Toshimichi Yamada
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View article: Pathway to Independence: a forecast for the future of developmental biology
Pathway to Independence: a forecast for the future of developmental biology Open
In 2022, Development launched its Pathway to Independence (PI) programme, aimed at supporting postdocs as they transition to their first independent position. In 2025, we welcome our third cohort of eight talented PI fellows. In this artic…
View article: Synthetic organizer cells guide development via spatial and biochemical instructions
Synthetic organizer cells guide development via spatial and biochemical instructions Open
View article: Harnessing synthetic biology to engineer organoids and tissues
Harnessing synthetic biology to engineer organoids and tissues Open
View article: Repression of PUM1-mediated mRNA decay activates translesion synthesis after DNA damage
Repression of PUM1-mediated mRNA decay activates translesion synthesis after DNA damage Open
Biological roles of Pumilio1 (PUM1) in ubiquitous cells remain unclear. Here we identify 48 degrading target mRNAs by combined analysis of transcriptome-wide mRNA stabilities and the binding of mRNAs. Further analysis revealed that cells r…
View article: Metabolic labeling of RNA using multiple ribonucleoside analogs enables the simultaneous evaluation of RNA synthesis and degradation rates
Metabolic labeling of RNA using multiple ribonucleoside analogs enables the simultaneous evaluation of RNA synthesis and degradation rates Open
Gene expression is determined by a balance between RNA synthesis and RNA degradation. To elucidate the underlying regulatory mechanisms and principles of this, simultaneous measurements of RNA synthesis and degradation are required. Here, …
View article: Systematic Analysis of Targets of Pumilio-Mediated mRNA Decay Reveals that PUM1 Repression by DNA Damage Activates Translesion Synthesis
Systematic Analysis of Targets of Pumilio-Mediated mRNA Decay Reveals that PUM1 Repression by DNA Damage Activates Translesion Synthesis Open
RNA-binding proteins (RBPs) play a pivotal role in gene expression by modulating the stability of transcripts. However, the identification of degradation target mRNAs of RBPs remains difficult. By the combined analysis of transcriptome-wid…
View article: Metabolic labeling of RNA using multiple ribonucleoside analogs enables simultaneous evaluation of transcription and degradation rates
Metabolic labeling of RNA using multiple ribonucleoside analogs enables simultaneous evaluation of transcription and degradation rates Open
Summary Gene expression is one of the factors determining cellular conditions, and its level is determined by the balance between transcription and RNA degradation. However, it has been not well elucidated how transcription and degradation…
View article: Systematic Analysis of Targets of Pumilio (PUM)-Mediated mRNA Decay Identifies a Role of PUM1 in Regulating DNA Damage Response Pathway
Systematic Analysis of Targets of Pumilio (PUM)-Mediated mRNA Decay Identifies a Role of PUM1 in Regulating DNA Damage Response Pathway Open
Summary RNA-binding proteins (RBPs) play a pivotal role in gene expression by modulating the stability of transcripts; however, the identification of degradation targets of RBPs remains difficult. Here, we identified 48 target mRNAs of hum…
View article: Diminished nuclear <scp>RNA</scp> decay upon <i>Salmonella</i> infection upregulates antibacterial noncoding <scp>RNA</scp> s
Diminished nuclear <span>RNA</span> decay upon <i>Salmonella</i> infection upregulates antibacterial noncoding <span>RNA</span> s Open
View article: Interplay between Transcription and RNA Degradation
Interplay between Transcription and RNA Degradation Open
Amount of mRNA depends on the both the rates of mRNA transcription in the nucleus and mRNA degradation in the cytoplasm. Although each of the processes was studied independently, recent studies demonstrated the interplay between transcript…
View article: Spatiotemporal analysis with a genetically encoded fluorescent RNA probe reveals TERRA function around telomeres
Spatiotemporal analysis with a genetically encoded fluorescent RNA probe reveals TERRA function around telomeres Open
Telomeric repeat-containing RNA (TERRA) controls the structure and length of telomeres through interactions with numerous telomere-binding proteins. However, little is known about the mechanism by which TERRA regulates the accessibility of…
View article: Development of red-shifted mutants derived from luciferase of Brazilian click beetle<i>Pyrearinus termitilluminans</i>
Development of red-shifted mutants derived from luciferase of Brazilian click beetle<i>Pyrearinus termitilluminans</i> Open
Luciferase, a bioluminescent protein, has been used as an analytical tool to visualize intracellular phenomena. Luciferase with red light emission is particularly useful for bioluminescence imaging because of its high transmittance in mamm…