A Prader-Willi locus lncRNA cloud modulates diurnal genes and energy expenditure

Human Molecular Genetics

Volumn 22, Issue 21, 2013, Pages 4318-4328

  Powell, Weston T ^a   Coulson, Rochelle L ^a   Crary, Florence K ^a   Wong, Spencer S ^a   Ach, Robert A ^b   Tsang, Peter ^b   Yamada, N Alice ^b   Yasui, Dag H ^a   LaSalle, Janine M ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b AGILENT LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CRYPTOCHROME 1; LONG UNTRANSLATED RNA; LONG UNTRANSLATED RNA 115HG; LONG UNTRANSLATED RNA 116HG; MAMMALIAN TARGET OF RAPAMYCIN; PER2 PROTEIN; SMALL NUCLEOLAR RNA; TRANSCRIPTION FACTOR CLOCK; UNCLASSIFIED DRUG;

ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; BODY WEIGHT; CIRCADIAN RHYTHM; CONTROLLED STUDY; CRYPTOCHROME 1 GENE; DNA ISOLATION; ENERGY EXPENDITURE; FLUORESCENCE IN SITU HYBRIDIZATION; GENE EXPRESSION; GENE LOCATION; GENE LOCUS; HUMAN; HUMAN TISSUE; LIPID OXIDATION; LUNG GAS EXCHANGE; MAMMALIAN TARGET OF RAPAMYCIN GENE; MOUSE; NERVE CELL; NEWBORN; NONHUMAN; PER2 GENE; PRADER WILLI SYNDROME; PRIORITY JOURNAL; PROTEIN DEGRADATION; QUANTITATIVE ANALYSIS; RBBP5 GENE; REGULATORY MECHANISM; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ISOLATION; RNA PURIFICATION; RNA SEQUENCE; RNA SPLICING; SIGNAL TRANSDUCTION; SUPRACHIASMATIC NUCLEUS; TRANSCRIPTION FACTOR CLOCK GENE; TRANSCRIPTION INITIATION SITE; WILD TYPE;

ANIMALS; AUTOPSY; BRAIN; CIRCADIAN RHYTHM; CLOCK PROTEINS; CRYPTOCHROMES; ENERGY METABOLISM; FEMALE; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENOMIC IMPRINTING; HUMANS; MALE; MICE; MICE, INBRED C57BL; MICE, TRANSGENIC; NEURONS; NUCLEAR PROTEINS; PERIOD CIRCADIAN PROTEINS; PRADER-WILLI SYNDROME; RNA, LONG NONCODING; SLEEP;

EID: 84882766445     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddt281     Document Type: Article

References (44)

1. Farooqi, I.S. and O'Rahilly, S. (2005) Monogenic obesity in humans. Ann. Rev. Med., 56, 443-458.
2. Dykens, E.M., Lee, E. and Roof, E. (2011) Prader-Willi syndrome and autism spectrum disorders: an evolving story. J. Neurodev. Dis., 3, 225-237.
3. Jiang, Y.H., Bressler, J. and Beaudet, A.L. (2004) Epigenetics and human disease. Ann. Rev. Genome Hum. Genet., 5, 479-510.
4. Edwards, C.A. and Ferguson-Smith, A.C. (2007) Mechanisms regulating imprinted genes in clusters. Curr. Opin. Cell Biol., 19, 281-289.
5. Leung, K.N., Chamberlain, S.J., Lalande, M. and LaSalle, J.M. (2011) Neuronal chromatin dynamics of imprinting in development and disease. J. Cell Biochem., 112, 365-373.
6. Sutcliffe, J.S., Nakao, M., Christian, S., Orstavik, K.H., Tommerup, N., Ledbetter, D.H. and Beaudet, A.L. (1994) Deletions of a differentially methylated CpG island at the SNRPN gene define a putative imprinting control region. Nat. Genet., 8, 52-58.
7. Duker, A.L., Ballif, B.C., Bawle, E.V., Person, R.E., Mahadevan, S., Alliman, S., Thompson, R., Traylor, R., Bejjani, B.A., Shaffer, L.G. et al. (2010) Paternally inherited microdeletion at 15q11.2 confirms a significant role for the SNORD116 C/D box snoRNA cluster in Prader-Willi syndrome. Eur. J. Hum. Genet., 18, 1196-1201.
8. Sahoo, T., del Gaudio, D., German, J.R., Shinawi, M., Peters, S.U., Person, R.E., Garnica, A., Cheung, S.W. and Beaudet, A.L. (2008) Prader-Willi phenotype caused by paternal deficiency for the HBII-85 C/D box small nucleolar RNA cluster. Nat. Genet., 40, 719-721.
9. de Smith, A.J., Purmann, C., Walters, R.G., Ellis, R.J., Holder, S.E., Van Haelst, M.M., Brady, A.F., Fairbrother, U.L., Dattani, M., Keogh, J.M. et al. (2009) A deletion of the HBII-85 class of small nucleolar RNAs (snoRNAs) is associated with hyperphagia, obesity and hypogonadism. Hum. Mol. Genet., 18, 3257-3265.
10. Vitali, P., Royo, H., Marty, V., Bortolin-Cavaille, M.L. and Cavaille, J. (2010) Long nuclear-retained non-coding RNAs and allele-specific higher-order chromatin organization at imprinted snoRNA gene arrays. J. Cell Sci., 123, 70-83.
11. Yin, Q.F., Yang, L., Zhang, Y., Xiang, J.F., Wu, Y.W., Carmichael, G.G. and Chen, L.L. (2012) Long Noncoding RNAs with snoRNA Ends. Mol. Cell., 48, 219-230.
12. Ding, F., Li, H.H., Zhang, S., Solomon, N.M., Camper, S.A., Cohen, P. and Francke, U. (2008) SnoRNA Snord116 (Pwcr1/MBII-85) deletion causes growth deficiency and hyperphagia in mice. PLoS One, 3, e1709.
13. Skryabin, B.V., Gubar, L.V., Seeger, B., Pfeiffer, J., Handel, S., Robeck, T., Karpova, E., Rozhdestvensky, T.S. and Brosius, J. (2007) Deletion of the MBII-85 snoRNA gene cluster in mice results in postnatal growth retardation. PLoS Genet., 3, e235.
14. Kishore, S. andStamm, S. (2006)ThesnoRNAHBII-52 regulates alternative splicing of the serotonin receptor 2C. Science, 311, 230-232.
15. Wang, K.C. and Chang, H.Y. (2011) Molecular mechanisms of long noncoding RNAs. Mol. Cell, 43, 904-914.
16. Lee, J.T. (2012) Epigenetic regulation by long noncoding RNAs. Science, 338, 1435-1439.
17. Qureshi, I.A., Mattick, J.S. and Mehler, M.F. (2010) Long non-codingRNAs in nervous system function and disease. Brain Res., 1338, 20-35.
18. Hughes, M.E., Grant, G.R., Paquin, C., Qian, J. and Nitabach, M.N. (2012) Deep sequencing the circadian and diurnal transcriptome of Drosophila brain. Genome Res., 22, 1266-1281.
19. Leung, K.N., Vallero, R.O., DuBose, A.J., Resnick, J.L. and LaSalle, J.M. (2009) Imprinting regulates mammalian snoRNA-encoding chromatin decondensation and neuronal nucleolar size. Hum. Mol. Genet., 18, 4227-4238.
20. Chu, C., Quinn, J. and Chang, H.Y. (2012) Chromatin isolation by RNA purification (ChIRP). JoVE., 61, pii: 3912.
21. Chu, C., Qu, K., Zhong, F.L., Artandi, S.E. and Chang, H.Y. (2011) Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol. Cell, 44, 667-678.
22. Simon, M.D., Wang, C.I., Kharchenko, P.V., West, J.A., Chapman, B.A., Alekseyenko, A.A., Borowsky, M.L., Kuroda, M.I. and Kingston, R.E. (2011) The genomic binding sites of a noncodingRNA. Proc. Natl Acad. Sci. USA, 108, 20497-20502.
23. Bertani, S., Sauer, S., Bolotin, E. and Sauer, F. (2011) The noncoding RNA Mistral activates Hoxa6 and Hoxa7 expression and stem cell differentiation by recruiting MLL1 to chromatin. Mol. Cell, 43, 1040-1046.
24. Hasegawa, Y., Brockdorff, N., Kawano, S., Tsutui, K., Tsutui, K. and Nakagawa, S. (2010) The matrix protein hnRNP U is required for chromosomal localization of Xist RNA. Dev. Cell, 19, 469-476.
25. Kino, T., Hurt, D.E., Ichijo, T., Nader, N. and Chrousos, G.P. (2010) NoncodingRNAgas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Sci. Signal., 3, ra8.
26. Cao, R., Anderson, F.E., Jung, Y.J., Dziema, H. and Obrietan, K. (2011) Circadian regulation of mammalian target of rapamycin signaling in the mouse suprachiasmatic nucleus. Neuroscience, 181, 79-88.
27. Yang, S., Wang, K., Valladares, O., Hannenhalli, S. and Bucan, M. (2007) Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortex. Genome Biol., 8, R247.
28. Brown, R.E., Basheer, R., McKenna, J.T., Strecker, R.E. and McCarley, R.W. (2012) Control of sleep and wakefulness. Physiol. Rev., 92, 1087-1187.
29. Gallagher, R.C., Pils, B., Albalwi, M. and Francke, U. (2002) Evidence for the role of PWCR1/HBII-85 C/D box small nucleolar RNAs in Prader-Willi syndrome. Am. J. Hum. Genet., 71, 669-678.
30. Gibbs, S., Wiltshire, E. and Elder, D. (2013) Nocturnal sleep measured by actigraphy in children with Prader-Willi syndrome. J Pediatr., 162, 765-769.
31. Kozlov, S.V., Bogenpohl, J.W., Howell, M.P., Wevrick, R., Panda, S., Hogenesch, J.B., Muglia, L.J., Van Gelder, R.N., Herzog, E.D. and Stewart, C.L. (2007) The imprinted gene Magel2 regulates normal circadian output. Nat. Genet., 39, 1266-1272.
32. Arble, D.M., Bass, J., Laposky, A.D., Vitaterna, M.H. and Turek, F.W. (2009) Circadian timing of food intake contributes to weight gain. Obesity (Silver Spring), 17, 2100-2102.
33. Hatori, M., Vollmers, C., Zarrinpar, A., DiTacchio, L., Bushong, E.A., Gill, S., Leblanc, M., Chaix, A., Joens, M., Fitzpatrick, J.A. et al. (2012) Time-restricted feeding without reducing caloric intake prevents metabolic diseases in mice fed a high-fat diet. Cell Metab., 15, 848-860.
34. Miller, J.L., Lynn, C.H., Driscoll, D.C., Goldstone, A.P., Gold, J.A., Kimonis, V., Dykens, E., Butler, M.G., Shuster, J.J. and Driscoll, D.J. (2011) Nutritional phases in Prader-Willi syndrome. Am. J. Med. Genet. A, 155A, 1040-1049.
35. Christ, E., Korf, H.-W. and von Gall, C. (2012) Andries Kalsbeek, M.M.T.R. and Russell, G.F. (eds), Progress in Brain Research, Vol. 199. Elsevier, Amsterdam, Netherlands, pp. 105-118.
36. Ding, F., Li, H.H., Li, J., Myers, R.M. and Francke, U. (2010) Neonatal maternal deprivation response and developmental changes in gene expression revealed by hypothalamic gene expression profiling in mice. PLoS One, 5, e9402.
37. Hellbruegge, T., Lange, J.E., Stehr, K. and Rutenfranz, J. (1964) Circadian periodicity of physiological functions in different stages of infancy and childhood. Ann. N. Y. Acad. Sci., 117, 361-373.
38. Langmead, B., Trapnell, C., Pop, M. and Salzberg, S.L. (2009) Ultrafast and memory-efficient alignment of shortDNAsequences to the human genome. Genome Biol., 10, R25.
39. Zhang, Y., Liu, T., Meyer, C.A., Eeckhoute, J., Johnson, D.S., Bernstein, B.E., Nusbaum, C., Myers, R.M., Brown, M., Li, W. et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol., 9, R137.
40. Huang da, W., Sherman, B.T. and Lempicki, R.A. (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res., 37, 1-13.
41. Huang da, W., Sherman, B.T. and Lempicki, R.A. (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc., 4, 44-57.
42. McLean, C.Y., Bristor, D., Hiller, M., Clarke, S.L., Schaar, B.T., Lowe, C.B., Wenger, A.M. and Bejerano, G. (2010) GREAT improves functional interpretation of cis-regulatory regions. Nat. Biotechnol., 28, 495-501.
43. Trapnell, C., Pachter, L. and Salzberg, S.L. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111.
44. Edgar, R., Domrachev, M. and Lash, A.E. (2002) Gene Expression Omnibus:NCBI gene expression and hybridization array data repository. Nucl. Acids Res., 30, 207-210.