Considerations for RNA-seq analysis of circadian rhythms

Methods in Enzymology

Volumn 551, Issue , 2015, Pages 349-367

  Li, Jiajia ^a   Grant, Gregory R ^b   Hogenesch, John B ^c   Hughes, Michael E ^a  

^a UNIVERSITY OF MISSOURI ST LOUIS   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

^c UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

Circadian rhythms; Clock controlled genes; Computational biology; Gene expression; Genomics; Next generation sequencing; Read depth; RNA sequencing

Indexed keywords

RNA; TRANSCRIPTION FACTOR CLOCK;

ALGORITHM; ANIMAL; ANIMAL TISSUE; ARTICLE; CIRCADIAN RHYTHM; CONTROLLED STUDY; DENSITY; FOLLOW UP; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; GENOME; HIGH THROUGHPUT SEQUENCING; HUMAN; MOUSE; NONHUMAN; PHYSIOLOGY; PRIORITY JOURNAL; RNA SEQUENCE; RNA SPLICING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SIMULATION; VALIDATION PROCESS;

ANIMALS; CIRCADIAN RHYTHM; CLOCK PROTEINS; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENETICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; PHYSIOLOGY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA;

EID: 84964267078     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/bs.mie.2014.10.020     Document Type: Chapter

References (72)

1. R.C. Anafi, Y. Lee, T.K. Sato, A. Venkataraman, C. Ramanathan, and I.H. Kavakli Machine learning helps identify CHRONO as a circadian clock component PLoS Biology 12 4 2014 e1001840 10.1371/journal.pbio.1001840
2. A. Atwood, R. DeConde, S.S. Wang, T.C. Mockler, J.S.M. Sabir, and T. Ideker Cell-autonomous circadian clock of hepatocytes drives rhythms in transcription and polyamine synthesis Proceedings of the National Academy of Sciences of the United States of America 108 45 2011 18560 18565 10.1073/pnas.1115753108
3. J.E. Baggs, T.S. Price, L. DiTacchio, S. Panda, G.A. Fitzgerald, and J.B. Hogenesch Network features of the mammalian circadian clock PLoS Biology 7 3 2009 e52 10.1371/journal.pbio.1000052
4. A. Balsalobre, L. Marcacci, and U. Schibler Multiple signaling pathways elicit circadian gene expression in cultured Rat-1 fibroblasts Current Biology 10 20 2000 1291 1294 10.1016/S0960-9822(00)00758-2
5. K. Bozek, A. Relogio, S.M. Kielbasa, M. Heine, C. Dame, and A. Kramer Regulation of clock-controlled genes in mammals PLoS One 4 3 2009 e4882 10.1371/journal.pone.0004882
6. A. Bugge, D. Feng, L.J. Everett, E.R. Briggs, S.E. Mullican, and F. Wang Rev-erbα and Rev-erbβ coordinately protect the circadian clock and normal metabolic function Genes & Development 26 7 2012 657 667 10.1101/gad.186858.112
7. M.F. Ceriani, J.B. Hogenesch, M. Yanovsky, S. Panda, M. Straume, and S.A. Kay Genome-wide expression analysis in Drosophila reveals genes controlling circadian behavior The Journal of Neuroscience 22 21 2002 9305 9319
8. R. Chen, M. D'Alessandro, and C. Lee miRNAs are required for generating a time delay critical for the circadian oscillator Current Biology 23 20 2013 1959 1968 10.1016/j.cub.2013.08.005
9. A. Claridge-Chang, H. Wijnen, F. Naef, C. Boothroyd, N. Rajewsky, and M.W. Young Circadian regulation of gene expression systems in the Drosophila head Neuron 32 4 2001 657 671 10.1016/S0896-6273(01)00515-3
10. B. Collins, E.A. Kane, D.C. Reeves, M.H. Akabas, and J. Blau Balance of activity between LN(v)s and glutamatergic dorsal clock neurons promotes robust circadian rhythms in Drosophila Neuron 74 4 2012 706 718 10.1016/j.neuron.2012.02.034
11. M.F. Covington, J.N. Maloof, M. Straume, S.A. Kay, and S.L. Harmer Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development Genome Biology 9 8 2008 R130 10.1186/gb-2008-9-8-r130
12. U. de Lichtenberg, L.J. Jensen, A. Fausboll, T.S. Jensen, P. Bork, and S. Brunak Comparison of computational methods for the identification of cell cycle-regulated genes Bioinformatics 21 7 2005 1164 1171 10.1093/bioinformatics/bti093
13. A. Deckard, R.C. Anafi, J.B. Hogenesch, S.B. Haase, and J. Harer Design and analysis of large-scale biological rhythm studies: A comparison of algorithms for detecting periodic signals in biological data Bioinformatics 29 24 2013 3174 3180 10.1093/bioinformatics/btt541
14. A. Dobin, C.A. Davis, F. Schlesinger, J. Drenkow, C. Zaleski, and S. Jha STAR: Ultrafast universal RNA-seq aligner Bioinformatics 29 1 2012 15 21 10.1093/bioinformatics/bts635
15. N.H. Du, A.B. Arpat, M. De Matos, and D. Gatfield MicroRNAs shape circadian hepatic gene expression on a transcriptome-wide scale elife 3 2014 e02510 10.7554/eLife.02510
16. S. Filichkin, and T. Mockler Unproductive alternative splicing and nonsense mRNAs: A widespread phenomenon among plant circadian clock genes Biology Direct 7 1 2012 1 15 10.1186/1745-6150-7-20
17. E.F. Glynn, J. Chen, and A.R. Mushegian Detecting periodic patterns in unevenly spaced gene expression time series using Lomb-Scargle periodograms Bioinformatics 22 3 2006 310 316 10.1093/bioinformatics/bti789
18. G.R. Grant, M.H. Farkas, A.D. Pizarro, N.F. Lahens, J. Schug, and B.P. Brunk Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM) Bioinformatics 27 18 2011 2518 2528 10.1093/bioinformatics/btr427
19. F. Halberg, G. Cornelissen, W. Ulmer, M. Blank, W. Hrushesky, and P. Wood Cancer chronomics III. Chronomics for cancer, aging, melatonin and experimental therapeutics researchers Journal of Experimental Therapeutics & Oncology 6 1 2006 73 84
20. S.N. Hart, T.M. Therneau, Y. Zhang, G.A. Poland, and J.P. Kocher Calculating sample size estimates for RNA sequencing data Journal of Computational Biology 20 12 2013 970 978 10.1089/cmb.2012.0283
21. M.H. Hastings, A.B. Reddy, and E.S. Maywood A clockwork web: Circadian timing in brain and periphery, in health and disease Nature Reviews. Neuroscience 4 8 2003 649 661 10.1038/nrn1177
22. K. Hayer, P. Pizarro, N.L. Lahens, J.B. Hogenesch, and G.R. Grant Benchmark analysis for determining and quantifying full-length mRNA splice forms from RNA-seq data bioRxiv 2014 007088 10.1101/007088
23. P.Y. Hsu, and S.L. Harmer Global profiling of the circadian transcriptome using microarrays Methods in Molecular Biology 1158 2014 45 56 10.1007/978-1-4939-0700-7-3
24. M. Hughes, L. Deharo, S.R. Pulivarthy, J. Gu, K. Hayes, and S. Panda High-resolution time course analysis of gene expression from pituitary Cold Spring Harbor Symposia on Quantitative Biology 72 2007 381 386 10.1101/sqb.2007.72.011
25. M.E. Hughes, L. DiTacchio, K.R. Hayes, C. Vollmers, S. Pulivarthy, and J.E. Baggs Harmonics of circadian gene transcription in mammals PLoS Genetics 5 4 2009 e1000442 10.1371/journal.pgen.1000442
26. M.E. Hughes, G.R. Grant, C. Paquin, J. Qian, and M.N. Nitabach Deep sequencing the circadian and diurnal transcriptome of Drosophila brain Genome Research 22 7 2012 1266 1281 10.1101/gr.128876.111
27. M.E. Hughes, J.B. Hogenesch, and K. Kornacker JTK-CYCLE: An efficient nonparametric algorithm for detecting rhythmic components in genome-scale data sets Journal of Biological Rhythms 25 5 2010 372 380 10.1177/0748730410379711
28. M.E. Hughes, H.K. Hong, J.L. Chong, A.A. Indacochea, S.S. Lee, and M. Han Brain-specific rescue of Clock reveals system-driven transcriptional rhythms in peripheral tissue PLoS Genetics 8 7 2012 e1002835 10.1371/journal.pgen.1002835
29. D. Jeyaraj, S.M. Haldar, X. Wan, M.D. McCauley, J.A. Ripperger, and K. Hu Circadian rhythms govern cardiac repolarization and arrhythmogenesis Nature 483 7387 2012 96 99 10.1038/nature10852
30. Y.L. Jung, L.J. Luquette, J.W. Ho, F. Ferrari, M. Tolstorukov, and A. Minoda Impact of sequencing depth in ChIP-seq experiments Nucleic Acids Research 42 9 2014 e74 10.1093/nar/gku178
31. S. Kadener, J.S. Menet, K. Sugino, M.D. Horwich, U. Weissbein, and P. Nawathean A role for microRNAs in the Drosophila circadian clock Genes & Development 23 18 2009 2179 2191 10.1101/gad.1819509
32. K.P. Keegan, S. Pradhan, J.P. Wang, and R. Allada Meta-analysis of Drosophila circadian microarray studies identifies a novel set of rhythmically expressed genes PLoS Computational Biology 3 11 2007 e208 10.1371/journal.pcbi.0030208
33. E.B. Klerman Clinical aspects of human circadian rhythms Journal of Biological Rhythms 20 4 2005 375 386 10.1177/0748730405278353
34. C.H. Ko, and J.S. Takahashi Molecular components of the mammalian circadian clock Human Molecular Genetics 15 Spec No 2 2006 R271 R277 10.1093/hmg/ddl207
35. N. Koike, S.-H. Yoo, H.-C. Huang, V. Kumar, C. Lee, and T.-K. Kim Transcriptional architecture and chromatin landscape of the core circadian clock in mammals Science 338 6105 2012 349 354 10.1126/science.1226339
36. B. Kornmann, O. Schaad, H. Bujard, J.S. Takahashi, and U. Schibler System-driven and oscillator-dependent circadian transcription in mice with a conditionally active liver clock PLoS Biology 5 2 2007 e34 10.1371/journal.pbio.0050034
37. E. Kula-Eversole, E. Nagoshi, Y. Shang, J. Rodriguez, R. Allada, and M. Rosbash Surprising gene expression patterns within and between PDF-containing circadian neurons in Drosophila Proceedings of the National Academy of Sciences of the United States of America 107 30 2010 13497 13502 10.1073/pnas.1002081107
38. B. Langmead, C. Trapnell, M. Pop, and S.L. Salzberg Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biology 10 3 2009 R25 10.1186/gb-2009-10-3-r25
39. F. Levi, and U. Schibler Circadian rhythms: Mechanisms and therapeutic implications Annual Review of Pharmacology and Toxicology 47 2007 593 628 10.1146/annurev.pharmtox.47.120505.105208
40. Y. Liu, J.F. Ferguson, C. Xue, I.M. Silverman, B. Gregory, and M.P. Reilly Evaluating the impact of sequencing depth on transcriptome profiling in human adipose PLoS One 8 6 2013 e66883 10.1371/journal.pone.0066883
41. D. Macarthur Methods: Face up to false positives Nature 487 7408 2012 427 428 10.1038/487427a
42. N.J. McGlincy, A. Valomon, J.E. Chesham, E.S. Maywood, M.H. Hastings, and J. Ule Regulation of alternative splicing by the circadian clock and food related cues Genome Biology 13 6 2012 R54 10.1186/gb-2012-13-6-r54
43. A.C. Meireles-Filho, A.F. Bardet, J.O. Yanez-Cuna, G. Stampfel, and A. Stark cis-Regulatory requirements for tissue-specific programs of the circadian clock Current Biology 24 1 2014 1 10 10.1016/j.cub.2013.11.017
44. J.S. Menet, S. Pescatore, and M. Rosbash CLOCK: BMAL1 is a pioneer-like transcription factor Genes & Development 28 1 2014 8 13 10.1101/gad.228536.113
45. J.S. Menet, J. Rodriguez, K.C. Abruzzi, and M. Rosbash Nascent-Seq reveals novel features of mouse circadian transcriptional regulation eLife 1 2012 e00011 10.7554/eLife.00011
46. G.J. Menger, G.C. Allen, N. Neuendorff, S.-S. Nahm, T.L. Thomas, and V.M. Cassone Circadian profiling of the transcriptome in NIH/3T3 fibroblasts: Comparison with rhythmic gene expression in SCN2.2 cells and the rat SCN Physiological Genomics 29 2007 280 289
47. M. Miyazaki, E. Schroder, S.E. Edelmann, M.E. Hughes, K. Kornacker, and C.W. Balke Age-associated disruption of molecular clock expression in skeletal muscle of the spontaneously hypertensive rat PLoS One 6 11 2011 e27168 10.1371/journal.pone.0027168
48. T.C. Mockler, T.P. Michael, H.D. Priest, R. Shen, C.M. Sullivan, and S.A. Givan The DIURNAL project: DIURNAL and circadian expression profiling, model-based pattern matching, and promoter analysis Cold Spring Harbor Symposia on Quantitative Biology 72 2007 353 363 10.1101/sqb.2007.72.006
49. E. Nagoshi, C. Saini, C. Bauer, T. Laroche, F. Naef, and U. Schibler Circadian gene expression in individual fibroblasts: Cell-autonomous and self-sustained oscillators pass time to daughter cells Cell 119 5 2004 693 705 10.1016/j.cell.2004.11.015
50. M.N. Nitabach, and P.H. Taghert Organization of the Drosophila circadian control circuit Current Biology 18 2 2008 R84 R93 10.1016/j.cub.2007.11.061
51. S. Panda, M.P. Antoch, B.H. Miller, A.I. Su, A.B. Schook, and M. Straume Coordinated transcription of key pathways in the mouse by the circadian clock Cell 109 3 2002 307 320
52. A. Pizarro, K. Hayer, N.F. Lahens, and J.B. Hogenesch CircaDB: A database of mammalian circadian gene expression profiles Nucleic Acids Research 41 Database issue 2013 D1009 D1013 10.1093/nar/gks1161
53. G. Rey, F. Cesbron, J. Rougemont, H. Reinke, M. Brunner, and F. Naef Genome-wide and phase-specific DNA-binding rhythms of BMAL1 control circadian output functions in mouse liver PLoS Biology 9 2 2011 e1000595 10.1371/journal.pbio.1000595
54. J. Rodriguez, C.-H.A. Tang, Y.L. Khodor, S. Vodala, J.S. Menet, and M. Rosbash Nascent-Seq analysis of Drosophila cycling gene expression Proceedings of the National Academy of Sciences 110 4 2013 275 284 10.1073/pnas.1219969110
55. S.S.C. Rund, T.Y. Hou, S.M. Ward, F.H. Collins, and G.E. Duffield Genome-wide profiling of diel and circadian gene expression in the malaria vector Anopheles gambiae Proceedings of the National Academy of Sciences 108 32 2011 421 430 10.1073/pnas.1100584108
56. E.A. Schroder, M. Lefta, X. Zhang, D.C. Bartos, H.Z. Feng, and Y. Zhao The cardiomyocyte molecular clock, regulation of Scn5a, and arrhythmia susceptibility American Journal of Physiology. Cell Physiology 304 10 2013 C954 C965 10.1152/ajpcell.00383.2012
57. E. Slat, G.M. Freeman Jr., and E. Herzog The clock in the brain: Neurons, glia, and networks in daily rhythms A. Kramer, M. Merrow, Circadian clocks Vol. 217 2013 Springer Berlin Heidelberg 105 123
58. K.F. Storch, O. Lipan, I. Leykin, N. Viswanathan, F.C. Davis, and W.H. Wong Extensive and divergent circadian gene expression in liver and heart Nature 417 6884 2002 78 83 10.1038/nature744
59. M. Stratmann, and U. Schibler Properties, entrainment, and physiological functions of mammalian peripheral oscillators Journal of Biological Rhythms 21 6 2006 494 506 10.1177/0748730406293889
60. M. Straume DNA microarray time series analysis: Automated statistical assessment of circadian rhythms in gene expression patterning Methods in Enzymology 383 2004 149 166 10.1016/s0076-6879(04)83007-6
61. C. Trapnell, L. Pachter, and S.L. Salzberg TopHat: Discovering splice junctions with RNA-Seq Bioinformatics 25 9 2009 1105 1111 10.1093/bioinformatics/btp120
62. C. Trapnell, B.A. Williams, G. Pertea, A. Mortazavi, G. Kwan, and M.J. van Baren Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Nature Biotechnology 28 5 2010 511 515 10.1038/nbt.1621
63. C. Vollmers, S. Gill, L. DiTacchio, S.R. Pulivarthy, H.D. Le, and S. Panda Time of feeding and the intrinsic circadian clock drive rhythms in hepatic gene expression Proceedings of the National Academy of Sciences of the United States of America 106 50 2009 21453 21458 10.1073/pnas.0909591106
64. J.R. Walker, and J.B. Hogenesch RNA profiling in circadian biology M.W. Young, Methods in enzymology Vol. 393 2005 Elsevier Academic Press San Diego 366 376
65. S. Wichert, K. Fokianos, and K. Strimmer Identifying periodically expressed transcripts in microarray time series data Bioinformatics 20 1 2004 5 20
66. H. Wijnen, F. Naef, and M.W. Young Molecular and statistical tools for circadian transcript profiling M.W. Young, Methods in enzymology Vol. 393 2005 Elsevier Academic Press San Diego 341 365
67. T.D. Wu, and S. Nacu Fast and SNP-tolerant detection of complex variants and splicing in short reads Bioinformatics 26 7 2010 873 881 10.1093/bioinformatics/btq057
68. K. Xu, J.R. DiAngelo, M.E. Hughes, J.B. Hogenesch, and A. Sehgal The circadian clock interacts with metabolic physiology to influence reproductive fitness Cell Metabolism 13 6 2011 639 654 10.1016/j.cmet.2011.05.001
69. R. Yang, and Z. Su Analyzing circadian expression data by harmonic regression based on autoregressive spectral estimation Bioinformatics 26 12 2010 i168 i174 10.1093/bioinformatics/btq189
70. S.H. Yoo, S. Yamazaki, P.L. Lowrey, K. Shimomura, C.H. Ko, and E.D. Buhr PERIOD2::LUCIFERASE real-time reporting of circadian dynamics reveals persistent circadian oscillations in mouse peripheral tissues Proceedings of the National Academy of Sciences of the United States of America 101 15 2004 5339 5346 10.1073/pnas.0308709101
71. E.E. Zhang, A.C. Liu, T. Hirota, L.J. Miraglia, G. Welch, and P.Y. Pongsawakul A genome-wide RNAi screen for modifiers of the circadian clock in human cells Cell 139 1 2009 199 210 10.1016/j.cell.2009.08.031
72. Zhang, R., Lahens, N. F., Ballance, H. I., Hughes, M. E., & Hogenesch, J. B. (2014). 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, http://dx.doi.org/10.1073/pnas.1408886111.