Alternative titles; symbols
HGNC Approved Gene Symbol: DHX36
Cytogenetic location: 3q25.2 Genomic coordinates (GRCh38): 3:154,272,546-154,324,487 (from NCBI)
Stable cyclic guanine quartets form by self-assembly of 4 guanine molecules, and these quartets can self-associate into a vertical stack known as a G quadruplex. DNA or RNA molecules with runs of 3 or more guanines can form complex G-quadruplex structures termed G4-DNA or G4-RNA. These G-quadruplex structures are thermodynamically stable and are found near genetic control regions, including mRNA splicing and polyadenylation sites, promoter regions, and telomeres. DHX36 is an enzyme that resolves G4 structures into separate nucleotide strands for metabolic processing of G-rich sequences (Creacy et al., 2008).
By sequencing clones obtained from a size-fractionated fetal brain cDNA library, Nagase et al. (2000) cloned DHX36, which they designated KIAA1488. The deduced 852-amino acid protein shares similarity with yeast and plant RNA helicases. RT-PCR ELISA detected relatively low expression in fetal liver and in adult liver, kidney, spinal cord, whole brain, and all specific brain regions examined. Expression was weaker in all other tissues examined, including fetal brain.
Using a G4-DNA affinity column to purify G4-DNA resolving enzymes from HeLa cells, followed by mass spectrometry, Vaughn et al. (2005) identified DHX36. The deduced protein has a calculated molecular mass of 115 kD. It had an apparent molecular mass of 120 kD by SDS-PAGE.
Vaughn et al. (2005) found that recombinant human DHX36 showed robust G4-DNA resolving activity. Formation of DNA monomers by DHX36 required ATP and Mg(2+). DHX36 did not resolve Y-form duplex DNA or duplex DNA with 5-prime or 3-prime overhangs. DHX36 readily resolved ribosomal G4-DNA. In contrast, DHX36 bound well to TP G4-DNA generated from the immunoglobulin heavy chain switch region, but it resolved it slowly.
Creacy et al. (2008) found that recombinant human DHX36 bound both G4-RNA and G4-DNA with high affinity and displayed robust resolving activity with both substrates. DHX36 bound G4-RNA with somewhat higher affinity than G4-DNA and appeared to bind G4-RNA as a monomer and as multimers. Competition studies showed that DHX36 preferred G4-RNA over G4-DNA of an identical sequence, but both were readily resolved into monomers. Creacy et al. (2008) concluded that DHX36 is a quadruplex nucleic acid surveillance protein capable of removing quadruplex 'knots,' allowing smooth metabolic processing of G-rich RNA and DNA.
By immunoprecipitation and protein pull-down analyses using biotinylated poly I:C, Zhang et al. (2011) identified a cytosolic, endosome-independent sensor of viral nucleotides consisting of the RNA helicases Ddx1 (601257), Ddx21 (606357), and Dhx36 and the adaptor molecule Trif (TICAM1; 607601) in mouse myeloid dendritic cells (mDCs). The double-stranded RNA (dsRNA) sensors Pkr (EIF2AK2; 176871) and Lgp2 (DHX58; 608588) were also precipitated. Knockdown of each helicase via short hairpin RNA blocked the ability of mDCs to mount type I interferon (see 147660) and cytokine responses to poly I:C, influenza A, and reovirus. Ddx1 bound poly I:C through its helicase A domain, while Dhx36 and Ddx21 bound the TIR domain of Trif via their HA2-DUF and PRK domains, respectively. Zhang et al. (2011) concluded that the DDX1-DDX21-DHX36 complex is a dsRNA sensor that uses the TRIF pathway to activate type I interferon responses in the cytosol of mDCs.
Crystal Structure
Chen et al. (2018) reported the cocrystal structure of bovine DHX36 bound to a DNA with a G-quadruplex and a 3-prime single-stranded DNA segment and showed that the N-terminal DHX36-specific motif folds into a DNA-binding-induced alpha-helix that, together with the OB-fold-like subdomain, selectively binds parallel G-quadruplexes. Comparison with unliganded and ATP-analog-bound DHX36 structures, together with single-molecule fluorescence resonance energy transfer analysis, suggested that G-quadruplex binding alone induces rearrangements of the helicase core; by pulling on the single-stranded DNA tail, these rearrangements drive G-quadruplex unfolding 1 residue at a time.
Hartz (2009) mapped the DHX36 gene to chromosome 3q25.2 based on an alignment of the DHX36 sequence (GenBank AB040921) with the genomic sequence (build 36.1).
Chen, M. C., Tippana, R., Demeshkina, N. A., Murat, P., Balasubramanian, S., Myong, S., Ferre-D'Amare, A. R. Structural basis of G-quadruplex unfolding by the DEAH/RHA helicase DHX36. Nature 558: 465-469, 2018. [PubMed: 29899445] [Full Text: https://doi.org/10.1038/s41586-018-0209-9]
Creacy, S. D., Routh, E. D., Iwamoto, F., Nagamine, Y., Akman, S. A., Vaughn, J. P. G4 resolvase 1 binds both DNA and RNA tetramolecular quadruplex with high affinity and is the major source of tetramolecular quadruplex G4-DNA and G4-RNA resolving activity in HeLa cell lysates. J. Biol. Chem. 283: 34626-34634, 2008. [PubMed: 18842585] [Full Text: https://doi.org/10.1074/jbc.M806277200]
Hartz, P. A. Personal Communication. Baltimore, Md. 4/28/2009.
Nagase, T., Kikuno, R., Ishikawa, K., Hirosawa, M., Ohara, O. Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. DNA Res. 7: 143-150, 2000. [PubMed: 10819331] [Full Text: https://doi.org/10.1093/dnares/7.2.143]
Vaughn, J. P., Creacy, S. D., Routh, E. D., Joyner-Butt, C., Jenkins, G. S., Pauli, S., Nagamine, Y., Akman, S. A. The DEXH protein product of the DHX36 gene is the major source of tetramolecular quadruplex G4-DNA resolving activity in HeLa cell lysates. J. Biol. Chem. 280: 38117-38120, 2005. [PubMed: 16150737] [Full Text: https://doi.org/10.1074/jbc.C500348200]
Zhang, Z., Kim, T., Bao, M., Facchinetti, V., Jung, S. Y., Ghaffari, A. A., Qin, J., Cheng, G., Liu, Y.-J. DDX1, DDX21, and DHX36 helicases form a complex with the adaptor molecule TRIF to sense dsRNA in dendritic cells. Immunity 34: 866-878, 2011. [PubMed: 21703541] [Full Text: https://doi.org/10.1016/j.immuni.2011.03.027]