Department of Reproductive Medicine

Miles Wilkinson

Miles Wilkinson, PhD.
Professor
Division of Reproductive Endocrinology

Sanford Consortium for Regenerative Medicine
2880 Torrey Pines Scenic Dr. Room 4011
University of California, San Diego
La Jolla, CA 92093-0864
Office Phone: 858-822-4819
Lab Phones: 858-822-4701

Visit our site at:  The Wilkinson Lab


Research Interests

Gene regulation
RNAi
MicroRNAs
Stem cells
Reproductive biology

Research Synopsis

Our laboratory primarily works on two topics: (1) transcriptional regulatory pathways that control embryonic stem cell and germ cell development in vivo, and (2) RNA surveillance pathways that serve as quality-control mechanisms to degrade or “correct” aberrant transcripts that would otherwise express truncated proteins causing developmental defects and/or cancer.

The Role of Homeobox Transcription Factors in Development
Homeobox genes encode transcription factors originally defined in fruit flies that have since been shown to have diverse roles in mammalian organisms. Many years ago we identified the homeobox gene Pem by subtraction hybridization screening of cDNAs differentially expressed between two different T-cell lymphoma clones. We later discovered that Pem (which we have since renamed Rhox5; see below) is widely expressed in a variety of different tumors but normally its expression is restricted to specific cell types in the embryo and in the reproductive tract.


The Rhox Homeobox Gene Cluster. (A) The 12 originally defined Rhox genes are contained within a ~0.7-Mb segment of the A2 region (MacLean et al. Cell 2005). The genes are further divided into three subclusters (alpha, beta and gamma) based on physical proximity. (B) The Rhox2, Rhox3 and Rhox4 paralogs in the alpha subcluster recently identified (MacLean et al. Genesis 2006). Boxes indicate the locations of three BACs that together cover the entire region.

RNA Surveillance
We are studying a highly conserved quality-control pathway called nonsense-mediated decay (NMD) that degrades aberrant transcripts harboring premature termination (nonsense) codons. NMD is an essential quality control mechanism, as without it, truncated proteins possessing dominant-negative and deleterious gain-of-functions are generated. As evidence for its importance, loss of Upf1, a gene essential for NMD, causes embryonic lethality in mice.

The targets of NMD – transcripts containing premature nonsense codons – are surprisingly common. One-third of disease-causing genes harbor premature nonsense codons as a result of nonsense and frameshift mutations. Even normal genes commonly give rise to transcripts with premature nonsense codons. Some of these are aberrant transcripts derived as a result of errors in RNA splicing, while others are functional transcripts that probably contain a stop codon in a “premature” position for regulatory reasons.

RNA Surveillance. TCR germline genes undergo programmed rearrangement events between the V, D and J segments to generate a diversity of antigen-specific receptors. Although these rearrangements are sometimes successful (right), two thirds of the time a frame-shift is generated, creating a downstream premature stop (nonsense) codon (left). An RNA surveillance pathway called nonsense-mediated decay (NMD) degrades the aberrant transcripts derived from these non-productively rearranged genes, thereby protecting cells from the putative dominant-negative effects of the truncated proteins. The mechanism underlying the NMD pathway is an interesting paradox, as it involves the nucleus (see text).

TCR transcripts are not alone in being regulated by this alternative branch of the NMD pathway. Using microarray analysis, we have identified many normal transcripts that also appear to use this UPF3a/UPF3b-independent pathway. Among these targets are NMD factors themselves, suggesting that NMD is subject to feedback regulation. We plan to study whether this feedback network buffers NMD from environmental and genetic insults.

Selected Recent Publications

Chang Y-F, Imam JS, Wilkinson MF (2007) “The Nonsense-Mediated Decay RNA Surveillance Pathway,” Annual Review of Biochemistry, Ed. Kornberg R, Annual Reviews Inc.

Bruno I, Wilkinson MF. (2006) P-bodies React to Stress and Nonsense. Cell 125:1036-1038.

Wang W, Cajigas IJ, García EJ, Peltz SW, Wilkinson MF, González CI. (2006) A Role for Upf2p Phosphorylation in Saccharomyces cerevisiae Nonsense-Mediated mRNA Decay. Molecular & Cellular Biology 26:3390-3400.

MacLean JA, Lorenzetti D, Hu Z, Salerno WJ, Miller J, Wilkinson MF. (2006) The Rhox Homeobox Gene Cluster: Recent Duplication of Three Family Members. Genesis 44:122-129.

Rao M, Pham J, Imam JS, MacLean JA, Murali D, Furuta Y, Sinha-Hikim AP, Wilkinson MF. (2006) Tissue-specific RNAi reveals that WT1 expression in nurse cells controls germ-cell survival and spermatogenesis. Genes & Development 20:147-12.

Gudikote JP, Imam JS, Garcia RF, Wilkinson MF. (2005) RNA Splicing Promotes Translation and RNA Surveillance. Nature Structural & Molecular Biology 12:801-809.

MacLean JA, Chen MA, Wayne CM, Bruce SR, Meistrich ML, Macleod CL, Wilkinson MF. (2005) Rhox: A New Homeobox Gene Cluster. Cell 120:369-382.

Commentaries on this paper:

MacLean JA, Rao MK, Doyle MH, Richards JS, Wilkinson MF. (2005) Regulation of the Rhox5 Homeobox Gene in Primary Granulosa Cells: Preovulatory Expression and Dependence on Sp1/Sp3 and Gabp. Biology of Reproduction 73:1126-1134.

Gudikote J, Wilkinson MF. (2005) Nonsense-Mediated Decay and the Immune System. In: “The Nonsense-Mediated Decay RNA Surveillance Pathway,” Maquat LE, ed., Landes Biosciences.

Bhardwaj A, Wilkinson MF. (2005) A Metabolic Enzyme Doing Double Duty as a Transcription Factor. BioEssays 27:467-471.

Sims-Mourtada JC, Bruce S, McKeller MR, Rangel R, Guzman-Rojas L, Cain K, Lopez C, Zimonjic DB, Popescu NC, Gordon J, Wilkinson MF, Hector Martinez-Valdez. (2005) The Human AKNA Gene Expresses Multiple Transcripts and Protein Isoforms as a Result of Alternative Promoter Usage, Splicing, and Polyadenylation. DNA & Cell Biology 24:325-328.

Wilkinson MF. (2005) A New Function for Nonsense-Mediated Decay Factors. Trends in Genetics 21:143-148.

MacLean JA, Wilkinson MF. (2005) Gene Regulation in Spermatogenesis. In: “Current Trends in Developmental Biology” 71:131-197.

Li S, Wilkinson MF, Xia X, David M, Xu L, Purkel-Sutton A, Bhardwaj A. (2005) Induction of IFN-Regulated Factors and Antitumoral Surveillance by Transfected Placebo Plasmid DNA. Molecular Therapy 11:112-119.

Bruce S, Wilkinson MF. (2005) RNA Stability. In: “Genomics and Proteomics in Molecular Medicine,” Ganten D & Ruckpaul K, ed., Springer International.

Inoue K, Khajavi M, Ohyama T, Hirabayashi S, Wilson J, Reggin JD, Mancias P, Butler IJ, Wilkinson MF, Wegner M, Lupski JR. (2004) Molecular Mechanism for Distinct Neurological Phenotypes Conveyed by Allelic Truncating Mutations. Nature Genetics 36:361-369.

Commentaries on this paper:

Wilkinson MF. (2003) The Cycle of Nonsense. Mol Cell 12:1059-1061.

Rao MK, Wayne CM, Meistrich ML, Wilkinson MF. (2003) Pem Homeobox Gene Promoter Sequences that Direct Transcription in a Sertoli Cell-Specific, Stage-Specific, and Androgen-Dependent Manner in the Testis In Vivo. Mol. Endocrinol 17:223-233.

Gudikote J, Wilkinson MF. (2003) Regulation of mRNA Splicing, Export, and Decay by RNA-Binding Proteins. In: “Encyclopedia of the Human Genome,” Nature Publishing Group.

Bruce S, Wilkinson MF. (2003) Nonsense-Mediated Decay: a Surveillance Pathway that Detects Faulty TCR and BCR Transcripts. In "Recent Research Developments in Immunology," Pandalai SG, ed., Research Signposts Publishers.

Wang J, Hamilton JI, Carter MS, Li S, Wilkinson MF. (2002) Alternatively Spliced TCR mRNA Induced by Disruption of Reading Frame. Science 297:108-110.

Commentaries on this paper:

Wang J, Chang Y-F, Hamilton,JI, Wilkinson MF. (2002) Nonsense-Associated Altered Splicing: A Frame-Dependent Response Distinct from Nonsense-Mediated Decay. Mol Cell 10:951-957.

Commentary on this paper:

Wilkinson MF, Shyu A-B. (2002) RNA Surveillance by Nuclear Scanning? Nature Cell Biology 4:E144-147.

Gudikote JP, Wilkinson MF. (2002) T-cell Receptor Sequences that elicit Strong Downregulation of Premature Termination Codon-bearing Transcripts. EMBO J 21:125-134.

Commentaries on this paper:

Wang J, Gudikote JP, Olivas OR, Wilkinson MF. (2002) Boundary-independent Polar Nonsense-mediated Decay. EMBO Reports 3:274-279.

Rao MK, Wayne CM, Wilkinson MF. (2002) Pem Homeobox Gene Regulatory Sequences that Direct Androgen-Dependent Developmentally Regulated Gene Expression in Different Subregions of the Epididymis. J Biol Chem 277:48771-48778.

Wayne C, Wilkinson MF. (2002) Expression of the Pem Homeobox Gene in Sertoli Cells Increases the Frequency of Adjacent Germ Cells with DNA-Strand Breaks. Endocrinology 143:4875-4885.

Bühler M, Wilkinson MF, Mühlemann O. (2002) Intranuclear Degradation of Nonsense Codon-Containing mRNA. EMBO Reports 3:646-651.

Rao MK, Maiti S, Ananthaswamy HN, Wilkinson MF. (2002) A Highly Active Homeobox Gene Promoter Regulated by Ets and Sp1 Family Members in Normal Granulosa Cells and Diverse Tumor Cell Types. J Biol Chem 277:26036-26045.

Wang J, Vock VM, Olivas OR, Wilkinson MF. (2002) A quality-control pathway that downregulates aberrant TCR transcripts by a mechanism requiring UPF2 and translation. J Biol Chem 277:18,489-18,493.

Wilkinson MF, Shyu AB. (2001) Bifunctional Regulatory Proteins that Control Gene Expression in both the Nucleus and the Cytoplasm. BioEssays 23:775-787.

Mühlemann O, Mock-Casagrande CS, Wang J, Li S, Custódio N, Carmo-Fonseca M, Wilkinson MF, Moore MJ. (2001) Precursor RNAs Harboring Nonsense Codons Accumulate Near the Site of Transcription. Mol Cell 8:33-43.

Commentaries on this paper:

Clement JQ, Maiti S, Wilkinson MF. (2001) Localization and Stability of Introns Spliced In Vivo from the Pem Homeobox Gene. J Biol Chem 276:16,919-16,930.

Maiti S, Meistrich ML, Wilson G, Shetty G, Marcelli M, McPhaul MJ, Morris PL, Wilkinson MF. (2001) Irradiation Selectively Inhibits Expression from the Androgen-Dependent Pem Homeobox Gene Promoter in Sertoli Cells. Endocrinology 142:1567-1577.

Shyu AB, Wilkinson MF. (2000) The Double Lives of Shuttling RNA-Binding Proteins. Cell 102:135-138.

Li S, Wilkinson MF. (1998) Nonsense Surveillance in Lymphocytes? Immunity 8:135-141

 

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