Genetic sequencing normally starts with grinding up the material which is being sampled, but that destroys all the cells and with them the location information about where gene activity takes place. Being able to track where RNA expression is taking place would help answer a lot of questions about how our bodies operate and permit creation of maps of processes within the body based on genetic expression.
Researchers at Harvard Medical School have just developed a technique called fluorescent in situ RNA sequencing (FISSEQ) that identifies RNA in place within the cell. The method involves chemically treating tissue to “freeze” everything in place and then copying the RNA many times over into identical DNA bunches located where the original RNA molecules were. To identify each bunch of DNA from the billions of others within the sample, they used unique sections of the original RNA as an addressing system and were able to map out the genetic activity in human primary fibroblasts.
Here’s an example of a FISSEQ flashing sequence: “As ‘letters,’ or bases, are added to RNAs throughout the cell during fluorescent in situ sequencing, the RNAs flash a specific color that indicates which base has been added (0:00 – 0:05 of this video). The sequence of colors, represented abstractly here as a growing stack of colored balls (0:08-0:16), reveals the base sequence.”
Here are the lead researchers talking about the latest findings:
More from the study abstract:
Using 30-base reads from 8742 genes in situ, we examined RNA expression and localization in human primary fibroblasts with a simulated wound-healing assay. FISSEQ is compatible with tissue sections and whole-mount embryos and reduces the limitations of optical resolution and noisy signals on single-molecule detection. Our platform enables massively parallel detection of genetic elements, including gene transcripts and molecular barcodes, and can be used to investigate cellular phenotype, gene regulation, and environment in situ.
Study in Science: Highly Multiplexed Subcellular RNA Sequencing in Situ
Harvard Medical School: New method IDs working copies of genes in human cells; could help diagnose sick tissues early