Commentary re: Protemics-based Identification of RS/DJ-1 as a Novel Circulating Tumor Antigen (2008)
Antigenic Marker, Ryuji Kobayashi
With the progress of the human genome project, a largescale analysis of proteins within a single experiment, called proteomics, has gained much attention. Mass spectrometry and related techniques...
∗ To whom correspondence should be addressed: (2008)
Kevin R. Coombes, John M. Koomen, Keith A. Baggerly, S. Morris, Ryuji Kobayashi, Kevin R. Coombes
the characteristics of mass spectrometry
Understanding the characteristics of mass spectrometry data through the use of simulation (2005)
Kevin R. Coombes, John M. Koomen, Keith A. Baggerly, Jeffrey S. Morris, Ryuji Kobayashi
Abstract: Background: Mass spectrometry is actively being used to discover disease-related proteomic patterns in complex mixtures of proteins derived from tissue samples or from easily obtained...
Understanding the characteristics of mass spectrometry data through the use of simulation (2005)
Kevin R. Coombes, John M. Koomen, Keith A. Baggerly, Jeffrey S. Morris, Ryuji Kobayashi
Abstract: Background: Mass spectrometry is actively being used to discover disease-related proteomic patterns in complex mixtures of proteins derived from tissue samples or from easily obtained...
Morris, Jeffrey S., Coombes, Kevin R., Koomen, John, Baggerly, Keith A., Kobayashi, Ryuji
Motivation: Mass spectrometry yields complex functional data for which the features of scientific interest are peaks. A common two-step approach to analyzing these data involves first extracting and...
Morris, Jeffrey S., Coombes, Kevin R., Koomen, John, Baggerly, Keith A., Kobayashi, Ryuji
Motivation: Mass spectrometry yields complex functional data for which the features of scientific interest are peaks. A common two-step approach to analyzing these data involves first extracting and...
Morris, Jeffrey S., Coombes, Kevin R., Koomen, John, Baggerly, Keith A., Kobayashi, Ryuji
Motivation: Mass spectrometry yields complex functional data for which the features of scientific interest are peaks. A common two-step approach to analyzing these data involves first extracting and...
Chattopadhyay, Chandrani, Hawke, David, Kobayashi, Ryuji, Maity, Sankar N.
To understand the role of the CCAAT-binding factor, CBF, in transcription, we developed a strategy to purify the heterotrimeric CBF complex from HeLa cell extracts using two successive immunoaffinity...
Interaction between the Drosophila CAF-1 and ASF1 chromatin assembly factors. (2001)
Tyler, Jessica K., Collins, Kimberly A., Prasad-Sinha, Jayashree, Amiott, Elizabeth, Bulger, Michael, Harte, Peter J., ...
The assembly of newly synthesized DNA into chromatin is essential for normal growth, development, and differentiation. To gain a better understanding of the assembly of chromatin during DNA...
Ito, Takashi, Levenstein, Mark E., Fyodorov, Dmitry V., Kutach, Alan K., Kobayashi, Ryuji, Kadonaga, James T.
Dong, Benhao, Horowitz, David S., Kobayashi, Ryuji, Krainer, Adrian R.
While searching for a human homolog of the S.cerevlslae splicing factor PRP18, we found a polypeptide that reacted strongly with antibodies against PRP18. We purified this polypeptide from HeLa cells...
Kobayashi, Ryuji, Kanatani, Akio, Yoshimoto, Tadashi, Tsuru, Daisuke
A neutral protease from Bacillus subtilis var. amylosacchariticus was modified with tetranitromethane (TNM) at pH 8.0 for 1 h at 25�C, by which treatment the proteolytic activity toward casein was...
Tyrosine phosphorylation of p62dok by p210bcr-abl inhibits RasGAP activity
Kashige, Nobuhiro, Carpino, Nick, Kobayashi, Ryuji
The t(9;22) chromosomal translocation is found in almost all patients with chronic myelogenous leukemia. The resultant Bcr-Abl fusion gene expresses a chimeric fusion protein p210bcr-abl with...
Ho, Yuen, Mason, Stephen, Kobayashi, Ryuji, Hoekstra, Merl, Andrews, Brenda
In the budding yeast, Saccharomyces cerevisiae, DNA damage or ribonucleotide depletion causes the transcriptional induction of an array of genes with known or putative roles in DNA repair. The...
Liao, Huey-Jane, Kobayashi, Ryuji, Mathews, Michael B.
Most human adenoviruses encode two virus-associated (VA) RNAs, VA RNAI and VA RNAII, that accumulate to high levels in the cytoplasm of infected cells. The function of VA RNAI in blocking the...
A novel yeast protein influencing the response of RNA polymerase II to transcriptional activators
Emili, Andrew, Kobayashi, Ryuji, Ingles, C. James
A sensitive in vitro crosslinking technique using a photoactive derivative of the chimeric activator LexA-E2F-1 was used to identify yeast proteins that might influence the response of RNA polymerase...
Oncogene-dependent apoptosis is mediated by caspase-9
Fearnhead, Howard O., Rodriguez, Joe, Govek, Eve-Ellen, Guo, Wenjun, Kobayashi, Ryuji, Hannon, Greg, ...
Understanding how oncogenic transformation sensitizes cells to apoptosis may provide a strategy to kill tumor cells selectively. We previously developed a cell-free system that recapitulates oncogene...
Rundlett, Stephen E., Carmen, Andrew A., Kobayashi, Ryuji, Bavykin, Sergei, Turner, Bryan M., Grunstein, Michael
Increased histone acetylation has been correlated with increased transcription, and regions of heterochromatin are generally hypoacetylated. In investigating the cause-and-effect relationship between...
Wu, Jiansheng, Carmen, Andrew A., Kobayashi, Ryuji, Suka, Noriyuki, Grunstein, Michael
Histone deacetylase HDA1, the prototype for the class II mammalian deacetylases, is likely the catalytic subunit of the HDA1-containing complex that is involved in TUP1-specific repression and global...
MacCallum, David E., Losada, Ana, Kobayashi, Ryuji, Hirano, Tatsuya
We previously characterized major components of mitotic chromosomes assembled in Xenopus laevis egg extracts and collectively referred to them as Xenopus chromosome–associated polypeptides (XCAPs)....
Ho, Yuen, Costanzo, Michael, Moore, Lynda, Kobayashi, Ryuji, Andrews, Brenda J.
In Saccharomyces cerevisiae, gene expression in the late G1 phase is activated by two transcription factors, SBF and MBF. SBF contains the Swi4 and Swi6 proteins and activates the transcription of G1...
Dallas, Peter B., Pacchione, Stephen, Wilsker, Deborah, Bowrin, Valerie, Kobayashi, Ryuji, Moran, Elizabeth
p270 is an integral member of human SWI-SNF complexes, first identified through its shared antigenic specificity with p300 and CREB binding protein. The deduced amino acid sequence of p270 reported...
Interaction between the Drosophila CAF-1 and ASF1 Chromatin Assembly Factors
Tyler, Jessica K., Collins, Kimberly A., Prasad-Sinha, Jayashree, Amiott, Elizabeth, Bulger, Michael, Harte, Peter J., ...
The assembly of newly synthesized DNA into chromatin is essential for normal growth, development, and differentiation. To gain a better understanding of the assembly of chromatin during DNA...
Carrodeguas, José A., Kobayashi, Ryuji, Lim, Susan E., Copeland, William C., Bogenhagen, Daniel F.
Peptide sequences obtained from the accessory subunit of Xenopus laevis mitochondrial DNA (mtDNA) polymerase γ (pol γ) were used to clone the cDNA encoding this protein. Amino-terminal sequencing...
p300/CREB Binding Protein-Related Protein p270 Is a Component of Mammalian SWI/SNF Complexes
Dallas, Peter B., Cheney, Ian Wayne, Liao, Da-Wei, Bowrin, Valerie, Byam, Whitney, Pacchione, Stephen, ...
p300 and the closely related CREB binding protein (CBP) are transcriptional adaptors that are present in intracellular complexes with TATA binding protein (TBP) and bind to upstream activators...
Trypanosome Capping Enzymes Display a Novel Two-Domain Structure
Silva, Erika, Ullu, Elisabetta, Kobayashi, Ryuji, Tschudi, Christian
The ubiquitous m7G cap of eukaryotic mRNAs and of precursors to the spliceosomal small nuclear RNAs (snRNAs) is the result of an essential RNA modification acquired during transcript elongation. In...
Wong, Mee Wa, Henry, R. William, Ma, Beicong, Kobayashi, Ryuji, Klages, Natacha, Matthias, Patrick, ...
The human RNA polymerase II and III snRNA promoters have similar enhancers, the distal sequence elements (DSEs), and similar basal promoter elements, the proximal sequence elements (PSEs). The DSE,...
Hu, Ping, Wu, Si, Sun, Yuling, Yuan, Chih-Chi, Kobayashi, Ryuji, Myers, Michael P., ...
Unlike Saccharomyces cerevisiae RNA polymerase III, human RNA polymerase III has not been entirely characterized. Orthologues of the yeast RNA polymerase III subunits C128 and C37 remain...
Carpino, Nick, Kobayashi, Ryuji, Zang, Heesuk, Takahashi, Yutaka, Jou, Shiann-Tarrng, Feng, Jian, ...
In a screen for proteins that interact with Jak2, we identified a previously uncharacterized 70-kDa protein and cloned the corresponding cDNA. The predicated sequence indicates that p70 contains an...
Nakayama, Jun-ichi, Xiao, Guoping, Noma, Ken-ichi, Malikzay, Asra, Bjerling, Pernilla, Ekwall, Karl, ...
The post-translational modifications of histones are key to the modulation of chromatin structure. Distinct patterns of modifications established by histone-modifying enzymes control diverse...
The type 2C Ser/Thr phosphatase PP2Cγ is a pre-mRNA splicing factor
Murray, Michael V., Kobayashi, Ryuji, Krainer, Adrian R.
To identify activities involved in human pre-mRNA splicing, we have developed a procedure to separate HeLa cell nuclear extract into five complementing fractions. An activity called SCF1 was purified...
Chen, Charlie Degui, Kobayashi, Ryuji, Helfman, David M.
In the rat β-tropomyosin (β-TM) gene, exons 6 and 7 are spliced alternatively in a mutually exclusive manner. Exon 6 is included in mRNA encoding nonmuscle TM-1, whereas exon 7 is used in mRNA...
Lopato, Sergiy, Kalyna, Maria, Dorner, Silke, Kobayashi, Ryuji, Krainer, Adrian R., Barta, Andrea
SR proteins are nuclear phosphoproteins with a characteristic Ser/Arg-rich domain and one or two RNA recognition motifs. They are highly conserved in animals and plants and play important roles in...
Ito, Takashi, Levenstein, Mark E., Fyodorov, Dmitry V., Kutach, Alan K., Kobayashi, Ryuji, Kadonaga, James T.
The assembly of core histones and DNA into periodic nucleosome arrays is mediated by ACF, an ISWI-containing factor, and NAP-1, a core histone chaperone, in an ATP-dependent process. We describe the...
Henry, R. William, Mittal, Vivek, Ma, Beicong, Kobayashi, Ryuji, Hernandez, Nouria
The basal transcription factor SNAPc binds to the PSE, a core element in the RNA polymerase II and III human snRNA promoters. SNAPc contains at least four subunits, but it has not been possible to...
Chattopadhyay, Chandrani, Hawke, David, Kobayashi, Ryuji, Maity, Sankar N.
To understand the role of the CCAAT-binding factor, CBF, in transcription, we developed a strategy to purify the heterotrimeric CBF complex from HeLa cell extracts using two successive immunoaffinity...
IκB kinase β phosphorylates Dok1 serines in response to TNF, IL-1, or γ radiation
Lee, Sanghoon, Andrieu, Charlotte, Saltel, Frédéric, Destaing, Olivier, Auclair, Jessie, Pouchkine, Véronique, ...
Dok1 is an abundant Ras-GTPase-activating protein-associated tyrosine kinase substrate that negatively regulates cell growth and promotes migration. We now find that IκB kinase β (IKKβ) associated...
Emili, Andrew, Shales, Michael, McCracken, Susan, Xie, Weijun, Tucker, Philip W, Kobayashi, Ryuji, ...
The carboxyl-terminal domain (CTD) of the largest subunit of eukaryotic RNA polymerase II (pol II) plays an important role in promoting steps of pre-mRNA processing. To identify proteins in human...
Tyrosine phosphorylation of p62dok by p210bcr-abl inhibits RasGAP activity
Kashige, Nobuhiro, Carpino, Nick, Kobayashi, Ryuji
The t(9;22) chromosomal translocation is found in almost all patients with chronic myelogenous leukemia. The resultant Bcr-Abl fusion gene expresses a chimeric fusion protein p210bcr-abl with...
Ho, Yuen, Mason, Stephen, Kobayashi, Ryuji, Hoekstra, Merl, Andrews, Brenda
In the budding yeast, Saccharomyces cerevisiae, DNA damage or ribonucleotide depletion causes the transcriptional induction of an array of genes with known or putative roles in DNA repair. The...
Liao, Huey-Jane, Kobayashi, Ryuji, Mathews, Michael B.
Most human adenoviruses encode two virus-associated (VA) RNAs, VA RNAI and VA RNAII, that accumulate to high levels in the cytoplasm of infected cells. The function of VA RNAI in blocking the...
A novel yeast protein influencing the response of RNA polymerase II to transcriptional activators
Emili, Andrew, Kobayashi, Ryuji, Ingles, C. James
A sensitive in vitro crosslinking technique using a photoactive derivative of the chimeric activator LexA-E2F-1 was used to identify yeast proteins that might influence the response of RNA polymerase...
Oncogene-dependent apoptosis is mediated by caspase-9
Fearnhead, Howard O., Rodriguez, Joe, Govek, Eve-Ellen, Guo, Wenjun, Kobayashi, Ryuji, Hannon, Greg, ...
Understanding how oncogenic transformation sensitizes cells to apoptosis may provide a strategy to kill tumor cells selectively. We previously developed a cell-free system that recapitulates oncogene...
Rundlett, Stephen E., Carmen, Andrew A., Kobayashi, Ryuji, Bavykin, Sergei, Turner, Bryan M., Grunstein, Michael
Increased histone acetylation has been correlated with increased transcription, and regions of heterochromatin are generally hypoacetylated. In investigating the cause-and-effect relationship between...
Wu, Jiansheng, Carmen, Andrew A., Kobayashi, Ryuji, Suka, Noriyuki, Grunstein, Michael
Histone deacetylase HDA1, the prototype for the class II mammalian deacetylases, is likely the catalytic subunit of the HDA1-containing complex that is involved in TUP1-specific repression and global...
MacCallum, David E., Losada, Ana, Kobayashi, Ryuji, Hirano, Tatsuya
We previously characterized major components of mitotic chromosomes assembled in Xenopus laevis egg extracts and collectively referred to them as Xenopus chromosome–associated polypeptides (XCAPs)....
Ho, Yuen, Costanzo, Michael, Moore, Lynda, Kobayashi, Ryuji, Andrews, Brenda J.
In Saccharomyces cerevisiae, gene expression in the late G1 phase is activated by two transcription factors, SBF and MBF. SBF contains the Swi4 and Swi6 proteins and activates the transcription of G1...
Dallas, Peter B., Pacchione, Stephen, Wilsker, Deborah, Bowrin, Valerie, Kobayashi, Ryuji, Moran, Elizabeth
p270 is an integral member of human SWI-SNF complexes, first identified through its shared antigenic specificity with p300 and CREB binding protein. The deduced amino acid sequence of p270 reported...
Interaction between the Drosophila CAF-1 and ASF1 Chromatin Assembly Factors
Tyler, Jessica K., Collins, Kimberly A., Prasad-Sinha, Jayashree, Amiott, Elizabeth, Bulger, Michael, Harte, Peter J., ...
The assembly of newly synthesized DNA into chromatin is essential for normal growth, development, and differentiation. To gain a better understanding of the assembly of chromatin during DNA...
Carrodeguas, José A., Kobayashi, Ryuji, Lim, Susan E., Copeland, William C., Bogenhagen, Daniel F.
Peptide sequences obtained from the accessory subunit of Xenopus laevis mitochondrial DNA (mtDNA) polymerase γ (pol γ) were used to clone the cDNA encoding this protein. Amino-terminal sequencing...
p300/CREB Binding Protein-Related Protein p270 Is a Component of Mammalian SWI/SNF Complexes
Dallas, Peter B., Cheney, Ian Wayne, Liao, Da-Wei, Bowrin, Valerie, Byam, Whitney, Pacchione, Stephen, ...
p300 and the closely related CREB binding protein (CBP) are transcriptional adaptors that are present in intracellular complexes with TATA binding protein (TBP) and bind to upstream activators...
Trypanosome Capping Enzymes Display a Novel Two-Domain Structure
Silva, Erika, Ullu, Elisabetta, Kobayashi, Ryuji, Tschudi, Christian
The ubiquitous m7G cap of eukaryotic mRNAs and of precursors to the spliceosomal small nuclear RNAs (snRNAs) is the result of an essential RNA modification acquired during transcript elongation. In...
Wong, Mee Wa, Henry, R. William, Ma, Beicong, Kobayashi, Ryuji, Klages, Natacha, Matthias, Patrick, ...
The human RNA polymerase II and III snRNA promoters have similar enhancers, the distal sequence elements (DSEs), and similar basal promoter elements, the proximal sequence elements (PSEs). The DSE,...
Hu, Ping, Wu, Si, Sun, Yuling, Yuan, Chih-Chi, Kobayashi, Ryuji, Myers, Michael P., ...
Unlike Saccharomyces cerevisiae RNA polymerase III, human RNA polymerase III has not been entirely characterized. Orthologues of the yeast RNA polymerase III subunits C128 and C37 remain...
Carpino, Nick, Kobayashi, Ryuji, Zang, Heesuk, Takahashi, Yutaka, Jou, Shiann-Tarrng, Feng, Jian, ...
In a screen for proteins that interact with Jak2, we identified a previously uncharacterized 70-kDa protein and cloned the corresponding cDNA. The predicated sequence indicates that p70 contains an...
Nakayama, Jun-ichi, Xiao, Guoping, Noma, Ken-ichi, Malikzay, Asra, Bjerling, Pernilla, Ekwall, Karl, ...
The post-translational modifications of histones are key to the modulation of chromatin structure. Distinct patterns of modifications established by histone-modifying enzymes control diverse...
The type 2C Ser/Thr phosphatase PP2Cγ is a pre-mRNA splicing factor
Murray, Michael V., Kobayashi, Ryuji, Krainer, Adrian R.
To identify activities involved in human pre-mRNA splicing, we have developed a procedure to separate HeLa cell nuclear extract into five complementing fractions. An activity called SCF1 was purified...
Chen, Charlie Degui, Kobayashi, Ryuji, Helfman, David M.
In the rat β-tropomyosin (β-TM) gene, exons 6 and 7 are spliced alternatively in a mutually exclusive manner. Exon 6 is included in mRNA encoding nonmuscle TM-1, whereas exon 7 is used in mRNA...
Lopato, Sergiy, Kalyna, Maria, Dorner, Silke, Kobayashi, Ryuji, Krainer, Adrian R., Barta, Andrea
SR proteins are nuclear phosphoproteins with a characteristic Ser/Arg-rich domain and one or two RNA recognition motifs. They are highly conserved in animals and plants and play important roles in...
Ito, Takashi, Levenstein, Mark E., Fyodorov, Dmitry V., Kutach, Alan K., Kobayashi, Ryuji, Kadonaga, James T.
The assembly of core histones and DNA into periodic nucleosome arrays is mediated by ACF, an ISWI-containing factor, and NAP-1, a core histone chaperone, in an ATP-dependent process. We describe the...
Henry, R. William, Mittal, Vivek, Ma, Beicong, Kobayashi, Ryuji, Hernandez, Nouria
The basal transcription factor SNAPc binds to the PSE, a core element in the RNA polymerase II and III human snRNA promoters. SNAPc contains at least four subunits, but it has not been possible to...
Chattopadhyay, Chandrani, Hawke, David, Kobayashi, Ryuji, Maity, Sankar N.
To understand the role of the CCAAT-binding factor, CBF, in transcription, we developed a strategy to purify the heterotrimeric CBF complex from HeLa cell extracts using two successive immunoaffinity...
IκB kinase β phosphorylates Dok1 serines in response to TNF, IL-1, or γ radiation
Lee, Sanghoon, Andrieu, Charlotte, Saltel, Frédéric, Destaing, Olivier, Auclair, Jessie, Pouchkine, Véronique, ...
Dok1 is an abundant Ras-GTPase-activating protein-associated tyrosine kinase substrate that negatively regulates cell growth and promotes migration. We now find that IκB kinase β (IKKβ) associated...
Emili, Andrew, Shales, Michael, McCracken, Susan, Xie, Weijun, Tucker, Philip W, Kobayashi, Ryuji, ...
The carboxyl-terminal domain (CTD) of the largest subunit of eukaryotic RNA polymerase II (pol II) plays an important role in promoting steps of pre-mRNA processing. To identify proteins in human...
Phosphorylation of the proline-rich domain of Xp95 modulates Xp95 interaction with partner proteins
DeJournett, Robert E., Kobayashi, Ryuji, Pan, Shujuan, Wu, Chuanfen, Etkin, Laurence D., Clark, Richard B., ...
The mammalian adaptor protein Alix [ALG-2 (apoptosis-linked-gene-2 product)-interacting protein X] belongs to a conserved family of proteins that have in common an N-terminal Bro1 domain and a...
ALY Is a Common Coactivator of RUNX1 and c-Myb on the Type B Leukemogenic Virus Enhancer▿
Mertz, Jennifer A., Kobayashi, Ryuji, Dudley, Jaquelin P.
Type B leukemogenic virus (TBLV), a mouse mammary tumor virus (MMTV) variant, often induces T-cell leukemias and lymphomas by c-myc activation following viral DNA integration. Transfection assays...
Identification and Characterization of Sa/Scc3p Subunits in the Xenopus and Human Cohesin Complexes
Losada, Ana, Yokochi, Tomoki, Kobayashi, Ryuji, Hirano, Tatsuya
A multisubunit protein complex, termed cohesin, plays an essential role in sister chromatid cohesion in yeast and in Xenopus laevis cell-free extracts. We report here that two distinct cohesin...
Yakubovskaya, Elena, Lukin, Mark, Chen, Zhixin, Berriman, John, Wall, Joseph S, Kobayashi, Ryuji, ...
We used electron microscopy to examine the structure of human DNA pol γ, the heterotrimeric mtDNA replicase implicated in certain mitochondrial diseases and aging models. Separate analysis of...
Herling, Marco, Patel, Kaushali A., Teitell, Michael A., Konopleva, Marina, Ravandi, Farhad, Kobayashi, Ryuji, ...
The T-cell leukemia 1 (TCL1) oncoprotein is overexpressed by chromosomal rearrangement in the majority of cases of T-cell prolymphocytic leukemia (T-PLL). In vitro, TCL1 can modulate the activity of...