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.

The Art of Science: Shapeshifter

Brian Jungen is a Canadian artist of mixed European and Native background.  He often uses everyday objects such as sporting goods, shoes and luggage to create new versions of iconic cultural objects, such as Native American masks, totem poles and fossil skeletons. This piece, Shapeshifter (2000), is one of a series of monumental whale skeleton sculptures made of cheap acrylic lawn chairs. Continue reading “The Art of Science: Shapeshifter”

Borrowed Time: Parquet Courts and aging academics

Simple songs (and most songs of the punk variety are pretty simple) are at their best when a single strong feeling or thought pervades. Along with some driving chords and a solid backbeat, a meaningful turn of phrase can be the chain that that makes the whole gear system work. Duffy and the Doubters hit it perfectly in Spider Baby Jesus, and New York’s Parquet Courts do it with Borrowed Time, from their 2012 release Light Up Gold. Continue reading “Borrowed Time: Parquet Courts and aging academics”

Don’t knock out your toddler

Your child tripped on the back steps and has ended up with a long deep gash on their leg. You head to the ER to get it stitched up. Turns out your toddler has other plans and wails and thrashes around whenever the doctors try to take a look. In many ERs around the country the doctor will recommend sedating your child to prevent the trauma your child is experiencing as well as the anguish you must be feeling watching your child suffer.

For the last ten years, evidence has been building that giving young children anesthesia can be bad for their developing nervous system. The evidence in juvenile rodents is extremely compelling while studies in humans show a trend but some variability. Links have been shown between anesthesia before 4 years of age and increased rates of ADHD and cognitive dysfunction. While there are many cases that require surgery before the age of 4, there are often elective surgeries that would be better postponed. Continue reading “Don’t knock out your toddler”

Parental controls

It’s not that extracting information from your kids is hard; but parents know that extracting high quality, useful information is almost impossible. My offspring can talk continuously1, but when it comes to a direct request for information the clam up, like clams with dimples. Their vocabulary is reduced a repetition of”yes” or “no”. How can I know if my questions are generating reliable information? How can I know if “no” really means “no” when I ask if anyone needs to use the potty2? Continue reading “Parental controls”