C16orf57, a gene mutated in poikiloderma with neutropenia, encodes a putative phosphodiesterase responsible for the U6 snRNA 3′ end modification

Abstract

C16orf57 encodes a human protein of unknown function, and mutations in the gene occur in poikiloderma with neutropenia (PN), which is a rare, autosomal recessive disease. Interestingly, mutations in C16orf57 were also observed among patients diagnosed with Rothmund-Thomson syndrome (RTS) and dyskeratosis congenita (DC), which are caused by mutations in genes involved in DNA repair and telomere maintenance. A genetic screen in Saccharomyces cerevisiae revealed that the yeast ortholog of C16orf57, USB1 (YLR132C), is essential for U6 small nuclear RNA (snRNA) biogenesis and cell viability. Usb1 depletion destabilized U6 snRNA, leading to splicing defects and cell growth defects, which was suppressed by the presence of multiple copies of the U6 snRNA gene SNR6. Moreover, Usb1 is essential for the generation of a unique feature of U6 snRNA; namely, the 39-terminal phosphate. RNAi experiments in human cells followed by biochemical and functional analyses confirmed that, similar to yeast, C16orf57 encodes a protein involved in the 29,39-cyclic phosphate formation at the 39 end of U6 snRNA. Advanced bioinformatics predicted that C16orf57 encodes a phosphodiesterase whose putative catalytic activity is essential for its function in vivo. Our results predict an unexpected molecular basis for PN, DC, and RTS and provide insight into U6 snRNA 39 end formation.

Aberrant 3′ oligoadenylation of spliceosomal U6 small nuclear RNA in poikiloderma with neutropenia

“…38 As Trf4 requires a free 3ЈOH terminal group, it is probable that a terminal Ͼ p or monophosphate group would inhibit Trf4-mediated oligoadenylation. Targeting of oligoadenylated U6 snRNA for degradation by the exosome in the absence of USB1 is consistent with our data showing that overexpression of U6 snRNA suppresses the lethality of usb1⌬ yeast cells and provides a potential mechanism to explain how USB1 might regulate the reduced U6 snRNA stability shown both in S cerevisiae, 34 in S pombe, and in human cells. 35 Thus, our data support the existence of a novel quality control pathway in which USB1 function alters the 3Ј end modification of U6 snRNA to target (3ЈOH) or protect (3Ј Ͼ p or 3Јp) it from Trf4-dependent 3Ј oligoadenylation and destruction by the exosome (Figure 7B).…”

Cajal bodies and snRNPs - friends with benefits

“…The LSm2-8 ring is pre-assembled without RNA in the cytoplasm and is localized to the nucleus by the LSm8 protein 44,45 . The 5′ end of U6 contains a γ-monomethyl cap while the 3′ end ribose is protected by cyclic 2′-3′ phosphate which is formed by USB1, a protein that is mutated in patients with the rare hereditary disease, Clericuzio-type poikiloderma with neutropenia 46 . The formation of the cyclic phosphate at the 3′ end destabilizes La binding and facilitates LSm2-8 association with the U6 snRNA 47 .…”

Clinical utility gene card for: poikiloderma with neutropenia

“…C16orf57 is a 3 0 -5 0 exonuclease essential for the biogenesis of the splicing apparatus. 4,5 Several classes of mutations have been identified, listed here in order of decreasing prevalence: nonsense mutations (c.232C4T, c.243G4A, c.258T4A, c.267T4A, c.415C4T, c.541C4T, c.673C4T); small out-of-frame deletions (c.176_177delG, c.179delC, c.489_492del4, c.496delA, c.531delA, c.683_893 þ 1del12); and splicing alterations, including substitutions at canonical splice junctions or at splice-site consensus sequences (c.265 þ 2T4G, c.266 À1G4A, c.450 À2A4G, c.502A4G, c.504 À2A4C, c.693 þ 1G4T). 2,3,[6][7][8][9][10] No missense mutations have yet been found; c.502A4G can be categorised as a splicing alteration because it leads to the excision of the fourth exon from the mature C16orf57-001 transcript.…”