Alternative titles; symbols
HGNC Approved Gene Symbol: U2AF2
Cytogenetic location: 19q13.42 Genomic coordinates (GRCh38): 19:55,655,035-55,674,716 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 19q13.42 | Developmental delay, dysmorphic facies, and brain anomalies | 620535 | Autosomal dominant | 3 |
U2AF65 is an essential pre-mRNA splicing factor that guides the early stages of splice-site choice by recognizing polypyrimidine tract consensus sequences near the 3-prime splice site (Sickmier et al., 2006).
Zamore and Green (1991) showed that all U2AF activity in vitro resides in the 65-kD U2AF polypeptide. Based on both immunologic and functional criteria, they showed that U2AF is evolutionarily conserved. Indeed, nuclear extracts from Drosophila melanogaster contain proteins that are antigenically related to both human U2AF polypeptides and can substitute for human U2AF in vitro. Zamore et al. (1992) isolated a cDNA encoding the 65-kD subunit of the U2 snRNP auxiliary factor and expressed it in vitro. They showed that it contains 2 functional domains: an RNA-binding region and an arginine/serine-rich motif necessary for splicing.
Gross (2014) mapped the U2AF2 gene to chromosome 19q13.42 based on an alignment of the U2AF2 sequence (GenBank BC008740) with the genomic sequence (GRCh37).
The 65- and 35-kD subunits of the splicing factor U2AF, U2AF65 and U2AF35 (191317), recognize, respectively, the pyrimidine-rich tract and the conserved terminal AG present at metazoan 3-prime splice sites. Soares et al. (2006) reported that DEK (125264), a chromatin- and RNA-associated protein mutated or overexpressed in certain cancers, enforces 3-prime splice site discrimination by U2AF. DEK phosphorylated at serines 19 and 32 associates with U2AF35, facilitates the U2AF35-AG interaction, and prevents binding of U2AF65 to pyrimidine tracts not followed by AG. DEK and its phosphorylation are required for intron removal, but not for splicing complex assembly, which indicates that proofreading of early 3-prime splice site recognition influences catalytic activation of the spliceosome.
Webby et al. (2009) discovered that the U2AF65 splicing factor undergoes posttranslational lysyl-5-hydroxylation catalyzed by the Fe(II)- and 2-oxoglutarate-dependent dioxygenase Jumonji domain-6 protein (JMJD6; 604914). JMJD6 is a nuclear protein that has an important role in vertebrate development and is a human homolog of the HIF asparaginyl-hydroxylase (factor-inhibiting HIF; 606615). JMJD6 was shown to change alternative RNA splicing of some, but not all, of the endogenous and reporter genes, supporting a specific role for JMJD6 in the regulation of RNA splicing.
Mackereth et al. (2011) studied the molecular mechanisms of the recognition of the 3-prime splice site-associated polypyrimidine tract RNA by the large subunit of the human U2 snRNP auxiliary factor (U2AF65) as a key early step in pre-mRNA splicing. Mackereth et al. (2011) showed that the tandem RNA recognition motif domains of the U2AF65 adopt 2 remarkably distinct domain arrangements in the absence or presence of a strong (i.e., high affinity) polypyrimidine tract. Recognition of sequence variations in the polypyrimidine tract RNA involves a population shift between these closed and open conformations. The equilibrium between the 2 conformations functions as a molecular rheostat that quantitatively correlates the natural variations in polypyrimidine tract nucleotide composition, length, and functional strength to the efficiency to recruit U2 snRNP to the intron during spliceosome assembly. Mutations that shift the conformational equilibrium without directly affecting RNA binding modulate splicing activity accordingly. Mackereth et al. (2011) suggest that similar mechanisms of cooperative multidomain conformational selection may operate more generally in the recognition of degenerate nucleotide or amino acid motifs by multidomain proteins.
Crystal Structure
Kielkopf et al. (2001) determined the x-ray structure of the human core U2AF heterodimer, consisting of the U2AF35 central domain and a proline-rich region of U2AF65, at 2.2-angstrom resolution. The structure revealed a novel protein-protein recognition strategy, in which an atypical RNA recognition motif (RRM) of U2AF35 and the U2AF65 polyproline segment interact via reciprocal 'tongue-in-groove' tryptophan residues. Complementary biochemical experiments demonstrated that the core U2AF heterodimer binds RNA, and that the interacting tryptophan side chains are essential for U2AF dimerization. The authors suggested that atypical RRMs in other splicing factors may serve as protein-protein interaction motifs elsewhere during spliceosome assembly.
U2AF65 preferentially binds uridine-rich RNA sequences, which are frequently interrupted by cytosines or purines. Sickmier et al. (2006) examined the x-ray structure of the U2AF65 RNA-binding domain in complex with polyuridine RNA. The structure revealed that U2AF65 recognizes uridines through a network of hydrogen bond interactions with the base edges rather than shape selection of the smaller pyrimidine compared with purine bases. A significant number of side chain and water-mediated hydrogen bonds seemed to allow U2AF65 to bind a variety of natural polypyrimidine tract sequences.
In a 7.5-year-old Japanese girl with developmental delay, dysmorphic facies, and brain anomalies (DEVDFB; 620535), Hiraide et al. (2021) identified a de novo heterozygous missense mutation in the U2AF2 gene (R149W; 191318.0001). The mutation, which was found by trio-based whole-exome sequencing and confirmed by Sanger sequencing, was not present in the gnomAD database. Functional studies of the variant and studies of patient cells were not performed.
By trio-based whole-exome sequencing, Kittock et al. (2023) identified a de novo heterozygous R149W mutation in the U2AF2 gene in a 4-year-old boy with DEVDFB. Functional studies of the variant and studies of patient cells were not performed.
In a 6-year-old Chinese boy with DEVDFB, Wang et al. (2023) identified a de novo heterozygous splice site mutation in the U2AF2 gene (191318.0002), resulting in skipping of exon 6. The mutation, which was found by trio-based whole-exome sequencing and confirmed by Sanger sequencing, was not present in the gnomAD, ExAC, or 1000 Genomes Project databases. Patient cells showed a 50% reduction in wildtype U2AF2 mRNA and protein expression (65-kD) compared to controls. A smaller 55-kD band corresponding to expression of the abnormal protein with the in-frame deletion was detected. The mutation significantly inhibited the proliferation of patient immortalized lymphocytes in vitro, with a slightly increased proportion of cells in the G1/G0 phase and a slightly less proportion of cells in the G2/M phase compared to controls.
Kuroda et al. (2023) reported a de novo heterozygous missense variant (P157L) in the U2AF2 gene in a 2-year-old Japanese girl with global developmental delay identified through exome sequencing. She did not have seizures. The variant was not present in the gnomAD database; functional studies of the variant were not performed. The patient also carried de novo heterozygous variants in 3 additional genes.
In a 7.5-year-old Japanese girl with developmental delay, dysmorphic facies, and brain anomalies (DEVDFB; 620535), Hiraide et al. (2021) identified a de novo heterozygous c.445C-T transition (c.445C-T, NM_007279.3) in the U2AF2 gene, resulting in an arg149-to-trp (R149W) substitution at a conserved residue in the RNA recognition motif 1 (RRM1). The mutation, which was found by trio-based whole-exome sequencing and confirmed by Sanger sequencing, was not present in the gnomAD database. Functional studies of the variant and studies of patient cells were not performed. The patient had seizures and hypoplasia of the corpus callosum.
By trio-based whole-exome sequencing, Kittock et al. (2023) identified a de novo heterozygous R149W mutation in the U2AF2 gene in a 4-year-old boy with DEVDFB. Functional studies of the variant and studies of patient cells were not performed. The patient had seizures and mega cisterna magna.
In a 6-year-old Chinese boy with developmental delay, dysmorphic facies, and brain anomalies (DEVDFB; 620535), Wang et al. (2023) identified a de novo heterozygous c.603G-T transversion (c.603G-T, NM_007279.3) in the last nucleotide of exon 6 of the U2AF2 gene. RT-PCR analysis of patient cells showed that the mutation caused abnormal splicing and skipping of exon 6, resulting in a 39-residue in-frame deletion (E163_E201del). The mutation, which was found by trio-based whole-exome sequencing and confirmed by Sanger sequencing, was not present in the gnomAD, ExAC, or 1000 Genomes Project databases. Patient cells showed a 50% reduction in wildtype U2AF2 mRNA and protein expression (65-kD) compared to controls. A smaller 55-kD band corresponding to expression of the abnormal protein with the in-frame deletion was detected. The mutation significantly inhibited the proliferation of patient immortalized lymphocytes, with a slightly increased proportion of cells in the G1/G0 phase and a slightly less proportion of cells in the G2/M phase compared to controls. The patient had seizures and hypoplasia of the corpus callosum.
Gross, M. B. Personal Communication. Baltimore, Md. 6/24/2014.
Hiraide, T., Tanaka, T., Masunaga, Y., Ohkubo, Y., Nakashima, M., Fukuda, T., Ogata, T., Saitsu, H. Global developmental delay, systemic dysmorphism and epilepsy in a patient with a de novo U2AF2 variant. J. Hum. Genet. 66: 1185-1187, 2021. [PubMed: 34112922] [Full Text: https://doi.org/10.1038/s10038-021-00948-4]
Kielkopf, C. L., Rodionova, N. A., Green, M. R., Burley, S. K. A novel peptide recognition mode revealed by the X-ray structure of a core U2AF35/U2AF65 heterodimer. Cell 106: 595-605, 2001. [PubMed: 11551507] [Full Text: https://doi.org/10.1016/s0092-8674(01)00480-9]
Kittock, C. M., Saifeddine, M., Straight, L., Ward, D. I. U2AF2 variant in a patient with developmental delay, dysmorphic features, and epilepsy. Am. J. Med. Genet. 191A: 1968-1972, 2023. [PubMed: 37092751] [Full Text: https://doi.org/10.1002/ajmg.a.63221]
Kuroda, Y., Matsufuji, M., Enomoto, Y., Osaka, H., Takanashi, J.-I., Yamamoto, T., Numata-Uematsu, Y., Tabata, K., Kurosawa, K., Inoue, K. A de novo U2AF2 heterozygous variant associated with hypomyelinating leukodystrophy. Am. J. Med. Genet. 191A: 2245-2248, 2023. [PubMed: 37134193] [Full Text: https://doi.org/10.1002/ajmg.a.63229]
Mackereth, C. D., Madl, T., Bonnal, S., Simon, B., Zanier, K., Gasch, A., Rybin, V., Valcarcel, J., Sattler, M. Multi-domain conformational selection underlies pre-mRNA splicing regulation by U2AF. Nature 475: 408-411, 2011. [PubMed: 21753750] [Full Text: https://doi.org/10.1038/nature10171]
Sickmier, E. A., Frato, K. E., Shen, H., Paranawithana, S. R., Green, M. R., Kielkopf, C. L. Structural basis for polypyrimidine tract recognition by the essential pre-mRNA splicing factor U2AF65. Molec. Cell 23: 49-59, 2006. [PubMed: 16818232] [Full Text: https://doi.org/10.1016/j.molcel.2006.05.025]
Soares, L. M. M., Zanier, K., Mackereth, C., Sattler, M., Valcarcel, J. Intron removal requires proofreading of U2AF/3-prime splice site recognition by DEK. Science 312: 1961-1965, 2006. [PubMed: 16809543] [Full Text: https://doi.org/10.1126/science.1128659]
Wang, X., You, B., Yin, F., Chen, C., He, H., Liu, F., Pan, Z., Ni, X., Pang, N., Peng, J. A presumed missense variant in the U2AF2 gene causes exon skipping in neurodevelopmental diseases. J. Hum. Genet. 68: 375-382, 2023. [PubMed: 36747105] [Full Text: https://doi.org/10.1038/s10038-023-01128-2]
Webby, C. J., Wolf, A., Gromak, N., Dreger, M., Kramer, H., Kessler, B., Nielsen, M. L., Schmitz, C., Butler, D. S., Yates, J. R., III, Delahunty, C. M., Hahn, P., Lengeling, A., Mann, M., Proudfoot, N. J., Schofield, C. J., Bottger, A. Jmjd6 catalyses lysyl-hydroxylation of U2AF65, a protein associated with RNA splicing. Science 325: 90-93, 2009. [PubMed: 19574390] [Full Text: https://doi.org/10.1126/science.1175865]
Zamore, P. D., Green, M. R. Biochemical characterization of U2 snRNP auxiliary factor: an essential pre-mRNA splicing factor with a novel intranuclear distribution. EMBO J. 10: 207-214, 1991. [PubMed: 1824937] [Full Text: https://doi.org/10.1002/j.1460-2075.1991.tb07937.x]
Zamore, P. D., Patton, J. G., Green, M. R. Cloning and domain structure of the mammalian splicing factor U2AF. Nature 355: 609-614, 1992. [PubMed: 1538748] [Full Text: https://doi.org/10.1038/355609a0]