Critical Evaluation of Imprinted Gene Expression by RNA–Seq: A New Perspective
In contrast to existing estimates of approximately 200 murine imprinted genes, recent work based on transcriptome sequencing uncovered parent-of-origin allelic effects at more than 1,300 loci in the developing brain and two adult brain regions, including hundreds present in only males or females. Our independent replication of the embryonic brain stage, where the majority of novel imprinted genes were discovered and the majority of previously known imprinted genes confirmed, resulted in only 12.9% concordance among the novel imprinted loci. Further analysis and pyrosequencing-based validation revealed that the vast majority of the novel reported imprinted loci are false-positives explained by technical and biological variation of the experimental approach. We show that allele-specific expression (ASE) measured with RNA–Seq is not accurately modeled with statistical methods that assume random independent sampling and that systematic error must be accounted for to enable accurate identification of imprinted expression. Application of a robust approach that accounts for these effects revealed 50 candidate genes where allelic bias was predicted to be parent-of-origin–dependent. However, 11 independent validation attempts through a range of allelic expression biases confirmed only 6 of these novel cases. The results emphasize the importance of independent validation and suggest that the number of imprinted genes is much closer to the initial estimates.
Vyšlo v časopise:
Critical Evaluation of Imprinted Gene Expression by RNA–Seq: A New Perspective. PLoS Genet 8(3): e32767. doi:10.1371/journal.pgen.1002600
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1002600
Souhrn
In contrast to existing estimates of approximately 200 murine imprinted genes, recent work based on transcriptome sequencing uncovered parent-of-origin allelic effects at more than 1,300 loci in the developing brain and two adult brain regions, including hundreds present in only males or females. Our independent replication of the embryonic brain stage, where the majority of novel imprinted genes were discovered and the majority of previously known imprinted genes confirmed, resulted in only 12.9% concordance among the novel imprinted loci. Further analysis and pyrosequencing-based validation revealed that the vast majority of the novel reported imprinted loci are false-positives explained by technical and biological variation of the experimental approach. We show that allele-specific expression (ASE) measured with RNA–Seq is not accurately modeled with statistical methods that assume random independent sampling and that systematic error must be accounted for to enable accurate identification of imprinted expression. Application of a robust approach that accounts for these effects revealed 50 candidate genes where allelic bias was predicted to be parent-of-origin–dependent. However, 11 independent validation attempts through a range of allelic expression biases confirmed only 6 of these novel cases. The results emphasize the importance of independent validation and suggest that the number of imprinted genes is much closer to the initial estimates.
Zdroje
1. SearleAGBeecheyCV 1978 Complementation studies with mouse translocations. Cytogenet Cell Genet 20 282 303
2. BeecheyCVaCB.M. 1993 Mouse' Genome 102
3. SuraniMABartonSCNorrisML 1984 Development of reconstituted mouse eggs suggests imprinting of the genome during gametogenesis. Nature 308 548 550
4. BarlowDPStogerRHerrmannBGSaitoKSchweiferN 1991 The mouse insulin-like growth factor type-2 receptor is imprinted and closely linked to the Tme locus. Nature 349 84 87
5. DeChiaraTMRobertsonEJEfstratiadisA 1991 Parental imprinting of the mouse insulin-like growth factor II gene. Cell 64 849 859
6. BartolomeiMSZemelSTilghmanSM 1991 Parental imprinting of the mouse H19 gene. Nature 351 153 155
7. Ferguson-SmithACCattanachBMBartonSCBeecheyCVSuraniMA 1991 Embryological and molecular investigations of parental imprinting on mouse chromosome 7. Nature 351 667 670
8. BarlowDP 1995 Gametic imprinting in mammals. Science 270 1610 1613
9. MorisonIMRamsayJPSpencerHG 2005 A census of mammalian imprinting. Trends Genet 21 457 465
10. RenfreeMBHoreTAShawGGravesJAPaskAJ 2009 Evolution of genomic imprinting: insights from marsupials and monotremes. Annu Rev Genomics Hum Genet 10 241 262
11. CowleyMOakeyRJ 2010 Retrotransposition and genomic imprinting. Brief Funct Genomics 9 340 346
12. BarlowDP 1993 Methylation and imprinting: from host defense to gene regulation? Science 260 309 310
13. SchulzRWoodfineKMenheniottTRBourc'hisDBestorT 2008 WAMIDEX: a web atlas of murine genomic imprinting and differential expression. Epigenetics 3 89 96
14. BabakTDevealeBArmourCRaymondCClearyMA 2008 Global survey of genomic imprinting by transcriptome sequencing. Curr Biol 18 1735 1741
15. WangXSunQMcGrathSDMardisERSolowayPD 2008 Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain. PLoS ONE 3 e3839 doi:10.1371/journal.pone.0003839
16. GreggCZhangJButlerJEHaigDDulacC 2010 Sex-specific parent-of-origin allelic expression in the mouse brain. Science 329 682 685
17. GreggCZhangJWeissbourdBLuoSSchrothGP 2010 High-resolution analysis of parent-of-origin allelic expression in the mouse brain. Science 329 643 648
18. MenheniottTRWoodfineKSchulzRWoodAJMonkD 2008 Genomic imprinting of Dopa decarboxylase in heart and reciprocal allelic expression with neighboring Grb10. Mol Cell Biol 28 386 396
19. DingFPrintsYDharMSJohnsonDKGarnacho-MonteroC 2005 Lack of Pwcr1/MBII-85 snoRNA is critical for neonatal lethality in Prader-Willi syndrome mouse models. Mamm Genome 16 424 431
20. WoodAJBourc'hisDBestorTHOakeyRJ 2007 Allele-specific demethylation at an imprinted mammalian promoter. Nucleic Acids Res 35 7031 7039
21. SchulzRMenheniottTRWoodfineKWoodAJChoiJD 2006 Chromosome-wide identification of novel imprinted genes using microarrays and uniparental disomies. Nucleic Acids Res 34 e88
22. Parker-KatiraeeLCarsonARYamadaTArnaudPFeilR 2007 Identification of the imprinted KLF14 transcription factor undergoing human-specific accelerated evolution. PLoS Genet 3 e65 doi:10.1371/journal.pgen.0030065
23. MonkDWagschalAArnaudPMullerPSParker-KatiraeeL 2008 Comparative analysis of human chromosome 7q21 and mouse proximal chromosome 6 reveals a placental-specific imprinted gene, TFPI2/Tfpi2, which requires EHMT2 and EED for allelic-silencing. Genome Res 18 1270 1281
24. EdgarRDomrachevMLashAE 2002 Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30 207 210
25. MituyamaTYamadaKHattoriEOkidaHOnoY 2009 The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs. Nucleic Acids Res 37 D89 92
26. FrazerKAEskinEKangHMBogueMAHindsDA 2007 A sequence-based variation map of 8.27 million SNPs in inbred mouse strains. Nature 448 1050 1053
27. KeaneTMGoodstadtLDanecekPWhiteMAWongK 2011 Mouse genomic variation and its effect on phenotypes and gene regulation. Nature 477 289 294
28. FujitaPARheadBZweigASHinrichsASKarolchikD 2011 The UCSC Genome Browser database: update 2011. Nucleic Acids Res 39 D876 882
29. NothnagelMWolfAHerrmannASzafranskiKVaterI 2011 Statistical inference of allelic imbalance from transcriptome data. Hum Mutat 32 98 106
30. RobinsonMDOshlackA 2010 A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 11 R25
31. DegnerJFMarioniJCPaiAAPickrellJKNkadoriE 2009 Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics 25 3207 3212
32. KozarewaINingZQuailMASandersMJBerrimanM 2009 Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods 6 291 295
33. MainBJBickelRDMcIntyreLMGrazeRMCalabresePP 2009 Allele-specific expression assays using Solexa. BMC Genomics 10 422
34. MamanovaLAndrewsRMJamesKDSheridanEMEllisPD 2010 FRT-seq: amplification-free, strand-specific transcriptome sequencing. Nat Methods 7 130 132
35. FontanillasPLandryCRWittkoppPJRussCGruberJD 2010 Key considerations for measuring allelic expression on a genomic scale using high-throughput sequencing. Mol Ecol 19 Suppl 1 212 227
36. HeapGAYangJHDownesKHealyBCHuntKA 2010 Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing. Hum Mol Genet 19 122 134
37. TurroESuSYGoncalvesACoinLJRichardsonS 2011 Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads. Genome Biol 12 R13
38. BabakTGarrett-EngelePArmourCDRaymondCKKellerMP 2010 Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation. BMC Genomics 11 473
39. NgSBTurnerEHRobertsonPDFlygareSDBighamAW 2009 Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461 272 276
40. MatsudaDHosodaNKimYKMaquatLE 2007 Failsafe nonsense-mediated mRNA decay does not detectably target eIF4E-bound mRNA. Nat Struct Mol Biol 14 974 979
41. YamashitaRSathiraNPKanaiATanimotoKArauchiT 2011 Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis. Genome Res 21 775 789
42. WilhelmBTMargueratSWattSSchubertFWoodV 2008 Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453 1239 1243
43. RoyoHCavailleJ 2008 Non-coding RNAs in imprinted gene clusters. Biol Cell 100 149 166
44. KimSJShonBHKangJHHahmKSYooOJ 1997 Cloning of novel trinucleotide-repeat (CAG) containing genes in mouse brain. Biochem Biophys Res Commun 240 239 243
45. Becker-HeckAZohnIEOkabeNPollockALenhartKB 2011 The coiled-coil domain containing protein CCDC40 is essential for motile cilia function and left-right axis formation. Nat Genet 43 79 84
46. MotoyamaNWangFRothKASawaHNakayamaK 1995 Massive cell death of immature hematopoietic cells and neurons in Bcl-x-deficient mice. Science 267 1506 1510
47. NukinaNIharaY 1986 One of the antigenic determinants of paired helical filaments is related to tau protein. J Biochem 99 1541 1544
48. MitchellKJPinsonKIKellyOGBrennanJZupicichJ 2001 Functional analysis of secreted and transmembrane proteins critical to mouse development. Nat Genet 28 241 249
49. Thierry-MiegDThierry-MiegJ 2006 AceView: a comprehensive cDNA-supported gene and transcripts annotation. Genome Biol 7 Suppl 1 S12 11 14
50. KinTYamadaKTeraiGOkidaHYoshinariY 2007 fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences. Nucleic Acids Res 35 D145 148
51. ParkhomchukDBorodinaTAmstislavskiyVBanaruMHallenL 2009 Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res 37 e123
52. RoyoJLHidalgoMRuizA 2007 Pyrosequencing protocol using a universal biotinylated primer for mutation detection and SNP genotyping. Nat Protoc 2 1734 1739
53. WangHElbeinSC 2007 Detection of allelic imbalance in gene expression using pyrosequencing. Methods Mol Biol 373 157 176
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2012 Číslo 3
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