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Yukako Oma

Publications and source records attributed to Yukako Oma.

7 recordsLinked to original sources
PubMed2006

Vertebrate Arp6, a novel nuclear actin-related protein, interacts with heterochromatin protein 1.

Actin-related proteins (Arps) were recently shown to contribute to the organization and regulation of chromatin structures. The nuclear functions of Arps have been investigated principally in budding yeast in which six of the ten Arp subfamilies are localized in the nucleus. In vertebrates, only two isoforms of Arp4 have so far been identified as showing localization to the nucleus. Here we show the predominant nuclear localization of another Arp subfamily, Arp6, in vertebrate cells. Vertebrate Arp6 directly interacted with heterochromatin protein 1 (HP1) orthologs and the two proteins colocalized in pericentric heterochromatin. Yeast Arp6 is involved in telomere silencing, while Drosophila Arp6 is localized in the pericentric heterochromatin. Our data strongly suggest that Arp6 has an evolutionarily conserved role in heterochromatin formation and also provide new insights into the molecular organization of heterochromatin.

Actins↗
PubMed2005

Sequence and comparative genomic analysis of actin-related proteins.

Actin-related proteins (ARPs) are key players in cytoskeleton activities and nuclear functions. Two complexes, ARP2/3 and ARP1/11, also known as dynactin, are implicated in actin dynamics and in microtubule-based trafficking, respectively. ARP4 to ARP9 are components of many chromatin-modulating complexes. Conventional actins and ARPs codefine a large family of homologous proteins, the actin superfamily, with a tertiary structure known as the actin fold. Because ARPs and actin share high sequence conservation, clear family definition requires distinct features to easily and systematically identify each subfamily. In this study we performed an in depth sequence and comparative genomic analysis of ARP subfamilies. A high-quality multiple alignment of approximately 700 complete protein sequences homologous to actin, including 148 ARP sequences, allowed us to extend the ARP classification to new organisms. Sequence alignments revealed conserved residues, motifs, and inserted sequence signatures to define each ARP subfamily. These discriminative characteristics allowed us to develop ARPAnno (http://bips.u-strasbg.fr/ARPAnno), a new web server dedicated to the annotation of ARP sequences. Analyses of sequence conservation among actins and ARPs highlight part of the actin fold and suggest interactions between ARPs and actin-binding proteins. Finally, analysis of ARP distribution across eukaryotic phyla emphasizes the central importance of nuclear ARPs, particularly the multifunctional ARP4.

Actins↗
PubMed2005

The nuclear actin-related protein Act3p/Arp4p is involved in the dynamics of chromatin-modulating complexes.

Chromatin remodelling and histone-modifying complexes govern the modulation of chromatin structure. While components of these complexes are diverse, nuclear actin-related proteins (Arps) have been repeatedly found in these complexes from yeast to mammals. In most cases, Arps are required for functioning of the complexes, but the molecular mechanisms of nuclear Arps have as yet been largely unknown. The Arps and actin, sharing a common ancestor, are supposed to be highly similar in the three-dimensional structure of their core regions, including the ATP-binding pocket. The Arp Act3p/Arp4p of Saccharomyces cerevisiae exists within the nucleus, partly as a component of several high molecular mass complexes, including the NuA4 histone acetyltransferase (HAT) complex, and partly as uncomplexed molecules. We observed that mutations in the putative ATP-binding pocket of Act3p/Arp4p increased its concentration in the high molecular mass complexes and, conversely, that an excess of ATP or ATPgammaS led to the release of wild-type Act3p/Arp4p from the complexes. These results suggest a requirement of ATP binding by Act3p/Arp4p for its dissociation from the complexes. In accordance, a mutation in the putative ATP binding site of Act3p/Arp4p inhibited the conversion of the NuA4 complex into the smaller piccoloNuA4, which does not contain Act3p/Arp4p and exhibits HAT activity distinct from that of NuA4. Although the in vitro binding activity of ATP by recombinant Act3p/Arp4p was found to be rather weak, our observations, taken together, suggest that the ATP-binding pocket of Act3p/Arp4p is involved in the function of chromatin modulating complexes by regulating their dynamics.

Acetyltransferases↗
PubMed2003

The brain-specific actin-related protein ArpN alpha interacts with the transcriptional co-repressor CtBP.

Actin-related protein (Arp) is found in many chromatin remodeling and histone acetyltransferase complexes. We previously identified ArpN alpha as an isoform of ArpN beta/BAF53, which is included in mammalian SWI/SNF chromatin remodeling complex, and showed that ArpN alpha is a potential component of the complex. Although it has a structure highly similar to ArpN beta/BAF53, ArpN alpha is expressed exclusively in brain and in neural differentiated embryonal carcinoma cells. Since ArpN alpha possesses a region that shows low similarity to ArpN beta/BAF53, we hypothesized that proteins interacting with this region contribute to the ArpN alpha-specific function in brain. Here we showed that ArpN alpha, but not ArpN beta/BAF53, interacts with the transcriptional co-repressor CtBP (C-terminal binding protein). Transactivation by the SWI/SNF complex and glucocorticoid receptor was repressed by the CtBP in the presence of ArpN alpha. These findings suggest that SWI/SNF complex containing ArpN alpha might regulate certain genes involved in brain development and/or its function differently from SWI/SNF complex containing ArpN beta/BAF53.

Actins↗
PubMed2002

Brain-specific expression of the nuclear actin-related protein ArpNalpha and its involvement in mammalian SWI/SNF chromatin remodeling complex.

Actin-related proteins share significant homology with conventional actins and are classified into subfamilies based on the similarity of their sequences and functions. The Arp4 subfamily of Arps is localized in the nucleus, and a mammalian isoform, ArpNbeta (also known as BAF53), is a component of the chromatin remodeling and histone acetyltransferase complexes. Another isoform identified in humans, ArpNalpha has scarcely been characterized yet. We identified mouse ArpNalpha, and showed that ArpNalpha is more similar between humans and mice than ArpNbeta. No difference was observed between ArpNalpha and beta in subcellular localization and interaction with BRM, which is an ATPase subunit of mammalian SWI/SNF chromatin remodeling complex. However, ArpNalpha was expressed exclusively in the brain and its expression was induced during neural differentiation of P19 mouse embryonic carcinoma cells. ArpNalpha is the first brain-specific component of a chromatin remodeling complex to be identified, suggesting that ArpNalpha has conserved and important roles in the differentiation of neural cells through regulation of chromatin structure.

Actins↗
PubMed2002

Correlation between chromatin association and transcriptional regulation for the Act3p/Arp4 nuclear actin-related protein of Saccharomyces cerevisiae.

Actin-related proteins (Arps), which share a basal structure with actin but have distinct functions, have been found in a wide variety of organisms. While their functions are not yet clear, some Arps are localized in the nucleus and are suggested to contribute to the regulation of transcription. An essential gene of Saccharomyces cerevisiae, Act3p/Arp4, encodes the first identified nuclear Arp, which has been shown to bind to core histones in vitro. Here we have analyzed the in vivo function of Act3p/Arp4 on the his4-912delta promoter. Chromatin immunoprecipitation assays show that Act3p/Arp4 is bound to the entire his4-912delta promoter region. Conditional act3/arp4 mutations affect transcription from the his4-912delta promoter, where decreased Act3p/Arp4 binding and a change in nuclease sensitivity of chromatin were observed, showing the involvement of Act3p/Arp4 in the regulation of gene expression through the organization of chromatin structure. Taken together with the presence of Act3p/Arp4 in chromatin remodeling and histone acetyltransferase complexes, it is suggested that Act3p/Arp4 functions in transcriptional regulation to recruit chromatin remodeling and histone acetyltransferase complexes onto chromatin.

Actins↗