Methylation
Elucidating the functional significance of methylation regulatory events
A review of Regulation of RNA splicing by the methylation-dependent transcriptional repressor methyl-CpG binding protein 2.
Note: This is a review of the published article listed below. All information, quotes, figures, methods, and findings mentioned in this review are from that article, and are the property of its authors and/or the publication in which the article originally appeared.
In an inaugural article to the National Academy of Sciences, Young and researchers from the Baylor College of Medicine (2005) examined the interactions between MeCP2 and the RNA-binding protein Y box-binding protein 1 as a regulator of reporter minigene splicing. The group used Agilent custom oligonucleotide microarrays, designed to monitor the expression of 19,763 genes (one probe each), 10,492 alternative 5’ and 3’ ends (one probe each), and 20,383 internal alternative splicing events (two probes per event, one reporting on the inclusion and one on the exclusion), and additional probes reporting on all exons and junctions of prioritized genes. Based on the results of this study, the researchers propose that MeCP2 is a multifunctional protein that, in addition to acting as a transcriptional repressor, acts as a splicing regulator. Through microarray analysis, the group was able to identify a novel MeCP2 transcriptional target, Dlx5, as an in vivo target of MeCP2-dependent splicing regulation. This paper presents many interesting links between DNA methylation and splicing events, adding another dimension to epigenetic control of gene expression.
Figure 1. Aberrant splicing in a mouse model of RTT.
(A) Supervised clustering of individual mouse samples based on splice monitoring. For every mutually exclusive splicing event identified, we designed a pair of probes to monitor the inclusion and the exclusion of the event. As an example, a cassette exon would have one probe to monitor the exon and one probe to monitor the junction between adjacent exons. To isolate splicing changes beyond gene expression changes, relative gene expression, as monitored by separate probes, was subtracted from each probe. Plotted is the log10-ratio-to-pool difference between probe pairs. Splicing events were selected that distinguish mutant from wild-type (wt) mouse brain samples with a t test (P < 0.0005). The CD44 variants (second to fifth from left) can distinguish samples. (B) Relative quantification of splice variant-specific mRNA by real-time PCR. The relative abundance of a set of splice variants found to be differentially expressed by microarray analysis were analyzed in cerebral cortices of six mice of wild-type (open bars) or mutant (filled bars) genotypes. Depicted are means of triplicate experiments for six mice of each genotype (±SD). *, P < 0.05; **, P < 0.03; ***, P < 0.01.
Title: : Regulation of RNA splicing by the methylation-dependent transcriptional repressor methyl-CpG binding protein 2.
Journal: Proc Natl Acad Sci U S A. 2005 Dec 6; 102(49): 17551-17558.
Authors: Young JI, Hong EP, Castle JC, Crespo-Barreto J, Bowman AB, Rose MF, Kang D, Richman R, Johnson JM, Berget S, Zoghbi HY.
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