Publications not available in pdf format may be obtained by contacting Ray Monnat
Publications 2014
Shiovitz S, Bertagnolli MM, Renfro LA, Nam E, Foster NR, Dzieciatkowski S, Luo Y, Lao VV, Monnat RJ Jr, Emond MJ, Maizels N, Niedzwiecki D, Goldberg RM, Saltz LB, Venook A, Warren RS, Grady WM; Alliance for Clinical Trials in Oncology. (2014) CpG Island Methylator Phenotype is Associated With Response to Adjuvant Irinotecan-Based Therapy for Stage 3 Colon Cancer. Gastroenterology Epub May 21. PMCID and PDF file are pending.
Lauper JM, Monnat RJ Jr. (2014) Diabetes mellitus and cancer in Werner syndrome. Acta Diabetol. Feb;51(1):159-61, Epub Feb 6, 2013 PMC3669637 [ pdf ]
Friedman JI, Li H, Monnat RJ Jr. (2014) Quantifying the information content of homing endonuclease target sites by single base pair profiling. Chapter 11 in Methods Mol Biol. 1123:135-49, David R. Edgell (ed.) [ pdf ]
Li H, Monnat RJ Jr. (2014) Homing endonuclease target site specificity defined by sequential enrichment and next-generation sequencing of highly complex target site libraries. Chapter 12 in Methods Mol Biol. 1123:151-63, David R. Edgell (ed.) [ pdf ]
Pellenz S, Monnat RJ Jr. (2014) Identification and analysis of genomic homing endonuclease target sites. Chapter 16 in Methods Mol Biol. 1123:245-64, David R. Edgell (ed.) [ pdf ]
Publications 2013
Metzger MJ, Stoddard BL, Monnat RJ Jr. (2013) PARP-mediated repair, homologous recombination, and back-up non-homologous end joining-like repair of single-strand nicks. DNA Repair (Amst). Jul;12(7):529-34. PMC3683368 [ pdf ]
Glukhova VA, Tomazela DM, Findlay GD, Monnat RJ Jr, MacCoss MJ (2013) Rapid assessment of RNAi-mediated protein depletion by selected reaction monitoring mass spectrometry. J Proteome Res. Jul 5;12(7):3246-54 PMC3767422 [ pdf ] [ supplemental data pdf ]
Lao VV, Welcsh P, Luo Y, Carter KT, Dzieciatkowski S, Dintzis S, Meza J, Sarvetnick NE, Monnat RJ Jr, Loeb LA, Grady WM (2013) Altered RECQ helicase expression in sporadic primary colorectal cancers. Transl Oncol. Aug 1;6(4):458-69 PMC3730021 [ pdf ]
Hughes BT, Sidorova J, Swanger J, Monnat RJ Jr, Clurman BE (2013) Essential role for Cdk2 inhibitory phosphorylation during replication stress revealed by a human Cdk2 knockin mutation. Proc Natl Acad Sci U S A. May 28;110(22):8954-9. PMC3670391 [ pdf ]
Lauper JM, Krause A, Vaughan TL, Monnat RJ Jr. (2013) Spectrum and risk of neoplasia in Werner syndrome: a systematic review. PLoS ONE 8(4):e59709 PMC3613408 [ pdf ]
Berti M, Chaudhuri AR, Thangavel S, Gomathinayagam S, Kenig S, Vujanovic M, Odreman F, Glatter T, Graziano S, Mendoza-Maldonado R, Marino F, Lucic B, Biasin V, Gstaiger M, Aebersold R, Sidorova JM, Monnat RJ Jr, Lopes M, Vindigni A (2013) Human RECQ1 promotes restart of replication forks reversed by DNA topoisomerase I inhibition. Nature Structural and Molecular Biology Mar;20(3):347-54. PMC3897332 [ pdf ]
Monnat RJ Jr. (2013) Chapter on Werner Syndrome in WHO Classification of Tumours of Soft Tissues and Bone p. 393-4, C.D.M. Fletcher, J.A. Bridge, P.C.W. Hogendoorn, F. Mertens (eds.) [ pdf ]
Publications 2012
Sidorova JM, Kehrli K, Mao F, Monnat R Jr. (2012) Distinct functions of human RECQ helicases WRN and BLM in replication fork recovery and progression after hydroxyurea-induced stalling. DNA Repair (Amst) Feb 1;12(2):128-39 PMC3551992 [ pdf ]
Duxin JP, Moore HR, Sidorova J, Karanja K, Honaker Y, Dao B, Piwnica-Worms H, Campbell JL, Monnat RJ Jr, Stewart SA (2012) Okazaki fragment processing-independent role for human Dna2 enzyme during DNA replication. J. Biol. Chem. 287:21980-91. PMC3381158 [ pdf ] [ supplemental data pdf ]
Li H, Ulge UY, Hovde BT, Doyle LA, Monnat RJ Jr. (2012) Comprehensive homing endonuclease target site specificity profiling reveals evolutionary constraints and enables genome engineering applications. Nucleic Acids Res. Mar 1;40(6):2587-98 PMC3315327 [ pdf ]
Publications 2011
Windbichler N, Menichelli M, Papathanos PA, Thyme SB, Li H, Ulge UY, Hovde BT, Baker D, Monnat RJ Jr, Burt A, Crisanti A. (2011) Genetic drive of a synthetic homing endonuclease-based element in populations of the human malaria vector Anopheles gambiae. Nature May 12;473(7346):212-5. PMC3093433 [ pdf ]
Ulge UY, Baker DA, Monnat RJ Jr. (2011) Comprehensive computational design of mCreI homing endonuclease cleavage specificity for genome engineering. Nucleic Acids Research May;39(10):4330-9. PMC3105429 [ pdf ]
Publications 2010
Monnat RJ Jr. (2010) Human RECQ helicases: Roles in DNA metabolism, disease pathogenesis and disease therapy. Seminars Cancer Biol. 20(5):329-39. PMC3040982 [ pdf ]
Sidorova JM, Monnat, RJ Jr. (2010) DNA Helicase-deficiency Disorders, in Encyclopedia of Life Sciences, Article # A6065
Mao FJ, Sidorova JM, Lauper JM, Emond ME, Monnat RJ Jr. (2010) The human WRN and BLM RecQ helicases differentially regulate cell proliferation and survival after chemotherapeutic DNA damage. Cancer Research 70(16):6548-55. PMC2941797 [ pdf ] [ supplemental data pdf ]
Thangavel S, Mendoza-Maldonado R, Tissino E, Sidorova JM, Yin J, Wang W, Monnat RJ Jr, Falaschi A, Vindigni A. (2010) Human RECQ1 and RECQ4 helicases play distinct roles in DNA replication initiation. Mol Cell Biol. Mar;30(6):1382-9 PMC2832491 [ pdf ]
Dhillon KK, Sidorova JM, Albertson TM, Anderson JB, Ladiges WC, Rabinovitch PS, Preston BD, Monnat RJ Jr. (2010) Werner syndrome protein loss leads to divergent mouse and human cell phenotypes. DNA Repair (Amst) Jan 2;9(1):11-22 PMC2818259 [ pdf ]
Publications 2009
Rey L, Sidorova JM, Puget N, Boudsocq F, Biard DSF, Monnat RJ Jr, Cazaux C, Hoffman JS. (2009) Human DNA polymerase eta is required for common fragile site stability during unperturbed DNA replication. Molec Cell Biol Jun;29(12):3344-54 PMC2698728 [ pdf ] [ supplemental data pdf ]
Sidorova JM, Li N, Schwartz DC, Folch A, Monnat RJ Jr. (2009) Microfluidic-assisted analysis of replicating DNA molecules. Nature Protocols 4(6):849-61 PMC2762429 [ pdf ]
Li H, Pellenz S, Ulge U, Stoddard BL, Monnat RJ Jr. (2009) Generation of single-chain LAGLIDADG homing endonucleases from native homodimeric precursor proteins. Nucleic Acids Res. 2009 Jan 19. PMC2655683 [ pdf ] [ supplemental data pdf ]
McConnell Smith A, Takeuchi R, Pellenz S, Davis L, Maizels N, Monnat RJ Jr, Stoddard BL. (2009) Generation of a nicking enzyme that stimulates site-specific targeted gene correction froms the I-AniI homing LAGLIDADG endonuclease. Proc Natl Acad Sci USA Mar 31;106(13):5099-104. PMC2664052 [ pdf ] [ supplemental data pdf ]
Publications 2008
Stoddard BL, Scharenberg AM, Monnat RJ Jr. (2008) Advances in engineering homing endonucleases for gene targeting: Ten years after structures. Chapter 6 in Progress in Gene Therapy 3: Autologous and Cancer Stem Cell Gene Therapy, R. Bertolotti and K. Ozawa (Eds.), World Scientific Press, Hackensack, NJ. pp. 135-167. [ pdf ]
Sidorova JM. (2008) Roles of the Werner syndrome RecQ helicase in DNA replication. DNA Repair 7:1776-1786 PMC2659608 [ pdf ]
Loeb LA, Monnat RJ Jr. (2008) DNA polymerases and human disease. Nature Reviews Genetics 9:594-604 [ pdf ]
Berkovich E, Monnat RJ Jr, Kastan MB. (2008) Assessment of protein dynamics and DNA repair following generation of DNA double-strand breaks at defined genomic sites. Nature Protocols 3:915-922. [ pdf ]
Sidorova JM, Li N, Folch A, Monnat RJ Jr. (2008) The RecQ helicase WRN is required for normal replication fork progression after DNA damage or replication fork arrest. Cell Cycle. 7(6):796-807 [ pdf ]
Publications 2007
Eklund JL, Ulge UY, Eastberg J, Monnat RJ Jr. (2007) Altered target site specificity variants of the I-PpoI His-Cys box homing endonuclease. Nucleic Acids Research 35(17):5839-50. PMC2034468 [ pdf ]
Sharma A, Awasthi S, Harrod CK, Matlock EF, Khan S, Xu L, Chan S, Yang H, Thammavaram CK, Rasor RA, Burns DK, Skiest DJ, Van Lint C, Girard AM, McGee M, Monnat RJ Jr, Harrod R. (2007) The Werner syndrome helicase is a cofactor for HIV-1 long terminal repeat transactivation and retroviral replication. J Biol Chem. Apr 20;282(16):12048-57. [ pdf ]
Kudlow B, Kennedy BK, Monnat RJ Jr. (2007) Werner and Hutchinson-Gilford progeria syndromes: mechanistic basis of human progeroid diseases. Nature Reviews Molecular and Cellular Biology 8: 394-404. [ pdf ]
Eastberg J, Eklund J, Monnat RJ Jr, Stoddard B. (2007) Mutability of an HNH nuclease imidazole general base and exchange of a deprotonation mechanism. Biochemistry 46:7215-7225. [ pdf ]
Monnat RJ Jr. (2007) From broken to old: DNA damage, IGF1 endocrine suppression and aging. DNA Repair Sep 1; 6(9): 1386-90. PMC2704237 [ pdf ]
Berkovich E, Monnat RJ Jr, Kastan M. (2007) Roles of ATM and NBS1 in chromatin structure modulation and DNA double strand break repair. Nature Cell Biology 9:683-690. [ pdf ]
Volna P, Jarjour J, Baxter S, Roffler S, Monnat RJ Jr, Stoddard B, Scharenberg A. (2007) Flow cytometric analysis of DNA binding and cleavage by cell surface-displayed homing endonucleases. Nucleic Acids Research 35: 2748-2758. PMC1885675 [ pdf ]
Dhillon K, Sidorova J, Saintigny Y, Poot M, Gollahon K, Rabinovitch PS, Monnat RJ Jr. (2007) Functional role of the Werner syndrome RecQ helicase in human fibroblasts. Aging Cell 6: 53-61. [ pdf ]
Publications 2006
Ashworth J, Havranek JJ, Duarte CM, Sussman D, Monnat RJ Jr, Stoddard BL, Baker D. (2006) Computational redesign of endonuclease DNA binding and cleavage specificity. Nature 441:656-659. PMC2999987 [ pdf ]
Monnat RJ Jr. (2006) 'Werner Syndrome as a Model of Human Aging', In Handbook of Models of Human Aging, P. Michael Conn, ed. Elsevier Academic Press, Chapter 80, pp. 961-976.
Publications 2005-2000
Chevalier B, Monnat RJ Jr, Stoddard BL. (2005) 'The LAGLIDADG Homing Endonuclease Family', in Homing Endonucleases and Inteins, M. Belfort, B.L. Stoddard, D.W. Wood, V. Derbyshire (Eds). Springer, Berlin. pp.33-47.
Awasthi S, Sharma A, Wong K, Zhang J, Matlock EF, Rogers L, Motloch P, Takemoto S, Taguchi H, Cole MD, Luscher B, Dittrich O, Tagami H, Nakatani Y, McGee M, Girard AM, Gaughan L, Robson CN, Monnat RJ Jr, Harrod R. (2005) A human T-cell lymphotropic virus type 1 enhancer of Myc transforming potential stabilizes Myc-TIP60 transcriptional interactions. Mol Cell Biol. 25:6178-98. PMC1168837 [ pdf ]
Monnat RJ Jr. (2005) ‘Werner Syndrome as a Model of Human Aging‘, in Handbook of Models of Human Aging, P. Michael Conn, ed. Elsevier Academic Press: chapter 80, pp.961-976.
Chevalier BS, Sussman J, Otis C, Nöel AJ, Turmel M, Lemieux C, Stephens K, Monnat RJ Jr, Stoddard BL. (2004) Metal-dependent DNA cleavage mechanism of the I-CreI LAGLIDADG homing endonuclease. Biochemistry 43:14015-14026. [ pdf ]
Sussman D, Chadsey M, Fauce S, Engel A, Bruett A, Monnat R Jr, Stoddard BL, Seligman LM. (2004) Isolation and characterization of new homing endonuclease specificities at individual target site positions. J. Mol. Biol. 342:31-41. [ pdf ]
Monnat RJ Jr, Saintigny Y. (2004) The Werner syndrome protein: in vivo function and disease links. Science's SAGE-KE (available at: http://sageke.sciencemag.org/cgi/content/full/2004/13/re3). [ pdf ]
Swanson C, Saintigny Y, Emond MJ, Monnat RJ Jr. (2004) The Werner syndrome protein has separable recombination and survival functions. DNA Repair 3:475-482. [ pdf ]
Grandori C, Wu KJ, Fernandez P, Ngouenet C, Grim J, Clurman BE, Moser MJ, Oshima J, Russell DW, Swisshelm K, Frank S, Amati B, Dalla-Favera R, Monnat RJ Jr. (2003) Werner syndrome protein limits MYC-induced cellular senescence. Genes & Development 17:1569-1574. PMC196129
Chevalier B, Turmel M, Lemieux C, Monnat RJ Jr, Stoddard BL.(2003) Flexible DNA target site recognition by divergent homing endonuclease isoschizomers I-CreI and I-MsoI. J. Mol. Biol. 329:253-269. [ pdf ]
Monnat RJ Jr. (2002) ‘Werner syndrome‘, in WHO/IARC Monograph on Pathology and Genetics of Tumours of Soft Tissue and Bone, edited by C. Fletcher, K. Unni and F.Mertens. IARC Press, Lyon. pp. 366-367.
Chevalier BS, Kortemme T, Chadsey MS, Baker D, Monnat RJ Jr, Stoddard BL. (2002) Design, activity and structure of E-DreI, a highly site-specific artificial endonuclease Molecular Cell 10:895-905. [ pdf ]
Saintigny Y, Makienko K, Swanson C, Emond MJ, Monnat RJ Jr. (2002) A homologous recombination resolution defect in Werner syndrome Molec. Cell. Biol. 22:6971-6978. PMC139822 [ pdf ]
Colgin LM, Hackmann AFM, Emond MJ, Monnat RJ Jr. (2002) The unexpected landscape of in vivo somatic mutation in a human epithelial cell lineage Proc. Natl. Acad. Sci. USA 99:1437-1442. PMC122209 [ pdf ]
Saintigny Y, Monnat RJ Jr. (2002) L'Hélicase RecQ, dont les altérations sont à l'origine du syndrome de Werner, participe à la réparation de l'ADN par recombinaison homologue. Médecine Sciences 18:79-85. [ pdf ]
Monnat RJ Jr. (2001) Cancer pathogenesis in the human RecQ helicase deficiency syndromes, in 'From Premature Gray Hair to Helicase: Werner Syndrome Implications for Aging and Cancer', edited by M. Goto and R.W. Miller. GANN Monograph on Cancer Research 49: 83-94.
Prince PR, Emond MJ, Monnat RJ Jr. (2001) Loss of Werner syndrome protein function promotes aberrant mitotic recombination Genes & Development 15:933-938. PMC312674 [ pdf ]
Chevalier BS, Monnat RJ Jr, Stoddard BL. (2001) The LAGLIDADG homing endonuclease I-CreI shares three metals between two active sites. Nature Structural Biology 8:312-316. [ pdf ]
Galburt EA, Chadsey MS, Jurica MS, Chevalier BS, Ehro D, Tang W, Monnat RJ Jr, Stoddard BL. (2000) Conformational changes and cleavage by the homing endonuclease I-PpoI: a critical role for a leucine residue in the active site. J. Mol. Biol. 300:877-887. [ pdf ]
Moser MJ, Bigbee WL, Grant SG, Emond MJ, Langlois RG, Jensen RH, Oshima J, Monnat RJ Jr. (2000) Genetic instability and hematologic disease risk in Werner syndrome patients and heterozygotes. Cancer Research 60:2492-2496. [ pdf ]
Publications 1999-1995
Galburt E, Chevalier B, Tang W, Jurica MS, Flick KE, Monnat RJ Jr, Stoddard BL. (1999) A novel endonuclease mechanism directly visualized for I-PpoI. Nature Structural Biology 6:1096-1099. [ pdf ]
Monnat RJ Jr. (1999) Unusual features of thyroid carcinomas in Japanese patients with Werner syndrome and possible genotype-phenotype relations to cell type and race (originally entitled 'No association of specific WRN mutations with thyroid cancer risk or histologic subtype in Werner syndrome patients' prior to editorial retitling). Cancer 86:728-729. [ pdf ]
Prince PR, Ogburn CE, Moser MJ, Emond MJ, Martin GM, Monnat RJ Jr. (1999) Cell fusion corrects the 4-nitroquinoline 1-oxide sensitivity of Werner syndrome fibroblast cell lines. Human Genetics 105:132-138. [ pdf ]
Colgin LM, Hackmann AFM, Monnat RJ Jr. (1999) Different somatic and germline HPRT1 mutations promote use of a common, cryptic intron 1 splice site. Human Mutation 13:504-505. [ pdf ]
Monnat RJ Jr, Hackmann AFM, Cantrell MA. (1999) Generation of highly site-specific DNA double strand breaks in human cells by the homing endonucleases I-PpoI and I-CreI. Biochem. Biophys. Res. Comm. 255:88-93. [ pdf ]
Bennett SE, Umar A, Kodama S, Barrett JC, Monnat RJ Jr, Kunkel TA. (1999) Evidence against a role for the Werner syndrome gene product in DNA mismatch repair. Molecular Biology of Aging, Alfred Benzon Symposium Proceedings, No. 44. Bohr, V.A, Clark, B.F.C. and Stevnsner, T. Munksgaard, Copenhagen. pp.214-224.
Jurica MS, Monnat RJ Jr, Stoddard BL. (1998) DNA recognition and cleavage by the LAGLIDADG homing endonuclease I-CreI. Molecular Cell 2:469-476. [ pdf ]
Flick KE, Jurica MS, Monnat RJ Jr, Stoddard BL. (1998) DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI. Nature 394:96-101. [ pdf ]
Argast GM, Stephens KM, Emond MJ, Monnat RJ Jr. (1998) I-PpoI and I-CreI homing site sequence degeneracy determined by random mutagenesis and sequential in vitro enrichment. J. Mol. Biol. 280:345-353. [ pdf ]
Flick KE, McHugh D, Heath JD, Stephens KM, Monnat RJ Jr, Stoddard BL. (1997) Crystallization and preliminary X-ray studies of I-PpoI: a nuclear, intron-encoded homing endonuclease from P. polycephalum. Protein Science 6(12):2677-80. PMC2143617 [ pdf ]
Seligman LM, Stephens KM, Monnat RJ Jr. (1997) Genetic analysis of the Chlamydomonas reinhardtii I-CreI mobile intron homing system in Escherichia coli. Genetics 147:1653-1664. PMC1208338 [ pdf ]
Bennett SE, Umar A, Oshima J, Monnat RJ Jr, Kunkel TA. (1997) Mismatch repair in extracts from Werner syndrome cell lines. Cancer Res 57: 256-2960.
Heath PJ, Stephens KM, Monnat RJ Jr, Stoddard BM. (1997) The structure of I-CreI: a Group I intron-encoded homing endonuclease. Nat Struct Biol 4:468-476.
Stephens KM, Monnat RJ Jr, Heath PD, Stoddard BM. (1997) Crystallization and preliminary X-ray analysis of the Chlamydomonas reinhardtii I-CreI mobile intron endonuclease. Proteins: Structure, Function and Genetics 28:137-139. [ pdf ]
Brooks-Wilson AR, Emond M, Monnat RJ Jr. (1997) Paradoxically low loss of hetero-zygosity (LOH) in genetically unstable Werner syndrome cell lines. Genes, Chromosomes & Cancer 18:133-142. [ pdf ]
Martin GM, Ogburn CE, Colgin LM, Gown AM, Edland SD, Monnat RJ Jr. (1996) Somatic mutations are frequent and increase with age in human kidney epithelial cells. Human Molec. Genetics 5:215-221. [ pdf ]
Publications prior to 1995
Monnat RJ Jr. (1992) Werner syndrome: molecular genetics and mechanistic hypotheses. Exp. Gerontol. 27:447-453. (first prediction that that the WRN protein may have helicase activity)
Monnat RJ Jr, Chiaverotti TA, Hackmann AFM, Maresh GA. (1992) Molecular structure and genetic stability of human hypoxanthine phosphoribosyltransferase (HPRT) gene duplications. Genomics 11:788-796. [ pdf ]
Monnat RJ Jr, Hackmann AFM, Chiaverotti TA. (1992) Nucleotide sequence analysis of human hypoxanthine phosphoribosyltransferase (HPRT) gene deletions. Genomics 11:777-787. [ pdf ]
Chiaverotti TA, Battula N, Monnat RJ Jr. (1991) Rat hypoxanthine phosphoribosyl-transferase cDNA cloning and sequence analysis. Genomics 11(4):1158-60. [ pdf ]
Fukuchi K, Tanaka K, Kumahara Y, Marumo K, Pride MB, Martin GM, Monnat RJ Jr. (1990) Increased frequency of 6-thioguanine-resistant peripheral blood lymphocytes in Werner syndrome patients. Human Genetics 84:249-252.
Fukuchi K, Martin GM, Monnat RJ Jr. (1989) Mutator phenotype of Werner syndrome is characterized by extensive deletions. Proc. Natl. Acad. Sci. USA 86:5893-5897. (errata in Proc. Natl. Acad. Sci. USA 86:7994, 1989). PMC297737 [ pdf ]