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Lis, John T
Barbara McClintock Professor of Molecular Biology & Genetics
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John Lis is a Professor in the Department of Molecular Biology and Genetics. He did his graduate research at Brandeis University and received his Ph.D. in Biochemistry in 1975. His postdoctoral work focused on Drosophila gene regulation and chromosome structure at Stanford University, during which time he was supported by a fellowship from the Helen Hay Whitney Foundation. Dr. Lis joined the faculty at Cornell in 1978. His research program has been supported by the National Institutes of Health, including a MERIT Award, March of Dimes, American Cancer Society, Cornell Biotechnology Institute, and a Proctor and Gamble University Exploratory Research Grant.
Research Areas
- biochemistry
- biological control
- biomedical sciences
- biophysics (CALS)
- biotechnology
- cell biology
- genetics
- intellectual property
- molecular biology
- molecular genetics
- nanobiotechnology
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- Teaching
- Service
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Affiliations
Research
research overview
- The Lis Lab develops and uses a variety of strategies to study the structure of promoters and genes and the mechanisms of their regulation in living cells. Our main model system has been the heat shock genes. These genes can undergo a 200-fold activation of transcription in response to small change in temperature and other cellular stresses. Over the years, we have developed genetic, optical and biochemical approaches that can be applied to study gene transcription and regulation with high precision and specificity in vivo. These include approaches that view the underlying mechanisms at the molecular level and in their native cellular environment. While our studies in the past were focused on a few genes, new genome-wide methods, several which we have developed, allow the interrogation of the entire genome – often with higher precision and sensitivity than our older focused gene studies. The genome-wide approaches are allowing the generality of hypotheses to be tested, and they are providing massive data for generating new hypotheses of how genes are regulated. We test our proposed molecular mechanisms by examining the consequences of targeted disruption of key protein factors or factor activities. This disruption of factors can be achieved by several strategies. Some strategies are easy and generally applied, such as RNAi, but are not effective at sorting primary from secondary effects. Others can be harder to implement, but are better at rigorously identifying the direct effects of a factor. We frequently use highly-specific small molecule inhibitors of the enzymes involved in transcription and regulation, when such molecules are available. Additionally, we have invested heavily in developing efficient selection methods for RNA aptamers that bind specific factors. RNA aptamers are of particular interest to us as they provide alternatives to small-molecular-weight "drugs" and can be selected in vitro from large combinatorial sequence pool for their affinity to a target protein. Next generation sequencing and use of our multiplex devices in selections have dramatically increased the rate production of RNA aptamers that bind target molecules with high affinity and specificity. These RNA aptamers are large enough to bind tightly to macromolecular surfaces and disrupt/inhibit interactions of a targeted macromolecule. Additionally, these aptamers can be targeted with precision by expressing the RNAs in cell under the control of specific promoters, allowing modulatation or perturbation of molecular interactions with high temporal and spatial precision in tissue culture cells or animals.
research activities
principal investigator on
- ANALYSIS OF THE ROLE AND ESTABLISHMENT OF THE PAUSED AND DIVERGENT RNA POLYMERASE II awarded by THE HELEN HAY WHITNEY FOUNDATION 2010 - 2013
- COORDINATE GENE REGULATION IN ANIMAL CELLS awarded by NATL INST OF GENERAL MEDICAL SCIENCES, NIH 2009 - 2013
- DEVELOPMENT OF HIGH THROUGHPUT APTAMER-BASED PROTEIN CAPTURE/DETECTION ASSAYS TOWARDS COMPREHENSIVE ANALYSIS OF HUMAN PROTEOME awarded by NATL INST OF HEALTH DHHS 2009 - 2014
- DISSECTION OF THE FACTORS AND ELEMENTS THAT DICTATE POL II PAUSING USING HIGH RESOLUTION NUCLEARRUN-ON ASSAYS awarded by HOWARD HUGHES MEDICAL INST 2011 - 2013
- IN VIVO DETECTION AND IMAGING OF EPIGENETIC HISTONE MODIFICATIONS AND MODIFYING ENZYMES USING MULTIVALENT RNA APTAMERS awarded by NATL INST OF HEALTH DHHS 2010 - 2015
- MOLECULAR DYNAMICS OF TRANSCRIPTION FACTORS AT HS LOCI IN LIVING CELLS awarded by NATL INST OF HEALTH DHHS 2009 - 2012
- PREDOCTORAL TRAINING IN CELLULAR AND MOLECULAR BIOLOGY awarded by NATL INST OF GENERAL MEDICAL SCIENCES, NIH 2010 - 2015
- QUANTIFYING THE GENOME-WIDE DISTRIBUTION OF TRANSCRIPTIONALLY-ENGAGED RNA POLYMERASES AT ULTRA-HIGH RESOLUTION awarded by NATL INST OF HEALTH DHHS 2009 - 2012
- REGULATION OF RNA POLYMERASE II ACTIVITY THROUGH PROMOTER-PROXIMAL PAUSING awarded by American Cancer Society 2012 - 2014
- USE OF APTAMERS IN DISSECTING THE HSF-REGULATED CANCER-ENABLING NETWORK awarded by NATL INST OF HEALTH DHHS 2009 - 2013
co-principal investigator on
- ULTRAVIEW VOX SPINNING DISK CONFOCAL FOR CORE FACILITY awarded by OFFICE OF THE DIRECTOR NIH 2012 - 2013
area(s) of concentration/expertise
keywords
- RNA aptamers
- RNA splicing
- SELEX
- Transcription
- chromatin
- gene expression
- gene regulation
- molecular genetics
submitted impact statement
Publications
individual publications
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academic article
- Accurate Prediction of Inducible Transcription Factor Binding Intensities In Vivo. PLoS Genetics. 8. 2012
- Accurate prediction of inducible transcription factor binding intensities in vivo.. PLoS Genetics. 8. 2012
- Activator Induced Spread of Poly(ADP-Ribose) Polymerase Promotes Nucleosome Loss at Hsp70.. Molecular Cell. 45:64-74. 2012
- Defining the status of RNA polymerase at promoters.. Cell Reports. 2:1025-1035. 2012
- Fcp1 dephosphorylation of the RNA polymerase II C-terminal domain is required for efficient transcription of heat shock genes.. Molecular and Cellular Biology. 32:3428-3437. 2012
- Mechanisms by which transcription factors gain access to target sequence elements in chromatin. Current Opinion in Genetic Development. 2012
- Overcoming the nucleosome barrier during transcript elongation.. Trends in Genetics. 28:285-294. 2012
- Peptidylarginine deiminase 2-catalyzed histone H3 arginine 26 citrullination facilitates estrogen receptor α target gene activation. Proceedings of the National Academy of Sciences of the United States of America. 109:13331-13336. 2012
- Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans. Nature Reviews. Genetics. 31:723-731. 2012
- RNA aptamers that functionally interact with green fluorescent protein and its derivatives. Nucleic Acids Research. 40. 2012
- The Drosophila 7SK snRNP and the essential role of dHEXIM in development. . Nucleic Acids Research. 40:5283-97. 2012
- A rapid,extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell. 145:622-634. 2011
- An RNA aptamer perturbs heat shock transcription factor activity in Drosophila melanogaster. Nucleic Acids Research. 39:6729-6740. 2011
- Drosophila Heat Shock System as a General Model to Investigate Transcriptional Regulation. Cold Spring Harbor Symposium on Quantitative Biology. 75:1-9. 2011
- Drosophila Set1 is the major histone H3 lysine 4 trimethyltransferase with role in transcription. EMBO Journal. 30:2817-2828. 2011
- Drosophila heat shock system as a general model to investigate transcriptional regulation.. Cold Spring Harbor Symposia on Quantitative Biology. 2011
- Minichromosome maintenance helicase paralog MCM9 is dispensible for DNA replication butfunctions in germ-line stem cells and tumor suppression. Proceedings at the National Academy of Science USA. 108:17702-17707. 2011
- Regulating RNAPolymerase Pausing and Transcription Elongation in Embryonic Stem Cells. Genes and Development. 25:742-754. 2011
- The polycomb group mutant esc leads to augmented levels of paused Pol II in the Drosophila embryo. Molecular Cell. 42:837-844. 2011
- X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila. Nature. 471:115-118. 2011
- CDK12 is a transcription elongation-associated CTD kinase, the metazoan ortholog of yeast Ctk1. Genes & Development. 24:2303-2316. 2010
- Chromatin landscape dictates HSF binding to target DNA elements. PLoS Genetics. 9. 2010
- Knocking down gene function with an RNA aptamer expressed as part of an intron.. Nucleic Acids Research. 38. 2010
- Recruitment Timing and Dynamics of Transcription Factors at the Hsp70 Loci in Living Cells. Molecular Cell. 40:965-975. 2010
- Recruitment timing and dynamics of transcription factors at the Hsp70 loci in living cells. Molecular Cell. 40:965-975. 2010
- Divergent transcription: a new feature of active promoters. Cell Cycle. 8:2557-2564. 2009
- A sol-gel-based microfluidics system enhances the efficiency of RNA aptamer selections. Molecular & Cellular Toxicology. 5:87-87. 2009
- Defining mechanisms that regulate RNA polymerase II transcription in vivo. Nature. 461:186-192. 2009
- High-resolution dynamic mapping of histone-DNA interactions in a nucleosome. Nature Structural and Molecular Biology. 16:124-129. 2009
- Paused Pol II captures enhancer activity and acts as a potent insulator. Genes & Development. 23:1606-1612. 2009
- Phosphorylation of the RNA polymerase II C-terminal domain by TFIIH kinase is not essential for transcription of Saccharomyces cerevisiae genome. Proceedings of the National Academy of Sciences of the United States of America. 106:14276-14280. 2009
- Selection and elution of aptamers using nanoporous sol-gel arrays with integrated microheaters. Lab on a Chip. 9:1206-12. 2009
- Imaging transcription dynamics at endogenous genes in living Drosophila tissues. Methods. 45:233-241. 2008
- Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters . Science. 322:1845-1848. 2008
- P-TEFb is Critical for the Maturation of RNA Polymerase II into Productive Elongation in vivo. Molecular and Cellular Biology. 28:1161-1170. 2008
- P-TEFb is critical for the maturation of RNA Polymerase II into productive elongation in viv. Molecular and Cellular Biology. 28. 2008
- Rapid, Transcription-Independent Loss of Nucleosomes over a Large Chromatin Domain at Hsp70 Loci. Cell. 134. 2008
- TFIIB aptamers inhibit transcription by perturbing PIC formation at distinct stages.. Nucleic Acids Research. 36:3118-3127. 2008
- Transcription regulation through promoter-proximal pausing. Science. 319:1791-1792. 2008
- Comparison of Femtosecond Laser and Continuous Wave UV Sources for Protein-Nucleic Acid Crosslinking. Photochemistry and Photobiology. 83:1394-404. 2007
- Imaging Drosophila gene activation and polymerase pausing in vivo. Nature. 450:198-202. 2007
- Intranuclear Distribution and Local Dynamics of RNA Polymerase II during Transcription Activation. Molecular Cell. 28:978-990. 2007
- RNA aptamers directed to discrete functional sites on a single protein structural domain. Proceedings at the National Academy of Science USA. 104:3742-3746. 2007
- An RNA aptamer that interferes with the DNA binding of the HSF transcription activator. Nucleic Acids Research. 34:3763-9. 2006
- Drosophila paf1 modulates chromatin structure at actively transcribed genes. Molecular and Cellular Biology. 26:250-60. 2006
- Dynamics of Heat Shock Factor Association with Native Gene Loci in Living Cells. Nature. 442:1050-1053. 2006
- Probing SWI/SNF remodeling of the nucleosome by unzipping single DNA molecules. Nature Structural and Molecular Biology. 6:549-54. 2006
- Promoter cleavage: a topoII-beta and PARP-1 collaboration. Cell. 125:1225-7. 2006
- Distinct transcriptional responses of RNA polymerases I, II and III to aptamersthat bind TBP. Nucleic Acids Research. 33:838-45. 2005
- Efficient release from promoter-proximal stall sites requires transcript cleavage factor TFIIS. Molecular Cell. 7:103-12. 2005
- Improving slide-based assays by stirring: application of liquid-on-liquid mixing to immunofluorescence staining of polytene chromosomes. Journal of Biochemical and Biophysical Methods. 64:59-68. 2005
- Interactions between subunits of Drosophila Mediator and activator proteins. Trends in Biochemical Sciences. 30:245-9. 2005
- Specific Contributions of Histone Tails and their Acetylation to the Mechanical Stability of Nucleosomes. Journal of Molecular Biology. 346:135-146. 2005
- Coordination of Transcription, RNA Processing, and Surveillance by P-TEFb Kinase on Heat Shock Genes. Molecular Cell. 13:55-65. 2004
- Indirect immunofluorescent labeling of Drosophila polytene chromosomes: visualizing protein interactions with chromatin in vivo. Methods in Enzymology. 376:393-404. 2004
- Molecular mechanism of transcription inhibition by Peptide antibiotic microcin j25. Molecular Cell. 14:753-762. 2004
- NAD+-dependent modulation of chromatin structure and transcription by nucleosome binding properties of PARP-1. Cell. 119:803-14. 2004
- Probing TBP interactions in transcription initiation and reinitiation with RNA aptamers that act in distinct modes. Proceedings at the National Academy of Science USA. 101:6934-6939. 2004
- Cdk7 Is Required for Full Activation of Drosophila Heat Shock Genes and Pol II Phosphorylation In Vivo. Molecular and Cellular Biology. 19:6876-86. 2003
- PARP Goes Transcription (Review). Cell. 113:677-683. 2003
- Specific SR protein-dependent splicing substrates identified through genomic SELEX. Nucleic Acids Research. 31:1955-61. 2003
- Tracking FACT and the RNA polymerase II elongation complex through chromatin in vivo. Science. 301:1094-6. 2003
- Transcription Factor and Polymerase Recruitment, Modification, and Movement on dhsp70 in vivo in the minutes following Heat Shock. Molecular and Cellular Biology. 23:7628-37. 2003
- Evolutionary dynamics and population control during in vitro selection and amplification with multiple targets. RNA. 11:1461-70. 2002
- How does Pol II overcome the nucleosome Barrier?. Molec. Cell. 9:451-457. 2002
- Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA. Proceedings at the National Academy of Science USA. 99:1960-65. 2002
- PR-Set7 is a nucleosome-specific methyltransferase that modifies lysine 20 of histone H4 and is associated with silent chromatin. Mol Cell.. 9:1201-13. 2002
- Single molecule analysis of RNA polymerase elongation reveals uniform kinetic behavior. Proceedings at the National Academy of Science USA. 99:13538-43. 2002
- The Drosophila BRM complex facilitates global transcription by RNA polymerase II. EMBO Journal. 21:5245-54. 2002
- The RNA processing exosome is linked to elongating RNA polymerase II in Drosophila. Nature. 420:837-41. 2002
- Mediator, Not Holoenzyme, Is Directly Recruited to the Heat Shock Promoter by HSF upon Heat Shock. Molec. Cell. 8:9-19. 2001
- A TRF1:BRF complex directs Drosophila RNA polymerase III transcription. Cell. 101:459-69. 2000
- High resolution localization of Drosophila Spt5 and Spt6 at heat shock genes in vivo: Roles in promoter proximal pausing and transcription elongation. Genes & Development. 14:2635-2649. 2000
- P-TEFb kinase recruitment and function at heat shock loci. Genes & Development. 14:792-803. 2000
- Pre-mRNA splicing by the essential Drosophila protein B52: tissue and target specificity. Molecular and Cellular Biology. 20:181-186. 2000
- DNA Distortion and Multimerization: Novel Functions of the Glutamine-Rich Domain of GAGA Factor. J. Mol. Biol. 285:515-525. 1999
- Different upstream transcriptional activators have distinct coactivator requirements. Genes & Development. 13:2934-2939. 1999
- Glycogen synthase phosphatase interacts with heat shock factor to activate cup1 gene transcription in saccharomyces cerevisiae. Molecular and Cellular Biology. 19:3237-3245. 1999
- Nuclear run-on assays: assessing transcription by measuring density of engaged RNA polymerases. Methods in Enzymology. 304:351-362. 1999
- RNA aptamers as effective protein antagonists in a multicellular organism. Proceedings at the National Academy of Science USA. 96:10033-10038. 1999
- TATA box-binding protein (TBP)-related factor 2 (TRF2), a third member of the TBP family. Proceedings at the National Academy of Science USA. 96:4791-6. 1999
- TFIIH Is Required for Promoter Melting In Vivo. Molecular and Cellular Biology. 19:5652-5658. 1999
- Direct cloning of DNA that interacts in vivo with a specific protein: application to RNA polymerase II and sites of pausing in Drosophila. Nucleic Acids Research. 26:919-924. 1998
- GAGA factor binding to DNA via a single trinucleotide sequence element. Nucleic Acids Research. 26:2672-2678. 1998
- In vitro selection of RNA molecules that displace cocaine from the membrane –bound nicotinic receptor. Proceedings at the National Academy of Science USA. 95:14051-14056. 1998
- Transcription activation that is independent of TFIIH kinase and the RNA polymerase II mediator in vivo. Nature. 393:389-392. 1998
- A specific RNA hairpin structure binds the RNA recognition motifs of the Drosophila SR protein B52. Molecular and Cellular Biology. 17:2649-2657. 1997
- Dynamics of potentiation and activation: GAGA factor and its role in heat shock gene regulation. Nucleic Acids Research. 25:3963-3968. 1997
- Interaction of Drosophila heat-shock factor, RNA polymerase II, and TATA-binding protein: Insights into heat-shock gene activation. Journal of Biological Chemistry. 272:33227-33233. 1997
- Promoter activity of Tat at steps subsequent to TBP-recruitment. Molecular and Cellular Biology. 17:6898-6905. 1997
- Transcription properties of a cell type specific tata-binding protein, TRF. Cell. 91:71-83. 1997
- HSF recruitment and loss at most Drosophila heat shock loci is coordinated and depends on proximal promoter sequences. Chromosoma. 105:158-171. 1996
- Binding of heat shock factor to and transcriptional activation of heat shock genes in Drosophila. Nucleic Acids Research. 23:4799-4804. 1995
- Distribution of GAGA protein on Drosophila genes in vivo. Genes & Development. 9:1098-1110. 1995
- Dynamic Protein-DNA Architecture of a Yeast Heat Shock Promoter. Molecular and Cellular Biology. 15:2737-2744. 1995
- HSF access to heat shock elements in vivo depends critically on promoter architecture defined by GAGA factor, TFIID, and RNA polymerase II binding sites. Genes & Development. 9:2756-2769. 1995
- Recruiting TATA-binding protein to the promoter: transcriptional activation without an upstream activator. Molecular and Cellular Biology. 15:5757-5761. 1995
- Short transcripts of the ternary complex provide insight into RNA polymerase II elongational pausing. J. Mol. Biol.. 252:522-535. 1995
- Sodium salicylate and yeast heat shock gene transcription. Journal of Biological Chemistry. 270:10369-10372. 1995
- A Highly Conserved Domain of RNA Polymerase II Shares a Functional Element with Acidic Activation Domains of Upstream Transcription Factors. Molecular and Cellular Biology. 14:7507-7516. 1994
- Distribution of B52 within a chromosomal locus depends on the level of transcription. Molecular and Cellular Biology. 5:71-79. 1994
- Fine structure analyses of the Drosophila and Saccharomyces heat shock factor - heat shock element interactions. Nucleic Acids Research. 22:167-173. 1994
- Phosphorylation of RNA polymerase II C-terminal domain and transcriptional elongation. Nature. 370:75-77. 1994
- The Concentration of B52, an Essential Splicing Factor and Regulator of Splice Site Choice In Vitro, Is Critical for Drosophila Development. Molecular and Cellular Biology. 14:5360-5370. 1994
- The SR Protein B52/SRp55 Is Essential for Drosophila Development. Molecular and Cellular Biology. 14:7499-7506. 1994
- The upstream activator CTF/NF1 and RNA polymerase II share a common element involved in transcriptional activation. Nucleic Acids Research. 22:1966-1973. 1994
- DNA melting on yeast RNA polymerase II promoters. Science. 261:759-762. 1993
- In vivo transcriptional pausing and cap formation on three Drosophila heat shock genes. Proceedings at the National Academy of Science USA. 90:7923-7927. 1993
- Polymerase processivity and termination on Drosophila heat shock genes. J. Biol. Chem. 268:23806-23811. 1993
- Protein traffic on the heat shock promoter: parking, stalling, and trucking along. Cell. 74:1-4. 1993
- Rapid changes in Drosophila transcription upon an "instantaneous " heat shock. Molecular and Cellular Biology. 13:3456-3463. 1993
- DNA Sequence requirements for generating paused polymerase at the start of hsp70. Genes & Development. 6:284-295. 1992
- Promoter melting and TFIID complexes on Drosophila genes in vivo. Genes & Development. 6:2190-2200. 1992
- Characterization of a Drosophila protein associated with boundaries of transcriptionally active chromatin. Genes & Development. 5:1611-1621. 1991
- Cooperative binding of Drosophila heat shock factor to arrays of a conserved 5 bp unit. Cell. 64:585-593. 1991
- RNA polymerase II pauses at the 5' end of the transcriptionally induced Drosophila hsp70 gene. Molecular and Cellular Biology. 11:5285-5290. 1991
- Closely related DNA sequences specify distinct patterns of developmental expression in Drosophila. Molecular and Cellular Biology. 10:3272-3276. 1990
- Multiple, compensatory regulatory elements specify spermatocyte-specific expression of the Drosophila hsp26 gene. Molecular and Cellular Biology. 10:131-137. 1990
- Optimal heat-induced expression of the Drosophila hsp26 gene requires a promoter sequence containing (CT)n.(GA)n repeats. J. Mol. Biol.. 211:751-761. 1990
- Post-initiation transcriptional control in Drosophila. Molecular and Cellular Biology. 10:6041-6045. 1990
- Heat shock and developmental regulation of the Drosophila melanogaster hsp83 gene. Molecular and Cellular Biology. 9:1746-1753. 1989
- Stable binding of Drosophila heat shock factor to head-to-head and tail-to-tail repeats of a conserved 5 bp recognition unit. Cell. 59:797-806. 1989
- Differential regulation of the two glyceraldehyde-3-phosphate dehydrogenase genes during Drosophila development. Molecular and Cellular Biology. 8:5200-5205. 1988
- Germline transformation used to define key features of heat shock response elements. Science. 239:1139-1142. 1988
- Localized heat shock induction in Drosophila melanogaster. Journal of Experimental Zoology. 247:279-284. 1988
- Sex-specific control of DrosophilaYP1 expression is limited to transcription. Molecular and Cellular Biology. 8:4756-4764. 1988
- Structure and expression of ubiquitin genes of Drosophila melanogaster. Molecular and Cellular Biology. 8:4727-4735. 1988
- The RNA polymerase II molecule at the 5' end of the uninduced hsp70 gene of D.melanogaster is transcriptionally engaged. Cell. 54:795-804. 1988
- The positive and negative regulation of the Drosophila Gapdh-2 gene. Genes & Development. 2:743-753. 1988
- Protein-DNA crosslinking reveal dramatic variation in RNA polymerase II density on different histone repeats of Drosophila melanogaster. Molecular and Cellular Biology. 7:3341-3344. 1987
- germline transformation analysis reveals flexibility in the organization of heat shock consensus elements. Nucleic Acids Research. 7:2971-2988. 1987
- A consensus sequence polymer inhibits in vivo expression of heat shock genes. Molecular and Cellular Biology. 6:3200-3206. 1986
- Electron microscopical analysis of Drosophila polytene chromosomes. Result of transformation of genetic material into chromosomes. Chromosoma. 93:461-468. 1986
- Expression of the major heat shock gene of Drosophila melanogaster in Saccharomyces cerevisiae. Nucleic Acids Research. 14:3587-3601. 1986
- RNA polymerase interacts with the promoter region of noninduced hsp70 gene in D. melanogaster cells. Molecular and Cellular Biology. 6:3984-3989. 1986
- Spatial and temporal pattern of hsp26 expression during normal development. EMBO Journal. 5:747-754. 1986
- Topoisomerase I interacts with transcribed regions in Drosophila cells. Cell. 44:401-407. 1986
- A hypersensitive site in hsp70 chromatin requires adjacent not internal DNA sequence. Nature. 313:147-149. 1985
- Determinants of heat shock-induced chromosome puffing. Cell. 40:805-817. 1985
- In vivo interactions of RNA polymerase II with genes of Drosophila melanogaster. Molecular and Cellular Biology. 5:2009-2018. 1985
- Localization and expression of transformed DNA sequences within heat shock puffs of D. melanogaster. Chromosoma. 93:26-30. 1985
- Detecting protein-DNA interactions in vivo: Distribution of RNA polymerase on specific bacterial genes. Proceedings at the National Academy of Science USA. 81:4275-4279. 1984
- High-resolution mapping of DNase I-hypersensitive sites of Drosophila heat shock genes in Drosophila melanogaster and Saccharomyces cerevisiae. Molecular and Cellular Biology. 4:1853-1860. 1984
- Update for users of the Cornell sequence analysis package. Nucleic Acids Research. 12:619-625. 1984
- Localization of the hsp83 transcript within a 3292 nucleotide sequence from the 63B heat shock locus of D. melanogaster. Nucleic Acids Research. 11:7011-7029. 1983
- New heat shock puffs and -galactosidase activity resulting from transformation of Drosophila with an hsp70-lacZ hybrid gene. Cell. 35:403-410. 1983
- Microcomputer software for nucleotide sequence analysis. Nucleic Acids Research. 10:6451-6463. 1982
- DNA sequences flanking the starts of the hsp 70 and ab heat shock genes are homologous. Developmental Biology. 83:291-300. 1981
- DNA sequencing reveals extensive homologies of regions preceding the hsp 70 and heat shock genes in Drosophila melanogaster. Proceedings at the National Academy of Science USA. 78:6196-6200. 1981
- Genomic organization and transcription of the ab heat shock DNA in Drosophila melanogaster. Nucleic Acids Research. 9:5297-5310. 1981
- Two closely linked transcription units within the 63B heat shock puff locus of D. melanogaster. Nucleic Acids Research. 9:5075-5092. 1981
- Genes for the 70,000 dalton heat shock protein in two cloned D. melanogaster DNA segments. Cell. 17:9-18. 1979
- Physical map of the two D. melanogaster DNA segments containing sequences coding for the 70,000 dalton heat shock protein. Cell. 17:1-8. 1979
- A novel arrangement of tandemly repeated genes at a major heat shock site in Drosophila melanogaster. Cell. 14:901-919. 1978
- Size fractionation of double-stranded DNA by precipitation with polyethylene glycol. Nucleic Acids Research. 2:383-389. 1975
- The isolation and characterization of plaque-forming arabinose transducing bacteriophage l. J. Mol. Biol.. 95:395-407. 1975
- The regulatory region of the L-arabinose operon--Its isolation on a 1017 base pair fragment from DNA heteroduplexes. J. Mol. Biol.. 95:409-416. 1975
- The regulatory region of the L-arabinose operon: A physical, genetic and physiological study. J. Mol. Biol.. 95:417-431. 1975
- Different cyclic AMP requirements for induction of the arabinose and lactose operons of Escherichia coli. J. Mol. Biol.. 79:149-162. 1973
- Lambda lysozyme synthesis in the absence of N protein. Virology. 45:532-533. 1971
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booksection
featured in archived article
- A new look at how genes unfold to enable their expression
- New technique provides snapshot of all genes being transcribed across human genome
- Research sheds light on the mechanics of gene transcription
- Researchers 'unzip' molecules to measure interactions keeping DNA packed in cells
- Researchers receive prestigious NIH grants, including two $2.5 million Pioneer awards
- Researchers see into living tissue using multiphoton fluorescence microscopy technique
Teaching
teaching overview
- My main teaching is focused in BioBM6390, The Nucleus. This course focuses on the structure and function of the eukaryotic nucleus and covers the following topics: genome organization, chromatin structure, transcription factors, gene regulatory mechanisms, RNA processing, DNA replication, and nuclear architecture. In the past I have also taught Explorations every year to 8 Freshman as part of BioG 1101-1104, however the Explorations Program does not presently exist as part of the course.
teaching activities
Service
service to the profession
- Genomics of Gene Regulation Advisors, NIH/NHGRI Board of Advisors 2009 -
- NIH mod ENCODE External Consultants Committee Member 2007 -
- NIH ENCODE External Consultants Panel Committee Member 2005 -
- AAAS/Board of Reviewing Editors Board Member 2007 - 2012
- NIH Site Visit for the Laboratory of Receptor Biology and Gene Expression Committee Member 2008
- NIH Study Section Member 2006 - 2007
reviewer or editor for
- NIH
- NIH CDF2 Study Section
- NIH CDF2 Study Section
- NIH Genetics Study Section
- NIH Genetics Study Section
- NIH Molecular Biology Study Section - now CDF-1
- NIH Molecular Biology Study Section - now CDF-1
- NIH Molecular Biology Study Section - now CDF-1
- NIH Molecular Biology Study Section - now CDF-1
- NIH Molecular Cytology Study Section – now CDF-2
- NIH Study Section
Background
education and training
- Ph.D. in, Brandeis University 1975
- Fairfield University 1970
awards and honors
- Distinguished Foreign Professorship, 2011
- Research Award for Basic Research, 2007
- Barbara McClintock Chaired Professor, 2004
- John Simon Guggenheim Memorial Foundation Fellowship, 2000
- Phi Beta Kappa, 1999
- MERIT Award, 1995
- Elected Fellow, 1992
- Procter & Gamble Exploratory Research Program Grant (1981-1984), 1981
- The Helen Hay Whitney Foundation Postdoctoral Fellowship (1975-1978), 1975
- Estherlee Russotto Gilbert Merit Award, 1973
- W. Conn. Sect. - American Chemical Society Award, Outstanding Senior chemistry Major, Fairfield University, 1970
Other
college
- CALS
research keyword
- RNA aptamers
- RNA splicing
- SELEX
- Transcription
- chromatin
- gene expression
- gene regulation
- molecular genetics
name prefix
- Dr.