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TRANSFORMER 2 BETA HOMOLOG; TRA2B

TRANSFORMER 2 BETA HOMOLOG; TRA2B

Alternative titles; symbolsTRANSFORMER 2, DROSOPHILA, HOMOLOG OF, BETATRA2-BETAHTRA2-BETA-1SPLICING FACTOR, ARGININE/SERINE-RICH, 10; SFRS10HGNC Approved Gene Sy...

Alternative titles; symbols

  • TRANSFORMER 2, DROSOPHILA, HOMOLOG OF, BETA
  • TRA2-BETA
  • HTRA2-BETA-1
  • SPLICING FACTOR, ARGININE/SERINE-RICH, 10; SFRS10

HGNC Approved Gene Symbol: TRA2B

Cytogenetic location: 3q27.2 Genomic coordinates (GRCh38): 3:185,914,557-185,938,026 (from NCBI)

▼ Cloning and Expression
Beil et al. (1997) performed a yeast 2-hybrid screen to find new factors involved in pre-mRNA splicing. Using SC35 as a bait, they isolated a human cDNA, termed TRA2-beta-1, bearing high homology to the Drosophila transformer-2 (tra2) protein. TRA2-beta-1 is a nuclear protein that colocalizes with SC35 in a speckled pattern. It interacts with several SR proteins (see 603364) in yeast. A second isoform, named TRA2-beta-2, is generated by alternative splicing. This isoform gives rise to a truncated protein without an SR domain. Both isoforms are evenly distributed throughout adult rat tissue. The ratio of these 2 isoforms changes after stimulation of primary human T-cell and primary rat spleen cell cultures, indicating that alternative splicing is involved in the regulation of TRA2-beta activity.

Stoilov et al. (2004) found that TRA2-beta-1 utilizes a negative feedback loop to regulate splicing of its exon 2. TRA2-beta-1 bound to 4 enhancers present in exon 2, which activated exon 2 inclusion resulting in mRNAs that were not translated into proteins. Mutations of exon 2 enhancers demonstrated that TRA2-beta-1 binds a degenerate sequence, GHVVGANR, which is found more frequently in exons than in introns. Hyperphosphorylation of TRA2-beta-1 strongly reduced its binding to RNA. Presence of CLK2 (602989) prevented usage of exons 2 and 3, generating TRA2-beta-3 mRNA. TRA2-beta-3 protein lacked the first RS domain of TRA2-beta-1, was expressed in several tissues, and had no influence on TRA2-beta splice site selection. When TRA2-beta-1 was sequestered by interacting proteins, exon 2 was no longer recognized, resulting in upregulation of TRA2-beta-1.

Full-length TRA2-BETA contains an N-terminal arginine- and serine-rich (RS) domain, followed by a central RNA-recognition motif (RRM), a glycine-rich region, and a C-terminal RS domain (Novoyatleva et al., 2008).

▼ Gene Structure
Nayler et al. (1998) determined that the TRA2-beta gene contains 10 exons and spans 21 kb. RT-PCR and analysis of TRA2-beta cDNAs in the EST database indicated that 5 different TRA2-beta RNA isoforms are generated by alternative splicing.

▼ Mapping
By analysis of a radiation hybrid panel, Nayler et al. (1998) mapped the TRA2B gene to chromosome 3q26.2-q27.

▼ Gene Function
Tacke et al. (1998) showed that human TRA2 proteins are present in HeLa cell nuclear extracts and that they bind efficiently and specifically to a previously characterized pre-mRNA splicing enhancer element. Both purified proteins bind preferentially to RNA sequences containing GAA repeats, characteristic of many enhancer elements. Neither TRA2 protein functions in constitutive splicing in vitro, but both activate enhancer-dependent splicing in a sequence-specific manner and restore it after inhibition with competitor RNA. These findings indicate that mammalian TRA2 proteins are sequence-specific splicing activators that are likely to participate in the control of cell-specific splicing patterns.

Nayler et al. (1998) observed that 2 TRA2-beta isoforms, TRA2-beta-3 and TRA2-beta-4, appear to be tissue specific and developmentally regulated, and encode proteins that lack the first SR domain. A chimeric GFP-TRA2-beta-3 protein localized to the nucleus, exhibiting a punctate staining pattern characteristic of splicing factors. The TRA2-beta-3 protein interacted with a subset of SR proteins in a yeast 2-hybrid assay and in vivo.

Venables et al. (2000) used a yeast 2-hybrid system to show that the gene product of RBMY (400006), the RBMX gene product HNRNPG (300199), and a novel testis-specific relative (termed HNRNPG-T) interact with TRA2-beta. The RBMY gene product and TRA2-beta colocalize in 2 major domains in human spermatocyte nuclei. Incubation with the protein interaction domain of the RBMY gene product inhibited splicing in vitro of a specific pre-mRNA substrate containing an essential enhancer bound by TRA2-beta. The RNA-binding domain of RBMY affected 5-prime splice site selection. The authors concluded that the HNRNPG family of proteins is involved in pre-mRNA splicing and hypothesized that RBM may be involved in TRA2-beta-dependent splicing in spermatocytes.

Using in vivo splicing assays, Hofmann and Wirth (2002) identified the protein HNRNPG and its paralog RBM as 2 novel splicing factors that promote the inclusion of SMN2 (601627) exon 7. Both HNRNPG and RBM nonspecifically bound RNA, but directly and specifically bound Htra2-beta-1, which itself stimulates inclusion of exon 7 through a direct interaction with SMN2 exon 7 pre-mRNA. Using deletion mutants of HNRNPG, the authors demonstrated a specific protein-protein interaction of HNRNPG with Htra2-beta1, which mediated the inclusion of SMN2 exon 7 rather than the nonspecific interaction of HNRNPG with SMN pre-mRNA. These trans-acting splicing factors were also effective on endogenous SMN2 transcripts and increased the endogenous SMN protein level. The authors presented a model of how exon 7 mRNA processing may be regulated by these splicing factors.

Proximal spinal muscular atrophy (SMA; 253300) is caused by the homozygous loss of SMN1 (600354). SMN2, a nearly identical copy gene, is present in all SMA patients; however, this gene cannot provide protection from disease due to the aberrant splicing of a critical exon. SMN2-derived transcripts predominantly lack SMN exon 7 due to a single nonpolymorphic nucleotide difference (C in SMN1 vs T in SMN2). Hofmann et al. (2000) showed that transient expression of TRA2-beta stimulated inclusion of exon 7 in SMN2-derived minigene transcripts through an interaction with the AG-rich exonic splice enhancer within exon 7. Young et al. (2002) demonstrated that SRp30c (SRSF9; 601943) can stimulate SMN exon 7 inclusion and that this activity required the same AG-rich enhancer as TRA2-beta. SRp30c did not directly associate with SMN exon 7; rather, its association with the exonic enhancer was mediated by a direct interaction with TRA2-beta. In the absence of the TRA2-beta binding site, SRp30c failed to associate with SMN exon 7. The authors concluded that SRp30c is a modulator of SMN exon 7 inclusion.

Mende et al. (2010) noted that SFRS10 binds SMN1/SMN2 RNA and restores full-length (FL)-SMN2 mRNA levels in vitro. They used the Cre/loxP system to generate a conditional Sfrs10 allele in mice. The ubiquitous homozygous deletion of Sfrs10 resulted in early embryonic lethality around E7.5, indicating an essential role of Sfrs10 during mouse embryogenesis. Deletion of Sfrs10 with recombinant Cre in murine embryonic fibroblasts (MEFs) derived from Sfrs10 homozygous full-length embryos increased the low levels of Smn-del7 without affecting full-length Smn levels. In MEFs from Smn(-/-);SMN2(tg/tg);Sfrs10(fl/fl) embryos, deletion of Sfrs10 by recombinant Cre showed no impact on SMN2 splicing but increased SMN levels.

Nasim et al. (2003) showed that HNRNPG and the splicing activator protein TRA2B have opposite effects upon the incorporation of several exons, and that both are capable of acting as either an activator or a repressor. HNRNPG acts via a specific sequence to repress the skeletal muscle-specific exon (SK) of human slow skeletal alpha-tropomyosin (TPM3; 191030), and stimulates inclusion of the alternative nonmuscle exon. The binding of HNRNPG to the exon is antagonized by TRA2B. The 2 proteins also have opposite effects upon a dystrophin (300377) pseudoexon. This exon was incorporated to a higher level in patient heart muscle than skeletal muscle, causing X-linked dilated cardiomyopathy. Cotransfection with HNRNPG repressed incorporation in cardiac myoblasts, whereas TRA2B increased it in skeletal myoblasts. The authors proposed that the HNRNPG/TRA2B ratio may contribute to cellular splicing preferences, and that the higher proportion of HNRNPG in skeletal muscle may play a role in preventing the incorporation of the pseudoexon and thus in preventing skeletal muscle dystrophy.

Venables et al. (2005) found that Tra2B recapitulated testis-specific splicing of the homeodomain-interacting kinase HIPK3 (604424) in a concentration-dependent manner and bound specifically to a long purine-rich sequence. This sequence was also specifically bound by HNRNPA1 (164017), HNRNPH1 (601035), ASF/SF2 (SFRS1; 600812), and SRp40 (SFRS5; 600914). In vitro studies showed that this sequence shifted splicing to a downstream 5-prime splice site within a heterologous pre-mRNA substrate in the presence of Tra2B, ASF/SF2, and SRp40, whereas HNRNPA1 specifically inhibited this choice. By mutating the purine-rich sequence in HIPK3, the authors showed that it is the major determinant of Tra2B- and HNRNPA1-mediated regulation. Venables et al. (2005) proposed an evolutionarily conserved role for Tra2 proteins in spermatogenesis, and suggested that an elevated concentration of Tra2B may convert it into a tissue-specific splicing factor.

Novoyatleva et al. (2008) identified a conserved protein phosphatase-1 (PP1; see 176875)-binding motif (RVDF) in the RRM domain of TRA2-beta. PP1 bound directly to the RVDF motif and dephosphorylated TRA2-beta, which promoted homomultimerization of TRA2-beta and interaction of TRA2-beta with other SR domain-containing proteins.

Tags: 3q27.2