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Yamazaki Lab
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The lab unravels the mechanisms of gene expression regulation through information analysis of mRNA.
AboutAbout the lab
Unraveling how gene expression works from mRNA information
The Yamazaki Lab, part of the RNA Informatics Group in the Division of Bioinformatics, Bioinformatics Center, Research Institute for Microbial Diseases, aims to understand the mechanisms of gene expression regulation through analysis of information on messenger RNA (mRNA) and to apply that understanding.
Proteins in the body are made when DNA information is transcribed into mRNA and then translated.
The lab investigates the complex regulatory mechanisms involved in mRNA transcription, degradation, and translation using the latest sequencing technologies and machine learning.
The findings are applied to the development of new medical and industrial technologies.
Key terms
- Gene expression
- The series of processes in which DNA information is transcribed into mRNA and then translated to synthesize proteins.
- Alternative splicing
- A post-transcriptional regulatory mechanism that produces multiple types of mRNA from a single gene. It greatly increases the variety of proteins.
- Translation efficiency
- The degree to which protein is produced from an mRNA. In many cases it correlates with the amount of protein that accumulates.
- Cell-free protein synthesis
- A technology that synthesizes proteins using extracted cellular components instead of living cells.
ResearchResearch themes
The timing and amount of protein production must be precisely controlled according to cell type and environmental conditions, and mRNA transcription efficiency, stability, and translation efficiency play a major role in this control. The lab elucidates the regulatory mechanisms involved in mRNA transcription, degradation, and translation using sequencing technologies and machine learning, and applies them to the development of medical and industrial technologies.
*Illustrative imageHow mRNA sequences are determined
The lab focuses on the mechanisms by which multiple types of mRNA are transcribed from a single gene through processes such as alternative splicing. Combining CAGE-seq and nanopore long-read cDNA sequencing data with machine learning, it analyzes how transcription start sites, splicing patterns, and polyA addition sites are determined, and is developing a system that predicts their positions.
*Illustrative imagemRNA stability and translation efficiency
mRNA stability and translation efficiency are determined by diverse regulatory sequences in the untranslated and coding regions of mRNA. The lab combines high-precision data with statistical methods and machine learning to investigate the features involved in this regulation. Using large-scale data from massively parallel reporter assays as well as genetic algorithms, it is developing a system for optimizing mRNA sequences.
Promoting applications of RNA
The lab is developing sequence design systems aimed at stabilizing RNA and improving translation efficiency. One example is mRNA design for cell-free protein synthesis, where the system under development has already greatly increased the yield of several proteins.
MembersFaculty
- Associate ProfessorShotaro Yamazaki
- Project Assistant ProfessorNEVIEN KAMEL MOHAMED ABDELKHALEK
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Report an errorAbout the images
The top and research theme images are illustrative and were not taken at the lab. They are cropped from Wikimedia Commons images. Cropped CC BY-SA images are provided under the same CC BY-SA license as the original (version shown on each line).
- Top image: “RNA pol” 作者不詳 / Public domain (cropped)
- How mRNA sequences are determined: “RNA Polymerase” Maria Voigt and PDB-101 / CC BY 4.0 (cropped)
- mRNA stability and translation efficiency: “Multiple Ribosomes Translation Protein Synthesis” Christinelmiller / CC BY-SA 4.0 (cropped)
- Related lab (Nakatani Lab): “Medaka (Oryzias latipes) egg, day 0” Ethmostigmus / CC BY-SA 4.0 (cropped)
- Related lab (Nakamura Lab): “370A automated DNA sequencer” Giac83 / CC BY-SA 2.5 (cropped)
- Related lab (Ikawa Lab): “Overview of TALENs” Ogletreerd / CC BY-SA 4.0 (cropped)
- Related lab (Ito Lab): “Potyvirus genome and virion” Jiri Sochor, Petr Babula, Vojtech Adam, Boris Krska, and Rene Kizek / CC BY 3.0 (cropped)
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