The truly provocative and disturbing stuff in ENCODE

… at least from my perspective. I’ll now stop ranting about the hype and media coverage of ENOCDE, and extend my compliments to the consortium for an amazingly well-coordinated effort to achieve an impressive level of consistency and quality for such a large consortium. Whatever else you might want to say about the idea of ENCODE, you cannot say that ENCODE was poorly executed.

It’s time to get into the interesting stuff – what’s actually in the papers. Among the results I’ve been most eagerly awaiting to see in print are the DNase hypersensitivity results now published in Thurman et al. (Nature 489, 75–82 (06 September 2012) doi:10.1038/nature11232)

Why is this interesting? Because it raises provocative and possibly disturbing questions regarding how transcription factors navigate and read out information from the genome. Continue reading “The truly provocative and disturbing stuff in ENCODE”

Polling junk DNA

I missed this poll by Chris Gunter yesterday, asking “If you are a non-genomicist, can you tell us if you thought/were taught much of the genome was “junk”?

Well, I’m 1) a day late and 2) not a non-genomicist, but I’ll reply anyway, because we need a little history review.

In my Eukaryotic Genomes course in grad school (in the year the draft Human Genome sequence came out), I was taught by Tom Eickbush, not so much about ‘junk DNA’, but about ‘selfish DNA’. The point is largely the same regardless of what we call it. Among the first papers we read in Eickbush’s class were the classic Doolittle and Sapienza and Orgel and Crick papers on selfish DNA.

The key argument of these papers was this: parasitic DNA that can replicate itself within the genome requires no other explanation for its existence other than is ability to replicate, period. It does not need to be functional, from the perspective of the organism. It may acquire a useful function. But in general, absent evidence of such a useful function, we don’t need to ask the question, ‘what is the function of this DNA?’ There’s no mystery why it’s there – because it can replicate. Continue reading “Polling junk DNA”

ENCODE Decodes the genome… but how much is functional?

The latest round of ENCODE papers are out, accessible via a handy ENCODE explorer gateway at Nature. I know what I’ll be doing for the next week. Stay tuned for more Finch & Pea coverage of what all this means, but I can’t resist a few brief comments about function.

First, you can immediately dismiss the NY Times’s misleading headline that suggests much, much more of the genome is functional than we previously thought. Being an intron counts as ‘function’ here, which is a pretty low bar to meet. The ENCODE results indicate that much of the genome is represented within introns, which I find fascinating, but that’s not something that forces us to dramatically revise our ideas about function in the genome.

Second, I’m going to claim (without any proof whatsoever) the title of the world’s record holder for “the largest number of randomly generated DNA sequences tested for function in an enhancer assay.” Hopefully in the not too distant future you can read in print about the 1000+ random sequences (plus several thousand genomic sequences) we tested in our new, smokin’ hot, high-throughput enhancer assay, but here’s the punch line: it’s not that difficult to randomly generate a DNA sequence that will drive substantial tissue-specific transcription.

In other words, whether it’s been selected for function or not, DNA is generally not biochemically inert.

P.S. This seems to be consistent with Ewan Birney’s comment, “It’s clear that 80% of the genome has a specific biochemical activity – whatever that might be.”

P.P.S. Brief methods: We took sequences under ChIP-seq peaks, thoroughly scrambled them while preserving the original di-nucleotide frequencies, and dropped them upstream of a basal promoter to test for enhancer activity.

Missouri may have opened a creationist Pandora’s Box

Missourians have voted overwhelmingly for a ‘right-to-pray’ constitutional amendment that creationists may use to let students opt-out of certain topics in science class. When I voted on Tuesday in my St. Louis suburb (against this amendment, of course), the ballot described the proposed amendment with a single, innocuous sentence that basically nobody could disagree with (except maybe Richard Dawkins or Jerry Coyne). No wonder the thing passed with 83% in favor – you can make anything sound good if you’re not constrained by honesty, which, when it comes to prayer, one would think ought to be a constraint.

From the St. Louis Post-Dispatch:

In the months leading up to the vote, Amendment 2 prompted unsuccessful lawsuits over its ballot wording, which its critics argued oversimplified the issue to the point of deceit. Continue reading “Missouri may have opened a creationist Pandora’s Box”

The Art of Science: Growth Factor

Betty Busby, a textile artist based in New Mexico, uses quilting to explore scientific themes.  Her large and often spectacularly detailed pieces represent biological processes, including cell division and the growth of plants and other organisms.

Busby uses photomicrographs of scientific images as inspiration for her work.  She says that because the colors in microscope photos are mostly artificially produced, either through chemical or lighting methods, it gives her the freedom to experiment with “the wildest color combinations I can think of, unhindered by expectations of realism.”

This piece, Growth Factor, looks at cell growth and development.  Busby printed the cell images on silk in a palette of green and gold, evoking a forest, then appliqued the purple organelles welling up in the middle. This piece will be shown at “Quilt Visions: Brainstorms”  at the Visions Art Museum in San Diego, CA, in October 2012.

You can see more of Busby’s work on her website  and at her etsy shop.

This post contains material that originally appeared in Guru magazine

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