Selected Publications

2017

Valdés-Mora F, Gould CM, Colino-Sanguino Y, Qu W, Song JZ, Taylor KM, Buske FA, Statham AL, Nair SS, Armstrong NJ, Kench JG, Lee KML, Horvath LG, Qiu M, Ilinykh A, Yeo-Teh NS, Gallego-Ortega D, Stirzaker C, Clark SJ (2017). Acetylated histone variant H2A.Z is involved in the activation of neo-enhancers in prostate cancer. Nature Communications 8:1346. doi: 10.1038/s41467-017-01393-8.

Clark SJ, Molloy PL (2017). Smoke-Induced Changes to the Epigenome Provide Fertile Ground for Oncogenic Mutation. Cancer Cell 32:278-280. doi: 10.1016/j.ccell.2017.08.016 (Commentary).

Achinger­Kawecka J, Taberlay PC, Clark SJ (2017). Alterations in Three­Dimensional Organization of the Cancer Genome and Epigenome. Cold Spring Harb Symp Quant Biol 81:41­51. doi: 10.1101/sqb.2016.81.031013

Skvortsova K, Zotenko E, Luu PL, Gould CM, Nair SS, Clark SJ*, Stirzaker C* (2017). Comprehensive evaluation of genome-wide hydroxymethylcytosine profiling approaches in human DNA. Epigenetics & Chromatin 10:16. doi: 10.1186/s13072-017-0123-7. * Equal Last Authors

Stirzaker C, Song J, Ng W, Du Q, Armstrong N, Locke W, Statham A, French H, Pidsley R, Valdes-Mora F, Zotenko E, Clark SJ (2017). Methyl-CpG-Binding Protein MBD2 plays a key role in maintenance and spread of DNA methylation of CpG islands and shores in cancer. Oncogene 36:1328-1338. doi: 10.1038/onc.2016.297.

2016

Pidsley R, Zotenko E, Peters T, Lawrence MG, Risbridger GP, Molloy P, Van Dijk S, Muhlhausler B, Stirzaker C*, Clark SJ* (2016). Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling. Genome Biology 17:208. * Equal Last Authors

Taberlay PC, Achinger-Kawecka A, Lun ATL, Buske FA, Sabir K, Gould CM, Zotenko E, Bert SA, Giles KA, Bauer DC, Smyth GK, Stirzaker C, O’Donoghue SI, Clark SJ (2016). Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations. Genome Research, 26:719-31.

BLUEPRINT consortium (Qu W, Nair S, Statham A, Stirzaker C, Clark SJ (2016). Quantitative comparison of DNA methylation assays for biomarker development and clinical applications. Nat Biotechnology, 34:726-37.

Colino-Sanguino Y, Clark SJ*, Valdes-Mora F* (2016). H2A.Z acetylation and transcription: ready, steady, go! Epigenomics, 8:583-6 *Equal Last Authors (Review).

2015

Stirzaker C, Zotenko E, Song JZ, Qu W, Nair SS, Locke WJ, Stone A, Armstong NJ, Robinson MD, Dobrovic A, Avery-Kiejda KA, Peters KM, French JD, Stein S, Korbie DJ, Trau M, Forbes JF, Scott RJ, Brown MA, Francis GD and Clark SJ (2015). Methylome sequencing in triple-negative breast cancer reveals distinct methylation clusters with prognostic value. Nat Communications 6:5899.

Stone A, Zotenko E, Locke WJ, Korbie D, Millar EK, Pidsley R, Stirzaker C, Graham P, Trau M, Musgrove EA, Nicholson RI, Gee JM and Clark SJ (2015). DNA methylation of oestrogen-regulated enhancers defines endocrine sensitivity in breast cancer. Nat Communications 6:7758.

Du Q, Luu PL, Stirzaker C and Clark SJ (2015). Methyl-CpG-binding domain proteins: readers of the epigenome. Epigenomics 1-23 (Review).

Locke WJ, Zotenko E, Stirzaker C, Robinson MD, Hinshelwood RA, Stone A, Reddel RR, Huschtscha LI and Clark SJ (2015). Coordinated epigenetic remodelling of transcriptional networks occurs during early breast carcinogenesis. Clinical Epigenetics 7(1):52.

2014

Mahon KL, Qu W, Devaney J, Paul C, Castillo L, Wykes RJ, Chatfield MD, Boyer MJ, Stockler MR, Marx G, Gurney H, Mallesara G, Molloy PL, Horvath LG and Clark SJ; PRIMe consortium (2014). Methylated Glutathione S-transferase 1 (mGSTP1) is a potential plasma free DNA epigenetic marker of prognosis and response to chemotherapy in castrate-resistant prostate cancer. British Journal of Cancer 111:1802-9.

Taberlay P, Statham A, Kelly TK, Clark SJ* and Jones PA* (2014). Reconfiguration of nucleosome depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer. Genome Res: doi:10.1101/gr.163485.113. * Equal Last Authors

Skulte KA, Phan L, Clark SJ* and Taberlay PC* (2014). Chromatin remodeler mutations in human cancers: epigenetic implications. Epigenomics 6:397-414. * Equal Last Authors (Review)

2013

Robinson MD, Strbenac D, Stirzaker C, Statham AL, Song J, Speed TP and Clark SJ (2013). Copy-number-aware differential analysis of DNA sequencing data. Genome Research 22:2489-2496.

Bert SA, Robinson MD, Strbenac D, Statham AL, Song JZ, Hulf T, Sutherland RL, Coolen MW, Stirzaker C and Clark SJ (2013). Regional activation of the cancer genome by long range epigenetic remodelling. Cancer Cell 23:9-22.

Hulf T, Sibbritt T, Wiklund ED, Patterson K, Song JZ, Stirzaker C, Qu W, Nair S, Horvath LG, Armstrong NJ, Kench JG, Sutherland RL and Clark SJ (2013). Epigenetic-induced repression of microRNA-205 is associated with MED1 activation and a poorer prognosis in localized prostate cancer. Oncogene 32:2891-9.

2012

Valdes-Mora F, Song JZ, Statham AL, Strbenac D, Robinson MD, Nair SS, Patterson KI, Tremethick DJ, Stirzaker C and Clark SJ (2012). Acetylation of H2A.Z is a key epigenetic modification associated with gene deregulation and epigenetic remodeling in cancer. Genome Res 22:307-321.

Statham AL, Robinson MD, Song JZ, Coolen MW, Stirzaker C and Clark SJ (2012). Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA. Genome Res 22:1120-1127.

Locke WJ and Clark SJ (2012). Epigenome remodelling in breast cancer: insights from an early in vitro model of carcinogenesis. Breast Cancer Res 14:10.1186/bcr3237 (Review)

Gloss BS, Patterson KI, Barton CA, Gonzalez M, Scurry JP, Hacker NF, Sutherland RL, O'Brien PM and Clark SJ (2012). Integrative genome-wide expression and promoter DNA methylation profiling identifies a novel panel of ovarian cancer epigenetic biomarkers. Cancer Lett 318:76-85.

2011

Wiklund ED, Gao S, Hulf T, Sibbritt T, Nair S, Costea DE, Villadsen SB, Bakholdt V, Bramsen JB, Sorensen JA, Krogdahl A, Clark SJ* and Kjems J* (2011). MicroRNA alterations and associated aberrant DNA methylation patterns across multiple sample types in oral squamous cell carcinoma. PLoS One 2011; 6:e27840. *Equal Last Authors

Patterson K, Molloy L, Qu W and Clark SJ (2011). DNA methylation: bisulphite modification and analysis. JoVE 56:e3170.

Nair SS, Coolen MW, Stirzaker C, Song JZ, Statham AL, Strbenac D, Robinson MD and Clark SJ (2011). Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias. Epigenetics 6:34-44.

Lee HJ, Hinshelwood RA, Bouras T, Gallego-Ortega D, Valdes-Mora F, Blazek K, Visvader JE, Clark SJ* and Ormandy CJ* (2011). Lineage specific methylation of the Elf5 promoter in mammary epithelial cells. Stem Cells 29:1611-1619. * Equal Last Authors

Hulf T, Sibbritt T, Wiklund ED, Bert S, Strbenac D, Statham AL, Robinson MD and Clark SJ (2011). Discovery pipeline for epigenetically deregulated miRNAs in cancer: integration of primary miRNA transcription. BMC Genomics 12:54.

Hansen TB, Wiklund ED, Bramsen JB, Villadsen SB, Statham AL, Clark SJ and Kjems J (2011). miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA. EMBO J 2011; 30:4414-4422.

Devaney J, Stirzaker C, Qu W, Song JZ, Statham AL, Patterson KI, Horvath LG, Tabor B, Coolen MW, Hulf T, Kench JG, Henshall SM, Benito RP, Haynes A-M, Mayor R, Peinado MA, Sutherland RL and Clark SJ (2011). Epigenetic deregulation across chromosome 2q14.2 differentiates normal from prostate cancer and provides a regional panel of novel DNA methylation cancer biomarkers. Cancer Epidemiol Biomarkers Prev 20:148-159.

2006-2010

Wiklund ED, Kjems J and Clark SJ (2010). Epigenetic architecture and miRNA: reciprocal regulators. Epigenomics 2:823-840 (Review).

Wiklund ED, Bramsen JB, Hulf T, Dyrskjøt L, Ramanathan R, Hansen TB, Villadsen SB, Gao S, Ostenfeld MS, Borre M, Peter ME, Ørntoft TF, Kjems J* and Clark SJ* (2010). Coordinated epigenetic repression of the miR-200 family and miR-205 in invasive bladder cancer. Int J Cancer128:1327-1334. * Equal Last Authors

Statham AL, Strbenac D, Coolen MW, Stirzaker C, Clark SJ and Robinson MD (2010). Repitools: an R package for the analysis of enrichment-based epigenomic data. Bioinformatics 26:1662-1663.

Robinson MD, Stirzaker C, Statham AL, Coolen MW, Song JZ, Nair SS, Strbenac D, Speed TP and Clark SJ (2010). Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation. Genome Research 20:1719-1729.

Robinson MD, Statham AL, Speed TP and Clark SJ (2010). Protocol matters: which methylome are you actually studying? Epigenomics 2:587-598 (Review).

Coolen MW, Stirzaker C, Song JZ, Statham AL, Kassir Z, Moreno CS, Young AN, Varma V, Speed TP, Cowley M, Lacaze P, Kaplan W, Robinson MD and Clark SJ (2010). Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity. Nature Cell Biology 12:235-246.

Hinshelwood RA, Melki JR, Huschtscha LI, Paul C, Song JZ, Stirzaker C, Reddel RR and Clark SJ (2009). Aberrant de novo methylation of the p16(INK4A) CpG island is initiated post gene silencing in association with chromatin remodelling and mimics nucleosome positioning. Hum Mol Genet 18:3098-3109.

Hinshelwood RA, Huschtscha LI, Melki J, Stirzaker C, Abdipranoto A, Vissel B, Ravasi T, Wells CA, Hume DA, Reddel RR and Clark SJ (2007). Concordant epigenetic silencing of transforming growth factor-beta signaling pathway genes occurs early in breast carcinogenesis. Cancer Research 67:11517-11527.

Coolen MW, Statham AL, Gardiner-Garden M and Clark SJ (2007). Genomic profiling of CpG methylation and allelic specificity using quantitative high- throughput mass spectrometry: critical evaluation and improvements. Nucleic Acids Res 35:e119.

Frigola J, Song J, Stirzaker C, Hinshelwood RA, Peinado MA and Clark SJ (2006). Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band. Nature Genetics 38:540-549.

Clark SJ, Statham A, Stirzaker C, Molloy PL and Frommer M (2006). DNA methylation: Bisulphite modification and analysis. Nature Protocols 1:2353-2364.

Prior to 2006

Stirzaker C, Song JZ, Davidson B and Clark SJ (2004). Transcriptional gene silencing promotes DNA hypermethylation through a sequential change in chromatin modifications in cancer cells. Cancer Res, 64:3871-3877.

Song JZ, Stirzaker C, Harrison J, Melki JR and Clark SJ (2002). Hypermethylation trigger of the glutathione-S-transferase gene (GSTP1) in prostate cancer cells. Oncogene, 21:1048-1061.

Stirzaker C, Millar DS, Paul CL, Warnecke PM, Harrison J, Vincent PC, Frommer M and Clark SJ (1997). Extensive DNA methylation spanning the Rb promoter in retinoblastoma tumors. Cancer Res, 57:2229-2237.

Clark SJ, Harrison J and Frommer M (1995). CpNpG methylation in mammalian-cells. Nat Genet, 10:20-27.

 


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