Regulation of alternative splicing at the single‐cell level

• Published in: Molecular systems biology Vol. 11; no. 12; pp. 845 - n/a
• Main Authors: Faigenbloom, Lior, Rubinstein, Nimrod D, Kloog, Yoel, Mayrose, Itay, Pupko, Tal, Stein, Reuven
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.12.2015; EMBO Press; John Wiley and Sons Inc; Springer Nature
• Subjects: Alternative Splicing; Cell Differentiation; Cell fate; Conserved sequence; Differentiation (biology); EMBO17; EMBO36; Evolution, Molecular; Evolutionary conservation; Exons; Experiments; Gene expression; Gene Expression Profiling - methods; Gene Expression Regulation; Genome, Human; HEK293 Cells; Humans; inclusion level; Isoforms; Life sciences; MCF-7 Cells; RNA, Messenger - metabolism; Sample variance; single cell; Single-Cell Analysis; Splicing; splicing regulation; Stem cells; Stem Cells - cytology; single cell; inclusion level; alternative splicing; splicing regulation; evolutionary conservation
• DOI: 10.15252/msb.20156278
• ISSN: 1744-4292

Alternative splicing is a key cellular mechanism for generating distinct isoforms, whose relative abundances regulate critical cellular processes. It is therefore essential that inclusion levels of alternative exons be tightly regulated. However, how the precision of inclusion levels among individual cells is governed is poorly understood. Using single‐cell gene expression, we show that the precision of inclusion levels of alternative exons is determined by the degree of evolutionary conservation at their flanking intronic regions. Moreover, the inclusion levels of alternative exons, as well as the expression levels of the transcripts harboring them, also contribute to this precision. We further show that alternative exons whose inclusion levels are considerably changed during stem cell differentiation are also subject to this regulation. Our results imply that alternative splicing is coordinately regulated to achieve accuracy in relative isoform abundances and that such accuracy may be important in determining cell fate. Synopsis Single‐cell quantification of expression levels of alternatively spliced isoforms identifies what governs the precision of cassette exon inclusion levels among single cells in a cell population. While most cassette exons in the human genome are flanked by lowly evolutionarily conserved intronic regions, a small fraction of cassette exons is flanked by highly evolutionarily conserved intronic regions. Evolutionary conservation at flanking intronic regions (FIRs) of cassette exons significantly increases the precision of cassette exon inclusion levels among homogenous single cells derived from human cell lines. Dominant cassette exon inclusion or exclusion levels, as well as high expression levels of the genes harboring them, also contribute to this precision. The precision of inclusion levels of cassette exons, which are involved in human stem cell differentiation, is similarly regulated by these three factors. Graphical Abstract Single‐cell quantification of expression levels of alternatively spliced isoforms identifies what governs the precision of cassette exon inclusion levels among single cells in a cell population.