Faculty Appointments
Associate Professor of Biological Sciences
Education
Ph.D., Molecular Microbiology, Tufts University School of Medicine, Boston, MassachusettsB.Sc., Microbiology, University of Massachusetts, Amherst, Massachusetts
Research Description
Regulation of genome duplication requires exquisite control to ensure proper transmission of genetic material from mother cell to daughter cell and to prevent the genome aberrations that are associated with cancer cells. Importantly, the replication machinery must respond to changes in chromatin structure and cell cycle parameters that are associated with cellular differentiation in order to maintain genome integrity. Although this is a fundamental aspect of genome duplication, the underlying molecular mechanisms and critical factors responsible for responding to these changes remain poorly understood.
Due to its well characterized replication systems, chromatin architecture and cell differentiation systems, Drosophila provides an ideal model system to understand, mechanistically, how the DNA replication program responds to changes in cellular differentiation and development. We are using a combination of proteomic, genomic, cell biological, genetic and biochemical approaches to uncover and characterize fundamental aspects of genome duplication and stability.
Due to its well characterized replication systems, chromatin architecture and cell differentiation systems, Drosophila provides an ideal model system to understand, mechanistically, how the DNA replication program responds to changes in cellular differentiation and development. We are using a combination of proteomic, genomic, cell biological, genetic and biochemical approaches to uncover and characterize fundamental aspects of genome duplication and stability.
Research Keywords
DNA replication, genome maintenance, cell cycle, development, Drosophila, Biochemistry, Genetics, Developmental Biology, Molecular Biology,
Publications
Han D, Schaffner SH, Davies JP, Benton ML, Plate L, Nordman JT. BRWD3 promotes KDM5 degradation to maintain H3K4 methylation levels. BioRxiv. 2023 Mar 3/28/2023; PMID: 37034668, PMCID: PMC10081218, PII: 2023.03.28.534572, DOI: 10.1101/2023.03.28.534572.
Munden A, Benton ML, Capra JA, Nordman JT. R-loop Mapping and Characterization During Drosophila Embryogenesis Reveals Developmental Plasticity in R-loop Signatures. J Mol Biol [print-electronic]. 2022 Jul 7/15/2022; 434(13): 167645. PMID: 35609632, PMCID: PMC9254486, PII: S0022-2836(22)00225-X, DOI: 10.1016/j.jmb.2022.167645, ISSN: 1089-8638.
Munden A, Wright MT, Han D, Tirgar R, Plate L, Nordman JT. Identification of replication fork-associated proteins in Drosophila embryos and cultured cells using iPOND coupled to quantitative mass spectrometry. Sci Rep. 2022 Apr 4/28/2022; 12(1): 6903. PMID: 35484306, PMCID: PMC9050644, PII: 10.1038/s41598-022-10821-9, DOI: 10.1038/s41598-022-10821-9, ISSN: 2045-2322.
Richards L, Das S, Nordman JT. Rif1-Dependent Control of Replication Timing. Genes (Basel). 2022 Mar 3/20/2022; 13(3): PMID: 35328102, PMCID: PMC8955891, PII: genes13030550, DOI: 10.3390/genes13030550, ISSN: 2073-4425.
Das S, Caballero M, Kolesnikova T, Zhimulev I, Koren A, Nordman J. Replication timing analysis in polyploid cells reveals Rif1 uses multiple mechanisms to promote underreplication in Drosophila. Genetics. 2021 Nov 11/5/2021; 219(3): PMID: 34740250, PMCID: PMC8570783, PII: 6369517, DOI: 10.1093/genetics/iyab147, ISSN: 1943-2631.
Armstrong RL, Das S, Hill CA, Duronio RJ, Nordman JT. Rif1 Functions in a Tissue-Specific Manner To Control Replication Timing Through Its PP1-Binding Motif. Genetics [print-electronic]. 2020 May; 215(1): 75-87. PMID: 32144132, PMCID: PMC7198277, PII: genetics.120.303155, DOI: 10.1534/genetics.120.303155, ISSN: 1943-2631.
Munden A, Rong Z, Sun A, Gangula R, Mallal S, Nordman JT. Rif1 inhibits replication fork progression and controls DNA copy number in Drosophila. Elife. 2018 Oct 10/2/2018; 7: PMID: 30277458, PMCID: PMC6185109, PII: 39140, DOI: 10.7554/eLife.39140, ISSN: 2050-084X.
Nordman JT, Orr-Weaver TL. Understanding replication fork progression, stability, and chromosome fragility by exploiting the Suppressor of Underreplication protein. Bioessays [print-electronic]. 2015 Aug; 37(8): 856-61. PMID: 26059810, PMCID: PMC4556369, DOI: 10.1002/bies.201500021, ISSN: 1521-1878.
Nordman JT, Kozhevnikova EN, Verrijzer CP, Pindyurin AV, Andreyeva EN, Shloma VV, Zhimulev IF, Orr-Weaver TL. DNA copy-number control through inhibition of replication fork progression. Cell Rep [print-electronic]. 2014 Nov 11/6/2014; 9(3): 841-9. PMID: 25437540, PMCID: PMC4366648, PII: S2211-1247(14)00859-6, DOI: 10.1016/j.celrep.2014.10.005, ISSN: 2211-1247.
Nordman J, Orr-Weaver TL. Regulation of DNA replication during development. Development. 2012 Feb; 139(3): 455-64. PMID: 22223677, PMCID: PMC3252349, PII: 139/3/455, DOI: 10.1242/dev.061838, ISSN: 1477-9129.
Sher N, Bell GW, Li S, Nordman J, Eng T, Eaton ML, Macalpine DM, Orr-Weaver TL. Developmental control of gene copy number by repression of replication initiation and fork progression. Genome Res [print-electronic]. 2012 Jan; 22(1): 64-75. PMID: 22090375, PMCID: PMC3246207, PII: gr.126003.111, DOI: 10.1101/gr.126003.111, ISSN: 1549-5469.
Nordman J, Wright A. Escherichia coli nucleoside diphosphate kinase mutants depend on translesion DNA synthesis to prevent mutagenesis. J. Bacteriol [print-electronic]. 2011 Sep; 193(17): 4531-3. PMID: 21725024, PMCID: PMC3165513, PII: JB.05393-11, DOI: 10.1128/JB.05393-11, ISSN: 1098-5530.
Kim JC, Nordman J, Xie F, Kashevsky H, Eng T, Li S, MacAlpine DM, Orr-Weaver TL. Integrative analysis of gene amplification in Drosophila follicle cells: parameters of origin activation and repression. Genes Dev. 2011 Jul 7/1/2011; 25(13): 1384-98. PMID: 21724831, PMCID: PMC3134082, PII: 25/13/1384, DOI: 10.1101/gad.2043111, ISSN: 1549-5477.
Nordman J, Li S, Eng T, Macalpine D, Orr-Weaver TL. Developmental control of the DNA replication and transcription programs. Genome Res [print-electronic]. 2011 Feb; 21(2): 175-81. PMID: 21177957, PMCID: PMC3032921, PII: gr.114611.110, DOI: 10.1101/gr.114611.110, ISSN: 1549-5469.
, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science [print-electronic]. 2010 Dec 12/24/2010; 330(6012): 1787-97. PMID: 21177974, PMCID: PMC3192495, PII: science.1198374, DOI: 10.1126/science.1198374, ISSN: 1095-9203.
Nordman J, Wright A. The relationship between dNTP pool levels and mutagenesis in an Escherichia coli NDP kinase mutant. Proc. Natl. Acad. Sci. U.S.A [print-electronic]. 2008 Jul 7/22/2008; 105(29): 10197-202. PMID: 18621712, PMCID: PMC2453072, PII: 0802816105, DOI: 10.1073/pnas.0802816105, ISSN: 1091-6490.
Dineen SS, Villapakkam AC, Nordman JT, Sonenshein AL. Repression of Clostridium difficile toxin gene expression by CodY. Mol Microbiol [print-electronic]. 2007 Oct; 66(1): 206-19. PMID: 17725558, PII: MMI5906, DOI: 10.1111/j.1365-2958.2007.05906.x, ISSN: 0950-382X.
Nordman J, Skovgaard O, Wright A. A novel class of mutations that affect DNA replication in E. coli. Mol. Microbiol. 2007 Apr; 64(1): 125-38. PMID: 17376077, PII: MMI5651, DOI: 10.1111/j.1365-2958.2007.05651.x, ISSN: 0950-382X.
Renzette N, Gumlaw N, Nordman JT, Krieger M, Yeh SP, Long E, Centore R, Boonsombat R, Sandler SJ. Localization of RecA in Escherichia coli K-12 using RecA-GFP. Mol. Microbiol. 2005 Aug; 57(4): 1074-85. PMID: 16091045, PII: MMI4755, DOI: 10.1111/j.1365-2958.2005.04755.x, ISSN: 0950-382X.
Munden A, Benton ML, Capra JA, Nordman JT. R-loop Mapping and Characterization During Drosophila Embryogenesis Reveals Developmental Plasticity in R-loop Signatures. J Mol Biol [print-electronic]. 2022 Jul 7/15/2022; 434(13): 167645. PMID: 35609632, PMCID: PMC9254486, PII: S0022-2836(22)00225-X, DOI: 10.1016/j.jmb.2022.167645, ISSN: 1089-8638.
Munden A, Wright MT, Han D, Tirgar R, Plate L, Nordman JT. Identification of replication fork-associated proteins in Drosophila embryos and cultured cells using iPOND coupled to quantitative mass spectrometry. Sci Rep. 2022 Apr 4/28/2022; 12(1): 6903. PMID: 35484306, PMCID: PMC9050644, PII: 10.1038/s41598-022-10821-9, DOI: 10.1038/s41598-022-10821-9, ISSN: 2045-2322.
Richards L, Das S, Nordman JT. Rif1-Dependent Control of Replication Timing. Genes (Basel). 2022 Mar 3/20/2022; 13(3): PMID: 35328102, PMCID: PMC8955891, PII: genes13030550, DOI: 10.3390/genes13030550, ISSN: 2073-4425.
Das S, Caballero M, Kolesnikova T, Zhimulev I, Koren A, Nordman J. Replication timing analysis in polyploid cells reveals Rif1 uses multiple mechanisms to promote underreplication in Drosophila. Genetics. 2021 Nov 11/5/2021; 219(3): PMID: 34740250, PMCID: PMC8570783, PII: 6369517, DOI: 10.1093/genetics/iyab147, ISSN: 1943-2631.
Armstrong RL, Das S, Hill CA, Duronio RJ, Nordman JT. Rif1 Functions in a Tissue-Specific Manner To Control Replication Timing Through Its PP1-Binding Motif. Genetics [print-electronic]. 2020 May; 215(1): 75-87. PMID: 32144132, PMCID: PMC7198277, PII: genetics.120.303155, DOI: 10.1534/genetics.120.303155, ISSN: 1943-2631.
Munden A, Rong Z, Sun A, Gangula R, Mallal S, Nordman JT. Rif1 inhibits replication fork progression and controls DNA copy number in Drosophila. Elife. 2018 Oct 10/2/2018; 7: PMID: 30277458, PMCID: PMC6185109, PII: 39140, DOI: 10.7554/eLife.39140, ISSN: 2050-084X.
Nordman JT, Orr-Weaver TL. Understanding replication fork progression, stability, and chromosome fragility by exploiting the Suppressor of Underreplication protein. Bioessays [print-electronic]. 2015 Aug; 37(8): 856-61. PMID: 26059810, PMCID: PMC4556369, DOI: 10.1002/bies.201500021, ISSN: 1521-1878.
Nordman JT, Kozhevnikova EN, Verrijzer CP, Pindyurin AV, Andreyeva EN, Shloma VV, Zhimulev IF, Orr-Weaver TL. DNA copy-number control through inhibition of replication fork progression. Cell Rep [print-electronic]. 2014 Nov 11/6/2014; 9(3): 841-9. PMID: 25437540, PMCID: PMC4366648, PII: S2211-1247(14)00859-6, DOI: 10.1016/j.celrep.2014.10.005, ISSN: 2211-1247.
Nordman J, Orr-Weaver TL. Regulation of DNA replication during development. Development. 2012 Feb; 139(3): 455-64. PMID: 22223677, PMCID: PMC3252349, PII: 139/3/455, DOI: 10.1242/dev.061838, ISSN: 1477-9129.
Sher N, Bell GW, Li S, Nordman J, Eng T, Eaton ML, Macalpine DM, Orr-Weaver TL. Developmental control of gene copy number by repression of replication initiation and fork progression. Genome Res [print-electronic]. 2012 Jan; 22(1): 64-75. PMID: 22090375, PMCID: PMC3246207, PII: gr.126003.111, DOI: 10.1101/gr.126003.111, ISSN: 1549-5469.
Nordman J, Wright A. Escherichia coli nucleoside diphosphate kinase mutants depend on translesion DNA synthesis to prevent mutagenesis. J. Bacteriol [print-electronic]. 2011 Sep; 193(17): 4531-3. PMID: 21725024, PMCID: PMC3165513, PII: JB.05393-11, DOI: 10.1128/JB.05393-11, ISSN: 1098-5530.
Kim JC, Nordman J, Xie F, Kashevsky H, Eng T, Li S, MacAlpine DM, Orr-Weaver TL. Integrative analysis of gene amplification in Drosophila follicle cells: parameters of origin activation and repression. Genes Dev. 2011 Jul 7/1/2011; 25(13): 1384-98. PMID: 21724831, PMCID: PMC3134082, PII: 25/13/1384, DOI: 10.1101/gad.2043111, ISSN: 1549-5477.
Nordman J, Li S, Eng T, Macalpine D, Orr-Weaver TL. Developmental control of the DNA replication and transcription programs. Genome Res [print-electronic]. 2011 Feb; 21(2): 175-81. PMID: 21177957, PMCID: PMC3032921, PII: gr.114611.110, DOI: 10.1101/gr.114611.110, ISSN: 1549-5469.
, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, Washietl S, Arshinoff BI, Ay F, Meyer PE, Robine N, Washington NL, Di Stefano L, Berezikov E, Brown CD, Candeias R, Carlson JW, Carr A, Jungreis I, Marbach D, Sealfon R, Tolstorukov MY, Will S, Alekseyenko AA, Artieri C, Booth BW, Brooks AN, Dai Q, Davis CA, Duff MO, Feng X, Gorchakov AA, Gu T, Henikoff JG, Kapranov P, Li R, MacAlpine HK, Malone J, Minoda A, Nordman J, Okamura K, Perry M, Powell SK, Riddle NC, Sakai A, Samsonova A, Sandler JE, Schwartz YB, Sher N, Spokony R, Sturgill D, van Baren M, Wan KH, Yang L, Yu C, Feingold E, Good P, Guyer M, Lowdon R, Ahmad K, Andrews J, Berger B, Brenner SE, Brent MR, Cherbas L, Elgin SC, Gingeras TR, Grossman R, Hoskins RA, Kaufman TC, Kent W, Kuroda MI, Orr-Weaver T, Perrimon N, Pirrotta V, Posakony JW, Ren B, Russell S, Cherbas P, Graveley BR, Lewis S, Micklem G, Oliver B, Park PJ, Celniker SE, Henikoff S, Karpen GH, Lai EC, MacAlpine DM, Stein LD, White KP, Kellis M. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science [print-electronic]. 2010 Dec 12/24/2010; 330(6012): 1787-97. PMID: 21177974, PMCID: PMC3192495, PII: science.1198374, DOI: 10.1126/science.1198374, ISSN: 1095-9203.
Nordman J, Wright A. The relationship between dNTP pool levels and mutagenesis in an Escherichia coli NDP kinase mutant. Proc. Natl. Acad. Sci. U.S.A [print-electronic]. 2008 Jul 7/22/2008; 105(29): 10197-202. PMID: 18621712, PMCID: PMC2453072, PII: 0802816105, DOI: 10.1073/pnas.0802816105, ISSN: 1091-6490.
Dineen SS, Villapakkam AC, Nordman JT, Sonenshein AL. Repression of Clostridium difficile toxin gene expression by CodY. Mol Microbiol [print-electronic]. 2007 Oct; 66(1): 206-19. PMID: 17725558, PII: MMI5906, DOI: 10.1111/j.1365-2958.2007.05906.x, ISSN: 0950-382X.
Nordman J, Skovgaard O, Wright A. A novel class of mutations that affect DNA replication in E. coli. Mol. Microbiol. 2007 Apr; 64(1): 125-38. PMID: 17376077, PII: MMI5651, DOI: 10.1111/j.1365-2958.2007.05651.x, ISSN: 0950-382X.
Renzette N, Gumlaw N, Nordman JT, Krieger M, Yeh SP, Long E, Centore R, Boonsombat R, Sandler SJ. Localization of RecA in Escherichia coli K-12 using RecA-GFP. Mol. Microbiol. 2005 Aug; 57(4): 1074-85. PMID: 16091045, PII: MMI4755, DOI: 10.1111/j.1365-2958.2005.04755.x, ISSN: 0950-382X.
Available Postdoctoral Position Details
Posted: 12/16/2015
We are currently looking for motivated and enthusiastic people to join our team. Contact Jared for more information.
We are currently looking for motivated and enthusiastic people to join our team. Contact Jared for more information.