Evidence for the role of PWCR1/HBII-85 C/D box small nucleolar RNAs in Prader-Willi syndrome

Abstract

Prior work has suggested that loss of expression of one or more of the many C/D box small nucleolar RNAs (snoRNAs) encoded within the complex, paternally expressed SNRPN (small nuclear ribonuclear protein N) locus may result in the phenotype of Prader-Willi syndrome (PWS). We suggest that the minimal critical region for PWS is approximately 121 kb within the >460-kb SNRPN locus, bordered by a breakpoint cluster region identified in three individuals with PWS who have balanced reciprocal translocations and by the proximal deletion breakpoint of a familial deletion found in an unaffected mother, her three children with Angelman syndrome, and her father. The subset of SNRPN-encoded snoRNAs within this region comprises the PWCR1/HBII-85 cluster of snoRNAs and the single HBII-438A snoRNA. These are the only known genes within this region, which suggests that loss of their expression may be responsible for much or all of the phenotype of PWS. This hypothesis is challenged by findings in two individuals with PWS who have balanced translocations with breakpoints upstream of the proposed minimal critical region but whose cells were reported to express transcripts within it, adjacent to these snoRNAs. By use of real-time quantitative reverse-transcriptase polymerase chain reaction, we reassessed expression of these transcripts and of the snoRNAs themselves in fibroblasts of one of these patients. We find that the transcripts reported to be expressed in lymphoblast-somatic cell hybrids are not expressed in fibroblasts, and we suggest that the original results were misinterpreted. Most important, we show that the PWCR1/HBII-85 snoRNAs are not expressed in fibroblasts of this individual. These results are consistent with the hypothesis that loss of expression of the snoRNAs in the proposed minimal critical region confers much or all of the phenotype of PWS.

Figure 1

The SNRPN locus, starting at the major promoter.A, The large SNRPN transcript (black arrow). Several of the stable transcripts are in blue: SNURF, exons 1–3; SNRPN, exons 4–10; PAR-5; PWCR1; IPW and PAR-1. A subset of SNRPN exon sequences is illustrated by thin black lines. SnoRNA sequences are indicated by red lines and are identified by red text. The PWCR1/HBII-85 snoRNAs are a cluster of 27 sequences, the HBII-52 snoRNAs are a cluster of 47 sequences. Most are located within SNRPN introns, and most introns contain only one snoRNA. Not all are depicted, and the drawing is not to scale. B, Derivation of the PWS minimal critical region (box). Its borders are defined proximally by the wavy line that indicates the distal breakpoint cluster region within the alternatively spliced intron 20a/exon 21 (three individuals with PWS). The proximal breakpoint cluster region is in intron 2, within the SNURF gene (two individuals with PWS, including the individual studied here). The distal border of the minimal region is defined by the AS submicroscopic deletion that did not confer PWS when paternally inherited (blackened rectangle). The known genes and detected transcripts found within its borders are depicted; these are the transcripts PWCR1, IPW, and PAR-1 (blue) and the genes for snoRNAs HBII-438A and the PWCR1/HBII-85 cluster (red).

Figure 2

Results of FISH of fibroblast chromosomes with a t(4;15)(q27;q11.2) balanced reciprocal translocation. The chromosome 15 centromeric (cen) probe (green) identifies the normal chromosome 15 (left) and the der(15) (middle). The SNRPN probe (pink) hybridizes to the normal chromosome 15 (left), the der(15) (middle), and the der(4) (right), demonstrating that the breakpoint is within SNRPN. The distal chromosome 15q22 probe (yellow) identifies the normal chromosome 15 (left) and the der(4) (right).

Figure 3

Amplification plots of quantitative RT-PCR of cDNA from fibroblasts of the individual with t(4;15) and fibroblasts of a normal control for three transcripts: A, IPW; B, U21 snoRNA; C, PWCR1/HBII-85 snoRNAs. The Y-axis is the amount of fluorescence. The X-axis is the PCR cycle number. Each +RT reaction was done in triplicate, but not all individual plots can be distinguished, because they are superimposed. IPW and PWCR1/HBII-85: t(4;15) +RTs are shown in red, yellow, and green; −RTs are shown in red and dark blue. The −RT reactions, performed in parallel, gave similar results for both cell types and have not been labeled individually. In all cases, a no-DNA control was included. The C_T values of these reactions were generally >40, but, with IPW primers, the value was 39. Samples with more starting cDNA of a transcript cross C_T at a lower PCR cycle (e.g., the t(4;15) fibroblasts have more U21 cDNA than do the control fibroblasts).