Posted: May 18, 2014 2:04 pm
by DavidMcC
Rumraket wrote:Relatedly:
http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004351
The Case for Junk DNA
Alexander F. Palazzo , T. Ryan Gregory

Overview

With the advent of deep sequencing technologies and the ability to analyze whole genome sequences and transcriptomes, there has been a growing interest in exploring putative functions of the very large fraction of the genome that is commonly referred to as “junk DNA.” Whereas this is an issue of considerable importance in genome biology, there is an unfortunate tendency for researchers and science writers to proclaim the demise of junk DNA on a regular basis without properly addressing some of the fundamental issues that first led to the rise of the concept. In this review, we provide an overview of the major arguments that have been presented in support of the notion that a large portion of most eukaryotic genomes lacks an organism-level function. Some of these are based on observations or basic genetic principles that are decades old, whereas others stem from new knowledge regarding molecular processes such as transcription and gene regulation.


The junk-DNA concept IS NOT AN ARGUMENT FROM IGNORANCE.

Indeed, not!
AFAIK, the main category of "junk DNA" refers to sequences that make up the chromatin "packaging" that wraps round the actual genes most of the time. This has the important function of helping to prevent "accidental" gene expression. Genes can only be expressed after the chromatin around them has "fluffed up". This should be seen as funtional DNA, even though it is not active in terms of translating into any RNA, because it could easily be fatal to a multicellular organism if any particular cell expresses any inappropriate genes at a significant level. Thus, "junk DNA" is a misnomer in any case, and should have been abandoned long ago, perhaps in favour of something like "permanently silent DNA", or whatever.