Unusual Intron Conservation near Tissue-Regulated Exons Found by Splicing Microarrays (2006)
Charles W. Sugnet, Karpagam Srinivasan, Tyson A. Clark, Georgeann O'Brien, Melissa S. Cline, Hui Wang, ...
Alternative splicing contributes to both gene regulation and protein diversity. To discover broad relationships between regulation of alternative splicing and sequence conservation, we applied a...
The structure of a rigorously conserved RNA element within the SARS virus genome (2005)
Robertson, Michael P, Igel, Haller, Baertsch, Robert, Haussler, David, Ares, Manuel, Scott, William G
We have solved the three- dimensional crystal structure of the stem- loop II motif ( s2m) RNA element of the SARS virus genome to 2.7- Angstrom resolution. SARS and related coronaviruses and...
The Structure of a Rigorously Conserved RNA Element within the SARS Virus Genome (2005)
Michael P. Robertson, Haller Igel, Robert Baertsch, David Haussler, Manuel Ares, William G. Scott
The SARS RNA genome contains a unique structure that resembles a portion of ribosomal RNA; this may allow the virus to hijack its hosts protein synthesis machinery.
The Structure of a Rigorously Conserved RNA Element within the SARS Virus Genome (2005)
Michael P. Robertson, Haller Igel, Robert Baertsch, David Haussler, Manuel Ares Jr., William G. Scott
We have solved the three-dimensional crystal structure of the stem-loop II motif (s2m) RNA element of the SARS virus genome to 2.7-Å resolution. SARS and related coronaviruses and astroviruses all...
Pauling, Michelle Haynes, McPheeters, David S., Ares, Manuel
To explore the dynamics of snRNP structure and function, we have studied Cus1p, identified as a suppressor of U2 snRNA mutations in budding yeast. Cus1p is homologous to human SAP145, a protein...
Vita.
Intron self-complementarity enforces exon inclusion in a yeast pre-mRNA
Howe, Kenneth James, Ares, Manuel
Skipping of internal exons during removal of introns from pre-mRNA must be avoided for proper expression of most eukaryotic genes. Despite significant understanding of the mechanics of intron...
Knowledge-based analysis of microarray gene expression data by using support vector machines
Brown, Michael P. S., Grundy, William Noble, Lin, David, Cristianini, Nello, Sugnet, Charles Walsh, Furey, Terrence S., ...
We introduce a method of functionally classifying genes by using gene expression data from DNA microarray hybridization experiments. The method is based on the theory of support vector machines...
Yan, Dong, Perriman, Rhonda, Igel, Haller, Howe, Kenneth J., Neville, Megan, Ares, Manuel
A screen for suppressors of a U2 snRNA mutation identified CUS2, an atypical member of the RNA recognition motif (RRM) family of RNA binding proteins. CUS2 protein is associated with U2 RNA in...
Functional Cus1p Is Found with Hsh155p in a Multiprotein Splicing Factor Associated with U2 snRNA
Pauling, Michelle Haynes, McPheeters, David S., Ares, Manuel
To explore the dynamics of snRNP structure and function, we have studied Cus1p, identified as a suppressor of U2 snRNA mutations in budding yeast. Cus1p is homologous to human SAP145, a protein...
Burns, C. Geoffrey, Ohi, Ryoma, Mehta, Sapna, O’Toole, Eileen T., Winey, Mark, Clark, Tyson A., ...
Genetic and biochemical studies of Schizosaccharomyces pombe and Saccharomyces cerevisiae have identified gene products that play essential functions in both pre-mRNA splicing and cell cycle control....
ATP requirement for Prp5p function is determined by Cus2p and the structure of U2 small nuclear RNA
Perriman, Rhonda, Barta, Imre, Voeltz, Gia K., Abelson, John, Ares, Manuel
Stable addition of U2 small nuclear ribonucleoprotein (snRNP) to form the prespliceosome is the first ATP-dependent step in splicing, and it requires the DEXD/H box ATPase Prp5p. However,...
ATP can be dispensable for prespliceosome formation in yeast
Perriman, Rhonda, Ares, Manuel
The first ATP-dependent step in pre-mRNA splicing involves the stable binding of U2 snRNP to form the prespliceosome. We show that a prespliceosome-like complex forms in the absence of ATP in yeast...
Alternative 3′-end processing of U5 snRNA by RNase III
Chanfreau, Guillaume, Elela, Sherif Abou, Ares, Manuel, Guthrie, Christine
The cellular components required to form the 3′ ends of small nuclear RNAs are unknown. U5 snRNA from Saccharomyces cerevisiae is found in two forms that differ in length at their 3′ ends (U5L...
Mer1p is a modular splicing factor whose function depends on the conserved U2 snRNP protein Snu17p
Spingola, Marc, Armisen, Javier, Ares, Manuel
Mer1p activates the splicing of at least three pre-mRNAs (AMA1, MER2, MER3) during meiosis in the yeast Saccharomyces cerevisiae. We demonstrate that enhancer recognition by Mer1p is separable from...
A new α-helical extension promotes RNA binding by the dsRBD of Rnt1p RNAse III
Leulliot, Nicolas, Quevillon-Cheruel, Sophie, Graille, Marc, Van Tilbeurgh, Herman, Leeper, Thomas C, Godin, Katherine S, ...
Rnt1 endoribonuclease, the yeast homolog of RNAse III, plays an important role in the maturation of a diverse set of RNAs. The enzymatic activity requires a conserved catalytic domain, while RNA...
Schattner, Peter, Decatur, Wayne A., Davis, Carrie A., Ares, Manuel, Fournier, Maurille J., Lowe, Todd M.
One of the largest families of small RNAs in eukaryotes is the H/ACA small nucleolar RNAs (snoRNAs), most of which guide RNA pseudouridine formation. So far, an effective computational method...
The Structure of a Rigorously Conserved RNA Element within the SARS Virus Genome
Robertson, Michael P, Igel, Haller, Baertsch, Robert, Haussler, David, Ares, Manuel, Scott, William G
We have solved the three-dimensional crystal structure of the stem-loop II motif (s2m) RNA element of the SARS virus genome to 2.7-Å resolution. SARS and related coronaviruses and astroviruses all...
Unusual Intron Conservation near Tissue-Regulated Exons Found by Splicing Microarrays
Sugnet, Charles W, Srinivasan, Karpagam, Clark, Tyson A, O'Brien, Georgeann, Cline, Melissa S, Wang, Hui, ...
Alternative splicing contributes to both gene regulation and protein diversity. To discover broad relationships between regulation of alternative splicing and sequence conservation, we applied a...
Prp43p Is a DEAH-Box Spliceosome Disassembly Factor Essential for Ribosome Biogenesis
Combs, D. Joshua, Nagel, Roland J., Ares, Manuel, Stevens, Scott W.
The known function of the DEXH/D-box protein Prp43p is the removal of the U2, U5, and U6 snRNPs from the postsplicing lariat-intron ribonucleoprotein complex. We demonstrate that affinity-purified...
HOWE, KENNETH JAMES, KANE, CAROLINE M., ARES, MANUEL
Unknown mechanisms exist to ensure that exons are not skipped during biogenesis of mRNA. Studies have connected transcription elongation with regulated alternative exon inclusion. To determine...
Davis, Carrie Anne, Ares, Manuel
Mutations in RRP6 result in the accumulation of aberrant polyadenylated transcripts from small nucleolar RNA genes. We exploited this observation to search for novel noncoding RNA genes in the yeast...
A dominant mutation at a new locus affecting resistance to cycloheximide has been isolated by exploiting a synergistic relationship with a previously known mutation for cycloheximide resistance in...
Intron self-complementarity enforces exon inclusion in a yeast pre-mRNA
Howe, Kenneth James, Ares, Manuel
Skipping of internal exons during removal of introns from pre-mRNA must be avoided for proper expression of most eukaryotic genes. Despite significant understanding of the mechanics of intron...
Knowledge-based analysis of microarray gene expression data by using support vector machines
Brown, Michael P. S., Grundy, William Noble, Lin, David, Cristianini, Nello, Sugnet, Charles Walsh, Furey, Terrence S., ...
We introduce a method of functionally classifying genes by using gene expression data from DNA microarray hybridization experiments. The method is based on the theory of support vector machines...
Yan, Dong, Perriman, Rhonda, Igel, Haller, Howe, Kenneth J., Neville, Megan, Ares, Manuel
A screen for suppressors of a U2 snRNA mutation identified CUS2, an atypical member of the RNA recognition motif (RRM) family of RNA binding proteins. CUS2 protein is associated with U2 RNA in...
Functional Cus1p Is Found with Hsh155p in a Multiprotein Splicing Factor Associated with U2 snRNA
Pauling, Michelle Haynes, McPheeters, David S., Ares, Manuel
To explore the dynamics of snRNP structure and function, we have studied Cus1p, identified as a suppressor of U2 snRNA mutations in budding yeast. Cus1p is homologous to human SAP145, a protein...
Burns, C. Geoffrey, Ohi, Ryoma, Mehta, Sapna, O’Toole, Eileen T., Winey, Mark, Clark, Tyson A., ...
Genetic and biochemical studies of Schizosaccharomyces pombe and Saccharomyces cerevisiae have identified gene products that play essential functions in both pre-mRNA splicing and cell cycle control....
ATP requirement for Prp5p function is determined by Cus2p and the structure of U2 small nuclear RNA
Perriman, Rhonda, Barta, Imre, Voeltz, Gia K., Abelson, John, Ares, Manuel
Stable addition of U2 small nuclear ribonucleoprotein (snRNP) to form the prespliceosome is the first ATP-dependent step in splicing, and it requires the DEXD/H box ATPase Prp5p. However,...
ATP can be dispensable for prespliceosome formation in yeast
Perriman, Rhonda, Ares, Manuel
The first ATP-dependent step in pre-mRNA splicing involves the stable binding of U2 snRNP to form the prespliceosome. We show that a prespliceosome-like complex forms in the absence of ATP in yeast...
Alternative 3′-end processing of U5 snRNA by RNase III
Chanfreau, Guillaume, Elela, Sherif Abou, Ares, Manuel, Guthrie, Christine
The cellular components required to form the 3′ ends of small nuclear RNAs are unknown. U5 snRNA from Saccharomyces cerevisiae is found in two forms that differ in length at their 3′ ends (U5L...
Mer1p is a modular splicing factor whose function depends on the conserved U2 snRNP protein Snu17p
Spingola, Marc, Armisen, Javier, Ares, Manuel
Mer1p activates the splicing of at least three pre-mRNAs (AMA1, MER2, MER3) during meiosis in the yeast Saccharomyces cerevisiae. We demonstrate that enhancer recognition by Mer1p is separable from...
A new α-helical extension promotes RNA binding by the dsRBD of Rnt1p RNAse III
Leulliot, Nicolas, Quevillon-Cheruel, Sophie, Graille, Marc, Van Tilbeurgh, Herman, Leeper, Thomas C, Godin, Katherine S, ...
Rnt1 endoribonuclease, the yeast homolog of RNAse III, plays an important role in the maturation of a diverse set of RNAs. The enzymatic activity requires a conserved catalytic domain, while RNA...
Schattner, Peter, Decatur, Wayne A., Davis, Carrie A., Ares, Manuel, Fournier, Maurille J., Lowe, Todd M.
One of the largest families of small RNAs in eukaryotes is the H/ACA small nucleolar RNAs (snoRNAs), most of which guide RNA pseudouridine formation. So far, an effective computational method...
The Structure of a Rigorously Conserved RNA Element within the SARS Virus Genome
Robertson, Michael P, Igel, Haller, Baertsch, Robert, Haussler, David, Ares, Manuel, Scott, William G
We have solved the three-dimensional crystal structure of the stem-loop II motif (s2m) RNA element of the SARS virus genome to 2.7-Å resolution. SARS and related coronaviruses and astroviruses all...
A dominant mutation at a new locus affecting resistance to cycloheximide has been isolated by exploiting a synergistic relationship with a previously known mutation for cycloheximide resistance in...
Unusual Intron Conservation near Tissue-Regulated Exons Found by Splicing Microarrays
Sugnet, Charles W, Srinivasan, Karpagam, Clark, Tyson A, O'Brien, Georgeann, Cline, Melissa S, Wang, Hui, ...
Alternative splicing contributes to both gene regulation and protein diversity. To discover broad relationships between regulation of alternative splicing and sequence conservation, we applied a...
Prp43p Is a DEAH-Box Spliceosome Disassembly Factor Essential for Ribosome Biogenesis
Combs, D. Joshua, Nagel, Roland J., Ares, Manuel, Stevens, Scott W.
The known function of the DEXH/D-box protein Prp43p is the removal of the U2, U5, and U6 snRNPs from the postsplicing lariat-intron ribonucleoprotein complex. We demonstrate that affinity-purified...
HOWE, KENNETH JAMES, KANE, CAROLINE M., ARES, MANUEL
Unknown mechanisms exist to ensure that exons are not skipped during biogenesis of mRNA. Studies have connected transcription elongation with regulated alternative exon inclusion. To determine...
Davis, Carrie Anne, Ares, Manuel
Mutations in RRP6 result in the accumulation of aberrant polyadenylated transcripts from small nucleolar RNA genes. We exploited this observation to search for novel noncoding RNA genes in the yeast...
Sing the Genome Electric: Excited Cells Adjust Their Splicing
Neuronal depolarization regulates the alternative splicing of NMDA receptor subunits, providing molecular insight into how experience alters gene expression.
Ni, Julie Z., Grate, Leslie, Donohue, John Paul, Preston, Christine, Nobida, Naomi, O’Brien, Georgeann, ...
Many alternative splicing events create RNAs with premature stop codons, suggesting that alternative splicing coupled with nonsense-mediated decay (AS-NMD) may regulate gene expression...
Rearrangement of competing U2 RNA helices within the spliceosome promotes multiple steps in splicing
Perriman, Rhonda J., Ares, Manuel
Nuclear pre-messenger RNA (pre-mRNA) splicing requires multiple spliceosomal small nuclear RNA (snRNA) and pre-mRNA rearrangements. Here we reveal a new snRNA conformational switch in which...
Boutz, Paul L., Stoilov, Peter, Li, Qin, Lin, Chia-Ho, Chawla, Geetanjali, Ostrow, Kristin, ...
Many metazoan gene transcripts exhibit neuron-specific splicing patterns, but the developmental control of these splicing events is poorly understood. We show that the splicing of a large group of...
Chakrabarti, Kausik, Pearson, Michael, Grate, Leslie, Sterne-Weiler, Timothy, Deans, Jonathan, Donohue, John Paul, ...
As the genomes of more eukaryotic pathogens are sequenced, understanding how molecular differences between parasite and host might be exploited to provide new therapies has become a major focus....