SR proteins as regulators of alternative transcript ends
March 2021. Scientists from Frankfurt identify the SR proteins SRSF3 and SRSF7 as important drivers of alternative polyadenylation in pluripotent mouse cells.
Cleavage and polyadenylation (CPA) is an important post-transcriptional process comprising the endonucleolytic cleavage of pre-mRNAs and the subsequent addition of a poly(A) at so-called polyadenylation sites. CPA is mediated by trans-acting factors recruited to conserved cis-acting sequence elements in the pre-mRNAs. Interestingly, around 70% of all mammalian genes contain more than one polyadenylation site enabling the expression of transcript isoforms differing in their 3’ ends, better known as alternative polyadenylation (APA). APA impacts mRNA stability, nuclear export and translation, and has important consequences on cellular function in human diseases like cancer. APA may be regulated in cis through the intrinsic strength of the competing polyadenylation sites or in trans via the level of CPA factors and other RNA-binding proteins.
Researchers from BMLS and the Institute for Molecular Bio Science at Goethe University Frankfurt elucidate how the splicing factors SRSF3 and SRSF7 can act as potent regulators of APA. In their study published in Genome Biology, they combined targeted high-throughput sequencing of transcript 3’ ends with transcriptome-wide RNA binding maps to find that both proteins bind directly at polyadenylation sites and exert opposite effects on 3’UTR length. This nicely illustrates how these proteins that are well known for their role as core splicing factors continue to act as key regulators in downstream processing events.
In their study within the SFB/CRC 902, the researchers elucidate the underlying mechanisms enabling the opposing roles of SRSF3 and SRSF7 in APA. While SRSF7 enhances the generation of short 3’UTRs, SRSF3 promotes 3’UTR lengthening. Combining biochemistry, transcriptomics and bioinformatics, they demonstrate that SRSF7 directly interacts with several CPA factors and thereby recruits the CPA machinery to proximal polyadenylation sites to generate short 3’UTRs. SRSF3 counteracts this regulation by preventing SRSF7 binding. Targeted deletion and domain-swap experiments reveal that protein features unique to SRSF7 are required for CPA factor recruitment and explain the functional diversification of SRSF3 and SRSF7. Additionally, the researchers find that SRSF3 acts as a critical regulator of CPA factor levels. SRSF3 ensures the productive splicing of mRNAs encoding the CPA factor CPSF6, which promotes distal polyadenylation sites. Their findings culminate in a mechanistic model that allows to explain how two apparently similar proteins with overlapping binding specificities can achieve opposing effects via distinct interactions with other regulators.
The functional diversification of SRSF3 and SRSF7 in APA regulation. When SRSF7 is present at high levels, it binds upstream of proximal polyadenylation sites (pPASs) and recruits the CPA factor FIP1 (CPSF complex), thereby acting as a sequence-specific enhancer of pPAS usage and promoting transcripts with short 3′UTRs. When SRSF3 levels are high, it prevents SRSF7 from recruiting FIP1 to pPASs through competitive binding. In addition, high SRSF3 levels ensure productive splicing of Cpsf6, encoding a subunit of the CPA complex CFIm, and maintenance of high CFIm levels, which in turn enhances distal PAS (dPAS) usage and generation of transcripts with long 3’UTRs. When SRSF3 levels are low, CFIm levels decrease due to unproductive splicing of Cpsf6, which prevents the activation of dPASs (Image rights: Mario Keller).
Contacts:
Dr Kathi Zarnack
Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt
kathi.zarnack(at)bmls.de
Prof. Dr Michaela Müller-McNicoll
Institute for Molecular Bio Science, Goethe University Frankfurt
Mueller-McNicoll(at)bio.uni-frankfurt.de
Publication:
Schwich, OD*, Blümel, N*, Keller, M*, Wegener, M, Setty, ST, Brunstein, ME, Poser, I, Ruiz De Los Mozos, I, Suess, B, Münch, C, McNicoll, F, Zarnack, K$, Müller-McNicoll, M$ (2021). SRSF3 and SRSF7 modulate 3′UTR length through suppression or activation of proximal polyadenylation sites and regulation of CFIm levels. Genome Biology 22(1):82, doi: 10.1186/s13059-021-02298-y.