A correlation with exon expression approach to identify cis-regulatory elements for tissue-specific alternative splicing.
Correlation of motif occurrences with gene expression intensity is an effective strategy for elucidating transcriptional cis-regulatory logic. Here we demonstrate that this approach can also identify cis-regulatory elements for alternative pre-mRNA splicing. Using data from a human exon microarray, we identified 56 cassette exons that exhibited higher transcript-normalized expression in muscle than in other normal adult tissues. Intron sequences flanking these exons were then analyzed to identify candidate regulatory motifs for muscle-specific alternative splicing. Correlation of motif parameters with gene-normalized exon expression levels was examined using linear regression and linear splines on RNA words and degenerate weight matrices, respectively. Our unbiased analysis uncovered multiple candidate regulatory motifs for muscle-specific splicing, many of which are phylogenetically conserved among vertebrate genomes. The most prominent downstream motifs were binding sites for Fox1- and CELF-related splicing factors, and a branchpoint-like element acuaac; pyrimidine-rich elements resembling PTB-binding sites were most significant in upstream introns. Intriguingly, our systematic study indicates a paucity of novel muscle-specific elements that are dominant in short proximal intronic regions. We propose that Fox and CELF proteins play major roles in enforcing the muscle-specific alternative splicing program, facilitating expression of unique isoforms of cytoskeletal proteins critical to muscle cell function.
Das
Debopriya
D
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Clark
Tyson A
TA
Schweitzer
Anthony
A
Yamamoto
Miki
M
Marr
Henry
H
Arribere
Josh
J
Minovitsky
Simon
S
Poliakov
Alexander
A
Dubchak
Inna
I
Blume
John E
JE
Conboy
John G
JG
D017398:Alternative Splicing; D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence; D003598:Cytoskeletal Proteins / Q000235:genetics / Q000378:metabolism; D005091:Exons; D020869:Gene Expression Profiling; D006801:Humans; D007438:Introns; D018482:Muscle, Skeletal / Q000378:metabolism; D009206:Myocardium / Q000378:metabolism; D012322:RNA Precursors / Q000737:chemistry; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000378:metabolism; D038621:Regulatory Sequences, Ribonucleic Acid; D017423:Sequence Analysis, RNA / Q000379:methods*; D014158:Transcription, Genetic
D003598:Cytoskeletal Proteins; D012322:RNA Precursors; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D038621:Regulatory Sequences, Ribonucleic Acid