thumb|[[Nuclear magnetic resonance spectroscopy of proteins|Solution structure of the RRM domain of the mouse SR protein Sfrs9 based on .]]
SR proteins are a conserved family of proteins involved in RNA splicing. SR proteins are named because they contain a protein domain with long repeats of serine and arginine amino acid residues, whose standard abbreviations are "S" and "R" respectively. SR proteins are ~200-600 amino acids in length and composed of two domains, the RNA recognition motif (RRM) region and the RS domain. This antibody allowed identification of four SR proteins (SRp20, SRp40, SRp55 and SRp75) and demonstrated their conservation among vertebrates and invertebrates.
Examples of genes
The following is a list of 14 human genes encoding SR proteins involved in splicing:
{| class="wikitable"
|-
! Gene !! Aliases !! Protein !! Locus
|-
| SRSF1 || SFRS1; ASF; SF2; SF2p33; SFRS1; SRp30a || Serine/arginine-rich splicing factor 1 || 17q22
|-
| SRSF2 || SFRS2; PR264; SC-35; SC35; SFRS2; SFRS2A; SRp30b || Serine/arginine-rich splicing factor 2 || 17q25
|-
| SRSF3 || SFRS3; SRp20 || Serine/arginine-rich splicing factor 3 || 6p21
|-
| SRSF4 || SFRS4; SRP75 || Serine/arginine-rich splicing factor 4 || 1p35
|-
| SRSF5 || HRS; SFRS5; SRP40 || Serine/arginine-rich splicing factor 5 || 14q24
|-
| SRSF6 || B52; SFRS6; SRP55 || Serine/arginine-rich splicing factor 6 || 20q13
|-
| SRSF7 || 9G8; AAG3; SFRS7 || Serine/arginine-rich splicing factor 7 || 2p22
|-
| SRSF8 || SFRS2B; SRp46 (human only) || Serine/arginine-rich splicing factor 8 || 11q21
|-
| SRSF9 || SFRS9; SRp30c || Serine/arginine-rich splicing factor 9 || 12q24
|-
| SRSF10 || TASR1; SRp38; SRrp40; SFRS13A || Serine/arginine-rich splicing factor 10 || 1p36.11
|-
| SRSF11 || NET2; SFRS11; dJ677H15.2; p54 || Serine/arginine-rich splicing factor 11 || 1p31
|-
| SRSF12 || SRrp35; SFRS13B || Serine/arginine-rich splicing factor 12 || 6q15
|-
| TRA2A || AWMS1; HSU53209 || Transformer 2 Alpha Homolog || 7p15.3
|-
| TRA2B || PPP1R156; SFRS10; SRFS10; TRAN2B || Transformer 2 Beta Homolog || 3q27.2
|}
Structure
SR proteins are characterized by an RS domain and at least one RNA recognition motif (RRM). The RRM is typically located near the N-terminus. The RS domain is located near the C-terminal end of an SR protein. RS domains regulate protein-protein interactions of SR proteins. Based on sequence analysis, SR proteins are suspected to be intrinsically disordered proteins resulting in an unstructured RS domain. Eight unphosphorylated repeats of arginine and serine in the RS domain take a helical form with arginine on the outside to reduce charge and in a phosphorylated state, the eight repeats of arginine and serine form a 'claw' shape.
SR proteins can have more than one RRM domain. The second RRM domain is called the RNA recognition motif homolog (RRMH). RRM domains are located near the N-terminus end of SR proteins. The RRM domain mediates the RNA interactions of the SR proteins by binding to exon splicing enhancer sequences. The RRMH usually has weaker interactions with RNA compared to the RRM domain. From NMR, the RRM domain of SRSF1, an SR protein, has a RNA binding fold structure. The RRM domain may also protect the phosphorylated RS domain, which suggests that the RS domain fits into the RRM domain.
thumbnail|SR proteins translocating out of the nucleus with TAP
Location and translocation
SR proteins can be found in both the cytosol and in nuclear speckles in the nucleus. SR proteins are mostly found in the nucleus. Localization depends on the phosphorylation of the RS domain of the SR protein. Phosphorylation of the RS domain causes the SR proteins to enter and remain in the nucleus. Partial dephosphorylation of the RS domain causes the SR proteins to leave the nucleus and SR proteins with unphosphorylated RS domains are found in the cytosol.
SR proteins are located in two different types of nuclear speckles, interchromatin granule clusters and perichromatin fibrils. Interchromatin granule clusters are for the storage and reassembly of pre-mRNA splicing proteins. Perichromatin fibrils are areas of gene transcription and where SR proteins associate with RNA polymerase II for co-transcriptional splicing.
<!-- Deleted image removed: thumbnail|SR proteins and hnRNPs -->
SR proteins' alternative splicing promoting activities are in contrast to those of hnRNPs. hnRNPs bind to exon splicing silencers, ESS, and inhibit the inclusion of exons, thus hnRNPs are splicing repressors. SR proteins and hnRNPs compete for binding to ESEs and ESSs sequences in exons. Binding is based on concentrations of SR proteins and hnRNPs in cells. If the cell has a high concentration of SR proteins then SR proteins are more likely to bind to ESEs compared to hnRNPs binding to ESS. If the cell has a high concentration of hnRNPs then hnRNPs can outcompete SR proteins for ESSs compared to ESEs.
SR proteins may work in an antagonistic fashion, competing with each other to bind to exonic splicing enhancers. Some evidence suggests that selection of the mRNA splicing variant depends upon the relative ratios of SR proteins. SR proteins appear to be redundant. Experiments have shown that knocking down SR proteins with RNAi shows no detectable phenotype in C. elegans. After knocking down one specific SR protein another different SR protein can make up for the lost function of the SR protein that was knocked down. Specific SR proteins' activities are important for specific tissues and developmental stages.
Exon dependent roles
SR proteins select alternative upstream 3' splice sites by recruiting U2AF<sup>35</sup> and U2AF<sup>65</sup> to specific ESE pyrimidine sequences in the exon of the pre-mRNA transcript.
SR proteins can also alternatively select different downstream 5' splice sites by binding to ESE upstream of the splice site. The suspected mechanism is that alternative 5' splice sites are chosen when SR proteins bind to upstream ESE and interacts with U1-70K and together recruit U1 to the 5' splice site.
SR proteins can also stabilize DNA during transcription through an interaction with Topoisomerase I. When Topoisomerase I, Topo I, reduces supercoiling caused by transcription when it is bound to DNA. When Topo I is not bound to DNA it can phosphorylate the SR protein SF2/ASF. Topo I and SF2/ASF interact when SF2/ASF is hypophosphorylated during transcription elongation. SR proteins can become hypophosphorylated during elongation decreasing their affinity for RNA polymerase II causing SR proteins to move to Topo I. When Topo I complexes with SF2/ASF, it can no longer undo the supercoiling of DNA causing elongation to pause. Topo I phosphorylates S2F/ASF increasing the SR proteins affinity for RNA poly II moving S2F/ASF from the Topo I back to RNA poly II allowing elongation to continue.
Translation
SR proteins can indirectly and directly influence translation. SR proteins SF2/ASF alternatively splices the transcript of MNK2. MNK2 is a kinase that initiates translation. High levels of SF2/ASF produce an isoform of MNK2 that increases cap-dependent translation by promoting phosphorylation of MAPK-independent eIF4E. SF2/ASF recruits components of the mTOR pathway, specifically S6K1. SF2/ASF creates an oncogenic form of S6K1 to increase the prevalence of cap-dependent translation. SF2/ASF can also interact with polyribosomes to directly influence translation of mRNA into protein by recruiting component of the mTOR pathway. SF2/ASF increases the phosphorylation of rpS6 and eIF4B by S6K1. 9G8 increases the translation of unspliced mRNA with a constitutive transport sequence.