RNA-Seq: Deep Sequencing the Human Transcriptome

Source: Sultan et al. (2008). A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome. Science 321:956-960.

Apparently, we're going back to re-doing all the experiments that we once did using tiling arrays. These papers are far from innovative but I think it's good for the people in the field to know that this data is out there (hence supporing its publication in science). Apart from expensive reactions, tiling arrays also miss vital information like splice sites and alternative splicing. RNA-seq circumvents most of the problems inherent to other methods and the authors have used this approach to provide snapshots of human transcriptome at the nucleotide level. The authors do many controls to validate their results. For example, they compare the reads for each gene to PolII Chip-seq data to make the case that the number of reads is a good measure for expression. The figure below (from the original paper) shows the distribution of PolII Chip-seq reads for the genes with different levels of expression (the x-asis is the position relative to TSS).


Their results generally include the identification 25% more genes and ~100, 000 splice sites (compared to ~4000 known before). They also show that exon skipping is the most prevalent method of splicing.