Structural variation-associated expression changes are paralleled by chromatin architecture modifications

PLoS ONE

Volumn 8, Issue 11, 2013, Pages

  Gheldof, Nele ^a,d   Witwicki, Robert M ^a   Migliavacca, Eugenia ^a,b   Leleu, Marion ^b,c   Didelot, Gérard ^a   Harewood, Louise ^a,e   Rougemont, Jacques ^b,c   Reymond, Alexandre ^a  

^a UNIVERSITY OF LAUSANNE   (Switzerland)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^c EPFL   (Switzerland)

^d NESTLÉ RESEARCH CENTER   (Switzerland)

^e Babraham Research Campus   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTISM; AUTS2 GENE; CHROMATIN STRUCTURE; CHROMOSOME CONFORMATION CAPTURE; CONFORMATION; CONTROLLED STUDY; COPY NUMBER VARIATION; DNA FLANKING REGION; FEMALE; GENE; GENE EXPRESSION; GENE INTERACTION; GENE REARRANGEMENT; GENETIC ASSOCIATION; GENETIC VARIABILITY; HISTONE MODIFICATION; HUMAN; HUMAN CELL; INTELLECTUAL IMPAIRMENT; NUCLEOTIDE SEQUENCE; PHENOTYPE; WILLIAMS BEUREN SYNDROME;

AUTISTIC DISORDER; CELL LINE; CHROMATIN; CHROMOSOMES, HUMAN, PAIR 7; DNA COPY NUMBER VARIATIONS; EPISTASIS, GENETIC; FEMALE; GENE EXPRESSION REGULATION; HISTONES; HUMANS; INTELLECTUAL DISABILITY; QUANTITATIVE TRAIT LOCI; WILLIAMS SYNDROME;

EID: 84893155197     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0079973     Document Type: Article

References (64)

1. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, et al. (2006) Global variation in copy number in the human genome. Nature 444: 444-454.
2. Graubert TA, Cahan P, Edwin D, Selzer RR, Richmond TA, et al. (2007) A high-resolution map of segmental DNA copy number variation in the mouse genome. PLoS Genet 3: e3.
3. Cutler G, Marshall LA, Chin N, Baribault H, Kassner PD (2007) Significant gene content variation characterizes the genomes of inbred mouse strains. Genome Res 17: 1743-1754.
4. She X, Cheng Z, Zollner S, Church DM, Eichler EE (2008) Mouse segmental duplication and copy number variation. Nat Genet 40: 909-914.
5. Henrichsen CN, Vinckenbosch N, Zollner S, Chaignat E, Pradervand S, et al. (2009) Segmental copy number variation shapes tissue transcriptomes. Nat Genet 41: 424-429.
6. Cahan P, Li Y, Izumi M, Graubert TA (2009) The impact of copy number variation on local gene expression in mouse hematopoietic stem and progenitor cells. Nat Genet 41: 430-437.
7. Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, et al. (2010) Origins and functional impact of copy number variation in the human genome. Nature 464: 704-712.
8. Zhang F, Gu W, Hurles ME, Lupski JR (2009) Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet 10: 451-481.
9. Fanciulli M, Petretto E, Aitman TJ (2009) Gene copy number variation and common human disease. Clin Genet.
10. Lee C, Scherer SW (2010) The clinical context of copy number variation in the human genome. Expert Rev Mol Med 12: e8.
11. Carvalho CM, Zhang F, Lupski JR (2010) Evolution in health and medicine Sackler colloquium: Genomic disorders: a window into human gene and genome evolution. Proc Natl Acad Sci U S A 107 Suppl 1: 1765-1771.
12. Mills RE, Pittard WS, Mullaney JM, Farooq U, Creasy TH, et al. (2011) Natural genetic variation caused by small insertions and deletions in the human genome. Genome research 21: 830-839.
13. Pober BR (2010) Williams-Beuren syndrome. The New England journal of medicine 362: 239-252.
14. Henrichsen CN, Chaignat E, Reymond A (2009) Copy number variants, diseases and gene expression. Hum Mol Genet 18: R1-8.
15. Chaignat E, Yahya-Graison EA, Henrichsen CN, Chrast J, Schutz F, et al. (2011) Copy number variation modifies expression time courses. Genome research 21: 106-113.
16. Merla G, Howald C, Henrichsen CN, Lyle R, Wyss C, et al. (2006) Submicroscopic deletion in patients with Williams-Beuren syndrome influences expression levels of the nonhemizygous flanking genes. Am J Hum Genet 79: 332-341.
17. Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, et al. (2007) Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315: 848-853.
18. Orozco LD, Cokus SJ, Ghazalpour A, Ingram-Drake L, Wang S, et al. (2009) Copy number variation influences gene expression and metabolic traits in mice. Hum Mol Genet 18: 4118-4129.
19. Ricard G, Molina J, Chrast J, Gu W, Gheldof N, et al. (2010) Phenotypic consequences of copy number variation: insights from Smith-Magenis and Potocki-Lupski syndrome mouse models. PLoS biology 8: e1000543.
20. Jacquemont S, Reymond A, Zufferey F, Harewood L, Walters RG, et al. (2011) Mirror extreme BMI phenotypes associated with gene dosage at the chromosome 16p11.2 locus. Nature 478: 97-102.
21. Kleinjan DA, Lettice LA (2008) Long-range gene control and genetic disease. Advances in genetics 61: 339-388.
22. Reymond A, Henrichsen CN, Harewood L, Merla G (2007) Side effects of genome structural changes. Curr Opin Genet Dev 17: 381-386.
23. Harewood L, Schutz F, Boyle S, Perry P, Delorenzi M, et al. (2010) The effect of translocation-induced nuclear reorganization on gene expression. Genome Res 20: 554-564.
24. de Wit E, Braunschweig U, Greil F, Bussemaker HJ, van Steensel B (2008) Global chromatin domain organization of the Drosophila genome. PLoS genetics 4: e1000045.
25. Noordermeer D, Leleu M, Splinter E, Rougemont J, De Laat W, et al. (2011) The dynamic architecture of Hox gene clusters. Science 334: 222-225.
26. Tolhuis B, Blom M, Kerkhoven RM, Pagie L, Teunissen H, et al. (2011) Interactions among Polycomb domains are guided by chromosome architecture. PLoS genetics 7: e1001343.
27. Sanyal A, Lajoie BR, Jain G, Dekker J (2012) The long-range interaction landscape of gene promoters. Nature 489: 109-113.
28. Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, et al. (2012) Landscape of transcription in human cells. Nature 489: 101-108.
29. Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, et al. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74.
30. Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, et al. (2012) The accessible chromatin landscape of the human genome. Nature 489: 75-82.
31. Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, et al. (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326: 289-293.
32. Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, et al. (2006) Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet 38: 1348-1354.
33. Dutly F, Schinzel A (1996) Unequal interchromosomal rearrangements may result in elastin gene deletions causing the Williams-Beuren syndrome. Human Molecular Genetics 5: 1893-1898.
34. Simonis M, Klous P, Homminga I, Galjaard RJ, Rijkers EJ, et al. (2009) High-resolution identification of balanced and complex chromosomal rearrangements by 4C technology. Nature methods 6: 837-842.
35. Soutoglou E, Misteli T (2007) Mobility and immobility of chromatin in transcription and genome stability. Current opinion in genetics & development 17: 435-442.
36. Chambeyron S, Bickmore WA (2004) Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription. Genes Dev 18: 1119-1130.
37. Ernst J, Kellis M (2010) Discovery and characterization of chromatin states for systematic annotation of the human genome. Nature biotechnology 28: 817-825.
38. Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, et al. (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125: 315-326.
39. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, et al. (2007) High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837.
40. Roh TY, Cuddapah S, Cui K, Zhao K (2006) The genomic landscape of histone modifications in human T cells. Proc Natl Acad Sci U S A 103: 15782-15787.
41. Shu W, Chen H, Bo X, Wang S (2011) Genome-wide analysis of the relationships between DNaseI HS, histone modifications and gene expression reveals distinct modes of chromatin domains. Nucleic acids research 39: 7428-7443.
42. Yalcin B, Wong K, Agam A, Goodson M, Keane TM, et al. (2011) Sequence-based characterization of structural variation in the mouse genome. Nature 477: 326-329.
43. Guryev V, Saar K, Adamovic T, Verheul M, van Heesch SA, et al. (2008) Distribution and functional impact of DNA copy number variation in the rat. Nat Genet 40: 538-545.
44. Splinter E, de Wit E, Nora EP, Klous P, van de Werken HJ, et al. (2011) The inactive X chromosome adopts a unique three-dimensional conformation that is dependent on Xist RNA. Genes & development 25: 1371-1383.
45. Pastinen T (2010) Genome-wide allele-specific analysis: insights into regulatory variation. Nature reviews Genetics 11: 533-538.
46. Wasserman NF, Aneas I, Nobrega MA (2010) An 8q24 gene desert variant associated with prostate cancer risk confers differential in vivo activity to a MYC enhancer. Genome research 20: 1191-1197.
47. McDaniell R, Lee BK, Song L, Liu Z, Boyle AP, et al. (2010) Heritable individual-specific and allele-specific chromatin signatures in humans. Science 328: 235-239.
48. Sanyal A, Bau D, Marti-Renom MA, Dekker J (2011) Chromatin globules: a common motif of higher order chromosome structure? Current opinion in cell biology 23: 325-331.
49. Yaffe E, Tanay A (2011) Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat Genet 43: 1059-1065.
50. Sung MH, Hager GL (2011) More to Hi-C than meets the eye. Nat Genet 43: 1047-1048.
51. Ben-David E, Granot-Hershkovitz E, Monderer-Rothkoff G, Lerer E, Levi S, et al. (2011) Identification of a functional rare variant in autism using genome-wide screen for monoallelic expression. Human molecular genetics 20: 3632-3641.
52. Huang XL, Zou YS, Maher TA, Newton S, Milunsky JM (2010) A de novo balanced translocation breakpoint truncating the autism susceptibility candidate 2 (AUTS2) gene in a patient with autism. American journal of medical genetics Part A 152A: 2112-2114.
53. Kalscheuer VM, FitzPatrick D, Tommerup N, Bugge M, Niebuhr E, et al. (2007) Mutations in autism susceptibility candidate 2 (AUTS2) in patients with mental retardation. Human genetics 121: 501-509.
54. Lyle R, Gehrig C, Neergaard-Henrichsen C, Deutsch S, Antonarakis SE (2004) Gene expression from the aneuploid chromosome in a trisomy mouse model of down syndrome. Genome Res 14: 1268-1274.
55. Gheldof N, Leleu M, Noordermeer D, Rougemont J, Reymond A (2012) Detecting Long-Range Chromatin Interactions Using the Chromosome Conformation Capture Sequencing (4C-seq) Method. Methods in molecular biology 786: 211-225.
56. Simonis M, Kooren J, de Laat W (2007) An evaluation of 3C-based methods to capture DNA interactions. Nature methods 4: 895-901.
57. Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
58. Consortium TEP (2011) A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 9: e1001046.
59. O'Geen H, Nicolet CM, Blahnik K, Green R, Farnham PJ (2006) Comparison of sample preparation methods for ChIP-chip assays. BioTechniques 41: 577-580.
60. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome biology 10: R25.
61. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
62. Zang C, Schones DE, Zeng C, Cui K, Zhao K, et al. (2009) A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 25: 1952-1958.
63. Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome biology 11: R106.
64. Pruitt KD, Tatusova T, Maglott DR (2005) NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic acids research 33: D501-504.