Biased allelic expression in human primary fibroblast single cells

American Journal of Human Genetics

Volumn 96, Issue 1, 2015, Pages 70-80

  Borel, Christelle ^a   Ferreira, Pedro G ^a,b,c   Santoni, Federico ^a   Delaneau, Olivier ^a,b,c   Fort, Alexandre ^d   Popadin, Konstantin Y ^a   Garieri, Marco ^a   Falconnet, Emilie ^a   Ribaux, Pascale ^a   Guipponi, Michel ^a,e   Padioleau, Ismael ^a   Carninci, Piero ^d   Dermitzakis, Emmanouil T ^a,b,c,f,g   Antonarakis, Stylianos E ^a,b,e  

^a UNIVERSITY OF GENEVA   (Switzerland)

^b Institute of Genetics and Genomics of Geneva   (Switzerland)

^c SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^d RIKEN   (Japan)

^e GENEVA UNIVERSITY HOSPITALS   (Switzerland)

^f KING ABDULAZIZ UNIVERSITY   (Saudi Arabia)

^g Academy of Athens Biomedical Research Foundation   (Greece)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; COMPLEMENTARY DNA;

ALLELE; ARTICLE; CONTROLLED STUDY; FEMALE; FETUS; FIBROBLAST; GENE EXPRESSION; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; HAPLOTYPE; HUMAN; HUMAN CELL; HUMAN CELL CULTURE; NEWBORN; PRIORITY JOURNAL; RNA SEQUENCE; CYTOLOGY; GENETICS; HETEROZYGOTE; HUMAN GENOME; METABOLISM; PHENOTYPE; SEQUENCE ANALYSIS; SINGLE CELL ANALYSIS;

MAMMALIA;

ALLELES; DNA, COMPLEMENTARY; FIBROBLASTS; GENOME, HUMAN; HAPLOTYPES; HETEROZYGOTE; HUMANS; PHENOTYPE; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; SINGLE-CELL ANALYSIS;

EID: 84920733410     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2014.12.001     Document Type: Article

References (49)

1. A.C. Ferguson-Smith Genomic imprinting: the emergence of an epigenetic paradigm Nat. Rev. Genet. 12 2011 565 575
2. W. Reik, and J. Walter Genomic imprinting: parental influence on the genome Nat. Rev. Genet. 2 2001 21 32
3. S. Augui, E.P. Nora, and E. Heard Regulation of X-chromosome inactivation by the X-inactivation centre Nat. Rev. Genet. 12 2011 429 442
4. J.C. Chow, Z. Yen, S.M. Ziesche, and C.J. Brown Silencing of the mammalian X chromosome Annu. Rev. Genomics Hum. Genet. 6 2005 69 92
5. A. Chess, I. Simon, H. Cedar, and R. Axel Allelic inactivation regulates olfactory receptor gene expression Cell 78 1994 823 834
6. I. Rodriguez, P. Feinstein, and P. Mombaerts Variable patterns of axonal projections of sensory neurons in the mouse vomeronasal system Cell 97 1999 199 208
7. I.J. Rimm, D.B. Bloch, and J.G. Seidman Allelic exclusion and lymphocyte development. Lessons from transgenic mice Mol. Biol. Med. 6 1989 355 364
8. A.A. Gimelbrant, A.W. Ensminger, P. Qi, J. Zucker, and A. Chess Monoallelic expression and asynchronous replication of p120 catenin in mouse and human cells J. Biol. Chem. 280 2005 1354 1359
9. A. Gimelbrant, J.N. Hutchinson, B.R. Thompson, and A. Chess Widespread monoallelic expression on human autosomes Science 318 2007 1136 1140
10. J. Wang, Z. Valo, D. Smith, and J. Singer-Sam Monoallelic expression of multiple genes in the CNS PLoS ONE 2 2007 e1293
11. M. Wijgerde, F. Grosveld, and P. Fraser Transcription complex stability and chromatin dynamics in vivo Nature 377 1995 209 213
12. J.M. Levsky, S.M. Shenoy, R.C. Pezo, and R.H. Singer Single-cell gene expression profiling Science 297 2002 836 840
13. C.S. Osborne, L. Chakalova, K.E. Brown, D. Carter, A. Horton, E. Debrand, B. Goyenechea, J.A. Mitchell, S. Lopes, W. Reik, and P. Fraser Active genes dynamically colocalize to shared sites of ongoing transcription Nat. Genet. 36 2004 1065 1071
14. C.S. Osborne, L. Chakalova, J.A. Mitchell, A. Horton, A.L. Wood, D.J. Bolland, A.E. Corcoran, and P. Fraser Myc dynamically and preferentially relocates to a transcription factory occupied by Igh PLoS Biol. 5 2007 e192
15. P. Fraser Transcriptional control thrown for a loop Curr. Opin. Genet. Dev. 16 2006 490 495
16. L. Chakalova, and P. Fraser Organization of transcription Cold Spring Harb. Perspect. Biol. 2 2010 a000729
17. J.M. Levsky, S.M. Shenoy, J.R. Chubb, C.B. Hall, P. Capodieci, and R.H. Singer The spatial order of transcription in mammalian cells J. Cell. Biochem. 102 2007 609 617
18. Q. Deng, D. Ramsköld, B. Reinius, and R. Sandberg Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells Science 343 2014 193 196
19. G.K. Marinov, B.A. Williams, K. McCue, G.P. Schroth, J. Gertz, R.M. Myers, and B.J. Wold From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing Genome Res. 24 2014 496 510
20. A.S. Dimas, S. Deutsch, B.E. Stranger, S.B. Montgomery, C. Borel, H. Attar-Cohen, C. Ingle, C. Beazley, M. Gutierrez Arcelus, and M. Sekowska Common regulatory variation impacts gene expression in a cell type-dependent manner Science 325 2009 1246 1250
21. S. Dahoun, S. Gagos, M. Gagnebin, C. Gehrig, C. Burgi, F. Simon, C. Vieux, P. Extermann, R. Lyle, and M.A. Morris Monozygotic twins discordant for trisomy 21 and maternal 21q inheritance: a complex series of events Am. J. Med. Genet. A. 146A 2008 2086 2093
22. S. Marco-Sola, M. Sammeth, R. Guigó, and P. Ribeca The GEM mapper: fast, accurate and versatile alignment by filtration Nat. Methods 9 2012 1185 1188
23. T. Lappalainen, M. Sammeth, M.R. Friedländer, P.A. 't Hoen, J. Monlong, M.A. Rivas, M. Gonzàlez-Porta, N. Kurbatova, T. Griebel, P.G. Ferreira Geuvadis Consortium Transcriptome and genome sequencing uncovers functional variation in humans Nature 501 2013 506 511
24. H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin 1000 Genome Project Data Processing Subgroup The Sequence Alignment/Map format and SAMtools Bioinformatics 25 2009 2078 2079
25. C. Trapnell, B.A. Williams, G. Pertea, A. Mortazavi, G. Kwan, M.J. van Baren, S.L. Salzberg, B.J. Wold, and L. Pachter Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Nat. Biotechnol. 28 2010 511 515
26. C. Trapnell, A. Roberts, L. Goff, G. Pertea, D. Kim, D.R. Kelley, H. Pimentel, S.L. Salzberg, J.L. Rinn, and L. Pachter Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks Nat. Protoc. 7 2012 562 578
27. J. Harrow, A. Frankish, J.M. Gonzalez, E. Tapanari, M. Diekhans, F. Kokocinski, B.L. Aken, D. Barrell, A. Zadissa, and S. Searle GENCODE: the reference human genome annotation for The ENCODE Project Genome Res. 22 2012 1760 1774
28. A.R. Quinlan, and I.M. Hall BEDTools: a flexible suite of utilities for comparing genomic features Bioinformatics 26 2010 841 842
29. S.C. Baker, S.R. Bauer, R.P. Beyer, J.D. Brenton, B. Bromley, J. Burrill, H. Causton, M.P. Conley, R. Elespuru, M. Fero External RNA Controls Consortium The External RNA Controls Consortium: a progress report Nat. Methods 2 2005 731 734
30. O. Delaneau, J. Marchini, and J.F. Zagury A linear complexity phasing method for thousands of genomes Nat. Methods 9 2012 179 181
31. G.R. Abecasis, A. Auton, L.D. Brooks, M.A. DePristo, R.M. Durbin, R.E. Handsaker, H.M. Kang, G.T. Marth, G.A. McVean 1000 Genomes Project Consortium An integrated map of genetic variation from 1,092 human genomes Nature 491 2012 56 65
32. M.F. Lyon Gene action in the X-chromosome of the mouse (Mus musculus L.) Nature 190 1961 372 373
33. B.T. Sherman, W. Huang, Q. Tan, Y. Guo, S. Bour, D. Liu, R. Stephens, M.W. Baseler, H.C. Lane, and R.A. Lempicki DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis BMC Bioinformatics 8 2007 426
34. H. Tani, R. Mizutani, K.A. Salam, K. Tano, K. Ijiri, A. Wakamatsu, T. Isogai, Y. Suzuki, and N. Akimitsu Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals Genome Res. 22 2012 947 956
35. H. Takahashi, T. Lassmann, M. Murata, and P. Carninci 5′ end-centered expression profiling using cap-analysis gene expression and next-generation sequencing Nat. Protoc. 7 2012 542 561
36. A. Fort, K. Hashimoto, D. Yamada, M. Salimullah, C.A. Keya, A. Saxena, A. Bonetti, I. Voineagu, N. Bertin, A. Kratz FANTOM Consortium Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance Nat. Genet. 46 2014 558 566
37. A.K. Shalek, R. Satija, X. Adiconis, R.S. Gertner, J.T. Gaublomme, R. Raychowdhury, S. Schwartz, N. Yosef, C. Malboeuf, and D. Lu Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells Nature 498 2013 236 240
38. A.R. Wu, N.F. Neff, T. Kalisky, P. Dalerba, B. Treutlein, M.E. Rothenberg, F.M. Mburu, G.L. Mantalas, S. Sim, M.F. Clarke, and S.R. Quake Quantitative assessment of single-cell RNA-sequencing methods Nat. Methods 11 2014 41 46
39. D.M. Suter, N. Molina, F. Naef, and U. Schibler Origins and consequences of transcriptional discontinuity Curr. Opin. Cell Biol. 23 2011 657 662
40. J.H. Levine, Y. Lin, and M.B. Elowitz Functional roles of pulsing in genetic circuits Science 342 2013 1193 1200
41. D.M. Suter, N. Molina, D. Gatfield, K. Schneider, U. Schibler, and F. Naef Mammalian genes are transcribed with widely different bursting kinetics Science 332 2011 472 474
42. C.V. Harper, B. Finkenstädt, D.J. Woodcock, S. Friedrichsen, S. Semprini, L. Ashall, D.G. Spiller, J.J. Mullins, D.A. Rand, J.R. Davis, and M.R. White Dynamic analysis of stochastic transcription cycles PLoS Biol. 9 2011 e1000607
43. T. Muramoto, D. Cannon, M. Gierlinski, A. Corrigan, G.J. Barton, and J.R. Chubb Live imaging of nascent RNA dynamics reveals distinct types of transcriptional pulse regulation Proc. Natl. Acad. Sci. USA 109 2012 7350 7355
44. N. Molina, D.M. Suter, R. Cannavo, B. Zoller, I. Gotic, and F. Naef Stimulus-induced modulation of transcriptional bursting in a single mammalian gene Proc. Natl. Acad. Sci. USA 110 2013 20563 20568
45. Y. Grimaldi, P. Ferrari, and M. Strubin Independent RNA polymerase II preinitiation complex dynamics and nucleosome turnover at promoter sites in vivo Genome Res. 24 2014 117 124
46. T. Trimborn, J. Gribnau, F. Grosveld, and P. Fraser Mechanisms of developmental control of transcription in the murine alpha- and beta-globin loci Genes Dev. 13 1999 112 124
47. J. Gribnau, E. de Boer, T. Trimborn, M. Wijgerde, E. Milot, F. Grosveld, and P. Fraser Chromatin interaction mechanism of transcriptional control in vivo EMBO J. 17 1998 6020 6027
48. P. Fraser, and F. Grosveld Locus control regions, chromatin activation and transcription Curr. Opin. Cell Biol. 10 1998 361 365
49. D.A. Jackson, A. Pombo, and F. Iborra The balance sheet for transcription: an analysis of nuclear RNA metabolism in mammalian cells FASEB J. 14 2000 242 254