Genome-wide identification of housekeeping genes in maize

Plant Molecular Biology

Volumn 86, Issue 4-5, 2014, Pages 543-554

  Lin, Feng ^a   Jiang, Lu ^a   Liu, Yuhe ^b   Lv, Yuanda ^a   Dai, Huixue ^c   Zhao, Han ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^c Vegetable Science Institute   (China)

Author keywords

Housekeeping gene; Maize; Nitrogen; qPCR; Reference gene

Indexed keywords

ZEA MAYS;

CLASSIFICATION; DNA MICROARRAY; ESSENTIAL GENE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE ONTOLOGY; GENETICS; MAIZE; PLANT GENE; PLANT GENOME; PROCEDURES; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; SPECIES DIFFERENCE;

GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENE ONTOLOGY; GENES, ESSENTIAL; GENES, PLANT; GENOME, PLANT; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, RNA; SPECIES SPECIFICITY; ZEA MAYS;

EID: 84919919782     PISSN: 01674412     EISSN: 15735028     Source Type: Journal    
DOI: 10.1007/s11103-014-0246-1     Document Type: Article

References (59)

1. Andersen CL, Jensen JK, Ørntoft TF (2004) Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res 64:5245–5250
2. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT et al (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25–29
3. Barber RD, Harmer DW, Coleman RA, Clark BJ (2005) GAPDH as a housekeeping gene: analysis of GAPDH mRNA expression in a panel of 72 human tissues. Physiol Genomics 21:389–395
4. Bremnera JM (1960) Determination of nitrogen in soil by the Kjeldahl method. J Agric Sci 55:11–33
5. Brunner AM, Yakovlev IA, Strauss SH (2004) Validating internal controls for quantitative plant gene expression studies. BMC Plant Biol 4:14
6. Butte AJ, Dzau VJ, Glueck SB (2001) Further defining housekeeping, or “maintenance”, genes focus on “A compendium of gene expression in normal human tissues”. Physiol Genomics 7:95–96
7. Chen K, Fessehaie A, Arora R (2012) Selection of reference genes for normalizing gene expression during seed priming and germination using qPCR in Zea mays and Spinacia oleracea. Plant Mol Biol Rep 30:478–487
8. Coker JS, Davies E (2003) Selection of candidate housekeeping controls in tomato plants using EST data. Biotechniques 35:740–748
9. Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676
10. Cox MP, Peterson DA, Biggs PJ (2010) SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics 11:485
11. Czechowski T, Stitt M, Altmann T, Udvardi MK, Scheible WR (2005) Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Plant Physiol 139:5–17
12. Danilevskaya ON, Meng X, Hou Z, Ananiev EV, Simmons CR (2008) A genomic and expression compendium of the expanded PEBP gene family from maize. Plant Physiol 146:250–264
13. Davidson RM, Hansey CN, Gowda M, Childs KL, Lin H, Vaillancourt B, Sekhon RS, de Leon N, Kaeppler SM, Jiang N, Buell CR (2011) Utility of RNA sequencing for analysis of maize reproductive transcriptomes. Plant Genome 4:191–203
14. Ding D, Zhang L, Wang H, Liu Z, Zhang Z, Zheng Y (2009) Differential expression of miRNAs in response to salt stress in maize roots. Ann Bot 103:29–38
15. Eisenberg E, Levanon EY (2003) Human housekeeping genes are compact. Trends Genet 19:362–365
16. Eisenberg E, Levanon EY (2013) Human housekeeping genes, revisited. Trends Genet 29:569–574
17. Galli V, Messias RS, Anjos e Silva SD, Rombaldi CV (2013) Selection of reliable reference genes for quantitative real-time polymerase chain reaction studies in maize grains. Plant Cell Rep 32:1869–1877
18. Goidin D, Mamessier A, Staquet MJ, Schmitt D, Berthier-Vergnes O (2001) Ribosomal 18S RNA prevails over glyceraldehyde-3-phosphate dehydrogenase and ß-Actin genes as internal standard for quantitative comparison of mRNA levels in invasive and noninvasive human melanoma cell subpopulations. Anal Biochem 295:17–21
19. Gutierrez L, Mauriat M, Guénin S, Pelloux J, Lefebvre JF, Louvet R, Rusterucci C, Moritz T, Guerineau F, Bellini C, Wuytswinkel OV (2008) The lack of a systematic validation of reference genes: a serious pitfall undervalued in reverse transcription polymerase chain reaction (RT-PCR) analysis in plants. Plant Biotechnol J 6:609–618
20. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol 28:503–510
21. Hong SY, Seo PJ, Yang MS, Xiang F, Park CM (2008) Exploring valid reference genes for gene expression studies in Brachypodium distachyon by real-time PCR. BMC Plant Biol 8:112
22. Infante C, Matsuoka MP, Asensio E, Cañavate JP, Reith M, Manchado M (2008) Selection of housekeeping genes for gene expression studies in larvae from flatfish using real-time PCR. BMC Mol Biol 9:28
23. Jain M, Nijhawan A, Tyagi AK, Khurana JP (2006) Validation of housekeeping genes as internal control for studying gene expression in rice by quantitative real-time PCR. Biochem Biophys Res Commun 345:646–651
24. Kim BR, Nam HY, Kim SU, Kim SI, Chang YJ (2003) Normalization of reverse transcription quantitative-PCR with housekeeping genes in rice. Biotechnol Lett 25:1869–1872
25. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25
26. Lee PD, Sladek R, Greenwood CMT, Hudson TJ (2002) Control genes and variability: absence of ubiquitous reference transcripts in diverse mammalian expression studies. Genome Res 12:292–297
27. Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18:1851–1858
28. Lister R, O’Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523–536
29. Liu S, Cai P, Hou N, Piao X, Wang H, Hung T, Chen Q (2012) Genome-wide identification and characterization of a panel of house-keeping genes in Schistosoma japonicum. Mol Biochem Parasit 182:75–82
30. −ΔΔCt method. Methods 25:402–408
31. Lunter G, Goodson M (2010) Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res 21:936–939
32. Makarevitch I, Phillips RL, Springer NM (2008) Profiling expression changes caused by a segmental aneuploid in maize. BMC Genom 9:7
33. Manoli A, Sturaroa A, Trevisana S, Quaggiotti S, Nonis A (2012) Evaluation of candidate reference genes for qPCR in maize. J Plant Physiol 169:807–815
34. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18:1509–1517
35. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat Methods 5:621–628
36. Murphy D (2002) Gene expression studies using microarrays: principles, problems, and prospects. Adv Physiol Educ 26:256–270
37. Murphy SP, Simmons CR, Bass HW (2010) Structure and expression of the maize (Zea mays L) SUN-domain protein gene family: evidence for the existence of two divergent classes of SUN proteins in plants. BMC Plant Biol 10:269
38. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344–1349
39. Nebreda AR (2006) CDK activation by non-cyclin proteins. Curr Opin Cell Biol 18:192–198
40. Paolacci AR, Tanzarella OA, Porceddu E, Ciaffi M (2009) Identification and validation of reference genes for quantitative RT-PCR normalization in wheat. BMC Mol Biol 10:11
41. Pfaffl MW, Tichopad A, Prgomet C, Neuvians TP (2004) Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper–Excel-based tool using pair-wise correlations. Biotechnol Lett 26:509–515
42. Ramsköld D, Wang ET, Burge CB, Sandberg R (2009) An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput Biol 5:e1000598
43. Remans T, Smeets K, Opdenakker K, Mathijsen D, Vangronsveld J, Cuypers A (2008) Normalization of real-time RT-PCR gene expression measurements in Arabidopsis thaliana exposed to increased metal concentrations. Planta 227:1343–1349
44. Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ et al (2010) De novo assembly and analysis of RNA-seq data. Nat Methods 7:909–912
45. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115
46. Scholtz JJ, Visser B (2013) Reference gene selection for qPCR gene expression analysis of rust-infected wheat. Physiol Mol Plant P 81:22–25
47. Sekhon RS, Lin H, Childs KL, Hansey CN, Buell CR, de Leon N, Kaeppler SM (2011) Genome-wide atlas of transcription during maize development. Plant J 66:553–563
48. Selvey S, Thompson EW, Matthaei K, Lea RA, Irving MG, Griffiths LR (2001) β-Actin—an unsuitable internal control for RT-PCR. Mol Cell Probes 15:307–311
49. Teste MA, Duquenne M, François JM, Parrou JL (2009) Validation of reference genes for quantitative expression analysis by real-time RT-PCR in Saccharomyces cerevisiae. BMC Mol Biol 10:99
50. Thellin O, Zorzi W, Lakaye B, Borman BD, Coumans B, Hennen G, Grisar T, Igout A, Heinen E (1999) Housekeeping genes as internal standards: use and limits. J Biotechnol 75:291–295
51. 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. Nat Biotechnol 28:511–515
52. Vandesompele J, Preter KD, Pattyn F, Poppe B, Roy NV, Raepe AD, Speleman F (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3:1–11
53. Velculescu VE, Madden SL, Zhang L, Lash AE, Yu J, Rago C, Lal A, Wang CJ, Beaudry GA, Ciriello KM et al (1999) Analysis of human transcriptomes. Nat Genet 23:387–388
54. Wang Z, Gerstein M, Snyder M (2009) RNA-seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63
55. Wang L, Wang Y, Zhou P (2013) Validation of reference genes for quantitative real-time PCR during Chinese wolfberry fruit development. Plant Physiol Biochem 70:304–310
56. Warrington JA, Nair A, Mahadevappa M, Tsyganskaya M (2000) Comparison of human adult and fetal expression and identification of 535 housekeeping/maintenance genes. Physiol Genomics 2:143–147
57. Yang XS, Wu J, Ziegler TE, Yang X, Zayed A, Rajani MS, Zhou D, Basra AS, Schachtman DP, Peng M et al (2011) Gene expression biomarkers provide sensitive indicators of in planta nitrogen status in maize. Plant Physiol 157:1841–1852
58. Zhong H, Simons JW (1999) Direct comparison of GAPDH, β-Actin, cyclophilin, and 28S rRNA as internal standards for quantifying RNA levels under hypoxia. Biochem Biophys Res Commun 259:523–526
59. Zhu J, He F, Song S, Wang J, Yu J (2008) How many human genes can be defined as housekeeping with current expression data? BMC Genom 9:172