研究課題
I have collected and conducted the next-generation sequencing on the bromo-uridine labelled and pulse-chased RNA for DLD-1 human cell line in hypoxia and normoxia. Following the sequencing, I have done primary analyses of the bromouridine labelled RNA and made an appropriate pipeline to obtain RNA half-life from the decay data. Data collection and creating the bioinformatic pipeline for the analysis of RNA decay is very important to understand the mechanisms behind RNA regulation, transcriptome-wide.Characterisation of RNA half-livesI have predominantly tried to generate RNA-seq library for BRIC-seq. I have conducted BRIC-seq in collaboration with Akimitsu Lab, using method previously published (Tani et. al. Genome Res. 2012) in DLD-1 adenocarcinoma cell-lines in Illumina Hi-seq 2000 for both hypoxia and normoxia. I sequenced and mapped on average of 27 million reads for hypoxia condition and 18.7 million for normoxia condition. I mapped the BRIC-seq reads to the human genome (GRCh37/hg19) and I quantified the sequence tag counts and tried to analyse the RNA decay by using three different decay models to fit the data.Comparison with other dataBy comparing our lab’s previous RNA-seq and epigenome data, I was able to make a list of genes where the half-life changes seems to be the causal reason behind the RNA expression change in hypoxia. I will be trying to verify some of these genes experimentally.
2: おおむね順調に進展している
I have managed to obtain and sequence the bromouridine pulse-chased RNA and I have managed to develop an primary bioinformatic pipelines to analyse the decay data that I have generated and I have been able to compare with previous data on transcriptome and epigenome to analyse the contribution of RNA decay in RNA genome-wide.
I have been trying to validate some of the claims through Western blot and qPCR, Luciferase assays, however it has not been successful yet. I am yet to find some of the regulatory motifs that are in RNA sequences and it is an effort that is still to be done next fiscal year and I will need to refine some of the computational simulations conducted in the last fiscal year.
すべて 2016 2015
すべて 学会発表 (4件) (うち国際学会 2件) 図書 (1件)
