Unusual Intron Conservation Near Tissue-regulated Exons Found by Splicing Microarrays

Abstract

Alternative splicing contributes to both gene regulation and protein diversity. To discover broad relationships between regulation of alternative splicing and sequence conservation, we applied a systems approach, using oligonucleotide microarrays designed to capture splicing information across the mouse genome. In a set of 22 adult tissues, we observe differential expression of RNA containing at least two alternative splice junctions for about 40% of the 6,216 alternative events we could detect. Statistical comparisons identify 171 cassette exons whose inclusion or skipping is different in brain relative to other tissues and another 28 exons whose splicing is different in muscle. A subset of these exons is associated with unusual blocks of intron sequence whose conservation in vertebrates rivals that of proteincoding exons. By focusing on sets of exons with similar regulatory patterns, we have identified new sequence motifs implicated in brain and muscle splicing regulation. Of note is a motif that is strikingly similar to the branchpoint consensus but is located downstream of the 59 splice site of exons included in muscle. Analysis of three paralogous membrane-associated guanylate kinase genes reveals that each contains a paralogous tissue-regulated exon with a similar tissue inclusion pattern. While the intron sequences flanking these exons remain highly conserved among mammalian orthologs, the paralogous flanking intron sequences have diverged considerably, suggesting unusually complex evolution of the regulation of alternative splicing in multigene families. Citation: Sugnet CW, Srinivasan K, Clark TA, O'Brien G, Cline MS, et al. (2006) Unusual intron conservation near tissue-regulated exons found by splicing microarrays. PLoS Comput Biol 2(1): e4.Editor:

A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart

“…Finally, CUAAC and ACUAA were highly conserved in multiple regions among mammals, and CUAAC in the first 250 bases of the upstream intron was associated with decreased exon inclusion. These motifs resemble the motif (A)CUAAC that was found to be associated with skeletal muscle-specific exons (12,22), and binding motifs for STAR family proteins (23).…”

“…CELF and MBNL proteins were first characterized as factors involved in the pathogenesis of myotonic dystrophy and were subsequently shown to be direct regulators of AS (6)(7)(8). Recent advances in microarray and computational technologies have allowed comprehensive analyses of individual exons on a genome-wide scale, providing the ability to identify commonly regulated splicing events (9)(10)(11)(12).…”

Frac-seq reveals isoform-specific recruitment to polyribosomes

“…Phylogenic conservation of DNA sequences often underscores their functional importance. This hallmark has been successfully applied to alternative splicing to identify putative regulatory elements in alternative exons and flanking intronic sequences (Sugnet et al 2006;Wang et al 2008). We compared the PhyloP conservation scores (placental mammals using a 46-way alignment) for different classes of alternative events associated with isoform-specific polyribosome association (Siepel et al 2005;Pollard et al 2010).…”

Software Note: Using probe secondary structure information to enhance Affymetrix GeneChip background estimates

“…Seven data sets were used in this study (Table 1): the human genome U133 Latin Square data set (http://www.affymetrix.com/support/technical/sample_data/datasets.affx), theChoe control data set (Choe et al, 2005), a Leukemia data set (Armstrong et al, 2002), a Malaria PM only data set (Le Roch et al, 2003), an Etoposide response data set (Fodor et al, 2006), a BK potassium channel knockout data set (Meredith et al, 2006;Pyott et al, 2006) and an alternative splicing PM only tiling microarray data set (Sugnet et al, 2006).…”