Divergent Transcription from Active Promoters (2010)
Amy C. Seila, J. Mauro Calabrese, Stuart S. Levine, Gene W. Yeo, Peter B. Rahl, Ryan A. Flynn, ...
Transcription initiation by RNA polymerase II (RNAPII) is thought to occur unidirectionally from most genes. Here, we present evidence of widespread divergent transcription at protein-encoding gene...
The Biology and Therapeutic Promise of Small RNAs (2009)
Presented by Phillip A. Sharp, PhD., Institute Professor at the Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology on October 2, 2009 11:00 am – 12:30 pm in the...
New Biology and Biotechnology (2009)
Phil Sharp, PhD, from MIT gave a brief presentation to the Friends of the Petit Institute Group on October 2, 2009 in IBB Seminar Room 1128.
The Biology and Therapeutic Promise of Small RNAs (2009)
The discovery of the multiple roles of small RNAs in regulation of gene expression is a revolutionary advance in biology. MicroRNAs probably interact with mRNAs from half of all human genes....
New Biology and Biotechnology (2009)
Phil Sharp, PhD, from MIT gave a brief presentation to the Friends of the Petit Institute Group on October 2, 2009 in IBB Seminar Room 1128.
Comparison of siRNA-induced off-target RNA and protein effects (2007)
Alemán, Lourdes M., Doench, John, Sharp, Phillip A.
The downregulation of many mRNAs has been observed through bioinformatic analysis of microarray results following transfection of short interfering RNAs (siRNAs). Many of these mRNA changes are due...
Dynamic regulation of miRNA expression in ordered stages of cellular development (2007)
Neilson, Joel R., Zheng, Grace X.Y., Burge, Christopher B., Sharp, Phillip A.
Short RNA expression in several distinct stages of T-lymphocyte development was comprehensively profiled. The total number of microRNAs (miRNAs) expressed per cell at different stages of development...
Comparison of siRNA-induced off-target RNA and protein effects (2007)
Alemán, Lourdes M., Doench, John, Sharp, Phillip A.
The downregulation of many mRNAs has been observed through bioinformatic analysis of microarray results following transfection of short interfering RNAs (siRNAs). Many of these mRNA changes are due...
Comparison of siRNA-induced off-target RNA and protein effects (2007)
Alemán, Lourdes M., Doench, John, Sharp, Phillip A.
The downregulation of many mRNAs has been observed through bioinformatic analysis of microarray results following transfection of short interfering RNAs (siRNAs). Many of these mRNA changes are due...
A positive feedback loop couples Ras activation and CD44 alternative splicing (2006)
Cheng, Chonghui, Yaffe, Michael B., Sharp, Phillip A.
The Ras signaling pathway is important in both cell proliferation and tumor progression. Alternatively spliced isoforms of CD44 containing variable exon 6 (v6) can serve as coreceptors for growth...
Calabrese, J. Mauro, Sharp, Phillip A.
Studies of mammalian RNA interference (RNAi) have focused largely on the actions of microRNAs; however, in other organisms, endogenous short-interfering RNAs (siRNAs) are involved in silencing...
Calabrese, J. Mauro, Sharp, Phillip A.
Studies of mammalian RNA interference (RNAi) have focused largely on the actions of microRNAs; however, in other organisms, endogenous short-interfering RNAs (siRNAs) are involved in silencing...
Calabrese, J. Mauro, Sharp, Phillip A.
Studies of mammalian RNA interference (RNAi) have focused largely on the actions of microRNAs; however, in other organisms, endogenous short-interfering RNAs (siRNAs) are involved in silencing...
Transcriptional silencing of a transgene by RNAi in the soma of C. elegans (2005)
Grishok, Alla, Sinskey, Jina L., Sharp, Phillip A.
The silencing of transgene expression at the level of transcription in the soma of Caenorhabditis elegans through an RNAi-dependent pathway has not been previously characterized. Most gene silencing...
Characterization of a highly variable eutherian microRNA gene (2005)
HOUBAVIY, HRISTO B., DENNIS, LUCAS, JAENISCH, RUDOLF, SHARP, PHILLIP A.
Mouse microRNAs (miRNAs) miR-290–miR295 are encoded by a cluster of partially homologous pre-miRNA hairpins and are likely to be functionally important in embryonic stem (ES) cells and...
Characterization of a highly variable eutherian microRNA gene (2005)
HOUBAVIY, HRISTO B., DENNIS, LUCAS, JAENISCH, RUDOLF, SHARP, PHILLIP A.
Mouse microRNAs (miRNAs) miR-290–miR295 are encoded by a cluster of partially homologous pre-miRNA hairpins and are likely to be functionally important in embryonic stem (ES) cells and...
Transcriptional silencing of a transgene by RNAi in the soma of C. elegans (2005)
Grishok, Alla, Sinskey, Jina L., Sharp, Phillip A.
The silencing of transgene expression at the level of transcription in the soma of Caenorhabditis elegans through an RNAi-dependent pathway has not been previously characterized. Most gene silencing...
Transcriptional silencing of a transgene by RNAi in the soma of C. elegans (2005)
Grishok, Alla, Sinskey, Jina L., Sharp, Phillip A.
The silencing of transgene expression at the level of transcription in the soma of Caenorhabditis elegans through an RNAi-dependent pathway has not been previously characterized. Most gene silencing...
Characterization of a highly variable eutherian microRNA gene (2005)
HOUBAVIY, HRISTO B., DENNIS, LUCAS, JAENISCH, RUDOLF, SHARP, PHILLIP A.
Mouse microRNAs (miRNAs) miR-290–miR295 are encoded by a cluster of partially homologous pre-miRNA hairpins and are likely to be functionally important in embryonic stem (ES) cells and...
Single Nucleotide Polymorphism–Based Validation of Exonic Splicing Enhancers (2004)
William G. Fairbrother, Dirk Holste, Christopher B. Burge, Phillip A. Sharp
A computational analysis of single nucleotide polymorphisms showed that one-fifth of mutations that disrupt predicted exonic splicing enhancers have been eliminated by natural selection.
Single Nucleotide Polymorphism–Based Validation of Exonic Splicing Enhancers (2004)
William G. Fairbrother, Dirk Holste, Christopher B. Burge, Phillip A. Sharp
Because deleterious alleles arising from mutation are filtered by natural selection, mutations that create such alleles will be underrepresented in the set of common genetic variation existing in a...
William G. Fairbrother, Gene W. Yeo, Rufang Yeh, Paul Goldstein, Matthew Mawson, Phillip A. Sharp, ...
identifies candidate exonic splicing
Specificity of microRNA target selection in translational repression (2004)
Doench, John G., Sharp, Phillip A.
MicroRNAs (miRNAs) are a class of noncoding RNAs found in organisms as evolutionarily distant as plants and mammals, yet most of the mRNAs they regulate are unknown. Here we show that the ability of...
RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons (2004)
Fairbrother, William G., Yeo, Gene W., Yeh, Rufang, Goldstein, Paul, Mawson, Matthew, Sharp, Phillip A., ...
A typical gene contains two levels of information: a sequence that encodes a particular protein and a host of other signals that are necessary for the correct expression of the transcript. While much...
Specificity of microRNA target selection in translational repression (2004)
Doench, John G., Sharp, Phillip A.
MicroRNAs (miRNAs) are a class of noncoding RNAs found in organisms as evolutionarily distant as plants and mammals, yet most of the mRNAs they regulate are unknown. Here we show that the ability of...
Specificity of microRNA target selection in translational repression (2004)
Doench, John G., Sharp, Phillip A.
MicroRNAs (miRNAs) are a class of noncoding RNAs found in organisms as evolutionarily distant as plants and mammals, yet most of the mRNAs they regulate are unknown. Here we show that the ability of...
Lentivirus-delivered stable gene silencing by RNAi in primary cells (2003)
STEWART, SHEILA A., DYKXHOORN, DEREK M., PALLISER, DEBORAH, MIZUNO, HANA, YU, EVAN Y., AN, DONG SUNG, ...
Genome-wide genetic approaches have proven useful for examining pathways of biological significance in model organisms such as Saccharomyces cerevisiae, Drosophila melanogastor, and Caenorhabditis...
Targeted mRNA degradation by double-stranded RNA in vitro (1999)
Tuschl, Thomas, Zamore, Phillip D., Lehmann, Ruth, Bartel, David P., Sharp, Phillip A.
A coactivator of pre-mRNA splicing (1998)
Blencowe, Benjamin J., Issner, Robbyn, Nickerson, Jeffrey A., Sharp, Phillip A.
HTF4: a new human helix-loop-helix protein (1991)
Zhang, Yi, Babin, Jane, Feldhaus, Andrew L., Singh, Harinder, Sharp, Phillip A., Bina, Minou
Function of a yeast TATA element-binding protein in a mammalian transcription system (1988)
Stephen Buratowski, Steven Hahn, Phillip A. Sharp, Leonard Guarente
A lymphoid-specific protein binding to the octamer motif of immunoglobulin genes (1986)
Louis M. Staudt, Harinder Singh, Ranjan Sen, Thomas Wirth, Phillip A. Sharp, David Baltimore
Characterization of the branch site in lariat RNAs produced by splicing of mRNA precursors (1985)
Maria M. Konarska, Paula J. Grabowski, Richard A. Padgett, Phillip A. Sharp
Berkner, Kathleen L., Sharp, Phillip A.
The EIa region of an Adenovirus 5 recombinant has been substituted by a modular gene encoding dihydrofolate reductase (DHFR). In this recombinant, the mouse DHFR cDNA was positioned behind sequences...
Cofactor requirements of splicing of purified messenger RNA precursors (1984)
Stephen F. Hardy, Paula J. Grabowski, Richard A. Padgett, Phillip A. Sharp
Barkner, Kathleen L., Sharp, Phillip A.
A gene with the Ad2 MLP end firat leader, and appropriate RNA processing signals (splicing, polyadenylation) positioned around a mouse DHFR cDNA clone was substituted for the EIa region of Ad5, and...
Generation of adenovirus by transfection of plasmids (1983)
Berkner, Kathleen L., Sharp, Phillip A.
Biologically active fragments of Adenovirus 5 (Ad5) DNA that span the entire genome have been cloned into plaanids. The covalently attached terminal protein wa3 removed and Eco RI linkers added in a...
Kim, Jung-Suh, Sharp, Phillip A., Davidson, Norman
A population of double-stranded replicative form of DNA molecules from bacteriophage phi X-174 carrying a deletion of about 9% of the wild-type DNA has been discovered in a sample cultivated under...
Sequence Heterogeneity in Closed Simian Virus 40 Deoxyribonucleic Acid (1972)
Tai, Henry T., Smith, Charles Allen, Sharp, Phillip A., Vinograd, Jerome
The heteroduplex molecules formed by self-annealing of denatured, singly nicked simian virus 40 (SV40) deoxyribonucleic acid (DNA) prepared from closed viral DNA were examined by formamide-protein...
Isolation of Catenated Forms of R Factor DNA from Minicells (1971)
STANLEY N. COHEN, RICHARD P. SILVER, ANNETTE E. MCCOUBREY, PHILLIP A. SHARP
Design of TATA box-binding protein/zinc finger fusions for targeted regulation of gene expression
Kim, Jin-Soo, Kim, Jaesang, Cepek, Karyn L., Sharp, Phillip A., Pabo, Carl O.
Fusing the TATA box-binding protein (TBP) to other DNA-binding domains may provide a powerful way of targeting TBP to particular promoters. To explore this possibility, a structure-based design...
Promoter-specific hypoacetylation of X-inactivated genes
Gilbert, Sandra L., Sharp, Phillip A.
The histone H4 acetylation status of the active X (Xa) and inactive X (Xi) chromosomes was investigated at the level of individual genes. A moderate level of acetylation was observed along the...
Mitsui, Akira, Sharp, Phillip A.
A sensitive assay using biotinylated ubiquitin revealed extensive ubiquitination of the large subunit of RNA polymerase II during incubations of transcription reactions in vitro. Phosphorylation of...
The SRm160/300 splicing coactivator is required for exon-enhancer function
Eldridge, Adam G., Li, Yu, Sharp, Phillip A., Blencowe, Benjamin J.
Exonic splicing enhancer (ESE) sequences are important for the recognition of splice sites in pre-mRNA. These sequences are bound by specific serine-arginine (SR) repeat proteins that promote the...
Ultraspiracle: An invertebrate nuclear receptor for juvenile hormones
Jones, Grace, Sharp, Phillip A.
Juvenile hormones (JH), a sesquiterpenoid group of ligands that regulate developmental transitions in insects, bind to the nuclear receptor ultraspiracle (USP). In fluorescence-based binding assays,...
Tat-SF1 Protein Associates with RAP30 and Human SPT5 Proteins
Kim, Jae B., Yamaguchi, Yuki, Wada, Tadashi, Handa, Hiroshi, Sharp, Phillip A.
The potent transactivator Tat recognizes the transactivation response RNA element (TAR) of human immunodeficiency virus type 1 and stimulates the processivity of elongation of RNA polymerase (Pol) II...
A Novel 50-Kilodalton Fragment of Host Cell Factor 1 (C1) in G0 Cells
Scarr, Rebecca B., Smith, Matthew R., Beddall, Margaret, Sharp, Phillip A.
Host cell factor 1 (HCF-1; also called C1) is a 230-kDa protein which is cleaved posttranslationally into separate but associated N- and C-terminal polypeptides. These polypeptides are components of...
Alternative Splicing of the Fibronectin EIIIB Exon Depends on Specific TGCATG Repeats
Lim, Lee P., Sharp, Phillip A.
The fibronectin EIIIB exon is alternatively spliced in a cell-type-specific manner, and TGCATG repeats in the intron downstream of EIIIB have been implicated in this regulation. Analysis of the...
Transcription-coupled and DNA damage-dependent ubiquitination of RNA polymerase II in vitro
Lee, Keng-Boon, Wang, Dong, Lippard, Stephen J., Sharp, Phillip A.
Transcription-coupled repair (TCR) is essential for the rapid, preferential removal of DNA damage in active genes. The large subunit of RNA polymerase (Pol) II is ubiquitinated in cells after...
Mouse Lymphoid Cell Line Selected To Have High Immunoglobulin Promoter Activity
Tantin, Dean, Sharp, Phillip A.
Immunoglobulin variable region promoters are predominantly B-cell specific, but the molecular basis for this specificity has not been elucidated. To further understand how B-cell-specific...
Cheng, Chonghui, Sharp, Phillip A.
The carboxyl-terminal domain (CTD) of RNA polymerase II (Pol II) can be phosphorylated at serine 2 (Ser-2) and serine 5 (Ser-5) of the CTD heptad repeat YSPTSPS, and this phosphorylation is important...
Ge, Qing, McManus, Michael T., Nguyen, Tam, Shen, Ching-Hung, Sharp, Phillip A., Eisen, Herman N., ...
Influenza A virus causes widespread infection in the human respiratory tract, but existing vaccines and drug therapy are of limited value. Here we show that short interfering RNAs (siRNAs) specific...
Song, Erwei, Lee, Sang-Kyung, Dykxhoorn, Derek M., Novina, Carl, Zhang, Dong, Crawford, Keith, ...
Small interfering RNAs (siRNAs) can induce potent gene silencing by degradation of cognate mRNA. However, in dividing cells, the silencing lasts only 3 to 7 days, presumably because of siRNA dilution...
Doench, John G., Petersen, Christian P., Sharp, Phillip A.
With the discovery of RNA interference (RNAi) and related phenomena, new regulatory roles attributed to RNA continue to emerge. Here we show, in mammalian tissue culture, that a short interfering RNA...
Aberrant Distribution of Human Adenovirus Type 2 Late Proteins in Monkey Kidney Cells
Cepko, Constance L., Sharp, Phillip A.
Monkey kidney cells (CV-C) infected with adenovirus type 2 displayed an aberrant distribution of 100K, 100K-hexon complex, hexon monomers, hexon trimers, penton base, and fiber proteins, relative to...
Expression of Early and Late Simian Virus 40 Transcripts in the Absence of Protein Synthesis
Handa, Hiroshi, Sharp, Phillip A.
We examined the synthesis of early and late simian virus 40 (SV40) mRNA's in SV40-infected cells treated with two kinds of protein synthesis inhibitors. SV40 stimulated the synthesis of mRNA's for...
A coactivator of pre-mRNA splicing
Blencowe, Benjamin J., Issner, Robbyn, Nickerson, Jeffrey A., Sharp, Phillip A.
The nuclear matrix antigen recognized by the monoclonal antibody (mAb) B1C8 is a novel serine (S) and arginine (R)-rich protein associated with splicing complexes and is named here SRm160 (SR-related...
Chasman, Daniel, Cepek, Karyn, Sharp, Phillip A., Pabo, Carl O.
We have determined the crystal structure, at 3.2 Å, of a ternary complex containing an OCA-B peptide, the Oct-1 POU domain, and an octamer DNA site. The OCA-B peptide binds in the major groove near...
Targeted mRNA degradation by double-stranded RNA in vitro
Tuschl, Thomas, Zamore, Phillip D., Lehmann, Ruth, Bartel, David P., Sharp, Phillip A.
Double-stranded RNA (dsRNA) directs gene-specific, post-transcriptional silencing in many organisms, including vertebrates, and has provided a new tool for studying gene function. The biochemical...
Wang, Victoria E. H., Schmidt, Tara, Chen, Jianzhu, Sharp, Phillip A., Tantin, Dean
Oct-1 is a sequence-specific DNA binding transcription factor that is believed to regulate a large group of tissue-specific and ubiquitous genes. Both Oct-1 and the related but tissue-restricted...
Herpes simplex virus infections are arrested in Oct-1-deficient cells
Nogueira, Mauricio L., Wang, Victoria E. H., Tantin, Dean, Sharp, Phillip A., Kristie, Thomas M.
Expression of the herpes simplex virus (HSV) immediate early (IE) genes is regulated by a multiprotein complex that is assembled on the TAATGARAT enhancer core element. The complex contains the...
Ozanne, Brad, Sharp, Phillip A., Sambrook, Joe
The amount of simian virus 40 (SV40) DNA present in various SV40-transformed mouse cell lines and “revertants” isolated from them was determined. The number of viral DNA copies in the different...
Conditional Lethal Mutants of Adenovirus 2-Simian Virus 40 Hybrids I. Host Range Mutants of Ad2+ND1
Grodzicker, Terri, Anderson, Carl, Sharp, Phillip A., Sambrook, Joe
Human adenovirus type 2 (Ad2) grows poorly in monkey cells, although this defect can be overcome by co-infection with simian virus 40 (SV40). The nondefective Ad2-SV40 hybrid virus, Ad2+ND1,...
Mulder, Carel, Sharp, Phillip A., Delius, Hajo, Pettersson, Ulf
The products of complete digestion of duplex DNA of each of seven human adenoviruses with restriction endonuclease R· EcoRI ranged from two fragments for adenovirus 7 DNA (Ad7) to six fragments for...
Sequence Heterogeneity in Closed Simian Virus 40 Deoxyribonucleic Acid
Tai, Henry T., Smith, Charles Allen, Sharp, Phillip A., Vinograd, Jerome
The heteroduplex molecules formed by self-annealing of denatured, singly nicked simian virus 40 (SV40) deoxyribonucleic acid (DNA) prepared from closed viral DNA were examined by formamide-protein...
B cell development and immunoglobulin transcription in Oct-1-deficient mice
Wang, Victoria E. H., Tantin, Dean, Chen, Jianzhu, Sharp, Phillip A.
The POU domain transcription factors Oct-1 and Oct-2 interact with the octamer element, a motif conserved within Ig promoters and enhancers, and mediate transcription from the Ig loci. Inactivation...
Specificity of microRNA target selection in translational repression
Doench, John G., Sharp, Phillip A.
MicroRNAs (miRNAs) are a class of noncoding RNAs found in organisms as evolutionarily distant as plants and mammals, yet most of the mRNAs they regulate are unknown. Here we show that the ability of...
Spliced early mRNAs of simian virus 40
Berk, Arnold J., Sharp, Phillip A.
Biochemical methods are presented for determining the structure of spliced RNAs present in cells at low concentrations. Two cytoplasmic spliced viral RNAs were detected in CV-1 cells during the early...
Electron Microscope Studies of Heteroduplex DNA from a Deletion Mutant of Bacteriophage ϕX-174
Kim, Jung-Suh, Sharp, Phillip A., Davidson, Norman
A population of double-stranded replicative form of DNA molecules from bacteriophage ϕX-174 carrying a deletion of about 9% of the wild-type DNA has been discovered in a sample cultivated under...
Transcription of Simian Virus 40. III. Mapping of “Early” and “Late” Species of RNA
Sambrook, Joe, Sugden, Bill, Keller, Walter, Sharp, Phillip A.
To determine the orientation of transcription of the E and L strands of DNA from simian virus 40 (SV40), we used linear DNA prepared by cleavage of superhelical viral DNA by endonuclease R·R1 from...
Cleavage of Adenovirus Type 2 DNA into Six Unique Fragments by Endonuclease R·RI
Pettersson, Ulf, Mulder, Carel, Delius, Hajo, Sharp, Phillip A.
The DNA of adenovirus type 2 was cleaved by restriction endonuclease R·RI into six fragments. These fragments were separated by electrophoresis on composite agarose-polyacrylamide gels. Their...
Botchan, Michael, Ozanne, Brad, Sugden, Bill, Sharp, Phillip A., Sambrook, Joe
32P-Labeled SV40 DNA was treated sequentially with restricting endonucleases EcoRI and Hpa I, and the resulting four fragments of DNA were separated by gel electrophoresis. The kinetics of...
RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons
Fairbrother, William G., Yeo, Gene W., Yeh, Rufang, Goldstein, Paul, Mawson, Matthew, Sharp, Phillip A., ...
A typical gene contains two levels of information: a sequence that encodes a particular protein and a host of other signals that are necessary for the correct expression of the transcript. While much...
Cre-lox-regulated conditional RNA interference from transgenes
Ventura, Andrea, Meissner, Alexander, Dillon, Christopher P., McManus, Michael, Sharp, Phillip A., Van Parijs, Luk, ...
We have generated two lentiviral vectors for conditional, Cre-lox-regulated, RNA interference. One vector allows for conditional activation, whereas the other permits conditional inactivation of...
Single Nucleotide Polymorphism–Based Validation of Exonic Splicing Enhancers
Fairbrother, William G, Holste, Dirk, Burge, Christopher B, Sharp, Phillip A
Because deleterious alleles arising from mutation are filtered by natural selection, mutations that create such alleles will be underrepresented in the set of common genetic variation existing in a...
Transcriptional silencing of a transgene by RNAi in the soma of C. elegans
Grishok, Alla, Sinskey, Jina L., Sharp, Phillip A.
The silencing of transgene expression at the level of transcription in the soma of Caenorhabditis elegans through an RNAi-dependent pathway has not been previously characterized. Most gene silencing...
Regulation of CD44 Alternative Splicing by SRm160 and Its Potential Role in Tumor Cell Invasion
Cheng, Chonghui, Sharp, Phillip A.
The multiple isoforms of the transmembrane glycoprotein CD44 are produced by alternative RNA splicing. Expression of CD44 isoforms containing variable 5 exon (v5) correlates with enhanced malignancy...
Gene silencing using micro-RNA designed hairpins.
McManus, Michael T, Petersen, Christian P, Haines, Brian B, Chen, Jianzhu, Sharp, Phillip A
During RNA interference (RNAi), long dsRNA is processed to approximately 21 nt duplexes, short interfering RNAs (siRNAs), which silence genes through a mRNA degradation pathway. Small temporal RNAs...
Lentivirus-delivered stable gene silencing by RNAi in primary cells
STEWART, SHEILA A., DYKXHOORN, DEREK M., PALLISER, DEBORAH, MIZUNO, HANA, YU, EVAN Y., AN, DONG SUNG, ...
Genome-wide genetic approaches have proven useful for examining pathways of biological significance in model organisms such as Saccharomyces cerevisiae, Drosophila melanogastor, and Caenorhabditis...
Characterization of a highly variable eutherian microRNA gene
HOUBAVIY, HRISTO B., DENNIS, LUCAS, JAENISCH, RUDOLF, SHARP, PHILLIP A.
Mouse microRNAs (miRNAs) miR-290–miR295 are encoded by a cluster of partially homologous pre-miRNA hairpins and are likely to be functionally important in embryonic stem (ES) cells and...
Grishok, Alla, Sharp, Phillip A.
Short RNA regulatory molecules, microRNAs, and short interfering RNAs participate in a range of developmental gene networks by base-pairing with their target sequences. Consistent with these...
Design of TATA box-binding protein/zinc finger fusions for targeted regulation of gene expression
Kim, Jin-Soo, Kim, Jaesang, Cepek, Karyn L., Sharp, Phillip A., Pabo, Carl O.
Fusing the TATA box-binding protein (TBP) to other DNA-binding domains may provide a powerful way of targeting TBP to particular promoters. To explore this possibility, a structure-based design...
Promoter-specific hypoacetylation of X-inactivated genes
Gilbert, Sandra L., Sharp, Phillip A.
The histone H4 acetylation status of the active X (Xa) and inactive X (Xi) chromosomes was investigated at the level of individual genes. A moderate level of acetylation was observed along the...
Mitsui, Akira, Sharp, Phillip A.
A sensitive assay using biotinylated ubiquitin revealed extensive ubiquitination of the large subunit of RNA polymerase II during incubations of transcription reactions in vitro. Phosphorylation of...
The SRm160/300 splicing coactivator is required for exon-enhancer function
Eldridge, Adam G., Li, Yu, Sharp, Phillip A., Blencowe, Benjamin J.
Exonic splicing enhancer (ESE) sequences are important for the recognition of splice sites in pre-mRNA. These sequences are bound by specific serine-arginine (SR) repeat proteins that promote the...
Ultraspiracle: An invertebrate nuclear receptor for juvenile hormones
Jones, Grace, Sharp, Phillip A.
Juvenile hormones (JH), a sesquiterpenoid group of ligands that regulate developmental transitions in insects, bind to the nuclear receptor ultraspiracle (USP). In fluorescence-based binding assays,...
Tat-SF1 Protein Associates with RAP30 and Human SPT5 Proteins
Kim, Jae B., Yamaguchi, Yuki, Wada, Tadashi, Handa, Hiroshi, Sharp, Phillip A.
The potent transactivator Tat recognizes the transactivation response RNA element (TAR) of human immunodeficiency virus type 1 and stimulates the processivity of elongation of RNA polymerase (Pol) II...
A Novel 50-Kilodalton Fragment of Host Cell Factor 1 (C1) in G0 Cells
Scarr, Rebecca B., Smith, Matthew R., Beddall, Margaret, Sharp, Phillip A.
Host cell factor 1 (HCF-1; also called C1) is a 230-kDa protein which is cleaved posttranslationally into separate but associated N- and C-terminal polypeptides. These polypeptides are components of...
Alternative Splicing of the Fibronectin EIIIB Exon Depends on Specific TGCATG Repeats
Lim, Lee P., Sharp, Phillip A.
The fibronectin EIIIB exon is alternatively spliced in a cell-type-specific manner, and TGCATG repeats in the intron downstream of EIIIB have been implicated in this regulation. Analysis of the...
Transcription-coupled and DNA damage-dependent ubiquitination of RNA polymerase II in vitro
Lee, Keng-Boon, Wang, Dong, Lippard, Stephen J., Sharp, Phillip A.
Transcription-coupled repair (TCR) is essential for the rapid, preferential removal of DNA damage in active genes. The large subunit of RNA polymerase (Pol) II is ubiquitinated in cells after...
Mouse Lymphoid Cell Line Selected To Have High Immunoglobulin Promoter Activity
Tantin, Dean, Sharp, Phillip A.
Immunoglobulin variable region promoters are predominantly B-cell specific, but the molecular basis for this specificity has not been elucidated. To further understand how B-cell-specific...
Cheng, Chonghui, Sharp, Phillip A.
The carboxyl-terminal domain (CTD) of RNA polymerase II (Pol II) can be phosphorylated at serine 2 (Ser-2) and serine 5 (Ser-5) of the CTD heptad repeat YSPTSPS, and this phosphorylation is important...
Ge, Qing, McManus, Michael T., Nguyen, Tam, Shen, Ching-Hung, Sharp, Phillip A., Eisen, Herman N., ...
Influenza A virus causes widespread infection in the human respiratory tract, but existing vaccines and drug therapy are of limited value. Here we show that short interfering RNAs (siRNAs) specific...
Song, Erwei, Lee, Sang-Kyung, Dykxhoorn, Derek M., Novina, Carl, Zhang, Dong, Crawford, Keith, ...
Small interfering RNAs (siRNAs) can induce potent gene silencing by degradation of cognate mRNA. However, in dividing cells, the silencing lasts only 3 to 7 days, presumably because of siRNA dilution...
Doench, John G., Petersen, Christian P., Sharp, Phillip A.
With the discovery of RNA interference (RNAi) and related phenomena, new regulatory roles attributed to RNA continue to emerge. Here we show, in mammalian tissue culture, that a short interfering RNA...
Aberrant Distribution of Human Adenovirus Type 2 Late Proteins in Monkey Kidney Cells
Cepko, Constance L., Sharp, Phillip A.
Monkey kidney cells (CV-C) infected with adenovirus type 2 displayed an aberrant distribution of 100K, 100K-hexon complex, hexon monomers, hexon trimers, penton base, and fiber proteins, relative to...
Expression of Early and Late Simian Virus 40 Transcripts in the Absence of Protein Synthesis
Handa, Hiroshi, Sharp, Phillip A.
We examined the synthesis of early and late simian virus 40 (SV40) mRNA's in SV40-infected cells treated with two kinds of protein synthesis inhibitors. SV40 stimulated the synthesis of mRNA's for...
A coactivator of pre-mRNA splicing
Blencowe, Benjamin J., Issner, Robbyn, Nickerson, Jeffrey A., Sharp, Phillip A.
The nuclear matrix antigen recognized by the monoclonal antibody (mAb) B1C8 is a novel serine (S) and arginine (R)-rich protein associated with splicing complexes and is named here SRm160 (SR-related...
Chasman, Daniel, Cepek, Karyn, Sharp, Phillip A., Pabo, Carl O.
We have determined the crystal structure, at 3.2 Å, of a ternary complex containing an OCA-B peptide, the Oct-1 POU domain, and an octamer DNA site. The OCA-B peptide binds in the major groove near...
Targeted mRNA degradation by double-stranded RNA in vitro
Tuschl, Thomas, Zamore, Phillip D., Lehmann, Ruth, Bartel, David P., Sharp, Phillip A.
Double-stranded RNA (dsRNA) directs gene-specific, post-transcriptional silencing in many organisms, including vertebrates, and has provided a new tool for studying gene function. The biochemical...
Wang, Victoria E. H., Schmidt, Tara, Chen, Jianzhu, Sharp, Phillip A., Tantin, Dean
Oct-1 is a sequence-specific DNA binding transcription factor that is believed to regulate a large group of tissue-specific and ubiquitous genes. Both Oct-1 and the related but tissue-restricted...
Herpes simplex virus infections are arrested in Oct-1-deficient cells
Nogueira, Mauricio L., Wang, Victoria E. H., Tantin, Dean, Sharp, Phillip A., Kristie, Thomas M.
Expression of the herpes simplex virus (HSV) immediate early (IE) genes is regulated by a multiprotein complex that is assembled on the TAATGARAT enhancer core element. The complex contains the...
Ozanne, Brad, Sharp, Phillip A., Sambrook, Joe
The amount of simian virus 40 (SV40) DNA present in various SV40-transformed mouse cell lines and “revertants” isolated from them was determined. The number of viral DNA copies in the different...
Conditional Lethal Mutants of Adenovirus 2-Simian Virus 40 Hybrids I. Host Range Mutants of Ad2+ND1
Grodzicker, Terri, Anderson, Carl, Sharp, Phillip A., Sambrook, Joe
Human adenovirus type 2 (Ad2) grows poorly in monkey cells, although this defect can be overcome by co-infection with simian virus 40 (SV40). The nondefective Ad2-SV40 hybrid virus, Ad2+ND1,...
Mulder, Carel, Sharp, Phillip A., Delius, Hajo, Pettersson, Ulf
The products of complete digestion of duplex DNA of each of seven human adenoviruses with restriction endonuclease R· EcoRI ranged from two fragments for adenovirus 7 DNA (Ad7) to six fragments for...
Sequence Heterogeneity in Closed Simian Virus 40 Deoxyribonucleic Acid
Tai, Henry T., Smith, Charles Allen, Sharp, Phillip A., Vinograd, Jerome
The heteroduplex molecules formed by self-annealing of denatured, singly nicked simian virus 40 (SV40) deoxyribonucleic acid (DNA) prepared from closed viral DNA were examined by formamide-protein...
B cell development and immunoglobulin transcription in Oct-1-deficient mice
Wang, Victoria E. H., Tantin, Dean, Chen, Jianzhu, Sharp, Phillip A.
The POU domain transcription factors Oct-1 and Oct-2 interact with the octamer element, a motif conserved within Ig promoters and enhancers, and mediate transcription from the Ig loci. Inactivation...
Specificity of microRNA target selection in translational repression
Doench, John G., Sharp, Phillip A.
MicroRNAs (miRNAs) are a class of noncoding RNAs found in organisms as evolutionarily distant as plants and mammals, yet most of the mRNAs they regulate are unknown. Here we show that the ability of...
Spliced early mRNAs of simian virus 40
Berk, Arnold J., Sharp, Phillip A.
Biochemical methods are presented for determining the structure of spliced RNAs present in cells at low concentrations. Two cytoplasmic spliced viral RNAs were detected in CV-1 cells during the early...
Electron Microscope Studies of Heteroduplex DNA from a Deletion Mutant of Bacteriophage ϕX-174
Kim, Jung-Suh, Sharp, Phillip A., Davidson, Norman
A population of double-stranded replicative form of DNA molecules from bacteriophage ϕX-174 carrying a deletion of about 9% of the wild-type DNA has been discovered in a sample cultivated under...
Transcription of Simian Virus 40. III. Mapping of “Early” and “Late” Species of RNA
Sambrook, Joe, Sugden, Bill, Keller, Walter, Sharp, Phillip A.
To determine the orientation of transcription of the E and L strands of DNA from simian virus 40 (SV40), we used linear DNA prepared by cleavage of superhelical viral DNA by endonuclease R·R1 from...
Cleavage of Adenovirus Type 2 DNA into Six Unique Fragments by Endonuclease R·RI
Pettersson, Ulf, Mulder, Carel, Delius, Hajo, Sharp, Phillip A.
The DNA of adenovirus type 2 was cleaved by restriction endonuclease R·RI into six fragments. These fragments were separated by electrophoresis on composite agarose-polyacrylamide gels. Their...
Botchan, Michael, Ozanne, Brad, Sugden, Bill, Sharp, Phillip A., Sambrook, Joe
32P-Labeled SV40 DNA was treated sequentially with restricting endonucleases EcoRI and Hpa I, and the resulting four fragments of DNA were separated by gel electrophoresis. The kinetics of...
RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons
Fairbrother, William G., Yeo, Gene W., Yeh, Rufang, Goldstein, Paul, Mawson, Matthew, Sharp, Phillip A., ...
A typical gene contains two levels of information: a sequence that encodes a particular protein and a host of other signals that are necessary for the correct expression of the transcript. While much...
Cre-lox-regulated conditional RNA interference from transgenes
Ventura, Andrea, Meissner, Alexander, Dillon, Christopher P., McManus, Michael, Sharp, Phillip A., Van Parijs, Luk, ...
We have generated two lentiviral vectors for conditional, Cre-lox-regulated, RNA interference. One vector allows for conditional activation, whereas the other permits conditional inactivation of...
Single Nucleotide Polymorphism–Based Validation of Exonic Splicing Enhancers
Fairbrother, William G, Holste, Dirk, Burge, Christopher B, Sharp, Phillip A
Because deleterious alleles arising from mutation are filtered by natural selection, mutations that create such alleles will be underrepresented in the set of common genetic variation existing in a...
Transcriptional silencing of a transgene by RNAi in the soma of C. elegans
Grishok, Alla, Sinskey, Jina L., Sharp, Phillip A.
The silencing of transgene expression at the level of transcription in the soma of Caenorhabditis elegans through an RNAi-dependent pathway has not been previously characterized. Most gene silencing...
Grishok, Alla, Sharp, Phillip A.
Short RNA regulatory molecules, microRNAs, and short interfering RNAs participate in a range of developmental gene networks by base-pairing with their target sequences. Consistent with these...
Regulation of CD44 Alternative Splicing by SRm160 and Its Potential Role in Tumor Cell Invasion
Cheng, Chonghui, Sharp, Phillip A.
The multiple isoforms of the transmembrane glycoprotein CD44 are produced by alternative RNA splicing. Expression of CD44 isoforms containing variable 5 exon (v5) correlates with enhanced malignancy...
Gene silencing using micro-RNA designed hairpins.
McManus, Michael T, Petersen, Christian P, Haines, Brian B, Chen, Jianzhu, Sharp, Phillip A
During RNA interference (RNAi), long dsRNA is processed to approximately 21 nt duplexes, short interfering RNAs (siRNAs), which silence genes through a mRNA degradation pathway. Small temporal RNAs...
Lentivirus-delivered stable gene silencing by RNAi in primary cells
STEWART, SHEILA A., DYKXHOORN, DEREK M., PALLISER, DEBORAH, MIZUNO, HANA, YU, EVAN Y., AN, DONG SUNG, ...
Genome-wide genetic approaches have proven useful for examining pathways of biological significance in model organisms such as Saccharomyces cerevisiae, Drosophila melanogastor, and Caenorhabditis...
Characterization of a highly variable eutherian microRNA gene
HOUBAVIY, HRISTO B., DENNIS, LUCAS, JAENISCH, RUDOLF, SHARP, PHILLIP A.
Mouse microRNAs (miRNAs) miR-290–miR295 are encoded by a cluster of partially homologous pre-miRNA hairpins and are likely to be functionally important in embryonic stem (ES) cells and...
A positive feedback loop couples Ras activation and CD44 alternative splicing
Cheng, Chonghui, Yaffe, Michael B., Sharp, Phillip A.
The Ras signaling pathway is important in both cell proliferation and tumor progression. Alternatively spliced isoforms of CD44 containing variable exon 6 (v6) can serve as coreceptors for growth...
Leung, Anthony K. L., Calabrese, J. Mauro, Sharp, Phillip A.
Argonaute proteins associate with microRNAs (miRNAs) that bind mRNAs through partial base-pairings to primarily repress translation in animals. A fraction of Argonaute proteins and miRNAs...
Calabrese, J. Mauro, Sharp, Phillip A.
Studies of mammalian RNA interference (RNAi) have focused largely on the actions of microRNAs; however, in other organisms, endogenous short-interfering RNAs (siRNAs) are involved in silencing...
Comparison of siRNA-induced off-target RNA and protein effects
Alemán, Lourdes M., Doench, John, Sharp, Phillip A.
The downregulation of many mRNAs has been observed through bioinformatic analysis of microarray results following transfection of short interfering RNAs (siRNAs). Many of these mRNA changes are due...
Dynamic regulation of miRNA expression in ordered stages of cellular development
Neilson, Joel R., Zheng, Grace X.Y., Burge, Christopher B., Sharp, Phillip A.
Short RNA expression in several distinct stages of T-lymphocyte development was comprehensively profiled. The total number of microRNAs (miRNAs) expressed per cell at different stages of development...
miRNA Profiling of Naïve, Effector and Memory CD8 T Cells
Wu, Haoquan, Neilson, Joel R., Kumar, Priti, Manocha, Monika, Shankar, Premlata, Sharp, Phillip A., ...
microRNAs have recently emerged as master regulators of gene expression during development and cell differentiation. Although profound changes in gene expression also occur during antigen-induced T...
RNA sequence analysis defines Dicer's role in mouse embryonic stem cells
Calabrese, J. Mauro, Seila, Amy C., Yeo, Gene W., Sharp, Phillip A.
Short RNA expression was analyzed from Dicer-positive and Dicer-knockout mouse embroyonic stem (ES) cells, using high-throughput pyrosequencing. A correlation of miRNA quantification with sequencing...
Suppression of non-small cell lung tumor development by the let-7 microRNA family
Kumar, Madhu S., Erkeland, Stefan J., Pester, Ryan E., Chen, Cindy Y., Ebert, Margaret S., Sharp, Phillip A., ...
Many microRNAs (miRNAs) target mRNAs involved in processes aberrant in tumorigenesis, such as proliferation, survival, and differentiation. In particular, the let-7 miRNA family has been proposed to...
A system for Cre-regulated RNA interference in vivo
Stern, Patrick, Astrof, Sophie, Erkeland, Stefan J., Schustak, Joshua, Sharp, Phillip A., Hynes, Richard O.
We report a system for Cre-regulated expression of RNA interference in vivo. Expression cassettes comprise selectable and FACS-sortable markers in tandem with additional marker genes and shRNAs in...
Grishok, Alla, Hoersch, Sebastian, Sharp, Phillip A.
In Caenorhabditis elegans, a vast number of endogenous short RNAs corresponding to thousands of genes have been discovered recently. This finding suggests that these short interfering RNAs (siRNAs)...