Junk DNA: goodbye!: another review paper (Introduction)

by David Turell , Thursday, July 16, 2015, 01:29 (3419 days ago) @ David Turell

Further evidence from research that ENCODE is correct that most of DNA has some function, even if we do not know them all as yet:-http://www.salvomag.com/new/articles/salvo32/the-encode-embroilment-part-II.php-"The fact that DNA transcription is immense—and nonrandom—was confirmed in a 2013 paper that studied RNA transcripts in yeast. It found that while the yeast genome contains only about 6,000 genes, there were over 1.8 million unique RNA transcripts, which were "arranged in a remarkably complex, overlapping pattern across the genome."-***-"ENCODE's results suggest that a cell's type and functional role in an organism are critically influenced by complex and carefully orchestrated patterns of expression of RNAs inside that cell. As Stamatoyannopoulos observes, ENCODE found that "the majority of regulatory DNA regions are highly cell type-selective," and "the genomic landscape rapidly becomes crowded with regulatory DNA as the number of cell types" studied increases.7 Thus, as two pro-ENCODE biochemists explain, "Assertions that the observed transcription represents random noise . . . is more opinion than fact and difficult to reconcile with the exquisite precision of differential cell- and tissue—specific transcription in human cells."-***-"In marked contrast to the prevailing wisdom, ENCODE chromatin and transcription studies now suggest that a large number of transposable elements encode highly cell type-selective regulatory DNA that controls not only their own cell-selective transcription, but also those of neighboring genes. Far from an evolutionary dustbin, transposable elements appear to be active and lively members of the genomic regulatory community, deserving of the same level of scrutiny applied to other genic or regulatory features.-***-"More of the human genome sequence appears to be used for some reproducible, biochemically defined activity than was previously imagined. Contrary to the initial expectations of many, the overwhelming majority of these activities appear to be state-specific—either restricted to specific cell types or lineages, or evokable in response to a stimulus. . . . Biochemical signatures of many ENCODE-defined elements exhibit complex trans-cellular patterns of activity. . . . Together, these observations suggest that the genome may, in fact, be extensively multiply encoded—i.e., that the same DNA element gives rise to different activities in different cell types.-***
"Finally, transcription doesn't just happen by accident. It can't start without special stretches of DNA, called promoter sequences, which bind to special enzymes called transcription factors (TFs). And just any enzyme won't do—TFs must be able to recognize the specific DNA promoter sequence that they're keyed to unlock for transcription. Without that precise biochemical correspondence, transcription can't occur. Once the right TFs bind to a promoter sequence, a molecular machine called RNA polymerase can then find the right place on the DNA to start converting the genomic message into a strand of RNA. The fact that the vast majority of the genome is transcribed suggests that these specified molecules—DNA promoter sequences and TFs—exist and are carefully matched throughout the genome. If all that RNA is junk, why do these innumerable specified molecules exist throughout our cells? "