Genes in the brain are very long and can be transcribed into diverse RNAs.

Introduction

We study the functions of RNPs in the regulation of splicing and 3’ end processing of pre-mRNAs. We demonstrated that most RNPs regulate RNA processing according to positional principles, as can be shown in the form of RNA maps.

Moreover, we showed that multivalent RNA motifs are often responsible for recruiting RBPs to specific positions on RNAs, and analysis of such motifs can predict many functions of RNPs.

How to choose an alternative exon.

Figure 1: How to choose an alternative exon. The image shows the choices taken in the selection of exons (yellow blocks), which become part of the mRNA, and need to be distinguished from introns (grey blocks), which are removed from the pre-mRNA and degraded. The red and blue blocks are proteins that either promote the inclusion of an alternative exon (the red path), or skipping of the exon (the blue path).

To define how the location of RNA binding site instructs the function of RNPs, we draw RNA maps by integrating multiple types of transcriptomic data, such as iCLIP and RNA-seq. iCLIP tells us where an RBP binds its target transcripts, while RNA-seq tells how such binding controls pre-mRNA processing. Integrating these approaches showed that most RBPs regulate RNA processing according to genome-wide positional principles. We developed the software that can derive RNA splicing maps by analysis of multivalent RNA motifs.

We have discovered a new type of regulatory mechanism that explains how introns can be removed in two steps by recursive splicing. We identified recursive splicing in introns of some of the longest human genes, which are expressed primarily in the brain; we showed that this requires definition of a cryptic. This cryptic exon is located next to the recursive splice site, which allows skipping of the exon in the second step of intron removal. Thus, cells initially select a cryptic exon that is present deep within a long intron, but later discard it via the recursive splicing mechanism.

We showed how the coupled exon definition and recursive splicing mechanism can be employed for coordinated coupling of multiple alternative exons, which can couple alternative promoters to alternative exons. An illustration of a long gene undergoing recursive splicing is shown in the banner image of this webpage. If the recursive site is preceded by other cryptic splicing events, then the cryptic exon can end up included – in this way, recursive splicing creates a ‘binary switch’ that can distinguish correct splicing events from the newly emerging cryptic promoters or other cryptic exons. The cryptic exon that is located next to the recursive splice site contains stop codons in all frames, so by coupling other cryptic events to this cryptic exons, the cells can ensure that the newly emerging aberrant mRNAs are not translated into the full protein.

We speculate that recursive splicing may enable a kind of evolutionary tinkering, by allowing creation of new mRNA isoforms from long introns, without translating them into potentially toxic proteins. Interestingly, this process happens in some of the longest genes that are expressed in the brain, which are often implicated in autism or other neurodevelopmental disorders.