Publications

Selected Recent Publications:

• Tan K, Wilkinson MF. Regulation of both transcription and RNA turnover contribute to germline specification. Nucleic Acids Res. 2022 Jul 22;50(13):7310-7325. doi: 10.1093/nar/gkac542. PMID: 35776114; PMCID: PMC9303369.
• Mortazavi M, Ren Y, Saini S, Antaki D, St Pierre CL, Williams A, Sohni A, Wilkinson MF, Gymrek M, Sebat J, Palmer AA. SNPs, short tandem repeats, and structural variants are responsible for differential gene expression across C57BL/6 and C57BL/10 substrains. Cell Genom. 2022 Mar 9;2(3):100102. doi: 10.1016/j.xgen.2022.100102. PMID: 35720252; PMCID: PMC9205302.
• Bhardwaj A, Sohni A, Lou CH, De Gendt K, Zhang F, Kim E, Subbarayalu P, Chan W, Kerkhofs S, Claessens F, Kimmins S, Rao MK, Meistrich M, Wilkinson MF. Concordant Androgen-Regulated Expression of Divergent Rhox5 Promoters in Sertoli Cells. Endocrinology. 2022 Jan 1;163(1):bqab237. doi: 10.1210/endocr/bqab237. PMID: 34902009; PMCID: PMC8667857.
• Tan K, Song HW, Wilkinson MF. RHOX10 drives mouse spermatogonial factor stem cell establishment through a transcription factor signaling cascade. Cell Reports, 2021.

• Tan K, Kim ME, Song HW, Skarbrevik D, Babajanian E, Bedrosian TA, Gage FH, Wilkinson MF. The Rhox gene cluster supresses germline LINE1 transposition. Proc Natl Acad Sci USA, 2021.
• Tan K, Jones S, Lake BB, Dumdie J, Shum EY, Zhang L, Chen S, Sohni A, Pandya S, Gallo RL, Zhang K, Cook-Andersen H, Wilkinson MF. The role of the NMD factor UPF3B in olfactory sensory neurons. eLife, 2020.
• Domingo D, Nawaz U, Corbett M, Espinoza JL, Tatton-Brown K, Coman D, Wilkinson MF, Gecz J, Jolly LA. UPF3B mutations including a novel synonymous variant associated with absent speech implicate nonsense mediated mRNA decay as a regulator of neurodevelopmental disorder gene networks. Hum Mol Genet, 2020.
• Tan K, Song HW, Thompson M, Munyoki SK, Sukhwani M, Hsieh TC, Orwig KE, Wilkinson MF. Transcriptome profiling reveals signaling conditions dictating human spermatogonia fate in vitro. Proc Natl Acad Sci USA, 2020.
• Tan K, Song HW, Wilkinson MF. Single-cell RNAseq analysis of testicular germ and somatic cell development during the perinatal period. Development, 2020.
• Ramaiah M, Tan K, Plank TM, Song HW, Dumdie JN, Jones S, Shum EY, Sheridan SD, Peterson KJ, Gromoll J, Haggarty SJ, Cook-Andersen H, Wilkinson MF. Response to: X‐linked miR‐506 family miRNAs promote FMRP expression in mouse spermatogonia. EMBO Rep, 2020.

• Fox CW, Zhang L, Sohni A, Doblado M, Wilkinson MF, Chang RJ, Duleba AJ. Inflammatory Stimuli Trigger Increased Androgen Production and Shifts in Gene Expression in Theca-Interstitial Cells. Endocrinology, 2019.
• Sohni A, Tan K, Song HW, Burow D, de Rooij DG, Laurent L, Hsieh TC, Rabah R, Hammoud SS, Vicini E, Wilkinson MF. The Neonatal and Adult Human Testis Defined at the Single-Cell Level. Cell Reports, 2019.
• Ramaiah M, Tan K, Plank TM, Song HW, Dumdie JN, Jones S, Shum EY, Sheridan SD, Peterson KJ, Gromoll J, Haggarty SJ, Cook-Andersen H, Wilkinson MF. A microRNA cluster in the Fragile-X region expressed during spermatogenesis targets FMR1. EMBO Reports, 2018.
• Dumdie JN, Cho K, Ramaiah M, Skarbrevik D, Mora-Castilla S, Stumpo DJ, Lykke-Anderson J, Laurent LC, Blackshear PJ, Wilkinson MF, Cook Anderson H. Chromatin Modification and Global Transcriptional Silencing in the Oocyte Mediated by the mRNA Decay Activator ZFP36L2, Developmental Cell, 2018.
• Huang L, Shum EY, Jones SH, Lou C-H, Dumdie J, Kim H, Roberts AJ, Jolly LA, Espinoza J, Skarbrevik DM, Phan MH, Cook-Andersen H, Swerdlow NR, Gecz J & Wilkinson MF. A Upf3b-Mutant Mouse Model with Behavioral and Neurogenesis Defects, Molecular Psychiatry, 2017.
• Lu J, Plank TD, Su F, Shi X, Liu C, Ji Y, Li S, Huynh A, Shi C, Zhu B, Yang G, Wu Y, Wilkinson MF & Lu Y. The nonsense-mediated RNA decay pathway is disrupted in inflammatory myofibroblastic tumors, The Journal of Clinical Investigation, 2016.
• Shum EY, Jones SH, Shao A, Dumdie J, Krause MD, Chan WK, Lou CH, Espinoza JL, Song HW, Phan MH, Ramaiah M, Huang L, McCarrey JR, Peterson KJ, De Rooij DG, Cook-Andersen H, Wilkinson MF. The Antagonistic Gene Paralogs Upf3a and Upf3b Govern Nonsense-Mediated RNA Decay, Cell, 2016.
• Song HW, Bettegowda A, Lake BB, Zhao AH, Skarbrevik D, Babajanian E, Sukhwani M, Shum EY, Phan MH, Plank TD, Richardson ME, Ramaiah M, Sridhar V, de Rooij DG, Orwig KE, Zhang K, Wilkinson MF. The Homeobox Transcription Factor RHOX10 Drives Mouse Spermatogonial Stem Cell Establishment, Cell Reports, 2016.
• Lu J, Plank TD, Su F, Shi X, Liu C, Ji Y, Li S, Huynh A, Shi C, Zhu B, Yang G, Wu Y, Wilkinson MF, Lu Y. The nonsense-mediated RNA decay pathway is disrupted in inflammatory myofibroblastic tumors, Journal of Clinical Investigation, 2016.
• Lou CH, Dumdie J, Goetz A, Shum EY, Brafman D, Liao X, Mora-Castilla S, Ramaiah M, Cook-Andersen H, Laurent L, Wilkinson MF. Nonsense-Mediated RNA Decay Influences Human Embryonic Stem Cell Fate, Stem Cell Reports, 2016.
• Jennifer Borgmann, Frank Tuttelmann, Bernd Dworniczak, Albrecht Ropke , Hye-Won Song, Sabine Kliesch, Miles F. Wilkinson, Sandra Laurentino, and Jorng Gromoll. The human RHOX gene cluster: target genes and functional analysis of gene variants in infertile men, Human Molecular Genetics 2016.
• Shum EY, Espinoza JL, Ramaiah M, Wilkinson MF.  Identification of novel post-transcriptional features in olfactory receptor family mRNAs.  Nucleic Acids Research, 2015.
• Song HW, Bettegowda A, Oliver D, Yan W, Phan MH, de Rooij DG, Corbett MA, Wilkinson MF.  shRNA Off-Target Effects In Vivo: Impaired Endogenous siRNA Expression and Spermatogenic Defects.  PLoS One, 2015.
• Karam R, Lou CH, Kroeger H, Huang L, Lin JH, Wilkinson MF.  The unfolded protein response is shaped by the NMD pathway.  EMBO Reports, 16:599-609 (2015).
• Rao MK, Matsumoto Y, Richardson ME, Panneerdoss S, Bhardwaj A, Ward JM, Shanker S, Bettegowda A, Wilkinson MF. Hormone- and DNA Demethylation-Induced Relief of a Tissue-Specific and Developmentally Regulated Block in Transcriptional Elongation. J Biol Chem, 2014. 
• Liu C, Karam R, Zhou Y, Su F, Ji Y, Li G, Xu G, Lu L, Wang C Song M, Zhu J, Wang Y, Zhao Y, Foo WC, Zuo M, Valasek MA, Javle M, Wilkinson MF, Lu Y. The UPF1 RNA surveillance gene is commonly mutated in pancreatic adenosquamous carcinoma. Nature Medicine, 2014.
• De Gendt K, Verhoeven G, Amieux PS, Wilkinson MF. Genome-wide identification of AR-regulated genes translated in Sertoli cells in vivo using the RiboTag approach. Molecular Endocrinology, 2014.
• Lou CH, Shao A, Shum EY, Espinoza JL, Huang L, Karam R, Wilkinson MF. Posttranscriptional control of the stem cell and neurogenic programs by the nonsense-mediated RNA decay pathway. Cell Reports, 2014.
• Lasalde C, Rivera AV, León AJ, González-Feliciano JA, Estrella LA, Rodríguez-Cruz EN, Correa ME, Cajigas IJ, Bracho DP, Vega IE, Wilkinson MF, González CI. Identification and functional analysis of novel phosphorylation sites in the RNA surveillance protein Upf1. Nucleic Acids Research, 2014.
• MacLean JA 2nd, Hu Z, Welborn JP, Song HW, Rao MK, Wayne CM, Wilkinson MF. The RHOX homeodomain proteins regulate the expression of insulin and other metabolic regulators in the testis. Journal of Biological Chemistry, 2013.
• Maeder ML, Angstman JF, Richardson ME, Linder SJ, Cascio VM, Tsai SQ, Ho QH, Sander JD, Reyon D, Bernstein BE, Costello JF, Wilkinson MF, Joung JK. Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins. Nature Biotechnology, 2013.
• Richardson ME, Bleiziffer A, Tüttelmann F, Gromoll J, Wilkinson MF. Epigenetic regulation of the RHOX homeobox gene cluster and its association with human male infertility. Human Molecular Genetics, 2013.
• Song HW, Anderson RA, Bayne RA, Gromoll J, Shimasaki S, Chang RJ, Parast MM, Laurent LC, de Rooij DG, Hsieh TC,Wilkinson MF. The RHOX homeobox gene cluster is selectively expressed in human oocytes and male germ cells. Human Reproduction, 2013.
• MacLean JA 2nd, Hayashi K, Turner TT, Wilkinson MF. The Rhox5 homeobox gene regulates the region-specific expression of its paralogs in the rodent epididymis. Biology of Reproduction, 2012.
• Song HW, Dann CT, McCarrey JR, Meistrich ML, Cornwall GA,Wilkinson MF. Dynamic expression pattern and subcellular localization of the Rhox10 homeobox transcription factor during early germ cell development. Reproduction, 2012.
• Bhardwaj A, Song HW, Beildeck M, Kerkhofs S, Castoro R, Shanker S, De Gendt K, Suzuki K, Claessens F, Issa JP, Orgebin-Crist MC, Wilkinson MF. DNA demethylation-dependent AR recruitment and GATA factors drive Rhox5 homeobox gene transcription in the epididymis. Molecular Endocrinology, 2012.
• Nguyen LS, Jolly L, Shoubridge C, Chan WK, Huang L, Laumonnier F, Raynaud M, Hackett A, Field M, Rodriguez J, Srivastava AK, Lee Y, Long R, Addington AM, Rapoport JL, Suren S, Hahn CN, Gamble J, Wilkinson MF, Corbett MA, Gecz J. Transcriptome profiling of UPF3B/NMD-deficient lymphoblastoid cells from patients with various forms of intellectual disability. Molecular Psychiatry, 2012.
• Huang L, Lou CH, Chan W, Shum EY, Shao A, Stone E, Karam R, Song HW, Wilkinson MF. RNA homeostasis governed by cell type-specific and branched feedback loops acting on NMD. Molecular Cell, 2011.
• De Gendt K, Denolet E, Willems A, Daniels VW, Clinckemalie L, Denayer S, Wilkinson MF, Claessens F, Swinnen JV, Verhoeven G. Expression of Tubb3, a beta-tubulin isotype, is regulated by androgens in mouse and rat Sertoli cells. Biology of Reproduction, 2013.
• Bruno IG, Karam R, Huang L, Bhardwaj A, Lou CH, Shum EY, Song HW, Corbett MA, Gifford WD, Gecz J, Pfaff SL, Wilkinson MF. Identification of a microRNA that activates gene expression by repressing nonsense-mediated RNA decay. Molecular Cell, 2011.
• Maclean JA, Bettegowda A, Kim BJ, Lou CH, Yang SM, Bhardwaj A, Shanker S, Hu Z, Fan Y, Eckardt S, McLaughlin KJ, Skoultchi AI, Wilkinson MF. The rhox homeobox gene cluster is imprinted and selectively targeted for regulation by histone h1 and DNA methylation. Molecular and Cellular Biology, 2011.
• Imam JS, Gudikote JP, Chan WK, Wilkinson MF. Frame-disrupting mutations elicit pre-mRNA accumulation independently of frame disruption. Nucleic Acids Research, 2009.
• Hu Z, Dandekar D, O’Shaughnessy PJ, De Gendt K, Verhoeven G, Wilkinson MF. Androgen-induced Rhox homeobox genes modulate the expression of AR-regulated genes. Molecular Endocrinology, 2010.
• Estrella LA, Wilkinson MF, González CI. The shuttling protein Npl3 promotes translation termination accuracy in Saccharomyces cerevisiae. Journal of Molecular Biology, 2009.
• Chan WK, Bhalla AD, Le Hir H, Nguyen LS, Huang L, Gécz J,Wilkinson MF. A UPF3-mediated regulatory switch that maintains RNA surveillance. Nature Structural and Molecular Biology, 2009.
• Bhalla AD, Gudikote JP, Wang J, Chan WK, Chang YF, Olivas OR, Wilkinson MF. Nonsense codons trigger an RNA partitioning shift. Journal of Biological Chemistry, 2009.
• Karam R, Carvalho J, Bruno I, Graziadio C, Senz J, Huntsman D, Carneiro F, Seruca R, Wilkinson MF, Oliveira C. The NMD mRNA surveillance pathway downregulates aberrant E-cadherin transcripts in gastric cancer cells and in CDH1 mutation carriers. Oncogene, 2008.
• Bhardwaj A, Rao MK, Kaur R, Buttigieg MR, Wilkinson MF. GATA factors and androgen receptor collaborate to transcriptionally activate the Rhox5 homeobox gene in Sertoli cells. Molecular and Cellular Biology, 2008.
• Hu Z, Shanker S, MacLean JA 2nd, Ackerman SL, Wilkinson MF. The RHOX5 homeodomain protein mediates transcriptional repression of the netrin-1 receptor gene Unc5c. Journal of Biological Chemistry, 2008.
• Chang YF, Chan WK, Imam JS, Wilkinson MF. Alternatively spliced T-cell receptor transcripts are up-regulated in response to disruption of either splicing elements or reading frame. Journal of Biological Chemistry, 2007.
• Chan WK, Huang L, Gudikote JP, Chang YF, Imam JS, MacLean JA 2nd, Wilkinson MF. An alternative branch of the nonsense-mediated decay pathway. EMBO Journal, 2007.
• Rao MK, Wilkinson MF. Tissue-specific and cell type-specific RNA interference in vivo. Nature Protocols, 2006.
• Rao MK, Pham J, Imam JS, MacLean JA, Murali D, Furuta Y, Sinha-Hikim AP, Wilkinson MF. Tissue-specific RNAi reveals that WT1 expression in nurse cells controls germ cell survival and spermatogenesis. Genes & Development, 2006.
• Gudikote JP, Imam JS, Garcia RF, Wilkinson MF. RNA splicing promotes translation and RNA surveillance. Nature Structural and Molecular Biology, 2005.
• Maclean JA 2nd, Chen MA, Wayne CM, Bruce SR, Rao M, Meistrich ML, Macleod C, Wilkinson MF. Rhox: a new homeobox gene cluster. Cell, 2005.

View All Publications on Pubmed