A multi-omics longitudinal study of the murine retinal response to chronic low-dose irradiation and simulated microgravity.

This research study aimed to understand how changes in a part of our DNA called methylation, which can affect gene activity without altering the actual genetic code itself, might be linked with eye diseases like age-related macular degeneration (AMD). Scientists looked at specific areas on 160 different human retinal cells from people who had AMD and compared them to healthy ones. They focused particularly on DNA spots known as CpG sites that are often involved in methylation changes, which can turn genes 'on' or 'off.' The researchers used a special method called RNA sequencing (RNA-seq) to see how the activity of different genes varied between AMD and healthy retinal cells. They also examined DNA for signs that methylation had occurred, which could explain changes in gene activity without altering the actual sequence of our DNA.

In this study, researchers aimed to elucidate the regulatory mechanisms of gene expression and DNA methylation in a specific biological context by integrating RNA sequencing (RNA-seq) data with bisulfite sequencing results. The methodology involved downloading unnormalized RNA-seq counts from GeneLab, which were generated using an established consensus pipeline that includes quality control, read trimming, mapping to the reference genome, and gene quantification steps. These raw count files served as input for differential expression analysis with DESeq2 (v1.30.1), a widely used tool in bioinformatics research for analyzing NGS data54. To investigate DNA methylation patterns associated with the observed changes in gene expression, RRBS FastQ files were also downloaded from GeneLab and subjected to differential methylation analysis using ORA (Oxford Reference Analyzer). This approach allowed researchers to identify genes that are either hypo- or hypermethylated based on their promoter regions.