Tuesday, May 24, 2016

University of Toronto press release distorts conclusions of RNA paper

My colleague, Ben Blencowe, just published a paper ...

Sharma, E., Sterne-Weiler, T., O’Hanlon, D., and Blencowe, B.J. (2016) Global Mapping of Human RNA-RNA Interactions. Molecular Cell, [doi: 10.1016/j.molcel.2016.04.030]

ABSTRACT (Summary)

The majority of the human genome is transcribed into non-coding (nc)RNAs that lack known biological functions or else are only partially characterized. Numerous characterized ncRNAs function via base pairing with target RNA sequences to direct their biological activities, which include critical roles in RNA processing, modification, turnover, and translation. To define roles for ncRNAs, we have developed a method enabling the global-scale mapping of RNA-RNA duplexes crosslinked in vivo, ‘‘LIGation of interacting RNA followed by high-throughput sequencing’’ (LIGR-seq). Applying this method in human cells reveals a remarkable landscape of RNA-RNA interactions involving all major classes of ncRNA and mRNA. LIGR-seq data reveal unexpected interactions between small nucleolar (sno) RNAs and mRNAs, including those involving the orphan C/D box snoRNA, SNORD83B, that control steady-state levels of its target mRNAs. LIGR-seq thus represents a powerful approach for illuminating the functions of the myriad of uncharacterized RNAs that act via base-pairing interactions.

Monday, May 16, 2016

Tim Minchin's "Storm," the animated movie, and another no-so-good Minchin cartoon

I've mentioned this before but it bears repeating. If you haven't listened to "Storm" then you are in for a treat because now you can listen AND watch. If you've heard it before, then hear it again. The message never gets old.

A word of caution. Minchin may be very good at recognizing pseudoscience and quacks but he can be a bit gullible when listening to scientists. He was completely take in by the ENCODE hype back in 2012. This cartoon is also narrated by Tim Minchin but it's not so good.

Monday, May 09, 2016

Research for a book

I'm on sabbatical this term, working on a possible book whose working title is "What's in Your Genome?: 90% of your genome is junk."

Here's some of the most important books I've read (or re-read) in the past few months.

I've also read a lot of papers and scribbled notes on what's important and what's bullshit not. The most difficult part about keeping up with the scientific literature is organizing it in some meaningful way so you can quickly find it again if you need to—something I do just about every day.

Everyone has their own method. What works for me is to keep an electronic reference with key words and links to a file folder on a particular topic. (I use EndNote.) Here are the folders with all the papers I've been reading in the past few months.

I don't know how other authors behave but for me the most difficult thing about writing a book is organizing my thoughts and planning how to present them in the most effective manner. I tend to write too much on too many topics so the initial drafts usually have to be pared down considerably. Keeping that in mind, what are YOUR favorite topics?

John Oliver teaches us to be skeptical of scientific publications

We all know that the purpose of education should be to teach students how to think critically. We're not doing a very good job. Take biochemistry, for example. We spend a lot of time transferring information from lecture notes to student notes and then examining students on whether the transfer has worked. We think that teaching students to read the primary literature will make them better scientists when, in fact, teaching them to be skeptical of the primary literature is what's really necessary.

The ENCODE fiasco is just one of many examples where the scientific literature got it wrong. We need to make sure that our students appreciate the important parts of science; namely, the necessity of repeating experiments and the value of scientific consensus. Our students, and many of my colleagues, are prone to hype and promotion just like every one else but that's exactly what critical thinking is supposed to avoid. And it's exactly what proper science—no matter how you define it—is designed to overcome.

If students and scientists are having trouble with these concepts, imagine how difficult it is for the general public. How are they supposed to know that not every "breakthrough" is a real breakthrough and not every new study is correct?

John Oliver did an excellent job of explaining the problem on a recent (May 8, 2016) episode of Last Week Tonight. Watch it. It's worth 20 minutes of your time. The last bit on "Todd Talks" is classic.

Monday, May 02, 2016

The Encyclopedia of Evolutionary Biology revisits junk DNA

The Enclyopedia of Evolutionary Biology is a four volume set of articles by leading evolutionary biologists. An online version is available at ScienceDirect. Many universities will have free access.

I was interested in what they had to say about junk DNA and the evolution of large complex genomes. The only article that directly addressed the topic was "Noncoding DNA Evolution: Junk DNA Revisited" by Michael Z. Ludwig of the Department of Ecology and Evolution at the University of Chicago. Ludwig is a Research Associate (Assistant Professor) who works with Martin Kreitman on "Developmental regulation of gene expression and the genetic basis for evolution of regulatory DNA."

As you could guess from the title of the article, Michael Ludwig divides the genome into two fractions; protein-coding genes and noncoding DNA. The fact that organismal complexity doesn't correlate with the number of genes (protein-coding) is a problem that requires an explanation, according to Ludwig. He assumes that the term "junk DNA" was used in the past to account for our lack of knowledge about noncoding DNA.
Eukaryotic genomes mostly consist of DNA that is not translated into protein sequence. However, noncoding DNA (ncDNA) has been little studied relative to proteins. The lack of knowledge about its functional significance has led to hypotheses that much nongenic DNA is useless "junk" (Ohno, 1972) or that it exists only to replicate itself (Doolittle and Sapienza, 1980; Orgel and Crick, 1980).
Ludwig says that we now know some of the functions of non-coding DNA and one of them is regulation of gene expression.
These regulatory sequences are distributed among selfish transposons and middle or short repetitive DNAs. The genome is an extremely complex machine; functionally as well as structurally it is generally not possible to disentangle the regulatory function from the junk selfish activity. The idea of junk DNA needs to be revisited.
Of course we all know about regulatory sequences. We've known about this function of non-coding DNA for half a century. The question that interests us is not whether non-coding DNA has a function but whether a large proportion of noncoding DNA is junk.

Ludwig seems to be arguing that a significant fraction of the mammalian genome is devoted to regulation. He doesn't ever specify what this fraction is but apparently it's large enough to "revisit" junk DNA.

The biggest obstacle to his thesis is the fact that only 8% of the human genome is conserved (Rands et al., 2014). Ludwig says that 1% of the genome is coding DNA and 7% "has a functional regulatory gene expression role" according to the Rands et al. study. This is somewhat misleading since Rands et al. specifically mention that not all of this conserved DNA will be regulatory.

All of this is consistent with a definition of function specifying that it must be under negative selection (i.e. conserved). It leads to the conclusion that about 90% of the human genome is junk. That doesn't require a re-evaluation of junk.

In order to "revisit" junk DNA, the proponents of the "complex machine" view of evolution must come up with plausible reasons why lack of sequence conservation does not rule out function. Ludwig offers up the standard rationales ...
  1. Some ultra-conserved sequences don't seem to have a function and this "shows that the extent of sequence conservation is not a good predictor of the functional importance of a sequence."
  2. The amount of conserved sequence depends on the alignment and alignment is difficult.
  3. About 40%-70% of the noncoding DNA in Drosophila melanogaster is under functional constraint within the species but not between D. melanogaster and D. simulans. Therefore, some large fraction of functional regulatory sequences might only be conserved in the human lineage and it won't show up in comparisons between species. (Does this explain onions?)
The idea here is that there is rapid turnover of functional DNA binding sites required for regulation but the overall fraction of DNA devoted to regulation remains large. This explains why there doesn't seem to be a correlation between the amount of conserved DNA and the amount that can possibly be devoted to regulating gene expression. The argument implies that much more than 7% of the genome is required for regulation. The amount has to be >50% or so in order to justify overthrowing the concept of junk DNA.

That's a ridiculous number, but so is 7%. Imagine that "only" 7% of the genome is functionally involved in regulating expression of the protein-coding genes. That's 224 million base pairs of DNA or approximately 10 thousand base pairs of cis-regulatory elements (CREs) for every protein-coding gene.

There is no evidence whatsoever that even this amount (7%) of DNA is required for regulation but Ludwig would like to think that the actual amount is much greater. The lack of conservation is dismissed by assuming rapid turnover while conserving function and/or stabilizing selection on polymorphic sequences.

The problem here is that Ludwig is constructing a just-so evolutionary story to explain something that doesn't require an explanation. If there's no evidence that a large fraction of the genome is required for regulation then there's no problem that needs explaining. Ludwig does not tell us why he believes that most of our genome is required for regulation. Maybe it's because of ENCODE?

Since this is published in the Encyclopedia of Evolutionary Biolgoy, I assume that this sort of evolutionary argument resonates with many evolutionary biologists. That's sad.

Rands, C. M., Meader, S., Ponting, C. P., and Lunter, G. (2014) 8.2% of the Human Genome Is Constrained: Variation in Rates of Turnover across Functional Element Classes in the Human Lineage. PLoS Genetics, 10(7), e1004525. [doi: 10.1371/journal.pgen.1004525]