A reader directed me to a 2015 ENCODE workshop with online videos of all the presentations [From Genome Function to Biomedical Insight: ENCODE and Beyond]. The workshop was sponsored by the National Human Genome Research Institute in Bethesda, Md (USA). The purpose of the workshop was ...
- Discuss the scientific questions and opportunities for better understanding genome function and applying that knowledge to basic biological questions and disease studies through large-scale genomics studies.
- Consider options for future NHGRI projects that would address these questions and opportunities.
I also expected a debate over the significance of associations between various molecular markers and disease. Are theses associations reproducible and relevant? Do the molecular markers have anything to do with the disease?
I looked at most of the videos but I saw nothing to suggest the workshop participants cared one hoot about either of these debates. Perhaps I missed something? If anyone can find such a discussion please alert me.
There was no mention of junk DNA and no mention of the failed publicity hype surrounding publication of the the 2012 papers. It was as though that episode never existed. The overwhelming impression you get from looking at the presentation is that all the researchers believe all their data is real and reflects biological function in some way or another.
The planning stage was all about collecting more and more data. Nothing about validating the data they already have. This workshop really needed to invite some of their critics to give presentations. These PI's needed to hear some "alternative truths"!
The closest thing I could find to the thinking of the participants was a slide from a talk by Michael Snyder. I assume it reflects the thinking of ENCODE leaders.
Prior to ENCODE there were dozens and dozens of known genes for functional noncoding RNAs. The number of proven genes in this category has crept up little by little as proven functions are found for some conserved transcripts. Today, it's conceivable there might be as many as 5,000 genes for functional noncoding RNAs. I don't think that's what Michael Snyder meant. I think he meant 100,000 or more genes but I can't be sure. In any case, even the most optimistic estimate, 100,000 genes, would only occupy a few percent of the genome.
The original 2012 ENCODE papers talked about millions of regulatory sequences. What Michael Snyder is saying here is that there's more "potential" regulatory sequences than coding DNA. That would be more than 1.5% of the genome or 48 million bp. Assuming 48 bp per regulatory site, that's one million regulatory sequences. It's enough for 40 regulatory sites for every known gene in our genome.
That doesn't make a lot of sense to me. Does anyone know of a single example of a gene whose expression is regulated by factors binding to DNA at 40 different sites?
The slide leaves out the most important thing about function; namely how much of the genome is functional. I'd love to know if the view of ENCODE researchers on junk DNA has changed between 2003 and 2015.