Temporal transcriptomics suggest that twin-peaking genes reset the clock

eLife

Volumn 4, Issue NOVEMBER2015, 2015, Pages

  Pembroke, William G ^a   Babbs, Arran ^a   Davies, Kay E ^a   Ponting, Chris P ^a   Oliver, Peter L ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIC AMP RESPONSIVE ELEMENT BINDING PROTEIN; G PROTEIN COUPLED RECEPTOR;

ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; BRAIN ELECTROPHYSIOLOGY; CALCIUM SIGNALING; CHRONOBIOLOGY; CIRCADIAN RHYTHM; FLUORESCENCE IN SITU HYBRIDIZATION; GENE EXPRESSION; GENE IDENTIFICATION; MALE; MOUSE; NONHUMAN; POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; SUPRACHIASMATIC NUCLEUS; SYNAPTIC TRANSMISSION; TRANSCRIPTOMICS; ANIMAL; BIOLOGICAL RHYTHM; C3H MOUSE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; LASER CAPTURE MICRODISSECTION; PHYSIOLOGY;

ANIMALS; BIOLOGICAL CLOCKS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; LASER CAPTURE MICRODISSECTION; MICE, INBRED C3H; SEQUENCE ANALYSIS, RNA; SUPRACHIASMATIC NUCLEUS; TRANSCRIPTION, GENETIC;

EID: 84955270628     PISSN: None     EISSN: 2050084X     Source Type: Journal    
DOI: 10.7554/eLife.10518.001     Document Type: Article

References (54)

1. Anders S, Pyl PT, Huber W. 2015. HTSeq-a python framework to work with high-throughput sequencing data. Bioinformatics 31:166-169. doi: 10.1093/bioinformatics/btu638
2. Azzi A, Dallmann R, Casserly A, Rehrauer H, Patrignani A, Maier B, Kramer A, Brown SA. 2014. Circadian behavior is light-reprogrammed by plastic DNA methylation. Nature Neuroscience 17:377-382. doi: 10.1038/ nn.3651
3. Barbosa-Morais NL, Irimia M, Pan Q, Xiong HY, Gueroussov S, Lee LJ, Slobodeniuc V, Kutter C, Watt S, Colak R, Kim T, Misquitta-Ali CM, Wilson MD, Kim PM, Odom DT, Frey BJ, Blencowe BJ. 2012. The evolutionary landscape of alternative splicing in vertebrate species. Science 338:1587-1593. doi: 10.1126/science.1230612
4. Belgard TG, Marques AC, Oliver PL, Abaan HO, Sirey TM, Hoerder-Suabedissen A, García-Moreno F, Molnár Z, Margulies EH, Ponting CP. 2011. A transcriptomic atlas of mouse neocortical layers. Neuron 71:605-616. doi: 10.1016/j.neuron.2011.06.039
5. Biello SM, Mrosovsky N. 1995. Blocking the phase-shifting effect of neuropeptide y with light. Proceedings of the Royal Society B: Biological Sciences 259:179-187. doi: 10.1098/rspb.1995.0026
6. Brawand D, Soumillon M, Necsulea A, Julien P, Csárdi G, Harrigan P, Weier M, Liechti A, Aximu-Petri A, Kircher M, Albert FW, Zeller U, Khaitovich P, Grützner F, Bergmann S, Nielsen R, Pääbo S, Kaessmann H. 2011. The evolution of gene expression levels in mammalian organs. Nature 478:343-348. doi: 10.1038/nature10532
7. Brown TM, Piggins HD. 2007. Electrophysiology of the suprachiasmatic circadian clock. Progress in Neurobiology 82:229-255. doi: 10.1016/j.pneurobio.2007.05.002
8. Cabej NR. 2013. Building the Most Complex Structure on Earth. Kidlington, United Kingdom: Elsevier,1-298.
9. Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. 2011. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes & Development 25: 1915-1927. doi: 10.1101/gad.17446611
10. Cagampang FRA, Antoni FA, Smith SM, Piggins HD, Coen CW. 1998. Circadian changes of type II adenylyl cyclase mRNA in the rat suprachiasmatic nuclei. Brain Research 810:279-282. doi: 10.1016/S0006-8993(98) 00934-2
11. Cagampang FRA, Piggins HD, Sheward WJ, Harmar AJ, Coen CW. 1998. Circadian changes in PACAP type 1 (pAC1) receptor mRNA in the rat suprachiasmatic and supraoptic nuclei. Brain Research 813:218-222. doi: 10. 1016/S0006-8993(98)01044-0
12. Cagampang FRA, Rattray M, Campbell IC, Powell JF, Coen CW. 1998. Variation in the expression of the mRNA for protein kinase c isoforms in the rat suprachiasmatic nuclei, caudate putamen and cerebral cortex. Molecular Brain Research 53:277-284. doi: 10.1016/S0169-328X(97)00309-4
13. Cagampang FRA, Sheward WJ, Harmar AJ, Piggins HD, Coen CW. 1998. Circadian changes in the expression of vasoactive intestinal peptide 2 receptor mRNA in the rat suprachiasmatic nuclei. Molecular Brain Research 54: 108-112. doi: 10.1016/S0169-328X(97)00327-6
14. Challet E. 2003. Interactions between photic and nonphotic stimuli to synchronize the master circadian clock in mammals. Frontiers in Bioscience 8:s246-257. doi: 10.2741/1039
15. Chodroff RA, Goodstadt L, Sirey TM, Oliver PL, Davies KE, Green ED, Molnár Z, Ponting CP. 2010. Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes. Genome Biology 11:R72. doi: 10.1186/gb-2010-11-7-r72
16. Ding J, Chen D, Weber E, Faiman L, Rea M, Gillette M. 1994. Resetting the biological clock: mediation of nocturnal circadian shifts by glutamate and NO. Science 266:1713-1717. doi: 10.1126/science.7527589
17. Ding JM, Buchanan GF, Tischkau SA, Chen D, Kuriashkina L, Faiman LE, Alster JM, McPherson PS, Campbell KP, Gillette MU. 1998. A neuronal ryanodine receptor mediates light-induced phase delays of the circadian clock. Nature 394:381-384. doi: 10.1038/28639
18. Dulneva A, Lee S, Oliver PL, Di Gleria K, Kessler BM, Davies KE, Becker EBE. 2015. The mutant moonwalker TRPC3 channel links calcium signaling to lipid metabolism in the developing cerebellum. Human Molecular Genetics 24:4114-4125. doi: 10.1093/hmg/ddv150
19. Ebling FJP, Maywood ES, Staley K, Humby T, Hancock DC, Waters CM, Evant GI, Hastings MH. 1991. The role of n-methyl-d-aspartate-type glutamatergic neurotransmission in the photic induction of immediate-early gene expression in the suprachiasmatic nuclei of the syrian hamster. Journal of Neuroendocrinology 3:641-652. doi: 10.1111/j.1365-2826.1991.tb00329.x
20. Eppig JT, Blake JA, Bult CJ, Kadin JA, Richardson JE.The Mouse Genome Database GroupThe Mouse Genome Database Group. 2015. The mouse genome database (mGD): facilitating mouse as a model for human biology and disease. Nucleic Acids Research 43:D726-D736. doi: 10.1093/nar/gku967
21. Gerber A, Esnault C, Aubert G, Treisman R, Pralong F, Schibler U. 2013. Blood-borne circadian signal stimulates daily oscillations in actin dynamics and SRF activity. Cell 152:492-503. doi: 10.1016/j.cell.2012.12.027
22. Gillette MU, Mitchell JW. 2002. Signaling in the suprachiasmatic nucleus: selectively responsive and integrative. Cell and Tissue Research 309:99-107. doi: 10.1007/s00441-002-0576-1
23. Golombek DA, Rosenstein RE. 2010. Physiology of circadian entrainment. Physiological Reviews 90:1063-1102. doi: 10.1152/physrev.00009.2009
24. Huang DW, Sherman BT, Lempicki RA. 2008. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols 4:44-57. doi: 10.1038/nprot.2008.211
25. Hughes ME, DiTacchio L, Hayes KR, Vollmers C, Pulivarthy S, Baggs JE, Panda S, Hogenesch JB, Barsh GS. 2009. Harmonics of circadian gene transcription in mammals. PLoS Genetics 5:e1000442. doi: 10.1371/journal.pgen. 1000442
26. Hughes ME, Hogenesch JB, Kornacker K. 2010. JTK_CYCLE: an efficient nonparametric algorithm for detecting rhythmic components in genome-scale data sets. Journal of Biological Rhythms 25:372-380. doi: 10.1177/ 0748730410379711
27. Hurley JM, Dasgupta A, Emerson JM, Zhou X, Ringelberg CS, Knabe N, Lipzen AM, Lindquist EA, Daum CG, Barry KW, Grigoriev IV, Smith KM, Galagan JE, Bell-Pedersen D, Freitag M, Cheng C, Loros JJ, Dunlap JC.2014. Analysis of clock-regulated genes in neurospora reveals widespread posttranscriptional control of metabolic potential. Proceedings of the National Academy of Sciences of the United States of America 111: 16995-17002. doi: 10.1073/pnas.1418963111
28. Iyer R, Wang TA, Gillette MU. 2014. Circadian gating of neuronal functionality: a basis for iterative metaplasticity1. Frontiers in Systems Neuroscience 8:350. doi: 10.3389/fnsys.2014.00164
29. Ko CH. 2006. Molecular components of the mammalian circadian clock. Human Molecular Genetics 15:R271- R277. doi: 10.1093/hmg/ddl207
30. Koike N, Yoo S-H, Huang H-C, Kumar V, Lee C, Kim T-K, Takahashi JS. 2012. Transcriptional architecture and chromatin landscape of the core circadian clock in mammals. Science 338:349-354. doi: 10.1126/science. 1226339
31. Kong L, Zhang Y, Ye Z-Q, Liu X-Q, Zhao S-Q, Wei L, Gao G. 2007. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Research 35:W345-W349. doi: 10.1093/nar/gkm391
32. Langfelder P, Horvath S. 2008. WGCNA: an r package for weighted correlation network analysis. BMC Bioinformatics 9:559. doi: 10.1186/1471-2105-9-559
33. Leming MT, Rund SSC, Behura SK, Duffield GE, O'Tousa JE. 2014. A database of circadian and diel rhythmic gene expression in the yellow fever mosquito aedes aegypti. BMC Genomics 15:1128. doi: 10.1186/1471-2164- 15-1128
34. Li J, Grant GR, Hogenesch JB, Hughes ME. 2015. Considerations for RNA-seq analysis of circadian rhythms. Methods of Enzymology 551:349-367. doi: 10.1016/bs.mie.2014.10.020
35. Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 15:550. doi: 10.1186/s13059-014-0550-8
36. Maywood ES, O'Neill JS, Chesham JE, Hastings MH. 2007. Minireview: the circadian clockwork of the suprachiasmatic nuclei-analysis of a cellular oscillator that drives endocrine rhythms. Endocrinology 148:5624-5634. doi: 10.1210/en.2007-0660
37. Menet JS, Rodriguez J, Abruzzi KC, Rosbash M. 2012. Nascent-seq reveals novel features of mouse circadian transcriptional regulation. eLife 1:e00011. doi: 10.7554/eLife.00011
38. Merkin J, Russell C, Chen P, Burge CB. 2012. Evolutionary dynamics of gene and isoform regulation in mammalian tissues. Science 338:1593-1599. doi: 10.1126/science.1228186
39. Omori Y, Chaya T, Yoshida S, Irie S, Tsujii T, Furukawa T, Sato M. 2015. Identification of g protein-coupled receptors (gPCRs) in primary cilia and their possible involvement in body weight control. PLOS ONE 10: e0128422. doi: 10.1371/journal.pone.0128422
40. Panda S, Antoch MP, Miller BH, Su AI, Schook AB, Straume M, Schultz PG, Kay SA, Takahashi JS, Hogenesch JB.2002. Coordinated transcription of key pathways in the mouse by the circadian clock. Cell 109:307-320. doi: 10.1016/S0092-8674(02)00722-5
41. Ponjavic J, Ponting CP, Lunter G. 2007. Functionality or transcriptional noise? evidence for selection within long noncoding RNAs. Genome Research 17:556-565. doi: 10.1101/gr.6036807
42. Ramos AD, Diaz A, Nellore A, Delgado RN, Park K-Y, Gonzales-Roybal G, Oldham MC, Song JS, Lim DA. 2013. Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo. Cell Stem Cell 12:616-628. doi: 10.1016/j.stem.2013.03.003
43. Shinohara K, Tominaga K, Isobe Y, Inouye ST. 1993. Photic regulation of peptides located in the ventrolateral subdivision of the suprachiasmatic nucleus of the rat: daily variations of vasoactive intestinal polypeptide, gastrin-releasing peptide, and neuropeptide y. Journal of Neuroscience 13:793-800.
44. Sims D, Ilott NE, Sansom SN, Sudbery IM, Johnson JS, Fawcett KA, Berlanga-Taylor AJ, Luna-Valero S, Ponting CP, Heger A. 2014. CGAT: computational genomics analysis toolkit. Bioinformatics 30:1290-1291. doi: 10. 1093/bioinformatics/btt756
45. Supek F, Bošnjak M, Škunca N, Šmuc T, Gibas C. 2011. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS ONE 6:e21800. doi: 10.1371/journal.pone.0021800
46. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. 2010. Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology 28:511-515. doi: 10.1038/nbt.1621
47. Ueda HR, Matsumoto A, Kawamura M, Iino M, Tanimura T, Hashimoto S. 2002. Genome-wide transcriptional orchestration of circadian rhythms in drosophila. Journal of Biological Chemistry 277:14048-14052. doi: 10. 1074/jbc.C100765200
48. Wang D, Liang X, Chen X, Guo J. 2013. Ribonucleoprotein complexes that control circadian clocks. International Journal of Molecular Sciences 14:9018-9036. doi: 10.3390/ijms14059018
49. Welsh DK, Takahashi JS, Kay SA. 2010. Suprachiasmatic nucleus: cell autonomy and network properties. Annual Review of Physiology 72:551-577. doi: 10.1146/annurev-physiol-021909-135919
50. Wu TD, Nacu S. 2010. Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26:873-881. doi: 10.1093/bioinformatics/btq057
51. Wu TD, Watanabe CK. 2005. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21:1859-1875. doi: 10.1093/bioinformatics/bti310
52. Yokota Shin-ichi, Yamamoto M, Moriya T, Akiyama M, Fukunaga K, Miyamoto E, Shibata S. 2001. Involvement of calcium-calmodulin protein kinase but not mitogen-activated protein kinase in light-induced phase delays and per gene expression in the suprachiasmatic nucleus of the hamster. Journal of Neurochemistry 77:618-627. doi: 10.1046/j.1471-4159.2001.00270.x
53. Zhang K, Huang K, Luo Y, Li S. 2014a. Identification and functional analysis of long non-coding RNAs in mouse cleavage stage embryonic development based on single cell transcriptome data. BMC Genomics 15:845. doi: 10.1186/1471-2164-15-845
54. Zhang R, Lahens NF, Ballance HI, Hughes ME, Hogenesch JB. 2014b. A circadian gene expression atlas in mammals: implications for biology and medicine. Proceedings of the National Academy of Sciences of the United States of America 111:16219-16224. doi: 10.1073/pnas.1408886111