene on the X chromosome; using 5’RACE and RT-PCR in human tissues and cell lines, we have found more than 70 novel exons (RACEfrags) connecting to at least one annotated exon.. We sequenced all MECP2-connected exons and flanking sequences in 3 groups: 46 patients with the Rett syndrome and without mutations in the currently annotated exons of the MECP2 and CDKL5 genes; 32 patients with the Rett syndrome and identified mutations in the MECP2 gene; 100 control individuals from the same geoethnic group. Approximately 13kb were sequenced per sample, (2.4Mb of DNA resequencing). A total of 75 individuals had novel rare variants (mostly private variants) but no statistically significant difference was found among the 3 groups. These results suggest that variants in the newly discovered exons may not contribute to Rett syndrome. Interestingly however, there are about twice more variants in the novel exons than in the flanking sequences (44 vs. 21 for approximately 1.3 Mb sequenced for each class of sequences, p = 0.0025). Thus the evolutionary forces that shape these novel exons may be different than those of neighboring sequences.

The Landscape of long noncoding RNA classification

“…Targeted methods (Box 1) based on Rapid Amplification of cDNA Ends (RACE) experiments [44] and RNA-seq [45] indicate that transcriptional forests constitute a general feature of the human genome. A prominent category of ncRNAs has emerged from these transcriptional forests composed of sense ncRNAs that overlap coding mRNAs on the same strand and share some sequence with the latter, yet do not encode proteins [44, 46–48]. This category includes unspliced sense partially intronic RNAs (PINs) [49], and spliced transcripts that combine exons from coding and non-coding regions of a gene [47, 48].…”

“…A prominent category of ncRNAs has emerged from these transcriptional forests composed of sense ncRNAs that overlap coding mRNAs on the same strand and share some sequence with the latter, yet do not encode proteins [44, 46–48]. This category includes unspliced sense partially intronic RNAs (PINs) [49], and spliced transcripts that combine exons from coding and non-coding regions of a gene [47, 48]. GENCODE recognizes the existence of such spliced lncRNAs in their “sense overlapping” biotype [33].…”