Examining the impact of gene variants on histone lysine methylation

Biochimica et Biophysica Acta - Gene Regulatory Mechanisms

Volumn 1839, Issue 12, 2014, Pages 1463-1476

  Van Rechem, Capucine ^a   Whetstine, Johnathan R ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

EZH2; Histone; KDM; KMT; SNP; Somatic mutation

Indexed keywords

HISTONE; HISTONE DEMETHYLASE; HISTONE H3; HISTONE LYSINE DEMETHYLASE; HISTONE LYSINE METHYLTRANSFERASE; HISTONE METHYLTRANSFERASE; IRINOTECAN; LYSINE; MIXED LINEAGE LEUKEMIA PROTEIN; UNCLASSIFIED DRUG;

ALTERNATIVE RNA SPLICING; CANCER CHEMOTHERAPY; CANCER PATIENT; CORRELATIONAL STUDY; ESOPHAGEAL SQUAMOUS CELL CARCINOMA; GAIN OF FUNCTION MUTATION; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENE MUTATION; GENE TARGETING; GENETIC VARIABILITY; GERMLINE MUTATION; GLIOMA; HISTONE METHYLATION; HUMAN; METASTATIC COLORECTAL CANCER; MOLECULAR DYNAMICS; MULTIPLE CANCER; OVERALL SURVIVAL; PROGRESSION FREE SURVIVAL; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; SOMATIC MUTATION; ANIMAL; GENETICS; METABOLISM; METHYLATION; MUTATION; NEOPLASM;

ANIMALS; HISTONE DEMETHYLASES; HISTONE-LYSINE N-METHYLTRANSFERASE; HISTONES; HUMANS; LYSINE; METHYLATION; MUTATION; NEOPLASMS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84913597263     PISSN: 18749399     EISSN: 18764320     Source Type: Journal    
DOI: 10.1016/j.bbagrm.2014.05.014     Document Type: Review

References (136)

1. Allis C.D., Jenuwein T., Reinberg D. Epigenetics 2007, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
2. Dawson M.A., Kouzarides T. Cancer epigenetics: from mechanism to therapy. Cell 2012, 150:12-27.
3. Black J.C., Van Rechem C., Whetstine J.R. Histone lysine methylation dynamics: establishment, regulation, and biological impact. Mol. Cell 2012, 48:491-507.
4. Rea S., Eisenhaber F., O'Carroll D., Strahl B.D., Sun Z.W., Schmid M., Opravil S., Mechtler K., Ponting C.P., Allis C.D., Jenuwein T. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 2000, 406:593-599.
5. Shi Y., Lan F., Matson C., Mulligan P., Whetstine J.R., Cole P.A., Casero R.A. Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 2004, 119:941-953.
6. Black J.C., Whetstine J.R. Tipping the lysine methylation balance in disease. Biopolymers 2013, 99:127-135.
7. Stratton M.R., Campbell P.J., Futreal P.A. The cancer genome. Nature 2009, 458:719-724.
8. Brookes A.J. The essence of SNPs. Gene 1999, 234:177-186.
9. Barreiro L.B., Laval G., Quach H., Patin E., Quintana-Murci L. Natural selection has driven population differentiation in modern humans. Nat. Genet. 2008, 40:340-345.
10. Lee J.C., Espeli M., Anderson C.A., Linterman M.A., Pocock J.M., Williams N.J., Roberts R., Viatte S., Fu B., Peshu N., Hien T.T., Phu N.H., Wesley E., Edwards C., Ahmad T., Mansfield J.C., Gearry R., Dunstan S., Williams T.N., Barton A., Vinuesa C.G., Parkes M., Lyons P.A., Smith K.G. Human SNP links differential outcomes in inflammatory and infectious disease to a FOXO3-regulated pathway. Cell 2013, 155:57-69.
11. Zeron-Medina J., Wang X., Repapi E., Campbell M.R., Su D., Castro-Giner F., Davies B., Peterse E.F., Sacilotto N., Walker G.J., Terzian T., Tomlinson I.P., Box N.F., Meinshausen N., De Val S., Bell D.A., Bond G.L. A polymorphic p53 response element in KIT ligand influences cancer risk and has undergone natural selection. Cell 2013, 155:410-422.
12. Liu J., Lee W., Jiang Z., Chen Z., Jhunjhunwala S., Haverty P.M., Gnad F., Guan Y., Gilbert H.N., Stinson J., Klijn C., Guillory J., Bhatt D., Vartanian S., Walter K., Chan J., Holcomb T., Dijkgraaf P., Johnson S., Koeman J., Minna J.D., Gazdar A.F., Stern H.M., Hoeflich K.P., Wu T.D., Settleman J., de Sauvage F.J., Gentleman R.C., Neve R.M., Stokoe D., Modrusan Z., Seshagiri S., Shames D.S., Zhang Z. Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events. Genome Res. 2012, 22:2315-2327.
13. Kandoth C., McLellan M.D., Vandin F., Ye K., Niu B., Lu C., Xie M., Zhang Q., McMichael J.F., Wyczalkowski M.A., Leiserson M.D., Miller C.A., Welch J.S., Walter M.J., Wendl M.C., Ley T.J., Wilson R.K., Raphael B.J., Ding L. Mutational landscape and significance across 12 major cancer types. Nature 2013, 502:333-339.
14. Fujimoto A., Totoki Y., Abe T., Boroevich K.A., Hosoda F., Nguyen H.H., Aoki M., Hosono N., Kubo M., Miya F., Arai Y., Takahashi H., Shirakihara T., Nagasaki M., Shibuya T., Nakano K., Watanabe-Makino K., Tanaka H., Nakamura H., Kusuda J., Ojima H., Shimada K., Okusaka T., Ueno M., Shigekawa Y., Kawakami Y., Arihiro K., Ohdan H., Gotoh K., Ishikawa O., Ariizumi S., Yamamoto M., Yamada T., Chayama K., Kosuge T., Yamaue H., Kamatani N., Miyano S., Nakagama H., Nakamura Y., Tsunoda T., Shibata T., Nakagawa H. Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators. Nat. Genet. 2012, 44:760-764.
15. Pasqualucci L., Trifonov V., Fabbri G., Ma J., Rossi D., Chiarenza A., Wells V.A., Grunn A., Messina M., Elliot O., Chan J., Bhagat G., Chadburn A., Gaidano G., Mullighan C.G., Rabadan R., Dalla-Favera R. Analysis of the coding genome of diffuse large B-cell lymphoma. Nat. Genet. 2011, 43:830-837.
16. Kramer J.M., van Bokhoven H. Genetic and epigenetic defects in mental retardation. Int. J. Biochem. Cell Biol. 2009, 41:96-107.
17. Wu G., Broniscer A., McEachron T.A., Lu C., Paugh B.S., Becksfort J., Qu C., Ding L., Huether R., Parker M., Zhang J., Gajjar A., Dyer M.A., Mullighan C.G., Gilbertson R.J., Mardis E.R., Wilson R.K., Downing J.R., Ellison D.W., Baker S.J. Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas. Nat. Genet. 2012, 44:251-253.
18. Ho A.S., Kannan K., Roy D.M., Morris L.G., Ganly I., Katabi N., Ramaswami D., Walsh L.A., Eng S., Huse J.T., Zhang J., Dolgalev I., Huberman K., Heguy A., Viale A., Drobnjak M., Leversha M.A., Rice C.E., Singh B., Iyer N.G., Leemans C.R., Bloemena E., Ferris R.L., Seethala R.R., Gross B.E., Liang Y., Sinha R., Peng L., Raphael B.J., Turcan S., Gong Y., Schultz N., Kim S., Chiosea S., Shah J.P., Sander C., Lee W., Chan T.A. The mutational landscape of adenoid cystic carcinoma. Nat. Genet. 2013, 45:791-798.
19. Lohr J.G., Stojanov P., Lawrence M.S., Auclair D., Chapuy B., Sougnez C., Cruz-Gordillo P., Knoechel B., Asmann Y.W., Slager S.L., Novak A.J., Dogan A., Ansell S.M., Link B.K., Zou L., Gould J., Saksena G., Stransky N., Rangel-Escareno C., Fernandez-Lopez J.C., Hidalgo-Miranda A., Melendez-Zajgla J., Hernandez-Lemus E., Schwarz-Cruz y Celis A., Imaz-Rosshandler I., Ojesina A.I., Jung J., Pedamallu C.S., Lander E.S., Habermann T.M., Cerhan J.R., Shipp M.A., Getz G., Golub T.R. Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing. Proc. Natl. Acad. Sci. U. S. A. 2012, 109:3879-3884.
20. Morin R.D., Mendez-Lago M., Mungall A.J., Goya R., Mungall K.L., Corbett R.D., Johnson N.A., Severson T.M., Chiu R., Field M., Jackman S., Krzywinski M., Scott D.W., Trinh D.L., Tamura-Wells J., Li S., Firme M.R., Rogic S., Griffith M., Chan S., Yakovenko O., Meyer I.M., Zhao E.Y., Smailus D., Moksa M., Chittaranjan S., Rimsza L., Brooks-Wilson A., Spinelli J.J., Ben-Neriah S., Meissner B., Woolcock B., Boyle M., McDonald H., Tam A., Zhao Y., Delaney A., Zeng T., Tse K., Butterfield Y., Birol I., Holt R., Schein J., Horsman D.E., Moore R., Jones S.J., Connors J.M., Hirst M., Gascoyne R.D., Marra M.A. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature 2011, 476:298-303.
21. Maitra A., Biswas N.K., Amin K., Kowtal P., Kumar S., Das S., Sarin R., Majumder P.P., Bagchi I., Bairagya B.B., Basu A., Bhan M.K., Chaturvedi P., Das D., D'Cruz A., Dhar R., Dutta D., Ganguli D., Gera P., Gupta T., Mahapatra S., Mujawar M.H., Mukherjee S., Nair S., Nikam S., Nobre M., Patil A., Patra S., Rama-Gowtham M., Rao T.S., Roy B., Roychowdhury B., Sarkar D., Sarkar S., Sarkar-Roy N., Sutradhar D. Mutational landscape of gingivo-buccal oral squamous cell carcinoma reveals new recurrently-mutated genes and molecular subgroups. Nat. Commun. 2013, 4:2873.
22. Schwartzentruber J., Korshunov A., Liu X.Y., Jones D.T., Pfaff E., Jacob K., Sturm D., Fontebasso A.M., Quang D.A., Tonjes M., Hovestadt V., Albrecht S., Kool M., Nantel A., Konermann C., Lindroth A., Jager N., Rausch T., Ryzhova M., Korbel J.O., Hielscher T., Hauser P., Garami M., Klekner A., Bognar L., Ebinger M., Schuhmann M.U., Scheurlen W., Pekrun A., Fruhwald M.C., Roggendorf W., Kramm C., Durken M., Atkinson J., Lepage P., Montpetit A., Zakrzewska M., Zakrzewski K., Liberski P.P., Dong Z., Siegel P., Kulozik A.E., Zapatka M., Guha A., Malkin D., Felsberg J., Reifenberger G., von Deimling A., Ichimura K., Collins V.P., Witt H., Milde T., Witt O., Zhang C., Castelo-Branco P., Lichter P., Faury D., Tabori U., Plass C., Majewski J., Pfister S.M., Jabado N. Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature 2012, 482:226-231.
23. Khuong-Quang D.A., Buczkowicz P., Rakopoulos P., Liu X.Y., Fontebasso A.M., Bouffet E., Bartels U., Albrecht S., Schwartzentruber J., Letourneau L., Bourgey M., Bourque G., Montpetit A., Bourret G., Lepage P., Fleming A., Lichter P., Kool M., von Deimling A., Sturm D., Korshunov A., Faury D., Jones D.T., Majewski J., Pfister S.M., Jabado N., Hawkins C. K27M mutation in histone H3.3 defines clinically and biologically distinct subgroups of pediatric diffuse intrinsic pontine gliomas. Acta Neuropathol. 2012, 124:439-447.
24. Gielen G.H., Gessi M., Hammes J., Kramm C.M., Waha A., Pietsch T. H3F3A K27M mutation in pediatric CNS tumors: a marker for diffuse high-grade astrocytomas. Am. J. Clin. Pathol. 2013, 139:345-349.
25. Chan K.M., Fang D., Gan H., Hashizume R., Yu C., Schroeder M., Gupta N., Mueller S., James C.D., Jenkins R., Sarkaria J., Zhang Z. The histone H3.3K27M mutation in pediatric glioma reprograms H3K27 methylation and gene expression. Genes Dev. 2013, 27:985-990.
26. Aihara K., Mukasa A., Gotoh K., Saito K., Nagae G., Tsuji S., Tatuno K., Yamamoto S., Takayanagi S., Narita Y., Shibui S., Aburatani H., Saito N. H3F3A K27M mutations in thalamic gliomas from young adult patients. Neuro-Oncology 2013, 16:140-146.
27. Behjati S., Tarpey P.S., Presneau N., Scheipl S., Pillay N., Van Loo P., Wedge D.C., Cooke S.L., Gundem G., Davies H., Nik-Zainal S., Martin S., McLaren S., Goodie V., Robinson B., Butler A., Teague J.W., Halai D., Khatri B., Myklebost O., Baumhoer D., Jundt G., Hamoudi R., Tirabosco R., Amary M.F., Futreal P.A., Stratton M.R., Campbell P.J., Flanagan A.M. Distinct H3F3A and H3F3B driver mutations define chondroblastoma and giant cell tumor of bone. Nat. Genet. 2013, 45:1479-1482.
28. Yuen B.T., Knoepfler P.S. Histone h3.3 mutations: a variant path to cancer. Cancer Cell 2013, 24:567-574.
29. Goldberg A.D., Banaszynski L.A., Noh K.M., Lewis P.W., Elsaesser S.J., Stadler S., Dewell S., Law M., Guo X., Li X., Wen D., Chapgier A., DeKelver R.C., Miller J.C., Lee Y.L., Boydston E.A., Holmes M.C., Gregory P.D., Greally J.M., Rafii S., Yang C., Scambler P.J., Garrick D., Gibbons R.J., Higgs D.R., Cristea I.M., Urnov F.D., Zheng D., Allis C.D. Distinct factors control histone variant H3.3 localization at specific genomic regions. Cell 2010, 140:678-691.
30. Lewis P.W., Muller M.M., Koletsky M.S., Cordero F., Lin S., Banaszynski L.A., Garcia B.A., Muir T.W., Becher O.J., Allis C.D. Inhibition of PRC2 activity by a gain-of-function H3 mutation found in pediatric glioblastoma. Science 2013, 340:857-861.
31. Black J.C., Manning A.L., Van Rechem C., Kim J., Ladd B., Cho J., Pineda C.M., Murphy N., Daniels D.L., Montagna C., Lewis P.W., Glass K., Allis C.D., Dyson N.J., Getz G., Whetstine J.R. KDM4A lysine demethylase induces site-specific copy gain and rereplication of regions amplified in tumors. Cell 2013, 154:541-555.
32. Bjerke L., Mackay A., Nandhabalan M., Burford A., Jury A., Popov S., Bax D.A., Carvalho D., Taylor K.R., Vinci M., Bajrami I., McGonnell I.M., Lord C.J., Reis R.M., Hargrave D., Ashworth A., Workman P., Jones C. Histone H3.3 mutations drive pediatric glioblastoma through upregulation of MYCN. Cancer Discov. 2013, 3:512-519.
33. Mikkelsen T.S., Ku M., Jaffe D.B., Issac B., Lieberman E., Giannoukos G., Alvarez P., Brockman W., Kim T.K., Koche R.P., Lee W., Mendenhall E., O'Donovan A., Presser A., Russ C., Xie X., Meissner A., Wernig M., Jaenisch R., Nusbaum C., Lander E.S., Bernstein B.E. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007, 448:553-560.
34. Creyghton M.P., Cheng A.W., Welstead G.G., Kooistra T., Carey B.W., Steine E.J., Hanna J., Lodato M.A., Frampton G.M., Sharp P.A., Boyer L.A., Young R.A., Jaenisch R. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:21931-21936.
35. Nikoloski G., Langemeijer S.M., Kuiper R.P., Knops R., Massop M., Tonnissen E.R., van der Heijden A., Scheele T.N., Vandenberghe P., de Witte T., van der Reijden B.A., Jansen J.H. Somatic mutations of the histone methyltransferase gene EZH2 in myelodysplastic syndromes. Nat. Genet. 2010, 42:665-667.
36. Ernst T., Chase A.J., Score J., Hidalgo-Curtis C.E., Bryant C., Jones A.V., Waghorn K., Zoi K., Ross F.M., Reiter A., Hochhaus A., Drexler H.G., Duncombe A., Cervantes F., Oscier D., Boultwood J., Grand F.H., Cross N.C. Inactivating mutations of the histone methyltransferase gene EZH2 in myeloid disorders. Nat. Genet. 2010, 42:722-726.
37. Ntziachristos P., Tsirigos A., Van Vlierberghe P., Nedjic J., Trimarchi T., Flaherty M.S., Ferres-Marco D., da Ros V., Tang Z., Siegle J., Asp P., Hadler M., Rigo I., De Keersmaecker K., Patel J., Huynh T., Utro F., Poglio S., Samon J.B., Paietta E., Racevskis J., Rowe J.M., Rabadan R., Levine R.L., Brown S., Pflumio F., Dominguez M., Ferrando A., Aifantis I. Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia. Nat. Med. 2012, 18:298-301.
38. Zhang J., Ding L., Holmfeldt L., Wu G., Heatley S.L., Payne-Turner D., Easton J., Chen X., Wang J., Rusch M., Lu C., Chen S.C., Wei L., Collins-Underwood J.R., Ma J., Roberts K.G., Pounds S.B., Ulyanov A., Becksfort J., Gupta P., Huether R., Kriwacki R.W., Parker M., McGoldrick D.J., Zhao D., Alford D., Espy S., Bobba K.C., Song G., Pei D., Cheng C., Roberts S., Barbato M.I., Campana D., Coustan-Smith E., Shurtleff S.A., Raimondi S.C., Kleppe M., Cools J., Shimano K.A., Hermiston M.L., Doulatov S., Eppert K., Laurenti E., Notta F., Dick J.E., Basso G., Hunger S.P., Loh M.L., Devidas M., Wood B., Winter S., Dunsmore K.P., Fulton R.S., Fulton L.L., Hong X., Harris C.C., Dooling D.J., Ochoa K., Johnson K.J., Obenauer J.C., Evans W.E., Pui C.H., Naeve C.W., Ley T.J., Mardis E.R., Wilson R.K., Downing J.R., Mullighan C.G. The genetic basis of early T-cell precursor acute lymphoblastic leukaemia. Nature 2012, 481:157-163.
39. Morin R.D., Johnson N.A., Severson T.M., Mungall A.J., An J., Goya R., Paul J.E., Boyle M., Woolcock B.W., Kuchenbauer F., Yap D., Humphries R.K., Griffith O.L., Shah S., Zhu H., Kimbara M., Shashkin P., Charlot J.F., Tcherpakov M., Corbett R., Tam A., Varhol R., Smailus D., Moksa M., Zhao Y., Delaney A., Qian H., Birol I., Schein J., Moore R., Holt R., Horsman D.E., Connors J.M., Jones S., Aparicio S., Hirst M., Gascoyne R.D., Marra M.A. Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nat. Genet. 2010, 42:181-185.
40. Sneeringer C.J., Scott M.P., Kuntz K.W., Knutson S.K., Pollock R.M., Richon V.M., Copeland R.A. Coordinated activities of wild-type plus mutant EZH2 drive tumor-associated hypertrimethylation of lysine 27 on histone H3 (H3K27) in human B-cell lymphomas. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:20980-20985.
41. Yap D.B., Chu J., Berg T., Schapira M., Cheng S.W., Moradian A., Morin R.D., Mungall A.J., Meissner B., Boyle M., Marquez V.E., Marra M.A., Gascoyne R.D., Humphries R.K., Arrowsmith C.H., Morin G.B., Aparicio S.A. Somatic mutations at EZH2 Y641 act dominantly through a mechanism of selectively altered PRC2 catalytic activity, to increase H3K27 trimethylation. Blood 2011, 117:2451-2459.
42. Bodor C., Grossmann V., Popov N., Okosun J., O'Riain C., Tan K., Marzec J., Araf S., Wang J., Lee A.M., Clear A., Montoto S., Matthews J., Iqbal S., Rajnai H., Rosenwald A., Ott G., Campo E., Rimsza L.M., Smeland E.B., Chan W.C., Braziel R.M., Staudt L.M., Wright G., Lister T.A., Elemento O., Hills R., Gribben J.G., Chelala C., Matolcsy A., Kohlmann A., Haferlach T., Gascoyne R.D., Fitzgibbon J. EZH2 mutations are frequent and represent an early event in follicular lymphoma. Blood 2013, 122:3165-3168.
43. van Haaften G., Dalgliesh G.L., Davies H., Chen L., Bignell G., Greenman C., Edkins S., Hardy C., O'Meara S., Teague J., Butler A., Hinton J., Latimer C., Andrews J., Barthorpe S., Beare D., Buck G., Campbell P.J., Cole J., Forbes S., Jia M., Jones D., Kok C.Y., Leroy C., Lin M.L., McBride D.J., Maddison M., Maquire S., McLay K., Menzies A., Mironenko T., Mulderrig L., Mudie L., Pleasance E., Shepherd R., Smith R., Stebbings L., Stephens P., Tang G., Tarpey P.S., Turner R., Turrell K., Varian J., West S., Widaa S., Wray P., Collins V.P., Ichimura K., Law S., Wong J., Yuen S.T., Leung S.Y., Tonon G., DePinho R.A., Tai Y.T., Anderson K.C., Kahnoski R.J., Massie A., Khoo S.K., Teh B.T., Stratton M.R., Futreal P.A. Somatic mutations of the histone H3K27 demethylase gene UTX in human cancer. Nat. Genet. 2009, 41:521-523.
44. Jankowska A.M., Makishima H., Tiu R.V., Szpurka H., Huang Y., Traina F., Visconte V., Sugimoto Y., Prince C., O'Keefe C., Hsi E.D., List A., Sekeres M.A., Rao A., McDevitt M.A., Maciejewski J.P. Mutational spectrum analysis of chronic myelomonocytic leukemia includes genes associated with epigenetic regulation: UTX, EZH2, and DNMT3A. Blood 2011, 118:3932-3941.
45. Kar S.A., Jankowska A., Makishima H., Visconte V., Jerez A., Sugimoto Y., Muramatsu H., Traina F., Afable M., Guinta K., Tiu R.V., Przychodzen B., Sakaguchi H., Kojima S., Sekeres M.A., List A.F., McDevitt M.A., Maciejewski J.P. Spliceosomal gene mutations are frequent events in the diverse mutational spectrum of chronic myelomonocytic leukemia but largely absent in juvenile myelomonocytic leukemia. Haematologica 2013, 98:107-113.
46. Gui Y., Guo G., Huang Y., Hu X., Tang A., Gao S., Wu R., Chen C., Li X., Zhou L., He M., Li Z., Sun X., Jia W., Chen J., Yang S., Zhou F., Zhao X., Wan S., Ye R., Liang C., Liu Z., Huang P., Liu C., Jiang H., Wang Y., Zheng H., Sun L., Liu X., Jiang Z., Feng D., Wu S., Zou J., Zhang Z., Yang R., Zhao J., Xu C., Yin W., Guan Z., Ye J., Zhang H., Li J., Kristiansen K., Nickerson M.L., Theodorescu D., Li Y., Zhang X., Li S., Wang J., Yang H., Cai Z. Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder. Nat. Genet. 2011, 43:875-878.
47. Dalgliesh G.L., Furge K., Greenman C., Chen L., Bignell G., Butler A., Davies H., Edkins S., Hardy C., Latimer C., Teague J., Andrews J., Barthorpe S., Beare D., Buck G., Campbell P.J., Forbes S., Jia M., Jones D., Knott H., Kok C.Y., Lau K.W., Leroy C., Lin M.L., McBride D.J., Maddison M., Maguire S., McLay K., Menzies A., Mironenko T., Mulderrig L., Mudie L., O'Meara S., Pleasance E., Rajasingham A., Shepherd R., Smith R., Stebbings L., Stephens P., Tang G., Tarpey P.S., Turrell K., Dykema K.J., Khoo S.K., Petillo D., Wondergem B., Anema J., Kahnoski R.J., Teh B.T., Stratton M.R., Futreal P.A. Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes. Nature 2010, 463:360-363.
48. Grasso C.S., Wu Y.M., Robinson D.R., Cao X., Dhanasekaran S.M., Khan A.P., Quist M.J., Jing X., Lonigro R.J., Brenner J.C., Asangani I.A., Ateeq B., Chun S.Y., Siddiqui J., Sam L., Anstett M., Mehra R., Prensner J.R., Palanisamy N., Ryslik G.A., Vandin F., Raphael B.J., Kunju L.P., Rhodes D.R., Pienta K.J., Chinnaiyan A.M., Tomlins S.A. The mutational landscape of lethal castration-resistant prostate cancer. Nature 2012, 487:239-243.
49. Dubuc A.M., Remke M., Korshunov A., Northcott P.A., Zhan S.H., Mendez-Lago M., Kool M., Jones D.T., Unterberger A., Morrissy A.S., Shih D., Peacock J., Ramaswamy V., Rolider A., Wang X., Witt H., Hielscher T., Hawkins C., Vibhakar R., Croul S., Rutka J.T., Weiss W.A., Jones S.J., Eberhart C.G., Marra M.A., Pfister S.M., Taylor M.D. Aberrant patterns of H3K4 and H3K27 histone lysine methylation occur across subgroups in medulloblastoma. Acta Neuropathol. 2013, 125:373-384.
50. Robinson G., Parker M., Kranenburg T.A., Lu C., Chen X., Ding L., Phoenix T.N., Hedlund E., Wei L., Zhu X., Chalhoub N., Baker S.J., Huether R., Kriwacki R., Curley N., Thiruvenkatam R., Wang J., Wu G., Rusch M., Hong X., Becksfort J., Gupta P., Ma J., Easton J., Vadodaria B., Onar-Thomas A., Lin T., Li S., Pounds S., Paugh S., Zhao D., Kawauchi D., Roussel M.F., Finkelstein D., Ellison D.W., Lau C.C., Bouffet E., Hassall T., Gururangan S., Cohn R., Fulton R.S., Fulton L.L., Dooling D.J., Ochoa K., Gajjar A., Mardis E.R., Wilson R.K., Downing J.R., Zhang J., Gilbertson R.J. Novel mutations target distinct subgroups of medulloblastoma. Nature 2012, 488:43-48.
51. Jones D.T., Jager N., Kool M., Zichner T., Hutter B., Sultan M., Cho Y.J., Pugh T.J., Hovestadt V., Stutz A.M., Rausch T., Warnatz H.J., Ryzhova M., Bender S., Sturm D., Pleier S., Cin H., Pfaff E., Sieber L., Wittmann A., Remke M., Witt H., Hutter S., Tzaridis T., Weischenfeldt J., Raeder B., Avci M., Amstislavskiy V., Zapatka M., Weber U.D., Wang Q., Lasitschka B., Bartholomae C.C., Schmidt M., von Kalle C., Ast V., Lawerenz C., Eils J., Kabbe R., Benes V., van Sluis P., Koster J., Volckmann R., Shih D., Betts M.J., Russell R.B., Coco S., Tonini G.P., Schuller U., Hans V., Graf N., Kim Y.J., Monoranu C., Roggendorf W., Unterberg A., Herold-Mende C., Milde T., Kulozik A.E., von Deimling A., Witt O., Maass E., Rossler J., Ebinger M., Schuhmann M.U., Fruhwald M.C., Hasselblatt M., Jabado N., Rutkowski S., von Bueren A.O., Williamson D., Clifford S.C., McCabe M.G., Collins V.P., Wolf S., Wiemann S., Lehrach H., Brors B., Scheurlen W., Felsberg J., Reifenberger G., Northcott P.A., Taylor M.D., Meyerson M., Pomeroy S.L., Yaspo M.L., Korbel J.O., Korshunov A., Eils R., Pfister S.M., Lichter P. Dissecting the genomic complexity underlying medulloblastoma. Nature 2012, 488:100-105.
52. Miyake N., Koshimizu E., Okamoto N., Mizuno S., Ogata T., Nagai T., Kosho T., Ohashi H., Kato M., Sasaki G., Mabe H., Watanabe Y., Yoshino M., Matsuishi T., Takanashi J., Shotelersuk V., Tekin M., Ochi N., Kubota M., Ito N., Ihara K., Hara T., Tonoki H., Ohta T., Saito K., Matsuo M., Urano M., Enokizono T., Sato A., Tanaka H., Ogawa A., Fujita T., Hiraki Y., Kitanaka S., Matsubara Y., Makita T., Taguri M., Nakashima M., Tsurusaki Y., Saitsu H., Yoshiura K., Matsumoto N., Niikawa N. MLL2 and KDM6A mutations in patients with Kabuki syndrome. Am. J. Med. Genet. A 2013, 161:2234-2243.
53. Miyake N., Mizuno S., Okamoto N., Ohashi H., Shiina M., Ogata K., Tsurusaki Y., Nakashima M., Saitsu H., Niikawa N., Matsumoto N. KDM6A point mutations cause Kabuki syndrome. Hum. Mutat. 2013, 34:108-110.
54. Gossage L., Murtaza M., Slatter A.F., Lichtenstein C.P., Warren A., Haynes B., Marass F., Roberts I., Shanahan S.J., Claas A., Dunham A., May A.P., Rosenfeld N., Forshew T., Eisen T. Clinical and pathological impact of VHL, PBRM1, BAP1, SETD2, KDM6A, and JARID1c in clear cell renal cell carcinoma. Gene Chromosome Cancer 2014, 53:38-51.
55. Shilatifard A. The COMPASS family of histone H3K4 methylases: mechanisms of regulation in development and disease pathogenesis. Annu. Rev. Biochem. 2012, 81:65-95.
56. Hu D., Gao X., Morgan M.A., Herz H.M., Smith E.R., Shilatifard A. The MLL3/MLL4 branches of the COMPASS family function as major histone H3K4 monomethylases at enhancers. Mol. Cell. Biol. 2013, 33:4745-4754.
57. Chen Y.H., Hung M.C., Li L.Y. EZH2: a pivotal regulator in controlling cell differentiation. Am. J. Transl. Res. 2012, 4:364-375.
58. Kanhere A., Viiri K., Araujo C.C., Rasaiyaah J., Bouwman R.D., Whyte W.A., Pereira C.F., Brookes E., Walker K., Bell G.W., Pombo A., Fisher A.G., Young R.A., Jenner R.G. Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2. Mol. Cell 2010, 38:675-688.
59. Wang A.H., Zare H., Mousavi K., Wang C., Moravec C.E., Sirotkin H.I., Ge K., Gutierrez-Cruz G., Sartorelli V. The histone chaperone Spt6 coordinates histone H3K27 demethylation and myogenesis. EMBO J. 2013, 32:1075-1086.
60. Margueron R., Reinberg D. The Polycomb complex PRC2 and its mark in life. Nature 2011, 469:343-349.
61. Mansour A.A., Gafni O., Weinberger L., Zviran A., Ayyash M., Rais Y., Krupalnik V., Zerbib M., Amann-Zalcenstein D., Maza I., Geula S., Viukov S., Holtzman L., Pribluda A., Canaani E., Horn-Saban S., Amit I., Novershtern N., Hanna J.H. The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming. Nature 2012, 488:409-413.
62. Lee M.G., Villa R., Trojer P., Norman J., Yan K.P., Reinberg D., Di Croce L., Shiekhattar R. Demethylation of H3K27 regulates polycomb recruitment and H2A ubiquitination. Science 2007, 318:447-450.
63. Hemming S., Cakouros D., Isenmann S., Cooper L., Menicanin D., Zannettino A., Gronthos S. EZH2 and KDM6A act as an epigenetic switch to regulate mesenchymal stem cell lineage specification. Stem Cells 2013, 32:802-815.
64. Zang Z.J., Cutcutache I., Poon S.L., Zhang S.L., McPherson J.R., Tao J., Rajasegaran V., Heng H.L., Deng N., Gan A., Lim K.H., Ong C.K., Huang D., Chin S.Y., Tan I.B., Ng C.C., Yu W., Wu Y., Lee M., Wu J., Poh D., Wan W.K., Rha S.Y., So J., Salto-Tellez M., Yeoh K.G., Wong W.K., Zhu Y.J., Futreal P.A., Pang B., Ruan Y., Hillmer A.M., Bertrand D., Nagarajan N., Rozen S., Teh B.T., Tan P. Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes. Nat. Genet. 2012, 44:570-574.
65. Ong C.K., Subimerb C., Pairojkul C., Wongkham S., Cutcutache I., Yu W., McPherson J.R., Allen G.E., Ng C.C., Wong B.H., Myint S.S., Rajasegaran V., Heng H.L., Gan A., Zang Z.J., Wu Y., Wu J., Lee M.H., Huang D., Ong P., Chan-on W., Cao Y., Qian C.N., Lim K.H., Ooi A., Dykema K., Furge K., Kukongviriyapan V., Sripa B., Wongkham C., Yongvanit P., Futreal P.A., Bhudhisawasdi V., Rozen S., Tan P., Teh B.T. Exome sequencing of liver fluke-associated cholangiocarcinoma. Nat. Genet. 2012, 44:690-693.
66. Jones S., Zhang X., Parsons D.W., Lin J.C., Leary R.J., Angenendt P., Mankoo P., Carter H., Kamiyama H., Jimeno A., Hong S.M., Fu B., Lin M.T., Calhoun E.S., Kamiyama M., Walter K., Nikolskaya T., Nikolsky Y., Hartigan J., Smith D.R., Hidalgo M., Leach S.D., Klein A.P., Jaffee E.M., Goggins M., Maitra A., Iacobuzio-Donahue C., Eshleman J.R., Kern S.E., Hruban R.H., Karchin R., Papadopoulos N., Parmigiani G., Vogelstein B., Velculescu V.E., Kinzler K.W. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 2008, 321:1801-1806.
67. Watanabe Y., Castoro R.J., Kim H.S., North B., Oikawa R., Hiraishi T., Ahmed S.S., Chung W., Cho M.Y., Toyota M., Itoh F., Estecio M.R., Shen L., Jelinek J., Issa J.P. Frequent alteration of MLL3 frameshift mutations in microsatellite deficient colorectal cancer. PLoS One 2011, 6:e23320.
68. Shin N., You K.T., Lee H., Kim W.K., Song M., Choi H.J., Rhee H., Nam S.W., Kim H. Identification of frequently mutated genes with relevance to nonsense mediated mRNA decay in the high microsatellite instability cancers. Int. J. Cancer 2011, 128:2872-2880.
69. Liu P., Morrison C., Wang L., Xiong D., Vedell P., Cui P., Hua X., Ding F., Lu Y., James M., Ebben J.D., Xu H., Adjei A.A., Head K., Andrae J.W., Tschannen M.R., Jacob H., Pan J., Zhang Q., Van den Bergh F., Xiao H., Lo K.C., Patel J., Richmond T., Watt M.A., Albert T., Selzer R., Anderson M., Wang J., Wang Y., Starnes S., Yang P., You M. Identification of somatic mutations in non-small cell lung carcinomas using whole-exome sequencing. Carcinogenesis 2012, 33:1270-1276.
70. Parsons D.W., Li M., Zhang X., Jones S., Leary R.J., Lin J.C., Boca S.M., Carter H., Samayoa J., Bettegowda C., Gallia G.L., Jallo G.I., Binder Z.A., Nikolsky Y., Hartigan J., Smith D.R., Gerhard D.S., Fults D.W., VandenBerg S., Berger M.S., Marie S.K., Shinjo S.M., Clara C., Phillips P.C., Minturn J.E., Biegel J.A., Judkins A.R., Resnick A.C., Storm P.B., Curran T., He Y., Rasheed B.A., Friedman H.S., Keir S.T., McLendon R., Northcott P.A., Taylor M.D., Burger P.C., Riggins G.J., Karchin R., Parmigiani G., Bigner D.D., Yan H., Papadopoulos N., Vogelstein B., Kinzler K.W., Velculescu V.E. The genetic landscape of the childhood cancer medulloblastoma. Science 2011, 331:435-439.
71. Pugh T.J., Weeraratne S.D., Archer T.C., Pomeranz Krummel D.A., Auclair D., Bochicchio J., Carneiro M.O., Carter S.L., Cibulskis K., Erlich R.L., Greulich H., Lawrence M.S., Lennon N.J., McKenna A., Meldrim J., Ramos A.H., Ross M.G., Russ C., Shefler E., Sivachenko A., Sogoloff B., Stojanov P., Tamayo P., Mesirov J.P., Amani V., Teider N., Sengupta S., Francois J.P., Northcott P.A., Taylor M.D., Yu F., Crabtree G.R., Kautzman A.G., Gabriel S.B., Getz G., Jager N., Jones D.T., Lichter P., Pfister S.M., Roberts T.M., Meyerson M., Pomeroy S.L., Cho Y.J. Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations. Nature 2012, 488:106-110.
72. Green M.R., Gentles A.J., Nair R.V., Irish J.M., Kihira S., Liu C.L., Kela I., Hopmans E.S., Myklebust J.H., Ji H., Plevritis S.K., Levy R., Alizadeh A.A. Hierarchy in somatic mutations arising during genomic evolution and progression of follicular lymphoma. Blood 2013, 121:1604-1611.
73. Neumann M., Heesch S., Schlee C., Schwartz S., Gokbuget N., Hoelzer D., Konstandin N.P., Ksienzyk B., Vosberg S., Graf A., Krebs S., Blum H., Raff T., Bruggemann M., Hofmann W.K., Hecht J., Bohlander S.K., Greif P.A., Baldus C.D. Whole-exome sequencing in adult ETP-ALL reveals a high rate of DNMT3A mutations. Blood 2013, 121:4749-4752.
74. Ng S.B., Bigham A.W., Buckingham K.J., Hannibal M.C., McMillin M.J., Gildersleeve H.I., Beck A.E., Tabor H.K., Cooper G.M., Mefford H.C., Lee C., Turner E.H., Smith J.D., Rieder M.J., Yoshiura K., Matsumoto N., Ohta T., Niikawa N., Nickerson D.A., Bamshad M.J., Shendure J. Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat. Genet. 2010, 42:790-793.
75. Hannibal M.C., Buckingham K.J., Ng S.B., Ming J.E., Beck A.E., McMillin M.J., Gildersleeve H.I., Bigham A.W., Tabor H.K., Mefford H.C., Cook J., Yoshiura K., Matsumoto T., Matsumoto N., Miyake N., Tonoki H., Naritomi K., Kaname T., Nagai T., Ohashi H., Kurosawa K., Hou J.W., Ohta T., Liang D., Sudo A., Morris C.A., Banka S., Black G.C., Clayton-Smith J., Nickerson D.A., Zackai E.H., Shaikh T.H., Donnai D., Niikawa N., Shendure J., Bamshad M.J. Spectrum of MLL2 (ALR) mutations in 110 cases of Kabuki syndrome. Am. J. Med. Genet. A 2011, 155A:1511-1516.
76. Banka S., Veeramachaneni R., Reardon W., Howard E., Bunstone S., Ragge N., Parker M.J., Crow Y.J., Kerr B., Kingston H., Metcalfe K., Chandler K., Magee A., Stewart F., McConnell V.P., Donnelly D.E., Berland S., Houge G., Morton J.E., Oley C., Revencu N., Park S.M., Davies S.J., Fry A.E., Lynch S.A., Gill H., Schweiger S., Lam W.W., Tolmie J., Mohammed S.N., Hobson E., Smith A., Blyth M., Bennett C., Vasudevan P.C., Garcia-Minaur S., Henderson A., Goodship J., Wright M.J., Fisher R., Gibbons R., Price S.M., Temple C.d.S.D.I.K., Collins A.L., Lachlan K., Elmslie F., McEntagart M., Castle B., Clayton-Smith J., Black G.C., Donnai D. How genetically heterogeneous is Kabuki syndrome?: MLL2 testing in 116 patients, review and analyses of mutation and phenotypic spectrum. Eur. J. Hum. Genet. 2012, 20:381-388.
77. Makrythanasis P., van Bon B., Steehouwer M., Rodriguez-Santiago B., Simpson M., Dias P., Anderlid B., Arts P., Bhat M., Augello B., Biamino E., Bongers E., Del Campo M., Cordeiro I., Cueto-Gonzalez A., Cusco I., Deshpande C., Frysira E., Izatt L., Flores R., Galan E., Gener B., Gilissen C., Granneman S., Hoyer J., Yntema H., Kets C., Koolen D., Marcelis C., Medeira A., Micale L., Mohammed S., de Munnik S., Nordgren A., Psoni S., Reardon W., Revencu N., Roscioli T., Ruiterkamp-Versteeg M., Santos H., Schoumans J., Schuurs-Hoeijmakers J., Silengo M., Toledo L., Vendrell T., van der Burgt I., van Lier B., Zweier C., Reymond A., Trembath R., Perez-Jurado L., Dupont J., de Vries B., Brunner H., Veltman J., Merla G., Antonarakis S., Hoischen A. MLL2 mutation detection in 86 patients with Kabuki syndrome: a genotype-phenotype study. Clin. Genet. 2013, 6:539-545.
78. Paulussen A.D., Stegmann A.P., Blok M.J., Tserpelis D., Posma-Velter C., Detisch Y., Smeets E.E., Wagemans A., Schrander J.J., van den Boogaard M.J., van der Smagt J., van Haeringen A., Stolte-Dijkstra I., Kerstjens-Frederikse W.S., Mancini G.M., Wessels M.W., Hennekam R.C., Vreeburg M., Geraedts J., de Ravel T., Fryns J.P., Smeets H.J., Devriendt K., Schrander-Stumpel C.T. MLL2 mutation spectrum in 45 patients with Kabuki syndrome. Hum. Mutat. 2011, 32:E2018-E2025.
79. Cleary S.P., Jeck W.R., Zhao X., Chen K., Selitsky S.R., Savich G.L., Tan T.X., Wu M.C., Getz G., Lawrence M.S., Parker J.S., Li J., Powers S., Kim H., Fischer S., Guindi M., Ghanekar A., Chiang D.Y. Identification of driver genes in hepatocellular carcinoma by exome sequencing. Hepatology 2013, 58:1693-1702.
80. Bea S., Valdes-Mas R., Navarro A., Salaverria I., Martin-Garcia D., Jares P., Gine E., Pinyol M., Royo C., Nadeu F., Conde L., Juan M., Clot G., Vizan P., Di Croce L., Puente D.A., Lopez-Guerra M., Moros A., Roue G., Aymerich M., Villamor N., Colomo L., Martinez A., Valera A., Martin-Subero J.I., Amador V., Hernandez L., Rozman M., Enjuanes A., Forcada P., Muntanola A., Hartmann E.M., Calasanz M.J., Rosenwald A., Ott G., Hernandez-Rivas J.M., Klapper W., Siebert R., Wiestner A., Wilson W.H., Colomer D., Lopez-Guillermo A., Lopez-Otin C., Puente X.S., Campo E. Landscape of somatic mutations and clonal evolution in mantle cell lymphoma. Proc. Natl. Acad. Sci. U. S. A. 2013, 110:18250-18255.
81. Lee J.E., Wang C., Xu S., Cho Y.W., Wang L., Feng X., Baldridge A., Sartorelli V., Zhuang L., Peng W., Ge K. H3K4 mono- and di-methyltransferase MLL4 is required for enhancer activation during cell differentiation. eLife 2013, 2:e01503.
82. Hu D., Garruss A.S., Gao X., Morgan M.A., Cook M., Smith E.R., Shilatifard A. The Mll2 branch of the COMPASS family regulates bivalent promoters in mouse embryonic stem cells. Nat. Struct. Mol. Biol. 2013, 20:1093-1097.
83. Wagner E.J., Carpenter P.B. Understanding the language of Lys36 methylation at histone H3. Nat. Rev. Mol. Cell Biol. 2012, 13:115-126.
84. Kurotaki N., Imaizumi K., Harada N., Masuno M., Kondoh T., Nagai T., Ohashi H., Naritomi K., Tsukahara M., Makita Y., Sugimoto T., Sonoda T., Hasegawa T., Chinen Y., Tomita Ha H.A., Kinoshita A., Mizuguchi T., Yoshiura Ki K., Ohta T., Kishino T., Fukushima Y., Niikawa N., Matsumoto N. Haploinsufficiency of NSD1 causes Sotos syndrome. Nat. Genet. 2002, 30:365-366.
85. Douglas J., Hanks S., Temple I.K., Davies S., Murray A., Upadhyaya M., Tomkins S., Hughes H.E., Cole T.R., Rahman N. NSD1 mutations are the major cause of Sotos syndrome and occur in some cases of Weaver syndrome but are rare in other overgrowth phenotypes. Am. J. Hum. Genet. 2003, 72:132-143.
86. Turkmen S., Gillessen-Kaesbach G., Meinecke P., Albrecht B., Neumann L.M., Hesse V., Palanduz S., Balg S., Majewski F., Fuchs S., Zschieschang P., Greiwe M., Mennicke K., Kreuz F.R., Dehmel H.J., Rodeck B., Kunze J., Tinschert S., Mundlos S., Horn D. Mutations in NSD1 are responsible for Sotos syndrome, but are not a frequent finding in other overgrowth phenotypes. Eur. J. Hum. Genet. 2003, 11:858-865.
87. Kurotaki N., Harada N., Shimokawa O., Miyake N., Kawame H., Uetake K., Makita Y., Kondoh T., Ogata T., Hasegawa T., Nagai T., Ozaki T., Touyama M., Shenhav R., Ohashi H., Medne L., Shiihara T., Ohtsu S., Kato Z., Okamoto N., Nishimoto J., Lev D., Miyoshi Y., Ishikiriyama S., Sonoda T., Sakazume S., Fukushima Y., Kurosawa K., Cheng J.F., Yoshiura K., Ohta T., Kishino T., Niikawa N., Matsumoto N. Fifty microdeletions among 112 cases of Sotos syndrome: low copy repeats possibly mediate the common deletion. Hum. Mutat. 2003, 22:378-387.
88. Rio M., Clech L., Amiel J., Faivre L., Lyonnet S., Le Merrer M., Odent S., Lacombe D., Edery P., Brauner R., Raoul O., Gosset P., Prieur M., Vekemans M., Munnich A., Colleaux L., Cormier-Daire V. Spectrum of NSD1 mutations in Sotos and Weaver syndromes. J. Med. Genet. 2003, 40:436-440.
89. Kamimura J., Endo Y., Kurotaki N., Kinoshita A., Miyake N., Shimokawa O., Harada N., Visser R., Ohashi H., Miyakawa K., Gerritsen J., Innes A.M., Lagace L., Frydman M., Okamoto N., Puttinger R., Raskin S., Resic B., Culic V., Yoshiura K., Ohta T., Kishino T., Ishikawa M., Niikawa N., Matsumoto N. Identification of eight novel NSD1 mutations in Sotos syndrome. J. Med. Genet. 2003, 40:e126.
90. Melchior L., Schwartz M., Duno M. dHPLC screening of the NSD1 gene identifies nine novel mutations-summary of the first 100 Sotos syndrome mutations. Ann. Hum. Genet. 2005, 69:222-226.
91. Sohn Y.B., Lee C.G., Ko J.M., Yang J.A., Yun J.N., Jung E.J., Jin H.S., Park S.J., Jeong S.Y. Clinical and genetic spectrum of 18 unrelated Korean patients with Sotos syndrome: frequent 5q35 microdeletion and identification of four novel NSD1 mutations. J. Hum. Genet. 2013, 58:73-77.
92. Opitz J.M., Weaver D.W., Reynolds J.F. The syndromes of Sotos and Weaver: reports and review. Am. J. Med. Genet. 1998, 79:294-304.
93. Baujat G., Rio M., Rossignol S., Sanlaville D., Lyonnet S., Le Merrer M., Munnich A., Gicquel C., Cormier-Daire V., Colleaux L. Paradoxical NSD1 mutations in Beckwith-Wiedemann syndrome and 11p15 anomalies in Sotos syndrome. Am. J. Hum. Genet. 2004, 74:715-720.
94. Tatton-Brown K., Douglas J., Coleman K., Baujat G., Cole T.R., Das S., Horn D., Hughes H.E., Temple I.K., Faravelli F., Waggoner D., Turkmen S., Cormier-Daire V., Irrthum A., Rahman N. Genotype-phenotype associations in Sotos syndrome: an analysis of 266 individuals with NSD1 aberrations. Am. J. Hum. Genet. 2005, 77:193-204.
95. Pasillas M.P., Shah M., Kamps M.P. NSD1 PHD domains bind methylated H3K4 and H3K9 using interactions disrupted by point mutations in human sotos syndrome. Hum. Mutat. 2011, 32:292-298.
96. Nielsen A.L., Jorgensen P., Lerouge T., Cervino M., Chambon P., Losson R. Nizp1, a novel multitype zinc finger protein that interacts with the NSD1 histone lysine methyltransferase through a unique C2HR motif. Mol. Cell. Biol. 2004, 24:5184-5196.
97. Visser R., Landman E.B., Goeman J., Wit J.M., Karperien M. Sotos syndrome is associated with deregulation of the MAPK/ERK-signaling pathway. PLoS One 2012, 7:e49229.
98. Fontebasso A.M., Schwartzentruber J., Khuong-Quang D.A., Liu X.Y., Sturm D., Korshunov A., Jones D.T., Witt H., Kool M., Albrecht S., Fleming A., Hadjadj D., Busche S., Lepage P., Montpetit A., Staffa A., Gerges N., Zakrzewska M., Zakrzewski K., Liberski P.P., Hauser P., Garami M., Klekner A., Bognar L., Zadeh G., Faury D., Pfister S.M., Jabado N., Majewski J. Mutations in SETD2 and genes affecting histone H3K36 methylation target hemispheric high-grade gliomas. Acta Neuropathol. 2013, 125:659-669.
99. Simon J.M., Hacker K.E., Singh D., Brannon A.R., Parker J.S., Weiser M., Ho T.H., Kuan P.F., Jonasch E., Furey T.S., Prins J.F., Lieb J.D., Rathmell W.K., Davis I.J. Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects. Genome Res. 2013, 24:241-250.
100. Kleine-Kohlbrecher D., Christensen J., Vandamme J., Abarrategui I., Bak M., Tommerup N., Shi X., Gozani O., Rappsilber J., Salcini A.E., Helin K. A functional link between the histone demethylase PHF8 and the transcription factor ZNF711 in X-linked mental retardation. Mol. Cell 2010, 38:165-178.
101. Laumonnier F., Holbert S., Ronce N., Faravelli F., Lenzner S., Schwartz C.E., Lespinasse J., Van Esch H., Lacombe D., Goizet C., Phan-Dinh Tuy F., van Bokhoven H., Fryns J.P., Chelly J., Ropers H.H., Moraine C., Hamel B.C., Briault S. Mutations in PHF8 are associated with X linked mental retardation and cleft lip/cleft palate. J. Med. Genet. 2005, 42:780-786.
102. Cukier H.N., Lee J.M., Ma D., Young J.I., Mayo V., Butler B.L., Ramsook S.S., Rantus J.A., Abrams A.J., Whitehead P.L., Wright H.H., Abramson R.K., Haines J.L., Cuccaro M.L., Pericak-Vance M.A., Gilbert J.R. The expanding role of MBD genes in autism: identification of a MECP2 duplication and novel alterations in MBD5, MBD6, and SETDB1. Autism Res. 2012, 5:385-397.
103. Piao Z., Fang W., Malkhosyan S., Kim H., Horii A., Perucho M., Huang S. Frequent frameshift mutations of RIZ in sporadic gastrointestinal and endometrial carcinomas with microsatellite instability. Cancer Res. 2000, 60:4701-4704.
104. Chadwick R.B., Jiang G.L., Bennington G.A., Yuan B., Johnson C.K., Stevens M.W., Niemann T.H., Peltomaki P., Huang S., de la Chapelle A. Candidate tumor suppressor RIZ is frequently involved in colorectal carcinogenesis. Proc. Natl. Acad. Sci. U. S. A. 2000, 97:2662-2667.
105. Tokumaru Y., Nomoto S., Jeronimo C., Henrique R., Harden S., Trink B., Sidransky D. Biallelic inactivation of the RIZ1 gene in human gastric cancer. Oncogene 2003, 22:6954-6958.
106. Sakurada K., Furukawa T., Kato Y., Kayama T., Huang S., Horii A. RIZ, the retinoblastoma protein interacting zinc finger gene, is mutated in genetically unstable cancers of the pancreas, stomach, and colorectum. Gene Chromosome Cancer 2001, 30:207-211.
107. Emterling A., Wallin A., Arbman G., Sun X.F. Clinicopathological significance of microsatellite instability and mutated RIZ in colorectal cancer. Ann. Oncol. 2004, 15:242-246.
108. Pan K.F., Lu Y.Y., Liu W.G., Zhang L., You W.C. Detection of frameshift mutations of RIZ in gastric cancers with microsatellite instability. World J. Gastroenterol. 2004, 10:2719-2722.
109. Grady W.M. Genomic instability and colon cancer. Cancer Metastasis Rev. 2004, 23:11-27.
110. Putiri E.L., Robertson K.D. Epigenetic mechanisms and genome stability. Clin. Epigenetics 2011, 2:299-314.
111. Vilar E., Gruber S.B. Microsatellite instability in colorectal cancer-the stable evidence. Nat. Rev. Clin. Oncol. 2010, 7:153-162.
112. Li F., Mao G., Tong D., Huang J., Gu L., Yang W., Li G.M. The histone mark H3K36me3 regulates human DNA mismatch repair through its interaction with MutSalpha. Cell 2013, 153:590-600.
113. Liu X., Gao Q., Li P., Zhao Q., Zhang J., Li J., Koseki H., Wong J. UHRF1 targets DNMT1 for DNA methylation through cooperative binding of hemi-methylated DNA and methylated H3K9. Nat. Commun. 2013, 4:1563.
114. Northcott P.A., Nakahara Y., Wu X., Feuk L., Ellison D.W., Croul S., Mack S., Kongkham P.N., Peacock J., Dubuc A., Ra Y.S., Zilberberg K., McLeod J., Scherer S.W., Sunil Rao J., Eberhart C.G., Grajkowska W., Gillespie Y., Lach B., Grundy R., Pollack I.F., Hamilton R.L., Van Meter T., Carlotti C.G., Boop F., Bigner D., Gilbertson R.J., Rutka J.T., Taylor M.D. Multiple recurrent genetic events converge on control of histone lysine methylation in medulloblastoma. Nat. Genet. 2009, 41:465-472.
115. Rodriguez-Paredes M., Martinez de Paz A., Simo-Riudalbas L., Sayols S., Moutinho C., Moran S., Villanueva A., Vazquez-Cedeira M., Lazo P.A., Carneiro F., Moura C.S., Vieira J., Teixeira M.R., Esteller M. Gene amplification of the histone methyltransferase SETDB1 contributes to human lung tumorigenesis. Oncogene 2013, 33:2807-2813.
116. Ceol C.J., Houvras Y., Jane-Valbuena J., Bilodeau S., Orlando D.A., Battisti V., Fritsch L., Lin W.M., Hollmann T.J., Ferre F., Bourque C., Burke C.J., Turner L., Uong A., Johnson L.A., Beroukhim R., Mermel C.H., Loda M., Ait-Si-Ali S., Garraway L.A., Young R.A., Zon L.I. The histone methyltransferase SETDB1 is recurrently amplified in melanoma and accelerates its onset. Nature 2011, 471:513-517.
117. Koivisto A.M., Ala-Mello S., Lemmela S., Komu H.A., Rautio J., Jarvela I. Screening of mutations in the PHF8 gene and identification of a novel mutation in a Finnish family with XLMR and cleft lip/cleft palate. Clin. Genet. 2007, 72:145-149.
118. Feng W., Yonezawa M., Ye J., Jenuwein T., Grummt I. PHF8 activates transcription of rRNA genes through H3K4me3 binding and H3K9me1/2 demethylation. Nat. Struct. Mol. Biol. 2010, 17:445-450.
119. Qiu J., Shi G., Jia Y., Li J., Wu M., Dong S., Wong J. The X-linked mental retardation gene PHF8 is a histone demethylase involved in neuronal differentiation. Cell Res. 2010, 20:908-918.
120. Qi H.H., Sarkissian M., Hu G.Q., Wang Z., Bhattacharjee A., Gordon D.B., Gonzales M., Lan F., Ongusaha P.P., Huarte M., Yaghi N.K., Lim H., Garcia B.A., Brizuela L., Zhao K., Roberts T.M., Shi Y. Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development. Nature 2010, 466:503-507.
121. Zhu Z., Wang Y., Li X., Xu L., Wang X., Sun T., Dong X., Chen L., Mao H., Yu Y., Li J., Chen P.A., Chen C.D. PHF8 is a histone H3K9me2 demethylase regulating rRNA synthesis. Cell Res. 2010, 20:794-801.
122. Jensen L.R., Amende M., Gurok U., Moser B., Gimmel V., Tzschach A., Janecke A.R., Tariverdian G., Chelly J., Fryns J.P., Van Esch H., Kleefstra T., Hamel B., Moraine C., Gecz J., Turner G., Reinhardt R., Kalscheuer V.M., Ropers H.H., Lenzner S. Mutations in the JARID1C gene, which is involved in transcriptional regulation and chromatin remodeling, cause X-linked mental retardation. Am. J. Hum. Genet. 2005, 76:227-236.
123. Santos C., Rodriguez-Revenga L., Madrigal I., Badenas C., Pineda M., Mila M. A novel mutation in JARID1C gene associated with mental retardation. Eur. J. Hum. Genet. 2006, 14:583-586.
124. Iwase S., Lan F., Bayliss P., de la Torre-Ubieta L., Huarte M., Qi H.H., Whetstine J.R., Bonni A., Roberts T.M., Shi Y. The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. Cell 2007, 128:1077-1088.
125. Halushka M.K., Fan J.B., Bentley K., Hsie L., Shen N., Weder A., Cooper R., Lipshutz R., Chakravarti A. Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat. Genet. 1999, 22:239-247.
126. Cargill M., Altshuler D., Ireland J., Sklar P., Ardlie K., Patil N., Shaw N., Lane C.R., Lim E.P., Kalyanaraman N., Nemesh J., Ziaugra L., Friedland L., Rolfe A., Warrington J., Lipshutz R., Daley G.Q., Lander E.S. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat. Genet. 1999, 22:231-238.
127. Sunyaev S., Ramensky V., Bork P. Towards a structural basis of human non-synonymous single nucleotide polymorphisms. Trends Genet. 2000, 16:198-200.
128. Ernst J., Kheradpour P., Mikkelsen T.S., Shoresh N., Ward L.D., Epstein C.B., Zhang X., Wang L., Issner R., Coyne M., Ku M., Durham T., Kellis M., Bernstein B.E. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 2011, 473:43-49.
129. Tsuge M., Hamamoto R., Silva F.P., Ohnishi Y., Chayama K., Kamatani N., Furukawa Y., Nakamura Y. A variable number of tandem repeats polymorphism in an E2F-1 binding element in the 5' flanking region of SMYD3 is a risk factor for human cancers. Nat. Genet. 2005, 37:1104-1107.
130. Crea F., Fornaro L., Paolicchi E., Masi G., Frumento P., Loupakis F., Salvatore L., Cremolini C., Schirripa M., Graziano F., Ronzoni M., Ricci V., Farrar W.L., Falcone A., Danesi R. An EZH2 polymorphism is associated with clinical outcome in metastatic colorectal cancer patients. Ann. Oncol. 2012, 23:1207-1213.
131. Fornaro L., Crea F., Masi G., Paolicchi E., Loupakis F., Graziano F., Salvatore L., Ronzoni M., Ricci V., Cremolini C., Schirripa M., Danesi R., Falcone A. EZH2 polymorphism and benefit from bevacizumab in colorectal cancer: another piece to the puzzle. Ann. Oncol. 2012, 23:1370-1371.
132. Wang Z., Moult J. SNPs, protein structure, and disease. Hum. Mutat. 2001, 17:263-270.
133. George Priya Doss C., Rajasekaran R., Sethumadhavan R. Computational identification and structural analysis of deleterious functional SNPs in MLL gene causing acute leukemia, Interdisciplinary sciences. Comput. Life Sci. 2010, 2:247-255.
134. Pointon J.J., Harvey D., Karaderi T., Appleton L.H., Farrar C., Wordsworth B.P. The histone demethylase JARID1A is associated with susceptibility to ankylosing spondylitis. Genes Immun. 2011, 12:395-398.
135. Sasaki O., Meguro K., Tohmiya Y., Funato T., Shibahara S., Sasaki T. Nucleotide alteration of retinoblastoma protein-interacting zinc finger gene, RIZ, in human leukemia. Tohoku J. Exp. Med. 2002, 196:193-201.
136. Lawrence M.S., Stojanov P., Mermel C.H., Robinson J.T., Garraway L.A., Golub T.R., Meyerson M., Gabriel S.B., Lander E.S., Getz G. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 2014, 505:495-501.