CNVs of noncoding cis-regulatory elements in human disease

Current Opinion in Genetics and Development

Volumn 23, Issue 3, 2013, Pages 249-256

  Spielmann, Malte ^a,b   Klopocki, Eva ^a,b,c  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^b MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^c UNIVERSITY OF WÜRZBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOSOMAL DOMINANT INHERITANCE; AXENFELD RIEGER SYNDROME; BLEPHAROPHIMOSIS BLEPHAROPHIMOSIS PTOSIS INVERSUS SYNDROME; BMP2 GENE; BRACHYDACTYLY; CAMPOMELIC DYSPLASIA; CHROMOSOME INVERSION; CIS ISOMER; COOKS SYNDROME; COPY NUMBER VARIATION; DYSCHONDROSTEOSIS; ENHANCER REGION; FOXG1 ENE; FOXL2 GENE; GENE; GENE DELETION; GENE DUPLICATION; GENE IDENTIFICATION; GENE LOCUS; GENE OVEREXPRESSION; GENE TRANSLOCATION; GENETIC DISORDER; GENOME ANALYSIS; GENOMICS; HEREDITARY MOTOR SENSORY NEUROPATHY; HOLOPROSENCEPHALY; HUMAN; LIEBENBERG SYNDROME; NONHUMAN; PHENOTYPIC VARIATION; PITX1 GENE; PITX2 GENE; PMP22 GENE; PRIORITY JOURNAL; REGULATORY SEQUENCE; RETT SYNDROME; REVIEW; SHH GENE; SHOX GENE; SOX9 GENE; TRANSGENIC MOUSE;

DNA COPY NUMBER VARIATIONS; GENE DOSAGE; GENETIC DISEASES, INBORN; GENOME, HUMAN; HUMANS; OPEN READING FRAMES; PHENOTYPE; REGULATORY SEQUENCES, NUCLEIC ACID;

EID: 84879884404     PISSN: 0959437X     EISSN: 18790380     Source Type: Journal    
DOI: 10.1016/j.gde.2013.02.013     Document Type: Review

References (48)

1. Lander E.S., Linton L.M., Birren B., Nusbaum C., Zody M.C., Baldwin J., Devon K., Dewar K., Doyle M., FitzHugh W., et al. Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921.
2. Venter J.C., Adams M.D., Myers E.W., Li P.W., Mural R.J., Sutton G.G., Smith H.O., Yandell M., Evans C.A., Holt R.A., et al. The sequence of the human genome. Science 2001, 291:1304-1351.
3. Girirajan S., Rosenfeld J.A., Coe B.P., Parikh S., Friedman N., Goldstein A., Filipink R.A., McConnell J.S., Angle B., Meschino W.S., et al. Phenotypic heterogeneity of genomic disorders and rare copy-number variants. N Engl J Med 2012, 367:1321-1331.
4. Manolio T.A., Collins F.S., Cox N.J., Goldstein D.B., Hindorff L.A., Hunter D.J., McCarthy M.I., Ramos E.M., Cardon L.R., Chakravarti A., et al. Finding the missing heritability of complex diseases. Nature 2009, 461:747-753.
5. Consortium E.P. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 2004, 306:636-640.
6. Ecker J.R., Bickmore W.A., Barroso I., Pritchard J.K., Gilad Y., Segal E. Genomics: ENCODE explained. Nature 2012, 489:52-55.
7. Consortium E.P., Bernstein B.E., Birney E., Dunham I., Green E.D., Gunter C., Snyder M. An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489:57-74.
8. Cooper G.M., Coe B.P., Girirajan S., Rosenfeld J.A., Vu T.H., Baker C., Williams C., Stalker H., Hamid R., Hannig V., et al. A copy number variation morbidity map of developmental delay. Nat Genet 2011, 43:838-846.
9. Rauch A., Wieczorek D., Graf E., Wieland T., Endele S., Schwarzmayr T., Albrecht B., Bartholdi D., Beygo J., Di Donato N., et al. Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study. Lancet 2012, 380:1674-1682.
10. de Ligt J., Willemsen M.H., van Bon B.W., Kleefstra T., Yntema H.G., Kroes T., Vulto-van Silfhout A.T., Koolen D.A., de Vries P., Gilissen C., et al. Diagnostic exome sequencing in persons with severe intellectual disability. N Engl J Med 2012, 367:1921-1929.
11. Maston G.A., Evans S.K., Green M.R. Transcriptional regulatory elements in the human genome. Annu Rev Genomics Hum Genet 2006, 7:29-59.
12. Klopocki E., Mundlos S. Copy-number variations, noncoding sequences, and human phenotypes. Annu Rev Genomics Hum Genet 2011, 12:53-72.
13. Spitz F., Furlong E.E. Transcription factors: from enhancer binding to developmental control. Nat Rev Genet 2012, 13:613-626.
14. Amano T., Sagai T., Tanabe H., Mizushina Y., Nakazawa H., Shiroishi T. Chromosomal dynamics at the Shh locus: limb bud-specific differential regulation of competence and active transcription. Dev Cell 2009, 16:47-57.
15. Lieberman-Aiden E., van Berkum N.L., Williams L., Imakaev M., Ragoczy T., Telling A., Amit I., Lajoie B.R., Sabo P.J., Dorschner M.O., et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 2009, 326:289-293.
16. Montavon T., Soshnikova N., Mascrez B., Joye E., Thevenet L., Splinter E., de Laat W., Spitz F., Duboule D. A regulatory archipelago controls Hox genes transcription in digits. Cell 2011, 147:1132-1145.
17. Chen J., Wildhardt G., Zhong Z., Roth R., Weiss B., Steinberger D., Decker J., Blum W.F., Rappold G. Enhancer deletions of the SHOX gene as a frequent cause of short stature: the essential role of a 250kb downstream regulatory domain. J Med Genet 2009, 46:834-839.
18. Benito-Sanz S., Royo J.L., Barroso E., Paumard-Hernandez B., Barreda-Bonis A.C., Liu P., Gracia R., Lupski J.R., Campos-Barros A., Gomez-Skarmeta J.L., et al. Identification of the first recurrent PAR1 deletion in Leri-Weill dyschondrosteosis and idiopathic short stature reveals the presence of a novel SHOX enhancer. J Med Genet 2011, 49:442-450.
19. Volkmann B.A., Zinkevich N.S., Mustonen A., Schilter K.F., Bosenko D.V., Reis L.M., Broeckel U., Link B.A., Semina E.V. Potential novel mechanism for Axenfeld-Rieger syndrome: deletion of a distant region containing regulatory elements of PITX2. Invest Ophthalmol Vis Sci 2011, 52:1450-1459.
20. D'Haene B., Attanasio C., Beysen D., Dostie J., Lemire E., Bouchard P., Field M., Jones K., Lorenz B., Menten B., et al. Disease-causing 7.4kb cis-regulatory deletion disrupting conserved non-coding sequences and their interaction with the FOXL2 promotor: implications for mutation screening. PLoS Genet 2009, 5:e1000522.
21. Sankaran V.G., Xu J., Byron R., Greisman H.A., Fisher C., Weatherall D.J., Sabath D.E., Groudine M., Orkin S.H., Premawardhena A., et al. A functional element necessary for fetal hemoglobin silencing. N Engl J Med 2011, 365:807-814.
22. Allou L., Lambert L., Amsallem D., Bieth E., Edery P., Destree A., Rivier F., Amor D., Thompson E., Nicholl J., et al. 14q12 and severe Rett-like phenotypes: new clinical insights and physical mapping of FOXG1-regulatory elements. Eur J Hum Genet 2012, 20:1216-1223.
23. Wagner T., Wirth J., Meyer J., Zabel B., Held M., Zimmer J., Pasantes J., Bricarelli F.D., Keutel J., Hustert E., et al. Autosomal sex reversal and campomelic dysplasia are caused by mutations in and around the SRY-related gene SOX9. Cell 1994, 79:1111-1120.
24. Benko S., Fantes J.A., Amiel J., Kleinjan D.J., Thomas S., Ramsay J., Jamshidi N., Essafi A., Heaney S., Gordon C.T., et al. Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence. Nat Genet 2009, 41:359-364.
25. Lettice L.A., Daniels S., Sweeney E., Venkataraman S., Devenney P.S., Gautier P., Morrison H., Fantes J., Hill R.E., FitzPatrick D.R. Enhancer-adoption as a mechanism of human developmental disease. Hum Mutat 2011, 32:1492-1499.
26. Spielmann M., Brancati F., Krawitz P.M., Robinson P.N., Ibrahim D.M., Franke M., Hecht J., Lohan S., Dathe K., Nardone A.M., et al. Homeotic arm-to-leg transformation associated with genomic rearrangements at the PITX1 locus. Am J Hum Genet 2012, 91:629-635.
27. Visel A., Minovitsky S., Dubchak I., Pennacchio L.A. VISTA Enhancer Browser-a database of tissue-specific human enhancers. Nucleic Acids Res 2007, 35:D88-D92.
28. Lupski J.R., de Oca-Luna R.M., Slaugenhaupt S., Pentao L., Guzzetta V., Trask B.J., Saucedo-Cardenas O., Barker D.F., Killian J.M., Garcia C.A., et al. DNA duplication associated with Charcot-Marie-Tooth disease type 1A. Cell 1991, 66:219-232.
29. Raeymaekers P., Timmerman V., Nelis E., De Jonghe P., Hoogendijk J.E., Baas F., Barker D.F., Martin J.J., De Visser M., Bolhuis P.A., et al. Duplication in chromosome 17p11.2 in Charcot-Marie-Tooth neuropathy type 1a (CMT 1a). The HMSN Collaborative Research Group. Neuromuscul Disord 1991, 1:93-97.
30. Chance P.F., Alderson M.K., Leppig K.A., Lensch M.W., Matsunami N., Smith B., Swanson P.D., Odelberg S.J., Disteche C.M., Bird T.D. DNA deletion associated with hereditary neuropathy with liability to pressure palsies. Cell 1993, 72:143-151.
31. Roa B.B., Garcia C.A., Suter U., Kulpa D.A., Wise C.A., Mueller J., Welcher A.A., Snipes G.J., Shooter E.M., Patel P.I., et al. Charcot-Marie-Tooth disease type 1A. Association with a spontaneous point mutation in the PMP22 gene. N Engl J Med 1993, 329:96-101.
32. Weterman M.A., van Ruissen F., de Wissel M., Bordewijk L., Samijn J.P., van der Pol W.L., Meggouh F., Baas F. Copy number variation upstream of PMP22 in Charcot-Marie-Tooth disease. Eur J Hum Genet 2010, 18:421-428.
33. Zhang F., Seeman P., Liu P., Weterman M.A., Gonzaga-Jauregui C., Towne C.F., Batish S.D., De Vriendt E., De Jonghe P., Rautenstrauss B., et al. Mechanisms for nonrecurrent genomic rearrangements associated with CMT1A or HNPP: rare CNVs as a cause for missing heritability. Am J Hum Genet 2010, 86:892-903.
34. Dixon J.R., Selvaraj S., Yue F., Kim A., Li Y., Shen Y., Hu M., Liu J.S., Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 2012, 485:376-380.
35. Dathe K., Kjaer K.W., Brehm A., Meinecke P., Nurnberg P., Neto J.C., Brunoni D., Tommerup N., Ott C.E., Klopocki E., et al. Duplications involving a conserved regulatory element downstream of BMP2 are associated with brachydactyly type A2. Am J Hum Genet 2009, 84:483-492.
36. Bandyopadhyay A., Tsuji K., Cox K., Harfe B.D., Rosen V., Tabin C.J. Genetic analysis of the roles of BMP2, BMP4, and BMP7 in limb patterning and skeletogenesis. PLoS Genet 2006, 2:e216.
37. Anderson E., Peluso S., Lettice L.A., Hill R.E. Human limb abnormalities caused by disruption of hedgehog signaling. Trends Genet 2012, 28:364-373.
38. Klopocki E., Ott C.E., Benatar N., Ullmann R., Mundlos S., Lehmann K. A microduplication of the long range SHH limb regulator (ZRS) is associated with triphalangeal thumb-polysyndactyly syndrome. J Med Genet 2008, 45:370-375.
39. Wu L., Liang D., Niikawa N., Ma F., Sun M., Pan Q., Long Z., Zhou Z., Yoshiura K., Wang H., et al. A ZRS duplication causes syndactyly type IV with tibial hypoplasia. Am J Med Genet A 2009, 149A:816-818.
40. Sun M., Ma F., Zeng X., Liu Q., Zhao X.L., Wu F.X., Wu G.P., Zhang Z.F., Gu B., Zhao Y.F., et al. Triphalangeal thumb-polysyndactyly syndrome and syndactyly type IV are caused by genomic duplications involving the long range, limb-specific SHH enhancer. J Med Genet 2008, 45:589-595.
41. Wieczorek D., Pawlik B., Li Y., Akarsu N.A., Caliebe A., May K.J., Schweiger B., Vargas F.R., Balci S., Gillessen-Kaesbach G., et al. A specific mutation in the distant sonic hedgehog (SHH) cis-regulator (ZRS) causes Werner mesomelic syndrome (WMS) while complete ZRS duplications underlie Haas type polysyndactyly and preaxial polydactyly (PPD) with or without triphalangeal thumb. Hum Mutat 2010, 31:81-89.
42. Klopocki E., Lohan S., Brancati F., Koll R., Brehm A., Seemann P., Dathe K., Stricker S., Hecht J., Bosse K., et al. Copy-number variations involving the IHH locus are associated with syndactyly and craniosynostosis. Am J Hum Genet 2011, 88:70-75.
43. Kurth I., Klopocki E., Stricker S., van Oosterwijk J., Vanek S., Altmann J., Santos H.G., van Harssel J.J., de Ravel T., Wilkie A.O., et al. Duplications of noncoding elements 5' of SOX9 are associated with brachydactyly-anonychia. Nat Genet 2009, 41:862-863.
44. Cox J.J., Willatt L., Homfray T., Woods C.G. A SOX9 duplication and familial 46, XX developmental testicular disorder. N Engl J Med 2011, 364:91-93.
45. Benko S., Gordon C.T., Mallet D., Sreenivasan R., Thauvin-Robinet C., Brendehaug A., Thomas S., Bruland O., David M., Nicolino M., et al. Disruption of a long distance regulatory region upstream of SOX9 in isolated disorders of sex development. J Med Genet 2011, 48:825-830.
46. Lupski J.R., Reid J.G., Gonzaga-Jauregui C., Rio Deiros D., Chen D.C., Nazareth L., Bainbridge M., Dinh H., Jing C., Wheeler D.A., et al. Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. N Engl J Med 2010, 362:1181-1191.
47. Mefford H.C. Diagnostic exome sequencing-are we there yet?. N Engl J Med 2012, 367:1951-1953.
48. Ruf S., Symmons O., Uslu V.V., Dolle D., Hot C., Ettwiller L., Spitz F. Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor. Nat Genet 2011, 43:379-386.