Toxicity in mice expressing short hairpin RNAs gives new insight into RNAi (2006)
Abstract Short hairpin RNAs can provide stable gene silencing via RNA interference. Recent studies have shown toxicity in vivo that appears to be related to saturation of the endogenous microRNA...
A nucleolar localizing Rev binding element inhibits HIV replication (2006)
Michienzi, Alessandro, De Angelis, Fernanda G, Bozzoni, Irene, Rossi, John J
Abstract The Rev protein of the human immunodeficiency virus (HIV) facilitates the nuclear export of intron containing viral mRNAs allowing formation of infectious virions. Rev traffics through the...
Functional polarity is introduced by Dicer processing of short substrate RNAs (2005)
Rose, Scott D., Kim, Dong-Ho, Amarzguioui, Mohammed, Heidel, Jeremy D., Collingwood, Michael A., Davis, Mark E., ...
Synthetic RNA duplexes that are substrates for Dicer are potent triggers of RNA interference (RNAi). Blunt 27mer duplexes can be up to 100-fold more potent than traditional 21mer duplexes (1). Not...
Ribozyme-mediated inhibition of HIV 1 suggests nucleolar trafficking of HIV-1 RNA
Michienzi, Alessandro, Cagnon, Laurence, Bahner, Ingrid, Rossi, John J.
The HIV regulatory proteins Tat and Rev have a nucleolar localization property in human cells. However, no functional role has been attributed to this localization. Recently it has been demonstrated...
Scherr, Michaela, Rossi, John J., Sczakiel, Georg, Patzel, Volker
The use of antisense oligodeoxyribonucleotides (ODN) or ribozymes to specifically suppress gene expression is simple in concept and relies on efficient binding of the antisense strand to the target...
Chen, Hsiu-Hua, Castanotto, Daniela, LeBon, Jeanne M., Rossi, John J., Riggs, Arthur D.
We have investigated the analysis of RNA by use of terminal transferase-dependent PCR (TDPCR), a procedure previously used for the analysis of DNA and chromatin [J.Komura and A.D.Riggs, Nucleic Acids...
Monitoring Retroviral RNA Dimerization In Vivo via Hammerhead Ribozyme Cleavage
Pal, Bijay K., Scherer, Lisa, Zelby, Laurie, Bertrand, Edouard, Rossi, John J.
We have used a strategy for colocalization of Psi (Ψ)-tethered ribozymes and targets to demonstrate that Ψ sequences are capable of specific interaction in the cytoplasm of both packaging and...
A nucleolar TAR decoy inhibitor of HIV-1 replication
Michienzi, Alessandro, Li, Shirley, Zaia, John A., Rossi, John J.
Tat is a critical regulatory factor in HIV-1 gene expression. It mediates the transactivation of transcription from the HIV-1 LTR by binding to the transactivation response (TAR) element in a complex...
Procedure for Isolating Mutants Defective in Metabolite Transport or Utilization
Berg, Claire M., Rossi, John J., Coleman, Joyce V., Conlon, Michele
Mutants defective in uptake or utilization of a given metabolite can readily be obtained from facultative auxotrophs (for that metabolite) by penicillin enrichment under nonpermissive conditions in...
Proline Excretion and Indirect Suppression in Escherichia coli and Salmonella typhimurium
Berg, Claire M., Rossi, John J.
The last step in proline biosynthesis in Escherichia coli K-12, Salmonella typhimurium LT7, and a number of other enterobacterial isolates is regulated so that no proline is excreted, even if excess...
Differential Recovery of Auxotrophs After Penicillin Enrichment in Escherichia coli
Rossi, John J., Berg, Claire M.
Various auxotrophs are recovered from a penicillin enrichment cycle with differing efficiencies. Reconstruction experiments indicate that, under starvation conditions in the presence of penicillin,...
Effect of Enrichment Procedure upon Auxotroph Recovery in Escherichia coli K-12
Rossi, John J., Berg, Claire M.
Proline-requiring auxotrophs are recovered preferentially after mutant enrichment procedures (e.g., penicillin) which perturb the cell envelope, but not after procedures (e.g., thymineless death)...
Soifer, Harris S., Zaragoza, Adriana, Peyvan, Maany, Behlke, Mark A., Rossi, John J.
Long interspersed nuclear elements (LINE-1 or L1) comprise 17% of the human genome, although only 80–100 L1s are considered retrotransposition-competent (RC-L1). Despite their small number, RC-L1s...
siRNA target site secondary structure predictions using local stable substructures
Heale, Bret S. E., Soifer, Harris S., Bowers, Chauncey, Rossi, John J.
The crystal structure based model of the catalytic center of Ago2 revealed that the siRNA and the mRNA must be able to form an A-helix for correct positing of the scissile phosphate bond for cleavage...
Kim, Dong-Ho, Langlois, Marc-Andre, Lee, Kwang-Back, Riggs, Arthur D., Puymirat, Jack, Rossi, John J.
Myotonic dystrophy type 1 (DM1) is an autosomal dominant neuromuscular disorder associated with a (CUG)n expansion in the 3′-untranslated region of the DMPK (DM1 protein kinase) gene. Mutant DMPK...
Functional polarity is introduced by Dicer processing of short substrate RNAs
Rose, Scott D., Kim, Dong-Ho, Amarzguioui, Mohammed, Heidel, Jeremy D., Collingwood, Michael A., Davis, Mark E., ...
Synthetic RNA duplexes that are substrates for Dicer are potent triggers of RNA interference (RNAi). Blunt 27mer duplexes can be up to 100-fold more potent than traditional 21mer duplexes (1). Not...
Functional siRNA expression from transfected PCR products.
Castanotto, Daniela, Li, Haitang, Rossi, John J
RNA interference (RNAi) is a process in which double-stranded RNA (dsRNA) induces the postranscriptional degradation of homologous transcripts. RNAi can be initiated by exposing cells to dsRNA either...
Uncoupling of RNAi from active translation in mammalian cells
Small inhibitory RNAs (siRNAs) are produced from longer RNA duplexes by the RNAse III family member Dicer. The siRNAs function as sequence-specific guides for RNA cleavage or translational...
Unwalla, Hoshang J., Li, Hai-Tang, Bahner, Ingrid, Li, Ming-Jie, Kohn, Donald, Rossi, John J.
We demonstrate a novel approach for coexpression of a short hairpin RNA (shRNA) with an open reading frame which exploits transcriptional read-through of a minimal polyadenylation signal from a Pol...
A nucleolar localizing Rev binding element inhibits HIV replication
Michienzi, Alessandro, De Angelis, Fernanda G, Bozzoni, Irene, Rossi, John J
The Rev protein of the human immunodeficiency virus (HIV) facilitates the nuclear export of intron containing viral mRNAs allowing formation of infectious virions. Rev traffics through the nucleolus...
WEINBERG, MARC S., VILLENEUVE, LOUISA M., EHSANI, ALI, AMARZGUIOUI, MOHAMMED, AAGAARD, LARS, CHEN, ZHAO-XIA, ...
To determine mechanistically how siRNAs mediate transcriptional gene silencing (TGS) in human cells, we have measured histone methylation at targeted promoters, the dependency on active...
Ribozyme-mediated inhibition of HIV 1 suggests nucleolar trafficking of HIV-1 RNA
Michienzi, Alessandro, Cagnon, Laurence, Bahner, Ingrid, Rossi, John J.
The HIV regulatory proteins Tat and Rev have a nucleolar localization property in human cells. However, no functional role has been attributed to this localization. Recently it has been demonstrated...
Scherr, Michaela, Rossi, John J., Sczakiel, Georg, Patzel, Volker
The use of antisense oligodeoxyribonucleotides (ODN) or ribozymes to specifically suppress gene expression is simple in concept and relies on efficient binding of the antisense strand to the target...
Chen, Hsiu-Hua, Castanotto, Daniela, LeBon, Jeanne M., Rossi, John J., Riggs, Arthur D.
We have investigated the analysis of RNA by use of terminal transferase-dependent PCR (TDPCR), a procedure previously used for the analysis of DNA and chromatin [J.Komura and A.D.Riggs, Nucleic Acids...
Monitoring Retroviral RNA Dimerization In Vivo via Hammerhead Ribozyme Cleavage
Pal, Bijay K., Scherer, Lisa, Zelby, Laurie, Bertrand, Edouard, Rossi, John J.
We have used a strategy for colocalization of Psi (Ψ)-tethered ribozymes and targets to demonstrate that Ψ sequences are capable of specific interaction in the cytoplasm of both packaging and...
A nucleolar TAR decoy inhibitor of HIV-1 replication
Michienzi, Alessandro, Li, Shirley, Zaia, John A., Rossi, John J.
Tat is a critical regulatory factor in HIV-1 gene expression. It mediates the transactivation of transcription from the HIV-1 LTR by binding to the transactivation response (TAR) element in a complex...
Procedure for Isolating Mutants Defective in Metabolite Transport or Utilization
Berg, Claire M., Rossi, John J., Coleman, Joyce V., Conlon, Michele
Mutants defective in uptake or utilization of a given metabolite can readily be obtained from facultative auxotrophs (for that metabolite) by penicillin enrichment under nonpermissive conditions in...
Proline Excretion and Indirect Suppression in Escherichia coli and Salmonella typhimurium
Berg, Claire M., Rossi, John J.
The last step in proline biosynthesis in Escherichia coli K-12, Salmonella typhimurium LT7, and a number of other enterobacterial isolates is regulated so that no proline is excreted, even if excess...
Differential Recovery of Auxotrophs After Penicillin Enrichment in Escherichia coli
Rossi, John J., Berg, Claire M.
Various auxotrophs are recovered from a penicillin enrichment cycle with differing efficiencies. Reconstruction experiments indicate that, under starvation conditions in the presence of penicillin,...
Effect of Enrichment Procedure upon Auxotroph Recovery in Escherichia coli K-12
Rossi, John J., Berg, Claire M.
Proline-requiring auxotrophs are recovered preferentially after mutant enrichment procedures (e.g., penicillin) which perturb the cell envelope, but not after procedures (e.g., thymineless death)...
Soifer, Harris S., Zaragoza, Adriana, Peyvan, Maany, Behlke, Mark A., Rossi, John J.
Long interspersed nuclear elements (LINE-1 or L1) comprise 17% of the human genome, although only 80–100 L1s are considered retrotransposition-competent (RC-L1). Despite their small number, RC-L1s...
siRNA target site secondary structure predictions using local stable substructures
Heale, Bret S. E., Soifer, Harris S., Bowers, Chauncey, Rossi, John J.
The crystal structure based model of the catalytic center of Ago2 revealed that the siRNA and the mRNA must be able to form an A-helix for correct positing of the scissile phosphate bond for cleavage...
Kim, Dong-Ho, Langlois, Marc-Andre, Lee, Kwang-Back, Riggs, Arthur D., Puymirat, Jack, Rossi, John J.
Myotonic dystrophy type 1 (DM1) is an autosomal dominant neuromuscular disorder associated with a (CUG)n expansion in the 3′-untranslated region of the DMPK (DM1 protein kinase) gene. Mutant DMPK...
Functional polarity is introduced by Dicer processing of short substrate RNAs
Rose, Scott D., Kim, Dong-Ho, Amarzguioui, Mohammed, Heidel, Jeremy D., Collingwood, Michael A., Davis, Mark E., ...
Synthetic RNA duplexes that are substrates for Dicer are potent triggers of RNA interference (RNAi). Blunt 27mer duplexes can be up to 100-fold more potent than traditional 21mer duplexes (1). Not...
Unwalla, Hoshang J., Li, Hai-Tang, Bahner, Ingrid, Li, Ming-Jie, Kohn, Donald, Rossi, John J.
We demonstrate a novel approach for coexpression of a short hairpin RNA (shRNA) with an open reading frame which exploits transcriptional read-through of a minimal polyadenylation signal from a Pol...
Functional siRNA expression from transfected PCR products.
Castanotto, Daniela, Li, Haitang, Rossi, John J
RNA interference (RNAi) is a process in which double-stranded RNA (dsRNA) induces the postranscriptional degradation of homologous transcripts. RNAi can be initiated by exposing cells to dsRNA either...
Uncoupling of RNAi from active translation in mammalian cells
Small inhibitory RNAs (siRNAs) are produced from longer RNA duplexes by the RNAse III family member Dicer. The siRNAs function as sequence-specific guides for RNA cleavage or translational...
WEINBERG, MARC S., VILLENEUVE, LOUISA M., EHSANI, ALI, AMARZGUIOUI, MOHAMMED, AAGAARD, LARS, CHEN, ZHAO-XIA, ...
To determine mechanistically how siRNAs mediate transcriptional gene silencing (TGS) in human cells, we have measured histone methylation at targeted promoters, the dependency on active...
A nucleolar localizing Rev binding element inhibits HIV replication
Michienzi, Alessandro, De Angelis, Fernanda G, Bozzoni, Irene, Rossi, John J
The Rev protein of the human immunodeficiency virus (HIV) facilitates the nuclear export of intron containing viral mRNAs allowing formation of infectious virions. Rev traffics through the nucleolus...
Toxicity in mice expressing short hairpin RNAs gives new insight into RNAi
A popular method of RNA interference shows levels of toxicity in mice that could limit its therapeutic potential.
Distance constraints between microRNA target sites dictate efficacy and cooperativity
Sætrom, Pål, Heale, Bret S.E., Snøve, Ola, Aagaard, Lars, Alluin, Jessica, Rossi, John J.
MicroRNAs (miRNAs) have the potential to regulate the expression of thousands of genes, but the mechanisms that determine whether a gene is targeted or not are poorly understood. We studied the...
Optimization and characterization of tRNA-shRNA expression constructs
Scherer, Lisa J., Frank, Richard, Rossi, John J.
Expression of short hairpin RNAs via the use of PolIII-based transcription systems has proven to be an effective mechanism for triggering RNAi in mammalian cells. The most popular promoters for this...
Kato, Mitsuo, Zhang, Jane, Wang, Mei, Lanting, Linda, Yuan, Hang, Rossi, John J., ...
Key features of diabetic nephropathy (DN) include the accumulation of extracellular matrix proteins such as collagen 1-α 1 and -2 (Col1a1 and -2). Transforming growth factor β1 (TGF-β), a key...
Held, Daniel M., Kissel, Jay D., Thacker, Sarah J., Michalowski, Daniel, Saran, Dayal, Ji, Jianfei, ...
Reverse transcriptase (RT) remains a primary target in therapies directed at human immunodeficiency virus type 1 (HIV-1). RNA aptamers that bind RT from HIV-1 subtype B have been shown to protect...
Castanotto, Daniela, Sakurai, Kumi, Lingeman, Robert, Li, Haitang, Shively, Louise, Aagaard, Lars, ...
Despite the great potential of RNAi, ectopic expression of shRNA or siRNAs holds the inherent risk of competition for critical RNAi components, thus altering the regulatory functions of some cellular...
Metalloproteases regulate T-cell proliferation and effector function via LAG-3
Li, Nianyu, Wang, Yao, Forbes, Karen, Vignali, Kate M, Heale, Bret S, Saftig, Paul, ...
Tight control of T-cell proliferation and effector function is essential to ensure an effective but appropriate immune response. Here, we reveal that this is controlled by the...