Junk DNA: goodbye!: more and more papers (Introduction)

by David Turell , Thursday, May 14, 2015, 01:04 (3269 days ago) @ David Turell

It really is disappearing. At least 80% is not junk, and although these areas do not code, they control gene expression. They run the genes:-http://theconversation.com/explainer-microrna-the-puppet-master-of-the-genome-39641-"For biologists, those important emails that slipped into the junk mail folder and were disregarded were miRNAs. That was until the first functional miRNA, lin-4, was officially discovered in 1993. Scientists were looking at the development of the nematode worm, Caenorhabditis elegans, and found that lin-4 inhibited protein synthesis of the lin-14 gene.-"They subsequently found that miRNA can physically bind to mRNA and stop it creating proteins. Thus it effectively suppresses the activity of a gene. This discovery was the first evidence of miRNA negatively regulating RNA coding for proteins.-"So, it turns out that the 98% of our genome that was regarded as “junk” might have a function after all.-"The second miRNA was not discovered for another seven years. But since then, more than 1,800 human miRNAs have been found. We now understand that miRNA control numerous genes and processes vital for cellular life such as metabolism, development and the immune system"-And from the 'junk' silencing function:-http://www.sciencemag.org/content/348/6230/41.summary-"All molecular machines have imperfections, and the biological ones are no exception. One type of flaw is a quantitative one: Although all the cells within an organ are genetically identical, the concentrations of many of their proteins can be “noisy”—that is, vary and fluctuate between all the cells. Biologists decompose such noise into two sources: an intrinsic one, which results from the stochastic nature of the biochemistry operating within cells, and an extrinsic one that manifests global differences between cells, such as the number of protein production facilities (e.g., ribosomes) (1). A major question is whether organisms have evolved means to control noise, especially when imprecisions are detrimental. On page 128 in this issue, Schmiedel et al. (2) report combining mathematical modeling and a synthetic gene approach to establish a complex role for microRNAs (miRNAs) in controlling cellular protein content. "-Abstract:
"MicroRNAs (miRNAs) repress the expression of many genes in metazoans by accelerating messenger RNA degradation and inhibiting translation, thereby reducing the level of protein. However, miRNAs only slightly reduce the mean expression of most targeted proteins, leading to speculation about their role in the variability, or noise, of protein expression. We used mathematical modeling and single-cell reporter assays to show that miRNAs, in conjunction with increased transcription, decrease protein expression noise for lowly expressed genes but increase noise for highly expressed genes. Genes that are regulated by multiple miRNAs show more-pronounced noise reduction. We estimate that hundreds of (lowly expressed) genes in mouse embryonic stem cells have reduced noise due to substantial miRNA regulation. Our findings suggest that miRNAs confer precision to protein expression and thus offer plausible explanations for the commonly observed combinatorial targeting of endogenous genes by multiple miRNAs, as well as the preferential targeting of lowly expressed genes. "-New book I've mentioned, Nessa Carey's "Junk DNA":-http://www.evolutionnews.org/2015/04/a_new_book_on_j095611.html-"Don't miss that last line: "The whole organization only works when all the components are in place. And so it is with our genomes." Doesn't that sound exactly like irreducible complexity? So here we have a biologist, unaffiliated with the intelligent-design community, arguing that junk DNA must be functional because it's like a car factory where all the components are needed in order for the entire system to function. Critics might claim that ID has had no impact on biological thinking, but the evidence shows otherwise."