Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2010 Jul 26;5(7):e11779.
doi: 10.1371/journal.pone.0011779.

Digital genome-wide ncRNA expression, including SnoRNAs, across 11 human tissues using polyA-neutral amplification

John C Castle  1 , Christopher D Armour, Martin Löwer, David Haynor, Matthew Biery, Heather Bouzek, Ronghua Chen, Stuart Jackson, Jason M Johnson, Carol A Rohl, Christopher K Raymond
Affiliations

Digital genome-wide ncRNA expression, including SnoRNAs, across 11 human tissues using polyA-neutral amplification

John C Castle et al. PLoS One. .

Abstract

Non-coding RNAs (ncRNAs) are an essential class of molecular species that have been difficult to monitor on high throughput platforms due to frequent lack of polyadenylation. Using a polyadenylation-neutral amplification protocol and next-generation sequencing, we explore ncRNA expression in eleven human tissues. ncRNAs 7SL, U2, 7SK, and HBII-52 are expressed at levels far exceeding mRNAs. C/D and H/ACA box snoRNAs are associated with rRNA methylation and pseudouridylation, respectively: spleen expresses both, hypothalamus expresses mainly C/D box snoRNAs, and testes show enriched expression of both H/ACA box snoRNAs and RNA telomerase TERC. Within the snoRNA 14q cluster, 14q(I-6) is expressed at much higher levels than other cluster members. More reads align to mitochondrial than nuclear tRNAs. Many lincRNAs are actively transcribed, particularly those overlapping known ncRNAs. Within the Prader-Willi syndrome loci, the snoRNA HBII-85 (group I) cluster is highly expressed in hypothalamus, greater than in other tissues and greater than group II or III. Additionally, within the disease locus we find novel transcription across a 400,000 nt span in ovaries. This genome-wide polyA-neutral expression compendium demonstrates the richness of ncRNA expression, their high expression patterns, their function-specific expression patterns, and is publicly available.

PubMed Disclaimer

Conflict of interest statement

Competing Interests: At the time of data acquisition, most authors were employed by Rosetta Inpharmatics LLC, a wholly owned subsidiary of Merck & Co., Inc. Since 2009, authors have been employed by TRON, a not-for-profit translational oncology institute in Germany; by Nugen Inc.; by the University of Washington; and by Merck & Co. Rosetta/Merck paid employee salaries and funded the original research. Merck employees have reviewed the manuscript and approved the data release. Further analysis was done by JCC at TRON, a not-for-profit institute.

Figures

Figure 1
Figure 1. ncRNA expression.
Expression (RPKM units) of the 20 monitored ncRNA with highest mean values across eleven tissues.
Figure 2
Figure 2. Individual ncRNA expression.
A: HY3 sequencing (RPKM) and qPCR expression. qPCR values are normalized to 18S and the mean sequencing value. B, C, and D: expression of BC200, snR39B, and TERC (telomerase RNA component).
Figure 3
Figure 3. Expression of the 14q snoRNA cluster.
A: genomic layout of the 41 members of the 14q snoRNA cluster (upper) and maximum RPKM values for each member, across all tissues (lower). Every second snoRNA is labeled. Y-axis is log10 scale. B: expression of the highly expressed 14q(I-6) snoRNA. qPCR values are normalized to 18S and the mean sequencing value. Y-axis is linear scale.
Figure 4
Figure 4. Expression of the HBII-52 and HBII-85 snoRNA clusters.
A: genomic layout of the HBII-52 and HBII-85 snoRNA clusters. B, C, and D: expression of the HBII-85 group I, II, and III clusters. E: expression of the HBII-52 cluster. F: expression of HBII-85 group I, II, and III in hypothalamus.
Figure 5
Figure 5. Expression in the PWS/Angelman locus, chromosome 15, 22.0–22.4 Mb.
A: gene location and strand and coverage by ESTs (Expressed Sequence Tags). B: sequence read coverage showing positive (red) and minus (green) strand transcription for each tissue. Transcription for genes NDN and UBE3A along with the novel region are circled in blue. C: summed positive strand expression between chromosome 15; 22.0 to 22.4 Mb.
See this image and copyright information in PMC

References

    1. Eddy SR. Non-coding RNA genes and the modern RNA world. Nat Rev Genet. 2001;2:919–929. - PubMed
    1. Mattick JS, Makunin IV. Non-coding RNA. Hum Mol Genet 15 Spec No. 2006;1:R17–29. - PubMed
    1. Sahoo T, del Gaudio D, German JR, Shinawi M, Peters SU, et al. Prader-Willi phenotype caused by paternal deficiency for the HBII-85 C/D box small nucleolar RNA cluster. Nat Genet. 2008;40:719–721. - PMC - PubMed
    1. Wong JM, Collins K. Telomerase RNA level limits telomere maintenance in X-linked dyskeratosis congenita. Genes Dev. 2006;20:2848–2858. - PMC - PubMed
    1. Agarwal S, Loh YH, McLoughlin EM, Huang J, Park IH, et al. Telomere elongation in induced pluripotent stem cells from dyskeratosis congenita patients. Nature 2010 - PMC - PubMed

Publication types