SR proteins in vertical integration of gene expression from transcription to RNA processing to translation

Abstract

SR proteins have been studied extensively as a family of RNA-binding proteins that participate in both constitutive and regulated pre-mRNA splicing in mammalian cells. However, SR proteins were first discovered as factors that interact with transcriptionally active chromatin. Recent studies have now uncovered properties that connect these once apparently disparate functions, showing that a subset of SR proteins seem to bind directly to the histone 3 tail, play an active role in transcriptional elongation, and colocalize with genes that are engaged in specific intra- and interchromosome interactions for coordinated regulation of gene expression in the nucleus. These transcription-related activities are also coupled with a further expansion of putative functions of specific SR protein family members in RNA metabolism downstream of mRNA splicing, from RNA export to stability control to translation. These findings, therefore, highlight the broader roles of SR proteins in vertical integration of gene expression and provide mechanistic insights into their contributions to genome stability and proper cell-cycle progression in higher eukaryotic cells.

Figure 1

(A) The SR protein B52/SRp55 brackets Pol II on induced Hsp70 puffs on Drosophila polytene chromosomes. Picture is reproduced with permission from Champlin et al., (1991). (B) Structure of “classic”, mAb104 reactive SR proteins, which are characterized by one or two RNA Recognition Motifs (RRM) at the N-terminus and the signature RS domain at the C-terminus.

Figure 2

A working model for SR protein-mediated dynamic coupling between transcription and co-transcriptional mRNA splicing events. SR protein may be first recruited at the initial Pol II pausing site after pTEFb-mediated Pol II phosphorylation at its CTD. The recruitment of pTEFb and SR proteins may mutually benefit one another. When a splicing signal emerges from nascent RNA, SR protein is switched from Pol II to the RNA (step 1) to nucleate spliceosome assembly, which may be accompanied by transient pausing of the Pol II complex, resulting in elevated H3K36 methylation (step 2). Altered chromatin may also enhance the recruitment of additional SR proteins to Pol II (step 3) to continue transcriptional elongation.

Figure 3

Potential mechanism for SR proteins to prevent R-loop formation during transcriptional elongation. The Pol II-associated SR proteins may help displace nascent RNA from the template DNA to suppress R-loop formation during transcriptional elongation. The absence of SR proteins may introduce positive and negative DNA supercoiling in front and back of induced R-loops, thereby retarding the movement of the Pol II complex. Prolonged RNA loops may potentiate DNA breaks and initial ssDNA breaks may be further converted to dsDNA breaks by both DNA replication dependent and independent mechanisms. Recognition of DSBs by the MRN complex recruits ATM to trigger the S-phase checkpoint. DSBs may be further trimmed by the exonuclease activity of the MRN to produce excessive single-stranded 3′ overhangs, which induces the binding of the single strand DNA binding protein RPA and recruits ATR. The activated ATM/ATR pathway triggers a cascade of events, leading to cell cycle arrest or apoptosis.

Figure 4

The spatial relationship between SR protein localization and gene networks in the nucleus. Two estrogen responsive genes TFF1 and GREB1 do not exhibit interaction with one another nor show any spatial relationship with the speckled SC35 domains in the absence of ligand (-E₂). The estrogen treatment (+E2) induces specific inter-chromosomal interactions between these two genes, which also become intermediately associated with nuclear speckles marked by anti-SC35. Pictures are reproduced from Hu et al., (2008). The diagram on the right illustrates the induction of gene networks at or near a nuclear speckle enriched with mRNPs.