Alternative titles; symbols
HGNC Approved Gene Symbol: RNASEH2A
Cytogenetic location: 19p13.13 Genomic coordinates (GRCh38): 19:12,806,584-12,813,640 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 19p13.13 | Aicardi-Goutieres syndrome 4 | 610333 | Autosomal recessive | 3 |
Ribonuclease (RNase) H enzymes specifically cleave ribonucleotides from RNA:DNA duplexes. Two classes of RNase H exist: type 1 (I) and 2 (II). RNase H2 is the major source of RNase H activity in mammalian cells and yeast. The protein complex is proposed to function in the removal of lagging-strand Okazaki fragment RNA primers during DNA replication and in the excision of single ribonucleotides from DNA:DNA duplexes. See also RNASEH2B (610326) and RNASEH2C (610330). The 3 homologs in S. cerevisiae are known as Rnh2Ap, Rnh2Bp, and RNh2Cp, respectively (Crow et al., 2006).
By biochemical purification of the 32-kD subunit of calf thymus RNase HI, microsequence analysis, EST database searching, and PCR with degenerate primers on an erythroleukemia cDNA library, Frank et al. (1998) obtained a cDNA encoding the large subunit of human RNase HI. The deduced 299-amino acid protein appeared to lack RNA- and DNA-binding domains. Genomic database comparisons revealed homologies between the large subunit of mammalian RNase HI and prokaryotic RNase HII. Western blot analysis showed expression of a 33-kD recombinant protein, close to the predicted size. Northern blot analysis detected a 1.2-kb transcript in a kidney cell line.
The RNASEH2A gene contains 8 exons (Crow et al., 2006).
Crow et al. (2006) mapped the RNASEH2A gene to chromosome 19p13.13.
RNase HI is involved in DNA replication and participates with FEN1 (600393) in DNA repair. The smaller RNase HII is associated with transcription (Frank et al., 1998).
By transient expression in HEK293T cells, Crow et al. (2006) showed that the human RNASEH2A, RNASEH2B, and RNASEH2C genes interact with each other and form an enzymatic protein complex with RNase H2 activity. The complex was able to recognize and cleave a single ribonucleotide embedded in a DNA-DNA complex.
RNase H2 is specialized to remove single ribonucleotides (ribonucleoside monophosphates, or rNMPs) from duplex DNA, and its absence in budding yeast has been associated with the accumulation of deletions within short tandem repeats. Kim et al. (2011) demonstrated that rNMP-associated deletion formation requires the activity of Top1 (126420), a topoisomerase that relaxes supercoils by reversibly nicking duplex DNA. The reported studies extended the role of Top1 to include the processing of rNMPs in genomic DNA into irreversible single-strand breaks, an activity that can have distinct mutagenic consequences and may be relevant to human disease.
By expressing fluorescence-tagged RNASEH2 subunits individually or together in HeLa cells, Kind et al. (2014) determined that the B subunit was required for nuclear expression of the A and C subunits. Mutation analysis revealed that the C terminus of the C subunit, but not a catalytically active A subunit, was also required for formation of a stable nuclear complex. Ring-shaped trimeric PCNA (176740) functions as a 'sliding clamp' along DNA that guides assembly of factors involved in DNA replication and repair. PCNA recruited RNASEH2 to sites of DNA damage, and the PIP-box motif of subunit B was required for interaction of RNASEH2 with PCNA and accumulation of RNASEH2 to sites of DNA damage. In addition, a catalytically active A subunit bound more tightly than a catalytically inactive A subunit to sites of DNA replication.
Using CRISPR screens to identify genes and pathways that mediate cellular resistance to olaparib, a clinically approved PARP (173870) inhibitor, Zimmermann et al. (2018) identified a high-confidence set of 73 genes that when mutated cause increased sensitivity to PARP inhibitors. In addition to an expected enrichment for genes related to homologous recombination, Zimmermann et al. (2018) discovered that mutations in all 3 genes encoding ribonuclease H2 (RNASEH2A; RNASEH2B, 610326; and RNASEH2C, 610330) sensitized cells to PARP inhibition and established that the underlying cause of the PARP-inhibitor hypersensitivity of cells deficient in ribonuclease H2 is impaired ribonucleotide excision repair. Embedded ribonucleotides, which are abundant in the genome of cells deficient in ribonucleotide excision repair, are substrates for cleavage by TOP1, resulting in PARP-trapping lesions that impede DNA replication and endanger genome integrity. Zimmermann et al. (2018) concluded that genomic ribonucleotides are a hitherto unappreciated source of PARP-trapping DNA lesions, and that the frequent deletion of RNASEH2B in metastatic prostate cancer and chronic lymphocytic leukemia may provide an opportunity to exploit these findings therapeutically.
In 2 children with Aicardi-Goutieres syndrome (AGS4; 610333) from a consanguineous family of Spanish ancestry reported by Sanchis et al. (2005), Crow et al. (2006) identified a homozygous mutation in the RNASEH2A gene (606034.0001).
Rice et al. (2007) found RNASEH2A mutations in 3 of 127 pedigrees with a clinical diagnosis of AGS. Four children in these 3 families had biallelic mutations. Four of 5 mutations, 1 of which occurred in homozygous form, were missense. In 1 family Rice et al. (2007) identified a single mutation in RNASEH2A that had been inherited.
Rice et al. (2013) studied 4 probands with AGS who had homozygous or compound heterozygous mutations in the RNASEH2A gene (606034.0002-606034.0006). All 4 patients carried at least 1 synonymous RNASEH2A mutation; functional analysis confirmed the pathogenicity of the synonymous mutations.
Pokatayev et al. (2016) found that knockin mice homozygous for the gly37-to-ser (G37S; 606034.0001) mutation in the Rnaseh2a gene exhibited perinatal lethality. The G37S mutation led to increased expression of interferon-stimulated genes dependent on Cgas (MB21D1; 613973)-Sting (TMEM173; 612374) signaling. Ablation of Sting in G37S mice resulted in partial rescue of perinatal lethality, with viable mice exhibiting white spotting on their ventral surface. Pokatayev et al. (2016) proposed that this mouse model may facilitate study of RNASEH2-associated autoimmune diseases.
In 2 brothers with Aicardi-Goutieres syndrome-4 (AGS4; 610333) from a consanguineous family of Spanish ancestry reported by Sanchis et al. (2005), Crow et al. (2006) identified a homozygous 109G-A transition in exon 1 of the RNASEH2A gene, resulting in a gly37-to-ser (G37S) substitution at the end of the first beta-sheet in the floor of the predicted substrate-binding cleft near the catalytic site. This amino acid is conserved across all 3 major phylogenetic divisions (archea, eubacteria, eukaryotes). In vitro functional expression studies showed that the G37S mutant protein resulted in markedly reduced protein activity. The mutation was not detected in 178 European control alleles, and both parents were heterozygous for the mutation.
In a 7-year-old Belgian girl with Aicardi-Goutieres syndrome-4 (AGS4; 610333), Rice et al. (2013) identified homozygosity for a c.75C-T transition in exon 1 of the RNASEH2A gene, resulting in an arg25-to-arg (R25R) substitution. Her unaffected parents were heterozygous for the variant. The mutation was predicted to create a new donor splice site within exon 1; sequencing of the smaller RT-PCR product obtained from patient cell lines confirmed preferential usage of the new donor splice site. The aberrant transcript had a 54-bp in-frame deletion, resulting in an 18-amino acid internal deletion (del26-43) in the RNASEH2A protein. Coexpression of the mutant RNASEH2A with the B and C subunits in E. coli showed that although a mutant trimeric complex was formed, it exhibited no detectable catalytic activity, consistent with the loss of key metal-binding residues asp34 and glu35 in the mutant enzyme. However, a small amount of full-length transcript was also detected and confirmed by quantitative RT-PCR analysis of patient cells and peripheral whole blood, and residual levels of cellular RNase H2 activity were confirmed using a fluorometric assay on whole cell lysates from patient fibroblasts and lymphoblastoid cells.
In a 12-year-old Spanish girl with Aicardi-Goutieres syndrome-4 (AGS4; 610333) and her affected sister, Rice et al. (2013) identified compound heterozygosity for 2 mutations in the RNASEH2A gene: a synonymous R25R substitution (606034.0002), and a c.704G-A transition in exon 7, resulting in an arg235-to-gln (R235Q) substitution at a highly conserved residue. Their unaffected parents were each heterozygous for 1 of the mutations. Coffin et al. (2011) performed kinetic analysis of wildtype and R235Q mutant RNASEH2A and observed that the mutant showed dramatically reduced activity, measured at 1/370, 1/600, and 1/750 relative to wildtype, as well as reduced binding affinity, measured at 1/4, 1/4, and 1/10 relative to wildtype, using polynucleotide substrates containing 1, 4, and 20 ribonucleotides, respectively. Catalytic efficiency with the R235Q mutant was 1/800 of the efficiency of the wildtype protein.
In an Italian boy with Aicardi-Goutieres syndrome-4 (AGS4; 610333) who died at 3.5 years of age, Rice et al. (2013) identified compound heterozygosity for 2 mutations in the RNASEH2A gene. The first mutation was a c.69G-A transition in exon 1, resulting in a val23-to-val (V23V) substitution and predicted to create a new donor splice site; sequencing confirmed an out-of-frame deletion and insertion of 20 amino acids followed by a premature stop codon at residue 42. The second mutation was a c.556C-T transition in exon 6, resulting in an arg186-to-trp (R186W; 606034.0005) substitution at a highly conserved residue. His unaffected parents were each heterozygous for 1 of the mutations. Coffin et al. (2011) performed kinetic analysis of wildtype and R186W mutant RNASEH2A and observed that the mutant showed dramatically reduced activity, measured at 1/160, 1/9, and 1/8 relative to wildtype, as well as reduced binding affinity, measured at 1/8, 1/25, and 1/100 relative to wildtype, using polynucleotide substrates containing 1, 4, and 20 ribonucleotides, respectively. Catalytic efficiency with the R186W mutant was 1/56 of the efficiency of the wildtype protein.
For discussion of the arg186-to-trp (R186W) mutation in the RNASEH2A gene that was found in compound heterozygous state in a patient with Aicardi-Goutieres syndrome-4 (AGS4; 610333) by Rice et al. (2013), see 606034.0004.
In an 11-year-old Caucasian boy with Aicardi-Goutieres syndrome-4 (AGS4; 610333), Rice et al. (2013) identified compound heterozygosity for 2 mutations in the RNASEH2A gene: a synonymous V23V mutation (606034.0004), and a c.635A-T transversion in exon 6, resulting in an asn212-to-ile (N212I) substitution at a conserved residue. His unaffected parents were each heterozygous for 1 of the mutations. RNase H2 enzyme activity was strongly reduced in cell lysates from the patient, whereas enzyme activity in parental cells was similar to control levels. Coffin et al. (2011) performed kinetic analysis of wildtype and N212I mutant RNASEH2A and observed that although activity and catalytic efficiency were comparable to wildtype, the mutant showed reduced binding affinity, measured at 1/2 and 1/3 relative to wildtype, using polynucleotide substrates containing 4 and 20 ribonucleotides, respectively.
Coffin, S. R., Hollis, T., Perrino, F. W. Functional consequences of the RNase H2A subunit mutations that cause Aicardi-Goutieres syndrome. J. Biol. Chem. 286: 16984-16991, 2011. [PubMed: 21454563] [Full Text: https://doi.org/10.1074/jbc.M111.228833]
Crow, Y. J., Leitch, A., Hayward, B. E., Garner, A., Parmar, R., Griffith, E., Ali, M., Semple, C., Aicardi, J., Babul-Hirji, R., Baumann, C., Baxter, P., and 33 others. Mutations in genes encoding ribonuclease H2 subunits cause Aicardi-Goutieres syndrome and mimic congenital viral brain infection. Nature Genet. 38: 910-916, 2006. [PubMed: 16845400] [Full Text: https://doi.org/10.1038/ng1842]
Frank, P., Braunshofer-Reiter, C., Wintersberger, U., Grimm, R., Busen, W. Cloning of the cDNA encoding the large subunit of human RNase HI, a homologue of the prokaryotic RNase HII. Proc. Nat. Acad. Sci. 95: 12872-12877, 1998. [PubMed: 9789007] [Full Text: https://doi.org/10.1073/pnas.95.22.12872]
Kim, N., Huang, S. N., Williams, J. S., Li, Y. C., Clark, A. B., Cho, J.-E., Kunkel, T. A., Pommier, Y., Jinks-Robertson, S. Mutagenic processing of ribonucleotides in DNA by yeast topoisomerase I. Science 332: 1561-1564, 2011. [PubMed: 21700875] [Full Text: https://doi.org/10.1126/science.1205016]
Kind, B., Muster, B., Staroske, W., Herce, H. D., Sachse, R., Rapp, A., Schmidt, F., Koss, S., Cardoso, M. C., Lee-Kirsch, M. A. Altered spatio-temporal dynamics of RNase H2 complex assembly at replication and repair sites in Aicardi-Goutieres syndrome. Hum. Molec. Genet. 23: 5950-5960, 2014. [PubMed: 24986920] [Full Text: https://doi.org/10.1093/hmg/ddu319]
Pokatayev, V., Hasin, N., Chon, H., Cerritelli, S. M., Sakhuja, K., Ward, J. M., Morris, H. D., Yan, N., Crouch, R. J. RNase H2 catalytic core Aicardi-Goutieres syndrome-related mutant invokes cGAS-STING innate immune-sensing pathway in mice. J. Exp. Med. 213: 329-336, 2016. [PubMed: 26880576] [Full Text: https://doi.org/10.1084/jem.20151464]
Rice, G. I., Reijns, M. A. M., Coffin, S. R., Forte, G. M. A., Anderson, B. H., Szynkiewicz, M., Gornall, H., Gent, D., Leitch, A., Botella, M. P., Fazzi, E., Gener, B., Lagae, L., Olivieri, I., Orcesi, S., Swoboda, K. J., Perrino, F. W., Jackson, A. P., Crow, Y. J. Synonymous mutations in RNASEH2A create cryptic splice sites impairing RNase H2 enzyme function in Aicardi-Goutieres syndrome. Hum. Mutat. 34: 1066-1070, 2013. [PubMed: 23592335] [Full Text: https://doi.org/10.1002/humu.22336]
Rice, G., Patrick, T., Parmar, R., Taylor, C. F., Aeby, A., Aicardi, J., Artuch, R., Montalto, S. A., Bacino, C. A., Barroso, B., Baxter, P., Benko, W. S., and 106 others. Clinical and molecular phenotype of Aicardi-Goutieres syndrome. Am. J. Hum. Genet. 81: 713-725, 2007. [PubMed: 17846997] [Full Text: https://doi.org/10.1086/521373]
Sanchis, A., Cervero, L., Bataller, A., Tortajada, J. L., Huguet, J., Crow, Y. J., Ali, M., Higuet, L. J., Martinez-Frias, M. L. Genetic syndromes mimic congenital infections. J. Pediat. 146: 701-705, 2005. [PubMed: 15870678] [Full Text: https://doi.org/10.1016/j.jpeds.2005.01.033]
Zimmermann, M., Murina, O., Reijns, M. A. M., Agathanggelou, A., Challis, R., Tarnauskaite, Z., Muir, M., Fluteau, A., Aregger, M., McEwan, A., Yuan, W., Clarke, M., and 12 others. CRISPR screens identify genomic ribonucleotides as a source of PARP-trapping lesions. Nature 559: 285-289, 2018. [PubMed: 29973717] [Full Text: https://doi.org/10.1038/s41586-018-0291-z]