Peter Lawrence Jones PHD
Title Associate Professor
Institution University of Massachusetts Medical School
Department Cell and Developmental Biology
Address Wellstone Program
55 Lake Avenue
Worcester MA 01655
Telephone 774/455-1581
Email
Other Positions
Institution UMMS - School of Medicine
Department Neurology
Narrative

Department of Cell and Developmental Biology / Wellstone Program

Academic Background

2013-Present
Associate Professor - University of Massachusetts Medical School
Research: Epigenetics; Muscle development and disease, FSHD; Rett Syndrome

2011-Present
Affiliate Investigator - Sen. Paul D. Wellstone Cooperative Research Center for FSHD

2010-2013
Principal Scientist - Boston Biomedical Research Institute

2001-2010
Assistant Professor - Department of Cell and Developmental Biology - University of Illinois at Urbana-Champaign

1997-2001
Postdoctoral fellow - Laboratory of Molecular Embryology, NICHD, NIH, Bethesda, MD.
Research: Epigenetics, chromatin, biochemistry

1991-1997
Emory University, Atlanta, GA - Program in Genetics and Molecular Biology
Degree: PhD in Eukaryotic gene regulation

1987-1991
Miami University, Oxford, OH
Degree: B.A. in Microbiology

Molecular Mechanisms of Facioscapulohumeral Muscular Dystrophy (FSHD) Pathology

FSHD is the most prevalent myopathy afflicting women, men, children and adults of all ages. FSHD is an autosomal dominant disease marked by slow but progressive atrophy in specific muscle groups in the face, upper arms, abdomen, hip girdle, and legs with individuals often showing bilateral asymmetry in muscle weakness. There is a wide range in both the age of disease onset and clinical severity, from the extremely severe infantile form (IFSHD), to the more common young adult onset FSHD manifesting in the second or third decade, to the individuals who show symptoms only much later in life, if ever. Initial symptoms often causing one to seek clinical help are difficulty raising ones arms above shoulder level, facial weakness and foot drop. Additional non-muscular symptoms that appear later in the disease progression include high-frequency hearing loss in more than half of all diagnosed cases, and vision problems in ~1% of patients. With many FSHD patients becoming wheelchair-bound as young adults, the personal, social, and economic costs of this disease are enormous, and no effective therapies exist.

FSHD is a genetic disease linked to chromosome 4q35 with a strong epigenetic component (Figure 1). FSHD research has now entered an important new stage as the DUX4 gene has emerged from studies in multiple laboratories, including our own, as the near consensus FSHD candidate gene whose misexpression is necessary for pathology. The DUX4 gene is present in numerous copies in the genome as each 3.3kb repeat unit of a D4Z4 repeat array contains a DUX4 gene and D4Z4 arrays are found in several places in the genome. However, only the DUX4 gene in the distal D4Z4 repeat of the 4q35 subtelomeric array can stably express pathogenic transcripts. A pathogenic change of the epigenetic status of the 4q35 D4Z4 array, predominantly caused by large deletions within the repeats and rarely by mutations in certain genes affecting DNA methylation, leads to a relaxation of the array and aberrant DUX4 expression and alternative mRNA splicing. The current evidence supports a model in which aberrant stable expression of the DUX4 mRNA splicing variant, termed DUX4-fl (fl = full-length), in skeletal muscle is required, but not necessarily sufficient, for FSHD pathology. This pathogenic mRNA encodes a transcription factor, DUX4-FL, whose expression leads to additional aberrant expression of downstream genes in FSHD muscle. Thus, there are a number of potential targets for therapy development.

My lab has several FSHD research projects: 1) investigating the epigenetic and genetic regulation of DUX4 gene expression and alternative mRNA splicing, 2) investigating additional FSHD candidate genes and transcripts that may be involved in pathology either in concert with or independent of DUX4-fl, 3) generating animal and cell culture models of FSHD using mice, Drosophila, C. elegans and human myogenic cultures, and 4) developing therapeutic strategies to target DUX4-fl mRNA and protein expression and function.
Peter jones Profile Pic
Figure 1: FSHD1 and FSHD2 are linked to epigenetic relaxation of the chromatin at chromosome 4q35 D4Z4 macrosatellite repeat array.
Each D4Z4 repeat unit encodes exons 1 and 2 of the DUX4 gene. At least one D4Z4 repeat, combined with an “A” type subtelomere, is required for FSHD. The “A” type subtelomere encodes a third exon containing a polyadenylation signal that is spliced onto and stabilizes the DUX4 mRNA when transcribed from the terminal D4Z4 repeat. *DUX4-fl mRNA and protein have been detected in a small number of control biopsies and myogenic cell cultures; however, the level is significantly lower than what is found in FSHD. Of note, a number of individuals (estimated up to 1-3%) in the general population have FSHD1-sized deletions and do not exhibit clinical symptoms of FSHD. Their expression levels of DUX4-fl in muscle are currently unknown.

Department of Cell and Developmental Biology
Wellstone Program

Publications
1. Morgan GT, Jones P, Bellini M. Association of modified cytosines and the methylated DNA-binding protein MeCP2 with distinctive structural domains of lampbrush chromatin. Chromosome Res. 2012 Dec; 20(8):925-42.
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2. Jones TI, Chen JC, Rahimov F, Homma S, Arashiro P, Beermann ML, King OD, Miller JB, Kunkel LM, Emerson CP, Wagner KR, Jones PL. Facioscapulohumeral muscular dystrophy family studies of DUX4 expression: evidence for disease modifiers and a quantitative model of pathogenesis. Hum Mol Genet. 2012 Oct 15; 21(20):4419-30.
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3. Liu Q, Jones TI, Bachmann RA, Meghpara M, Rogowski L, Williams BD, Jones PL. C. elegans PAT-9 is a nuclear zinc finger protein critical for the assembly of muscle attachments. Cell Biosci. 2012; 2(1):18.
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4. Long SW, Ooi JY, Yau PM, Jones PL. A brain-derived MeCP2 complex supports a role for MeCP2 in RNA processing. Biosci Rep. 2011 Oct 1; 31(5):333-43.
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5. Sun CY, van Koningsbruggen S, Long SW, Straasheijm K, Klooster R, Jones TI, Bellini M, Levesque L, Brieher WM, van der Maarel SM, Jones PL. Facioscapulohumeral muscular dystrophy region gene 1 is a dynamic RNA-associated and actin-bundling protein. J Mol Biol. 2011 Aug 12; 411(2):397-416.
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6. Bogdanovic O, Long SW, van Heeringen SJ, Brinkman AB, Gómez-Skarmeta JL, Stunnenberg HG, Jones PL, Veenstra GJ. Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis. Genome Res. 2011 Aug; 21(8):1313-27.
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7. Hanel ML, Sun CY, Jones TI, Long SW, Zanotti S, Milner D, Jones PL. Facioscapulohumeral muscular dystrophy (FSHD) region gene 1 (FRG1) is a dynamic nuclear and sarcomeric protein. Differentiation. 2011 Feb; 81(2):107-18.
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8. Wuebbles RD, Long SW, Hanel ML, Jones PL. Testing the effects of FSHD candidate gene expression in vertebrate muscle development. Int J Clin Exp Pathol. 2010; 3(4):386-400.
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9. Liu Q, Jones TI, Tang VW, Brieher WM, Jones PL. Facioscapulohumeral muscular dystrophy region gene-1 (FRG-1) is an actin-bundling protein associated with muscle-attachment sites. J Cell Sci. 2010 Apr 1; 123(Pt 7):1116-23.
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10. Hanel ML, Wuebbles RD, Jones PL. Muscular dystrophy candidate gene FRG1 is critical for muscle development. Dev Dyn. 2009 Jun; 238(6):1502-12.
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11. Wuebbles RD, Hanel ML, Jones PL. FSHD region gene 1 (FRG1) is crucial for angiogenesis linking FRG1 to facioscapulohumeral muscular dystrophy-associated vasculopathy. Dis Model Mech. 2009 May-Jun; 2(5-6):267-74.
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12. El-Osta A, Brasacchio D, Yao D, Pocai A, Jones PL, Roeder RG, Cooper ME, Brownlee M. Transient high glucose causes persistent epigenetic changes and altered gene expression during subsequent normoglycemia. J Exp Med. 2008 Sep 29; 205(10):2409-17.
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13. Wuebbles R, Jones PL. Engineered telomeres in transgenic Xenopus laevis. Transgenic Res. 2007 Jun; 16(3):377-84.
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14. Beenders B, Jones PL, Bellini M. The tripartite motif of nuclear factor 7 is required for its association with transcriptional units. Mol Cell Biol. 2007 Apr; 27(7):2615-24.
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15. Wang Y, Jorda M, Jones PL, Maleszka R, Ling X, Robertson HM, Mizzen CA, Peinado MA, Robinson GE. Functional CpG methylation system in a social insect. Science. 2006 Oct 27; 314(5799):645-7.
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16. Insights into social insects from the genome of the honeybee Apis mellifera. Nature. 2006 Oct 26; 443(7114):931-49.
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17. Harikrishnan KN, Chow MZ, Baker EK, Pal S, Bassal S, Brasacchio D, Wang L, Craig JM, Jones PL, Sif S, El-Osta A. Brahma links the SWI/SNF chromatin-remodeling complex with MeCP2-dependent transcriptional silencing. Nat Genet. 2005 Mar; 37(3):254-64.
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18. Jones PL, Shi YB. N-CoR-HDAC corepressor complexes: roles in transcriptional regulation by nuclear hormone receptors. Curr Top Microbiol Immunol. 2003; 274:237-68.
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19. Sachs LM, Jones PL, Havis E, Rouse N, Demeneix BA, Shi YB. Nuclear receptor corepressor recruitment by unliganded thyroid hormone receptor in gene repression during Xenopus laevis development. Mol Cell Biol. 2002 Dec; 22(24):8527-38.
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20. Jones PL, Wade PA, Wolffe AP. Purification of MeCP2-containing deacetylase from Xenopus laevis. Methods Mol Biol. 2002; 200:131-41.
  View in: PubMed
 
21. Stunkel W, Ait-Si-Ali S, Jones PL, Wolffe AP. Programming the transcriptional state of replicating methylated dna. J Biol Chem. 2001 Jun 8; 276(23):20743-9.
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22. Jones PL, Sachs LM, Rouse N, Wade PA, Shi YB. Multiple N-CoR complexes contain distinct histone deacetylases. J Biol Chem. 2001 Mar 23; 276(12):8807-11.
  View in: PubMed
 
23. Jones PL, Wade PA, Wolffe AP. Purification of the MeCP2/histone deacetylase complex from Xenopus laevis. Methods Mol Biol. 2001; 181:297-307.
  View in: PubMed
 
24. Robertson KD, Ait-Si-Ali S, Yokochi T, Wade PA, Jones PL, Wolffe AP. DNMT1 forms a complex with Rb, E2F1 and HDAC1 and represses transcription from E2F-responsive promoters. Nat Genet. 2000 Jul; 25(3):338-42.
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25. Sachs LM, Damjanovski S, Jones PL, Li Q, Amano T, Ueda S, Shi YB, Ishizuya-Oka A. Dual functions of thyroid hormone receptors during Xenopus development. Comp Biochem Physiol B Biochem Mol Biol. 2000 Jun; 126(2):199-211.
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26. Jones PL, Wolffe AP. Relationships between chromatin organization and DNA methylation in determining gene expression. Semin Cancer Biol. 1999 Oct; 9(5):339-47.
  View in: PubMed
 
27. Vermaak D, Wade PA, Jones PL, Shi YB, Wolffe AP. Functional analysis of the SIN3-histone deacetylase RPD3-RbAp48-histone H4 connection in the Xenopus oocyte. Mol Cell Biol. 1999 Sep; 19(9):5847-60.
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28. Wade PA, Gegonne A, Jones PL, Ballestar E, Aubry F, Wolffe AP. Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation. Nat Genet. 1999 Sep; 23(1):62-6.
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29. Wolffe AP, Jones PL, Wade PA. DNA demethylation. Proc Natl Acad Sci U S A. 1999 May 25; 96(11):5894-6.
  View in: PubMed
 
30. Wade PA, Jones PL, Vermaak D, Wolffe AP. Purification of a histone deacetylase complex from Xenopus laevis: preparation of substrates and assay procedures. Methods Enzymol. 1999; 304:715-25.
  View in: PubMed
 
31. Wade PA, Jones PL, Vermaak D, Wolffe AP. A multiple subunit Mi-2 histone deacetylase from Xenopus laevis cofractionates with an associated Snf2 superfamily ATPase. Curr Biol. 1998 Jul 2; 8(14):843-6.
  View in: PubMed
 
32. Shi YB, Sachs LM, Jones P, Li Q, Ishizuya-Oka A. Thyroid hormone regulation of Xenopus laevis metamorphosis: functions of thyroid hormone receptors and roles of extracellular matrix remodeling. Wound Repair Regen. 1998 Jul-Aug; 6(4):314-22.
  View in: PubMed
 
33. Jones PL, Veenstra GJ, Wade PA, Vermaak D, Kass SU, Landsberger N, Strouboulis J, Wolffe AP. Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat Genet. 1998 Jun; 19(2):187-91.
  View in: PubMed
 
34. Wade PA, Jones PL, Vermaak D, Veenstra GJ, Imhof A, Sera T, Tse C, Ge H, Shi YB, Hansen JC, Wolffe AP. Histone deacetylase directs the dominant silencing of transcription in chromatin: association with MeCP2 and the Mi-2 chromodomain SWI/SNF ATPase. Cold Spring Harb Symp Quant Biol. 1998; 63:435-45.
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35. Jones PL, Ping D, Boss JM. Tumor necrosis factor alpha and interleukin-1beta regulate the murine manganese superoxide dismutase gene through a complex intronic enhancer involving C/EBP-beta and NF-kappaB. Mol Cell Biol. 1997 Dec; 17(12):6970-81.
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36. Smith ER, Jones PL, Boss JM, Merrill AH. Changing J774A.1 cells to new medium perturbs multiple signaling pathways, including the modulation of protein kinase C by endogenous sphingoid bases. J Biol Chem. 1997 Feb 28; 272(9):5640-6.
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37. Ping D, Jones PL, Boss JM. TNF regulates the in vivo occupancy of both distal and proximal regulatory regions of the MCP-1/JE gene. Immunity. 1996 May; 4(5):455-69.
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38. Jones PL, Kucera G, Gordon H, Boss JM. Cloning and characterization of the murine manganous superoxide dismutase-encoding gene. Gene. 1995 Feb 14; 153(2):155-61.
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