Junk DNA: goodbye!: ENCODE now hedging on 80% (Introduction)

by David Turell , Saturday, January 02, 2016, 23:52 (3248 days ago) @ dhw
edited by David Turell, Saturday, January 02, 2016, 23:59

A review article by the authors of ENCODE is now saying that some of the biochemically functional areas may not result in gene produced results:-http://www.pnas.org/content/111/17/6131-"Abstract:-"With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. As a complement to genetic and comparative genomics approaches, the Encyclopedia of DNA Elements Project was launched to contribute maps of RNA transcripts, transcriptional regulator binding sites, and chromatin states in many cell types. The resulting genome-wide data reveal sites of biochemical activity with high positional resolution and cell type specificity that facilitate studies of gene regulation and interpretation of noncoding variants associated with human disease. However, the biochemically active regions cover a much larger fraction of the genome than do evolutionarily conserved regions, raising the question of whether nonconserved but biochemically active regions are truly functional. Here, we review the strengths and limitations of biochemical, evolutionary, and genetic approaches for defining functional DNA segments, potential sources for the observed differences in estimated genomic coverage, and the biological implications of these discrepancies. We also analyze the relationship between signal intensity, genomic coverage, and evolutionary conservation. Our results reinforce the principle that each approach provides complementary information and that we need to use combinations of all three to elucidate genome function in human biology and disease."-Their conclusion:-"In contrast to evolutionary and genetic evidence,biochemical data offer clues about
both the molecular function served by underlying DNA elements and the cell types
in which they act, thus providing a launching point to study differentiation and development,cellular circuitry, and human disease (14, 35, 69, 111, 112). The major
contribution of ENCODE to date has been high-resolution, highly-reproducible maps of
DNA segments with biochemical signatures associated with diverse molecular functions.
We believe that this public resource is far more important than any interim estimate
of the fraction of the human genome that is functional.-"By identifying candidate genomic elements and placing them into classes with shared
molecular characteristics, the biochemical maps provide a starting point for testing
how these signatures relate to molecular,cellular, and organismal function. The data
identify very large numbers of sequence elements of differing sizes and signal strengths. Emerging genome-editing methods should considerably increase the
throughput and resolution with which these candidate elements can be evaluated
by genetic criteria. Given the limitations of our current understanding of genome function,future work should seek to better define genome elements by integrating all three methods to gain insight into the roles they play in human biology and disease."-Comment: The resulting function of 'active' areas, being still unknown, it is best not to conclude that non-junk is up to 80%. The percent may be less and needs more research. Honest hindsight.