Review
SRSF3: Newly discovered functions and roles in human health and diseases

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Abstract

The serine/arginine rich proteins (SR proteins) are members of a family of RNA binding proteins involved in regulating various features of RNA metabolism, including pre-mRNA constitutive and alternative splicing. In humans, a total of 12 SR splicing factors (SRSFs) namely SRSF1-SRSF12 have been reported. SRSF3, the smallest member of the SR family and the focus of this review, regulates critical steps in mRNA metabolism and has been shown to have mRNA-independent functions as well. Recent studies on SRSF3 have uncovered its role in a wide array of complex biological processes. We have also reviewed the involvement of SRSF3 in disease conditions like cancer, ageing, neurological and cardiac disorders. Finally, we have discussed in detail the autoregulation of SRSF3 and its implications in cancer and commented on the potential of SRSF3 as a therapeutic target, especially in the context of cancer.

Introduction

The serine/arginine rich proteins (SR proteins) belong to a family of phylogenetically conserved RNA binding proteins found in all metazoans and plants. SF2 (SRSF1) was the first human SR protein identified by complementation of cytoplasmic S-100 extract from HeLa cells that is deficient in splicing (Krainer et al., 1990). Zahler et al. (1992) first referred to SR proteins as set of proteins containing consecutive serine (S) and arginine (R) dipeptides sequences and classified them as a family based on the presence of phosphoepitope recognized by a monoclonal antibody, their conservation across animal kingdom and their ability to complement the splicing-deficient cytoplasmic S-100 extract. The new nomenclature proposed by Manley and Krainer (2010) defines SR proteins as “any protein with one or two N-terminal RNA-binding domains (RBDs; also called as RNA recognition motifs [RRMs]), followed by a downstream RS domain of at least 50 amino acids with >40 % RS content, characterized by consecutive RS or SR repeats”. According to these rigorous criteria, humans contain 12 SR proteins designated as “SRSF” (serine/arginine rich splicing factor) followed by the numbers 1–12 (see Fig. 1; Table 1), reflecting the sequential order in which the proteins/genes were discovered. During constitutive and alternative splicing, the RRM domain imparts substrate specificity, while the RS domain is involved in protein-protein interactions. The zinc knuckle, a CCHC-type zinc finger (Fig. 1) is a unique feature of SRSF7 and contributes to the specificity of its RRM domain (Cavaloc et al., 1999).

SR proteins are localized in the nucleus and are distributed both in the nucleoplasm and in interchromatin granule clusters (IGCs) or nuclear speckles at steady state (Spector and Lamond, 2011). However, a subset of SR proteins can shuttle between the nucleus and the cytoplasm. Using domain swapped chimeric proteins, Ca´ceres et al. (1998) have demonstrated that the RS domain along with the RRM domain plays an important role in nucleocytoplasmic shuttling of these proteins. Phosphorylation of the RS domain is critical for both the nucleocytoplasmic shuttling and localization of SR proteins to the nuclear speckles (Ca´ceres et al., 1998; Lai et al., 2001; Koizumi et al., 1999). While SRSF1, SRSF3, SRSF7 and SRSF10 have rapid shuttling rates between the nucleus and cytoplasm, SRSF4 and SRSF6 shuttle at slower dynamic rates (Ca´ceres et al., 1998; Cowper et al., 2001; Cazalla et al., 2002; Sapra et al., 2009).

SR proteins are phosphorylated predominantly within the RS domain by two families of protein kinases, namely SR-specific protein kinases (SRPKs) and Cdc2-like kinases (CLKs), and the phosphorylation is crucial for both splicing and splicing-independent functions of SR proteins (Zhou and Fu, 2013; Aubol et al., 2013). SRPKs localize mainly to the cytoplasm, while CLKs are predominantly localized to the nucleus and each phosphorylate SR proteins by distinct mechanisms (Aubol et al., 2013; Long et al., 2019). Colwill et al. (1996) have reported that CLKs also play a critical role in regulating the subnuclear distribution of SR proteins. Corkery et al. (2015) have reviewed the implications of dysregulation of splicing kinases in tumorigenesis and therapeutic response to chemotherapy and radiation, further underscoring the importance of splicing kinases in regulation of SR proteins.

Here we review the regulation and recently identified functions of SRSF3 and its implications in human health and diseases.

Section snippets

SRSF3: smallest SR protein

SRSF3, the smallest of the SR proteins, was first identified and cloned by Zahler et al. (1992). It plays an essential role in early vertebrate development as SRSF3-null mouse embryos fail to form blastocysts and die at the morula stage (Jumaa et al., 1999). The SRSF3 gene, located on chromosome 6p21.31, contains 6 exons and spans 10,155 base pairs on the plus (+) strand. It encodes for two transcript variants which result from alternative splicing. The transcript variant-1 is the

Roles of SRSF3 in various cellular processes

SRSF3 is a multifunctional protein and participates in regulation of several cellular processes (Fig. 2). Apart from its canonical role in both constitutive and alternative splicing, SRSF3 also regulates additional aspects of RNA metabolism like alternative polyadenylation, mRNA export, transcription termination and miRNA biogenesis. These functions along with some newly identified roles in various cellular processes are the focus of this review.

Role in alternative polyadenylation

Alternative polyadenylation (APA) is one of the major mechanisms of gene regulation found across eukaryotes which leads to generation of distinct 3’ ends on mRNAs and other RNA pol II transcripts through differential use of multiple poly(A) sites present mostly in the 3’ untranslated regions (3’UTRs) of mRNAs (Tian and Manley, 2017). Apart from its general role in gene regulation, APA also regulates various cellular processes, including mRNA metabolism, protein diversity and protein

Role in mRNA export

The mRNA export pathway involves the active transport of mRNAs from the nucleus to the cytoplasm and is essential for gene expression in eukaryotes. The mRNA export machinery comprises of three classes of factors, namely the adaptor proteins which bind directly to the RNA, receptor proteins (NFX1/TAP) that recognize the adaptor proteins and the nuclear pore complex (NPC) (Cullen, 2000). The role of SRSF3 along with 9G8/SRSF7 as adaptor proteins in mRNA export was first studied by Huang and

Role in transcription termination

Termination of transcription by RNA polymerase II is a complex process and is coupled to 3’ end processing machinery (Richard and Manley, 2009). Cui et al. (2008) showed that SRSF3 is involved in events following cleavage of 3’end, leading to transcription termination. They proposed that SRSF3 facilitates transcription termination either by degrading RNA downstream of the cleavage site or by releasing the polymerase from the DNA (Cui et al., 2008).

Role in miRNA biogenesis

The role of SRSF3 in miRNA biogenesis was first reported by Auyeung et al. (2013). They observed the presence of SRSF3 binding motif (CNNC) downstream of most pri-miRNA hairpins in bilaterian animals. This binding motif was found to be one of the three primary-sequence determinants which distinguish pri-miRNAs from other hairpin-containing transcripts, thus facilitating pri-miRNA processing (Auyeung et al., 2013). The importance of SRSF3 in pri-miRNA processing was further strengthened by

Role in pluripotency

SRSF3 plays a critical role in development as SRSF3-null mice fail to form blastocysts (Jumaa et al., 1999). Recently, SRSF3 was shown to regulate gene expression during reprogramming stem-cell renewal and early development (Ratnadiwakara et al., 2018). Using a reprogrammable tamoxifen inducible Srsf3 knockout mouse model, Ratnadiwakara et al. (2018) showed that SRSF3 facilitates reprogramming and is essential for maintenance of pluripotency. Apart from regulating the nucleocytoplasmic export

Role in DNA repair

The role of SRSF3 as a novel regulator of homologous recombination-mediated DNA repair (HRR) pathway especially in the context of neoplastic transformation was recently established by He and Zhang (2015). They showed that knockdown of SRSF3 leads to downregulation of key genes involved in the HRR pathway, namely breast cancer 1, early onset (BRCA1), BRCA1 interacting protein C-terminal helicase1 (BRIP1), and RAD51 recombinase (RAD51) through an epigenetic pathway (He and Zhang, 2015). During

Role in quality control of nuclear RNA

The process of mRNA processing and formation of an mRNP competent for export into the cytoplasm is an error-prone process. Aberrantly processed mRNPs that fail the quality control steps of the surveillance mechanism are retained in the nucleus and are degraded by various ribonucleases (Eberle and Visa, 2014). RNA exosome pathway is one of the two major pathways involved in degradation of defective mRNA transcripts. Using Epstein Barr virus mRNA as a model, Mure et al. (2018) proposed a novel

Role in stress granule assembly

SRSF3 was identified as a potential regulator as well as major structural component of translationally stalled mRNA-protein complexes, namely the stress granule (SG) and P-body (PB) (Yoon et al., 2013). Jayabalan et al. (2016) have further studied the effect of arsenite-induced oxidative stress on SG assembly. They observe that, in response to arsenite, SRSF3 is selectively neddylated at Lys8, which in turn induces SG assembly, emphasizing the importance of neddylation pathway in SG assembly (

Role in maintaining transcriptional integrity of oocytes

Jumaa et al. (1999) have shown that SRSF3 is present throughout various embryonic stages like oocytes, fertilized egg, 8-cell embryo and blastocyst indicating that maternal SRSF3 is packaged into the developing egg. The role of maternal SRSF3 during oocyte maturation was recently established by Do et al. (2018). Using maternal Srsf3-knockout oocytes, they established that depletion of maternal SRSF3 protein results in developmental arrest at one/two-cell stage, indicating that maternal SRSF3 is

Role in cancer

The role of SRSF3 as a proto-oncogene crucial for cell proliferation and tumor induction and maintenance was established by Jia and colleagues (2010). SRSF3 was found to be overexpressed in cancers of the lung, cervix, breast, skin, stomach, bladder, colon, liver, thyroid and kidney, as well as in various mesenchymal tissue-derived tumors (Jia et al., 2010). The significance of chromosome 6p amplification in progression of several cancers is reviewed by Santos et al. (2007). The SRSF3 gene is

Autoregulation of SRSF3

SRSF3 is involved in regulation of alternative splicing of its own mRNA and autoregulates the expression to maintain homeostasis (Jumaa and Nielsen, 1997). This autoregulation of SRSF3 was first reported by Jumaa and Nielsen (1997) who showed that overexpression of SRSF3 results in the reduction in the level of exon 4-skipped transcript variant-1 and activates the production of transcript variant-2 which includes exon 4. Jumaa et al. (1997) also showed that expression of the exon 4-included

Newly identified independent functions of truncated SRSF3

Recent reports have attributed independent biological functions to the transcript variant-2 encoded truncated SRSF3 protein (SRSF3-TR), specifically in cancer cells. Kano et al. (2014) reported that on exposure of HCT116 colon cancer cells to an oxidant, namely sodium arsenite, there is an increase in the expression of SRSF3-TR which in turn positively regulates oxidative stress-stimulated interleukin-8 production through regulation of c-Jun production. SRSF3-TR might therefore positively

Concluding remarks

Apart from their role as modulators of constitutive and alternative splicing, many splicing factors including SRSF3 control other aspects of RNA metabolism and gene regulation. Alterations in their expression thus has far reaching consequences for the cell functioning. The implication of deregulated splicing factors expression in various diseases including cancers has now been widely established. Modulation of splicing factors is therefore a potential therapeutic approach for targeting a

Source of funding

Financially support in AK laboratory from DBT (Grant# BT/PR10272/BRB/10/1266/2013 and BT/PR8670/AGR/36/757/2013), DST-FIST [SR/FST/LS11-036/2014(C)], UGC-SAP [F.4.13/2018/DRS-III (SAP-II)] and DBT-IISc Partnership Program Phase-II (BT/PR27952-INF/22/212/2018) is gratefully acknowledged.

Declaration of Competing Interest

Both authors declare that there are no conflicts of interests, no financial affiliation or involvement with any commercial organization with direct financial interest in the subject or materials discussed in this manuscript.

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