View Full Version : Is a genome enough? (Not Just DNA #1)


Amtram
10-21-13, 05:42 PM
Code for Life is one of the blogs I go to regularly. It's written by Grant Jacobs, a researcher in computational biology and a bioinformatics consultant. Because he has to take biological complexity and turn it into usable bits of data, he's very good at explaining that complexity - and illustrating how important it is to include it all for accurate results and information.

He hasn't put up post #2 yet, but post #1 (http://sciblogs.co.nz/code-for-life/2013/10/02/is-a-genome-enough-not-just-dna-1/) provides a HUGE amount of information about genomics, with illustration and lots of linky goodness. About 2/3rds of the way down the page, you will find this:

4. A few weeks ago Darcy Cowan, writing at the Tuatara Genome project blog asked,
“What about epigenetic markers? How important are these when considering if all the genomic information has been captured? Should we get to the point of creating artificial sequences for organisms larger than microbes will we need to concern ourselves with these?”
David Winter, the author of the Tuatara genome project blog, replied,
“If you don’t mind, I might split into two sub-questions for answers. (a) How much information does the genome sequence itself give us, and will understanding epigenetic tags (and other data on top of the genome sequence) be important?”
I asked if David minded me jumping in and making a few comments on the first aspect.

My research interests include the detailed structure and bioinformatics of epigenetics and gene regulation.

You’ll see that I have only addressed the question briefly and have not explained the epigenetic ‘tags’ at all. As I want Not Just DNA to be an on-going theme I feel obliged to lay out the larger scene first. This is particularly important to me as I’d like to explore the physical nature of genomes whereas the question refers only one part of this.


This entry not only delves into some good information about how epigenetics works (and combats some misinterpretations we've seen in these very forums) but also links to other articles that provide even MORE detailed coverage of the mechanisms of epigenetics and what we really know about how they work.


It's very good information to have if you're confronted with the incorrect argument that environmental factors are the cause of epigenetics. And it's fascinating stuff.

Dizfriz
10-21-13, 07:21 PM
Very good article. I do have to admit that without the reading I have been doing lately on epigenetics I would be totally lost. As it is, I was only mostly so (grin).


Thanks for posting it.

Dizfriz

Amtram
10-21-13, 07:48 PM
BTW, the Tuatara genome project (http://sciblogs.co.nz/tuataragenome/) is covered on another blog on the same site, and it's interesting to read as the work progresses. (Remember, most recent entries are at the top, so scroll down to the bottom and read up!) What is cool about this is that it explains the process of discovering a genome and how its structure is reconstructed. Closer to the top, there's information about what a transcriptome is and how they used it to build a full genome from segments of DNA. The post at the top (as of today) introduces the concept of epigenetics and how important understanding the genome is to learning about epigenetics.

Amtram
10-21-13, 08:08 PM
Another article (http://sciblogs.co.nz/code-for-life/2010/10/14/improving-screening-for-gene-regulatory-sites-using-histone-acetylation-data/) linked in the original explains the importance of transcription factors in regulating gene expression, and how that ties in with epigenetics.

There is a preview PDF (http://www.cshlpress.com/pdf/sample/epigen.pdf) from Cold Spring Harbor press that has some information about genetics versus epigenetics.

This infographic (http://images.the-scientist.com/content/images/articles/58007/epigenetics_primer.jpg) might be helpful to some of you as well, as an illustrated explanation of epigenetics.

Unfortunately, many of the links are to journals, which means $$$, but Jacobs covers a lot of the basic information in the articles in his blog entries, and does respond to specific questions if you ask for clarification.