Comprehensive human epigenome map completed

_{Denyse O'Leary

November 21, 2016

Epigenetics, Intelligent Design, News}

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methylated DNA molecule/Christoph Bock/CeMM

Comprehensive for now. From ScienceDaily:

One of the great mysteries in biology is how the many different cell types that make up our bodies are derived from a single cell and from one DNA sequence, or genome. We have learned a lot from studying the human genome, but have only partially unveiled the processes underlying cell determination. The identity of each cell type is largely defined by an instructive layer of molecular annotations on top of the genome — the epigenome — which acts as a blueprint unique to each cell type and developmental stage.

Unlike the genome the epigenome changes as cells develop and in response to changes in the environment. Defects in the factors that read, write, and erase the epigenetic blueprint are involved in many diseases. The comprehensive analysis of the epigenomes of healthy and abnormal cells will facilitate new ways to diagnose and treat various diseases, and ultimately lead to improved health outcomes.

A collection of 41 coordinated papers now published by scientists from across the International Human Epigenome Consortium (IHEC) sheds light on these processes, taking global research in the field of epigenomics a major step forward. Paper. (public access) – Matthias Farlik et al., DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation. Cell Stem Cell, 2016; DOI: 10.1016/j.stem.2016.10.019 More.

These days, genetic fundamentalism is out looking for a job.

Oh and, while we are here, this just hit the news inbox, from Columbia U:

http://newsroom.cumc.columbia.edu/blog/2016/09/06/pioneers-epigenetics-awarded-horwitz-prize/

NEW YORK, NY (September 6, 2016)—Columbia University will award the 2016 Louisa Gross Horwitz Prize to Howard Cedar, PhD, and Aharon Razin, PhD, of the Hebrew University of Jerusalem, and Gary Felsenfeld, PhD, of the National Institutes of Health, for their fundamental work on how molecules can regulate the structure, behavior, and activity of DNA without modifying its genetic code. Their research, which has yielded key insights into how cells and embryos develop, led to the formation of the field of biology called epigenetics.

The Horwitz Prize, first awarded in 1967, is Columbia University’s top honor for achievement in biological and biochemical research. Forty-three Horwitz Prize awardees have gone on to win Nobel Prizes. More.

See also: Epigenetics: Teen binge drinking may affect their own kids’ development later

Epigenetics: Aeon writer says Darwin’s theory is “incomplete”

and

Epigenetic change: Lamarck, wake up, you’re wanted in the conference room!

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Interesting. This is the link to the IHEC portal, where the data collection is hosted: http://epigenomesportal.ca/ihec/gpuccio_{November 22, 2016
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of note:
Beyond the DNA: Comprehensive map of the human epigenome completed - November 17, 2016 Source: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences Summary: Scientists have established comprehensive maps of the human epigenome, shedding light on how the body regulates which genes are active in which cells. Over the last five years, a worldwide consortium of scientists has established epigenetic maps of 2,100 cell types. https://www.sciencedaily.com/releases/2016/11/161117150743.htm
a little background:
Junk No More: ENCODE Project Nature Paper Finds “Biochemical Functions for 80% of the Genome” – Casey Luskin – September 5, 2012 Excerpt: The Discover Magazine article further explains that the rest of the 20% of the genome is likely to have function as well: “And what’s in the remaining 20 percent? Possibly not junk either, according to Ewan Birney, the project’s Lead Analysis Coordinator and self-described “cat-herder-in-chief”. He explains that ENCODE only (!) looked at 147 types of cells, and the human body has a few thousand. A given part of the genome might control a gene in one cell type, but not others. If every cell is included, functions may emerge for the phantom proportion. “It’s likely that 80 percent will go to 100 percent,” says Birney. “We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful.”” ,,, under an intelligent design paradigm, none of this is surprising. In fact, it is exactly what ID predicted. http://www.evolutionnews.org/2012/09/junk_no_more_en_1064001.html Why Are Biologists Lashing Out Against Empirically Verified Research Results? – Casey Luskin July 13, 2015 Excerpt: the “vast majority” of the human genome shows biochemical function: “These data enabled us to assign biochemical functions for 80 percent of the genome, in particular outside of the well-studied protein-coding regions.”3 Ewan Birney, ENCODE’s lead analyst, explained in Discover Magazine that since ENCODE studied 147 types of cells, and the human body has a few thousand cell types, “it’s likely that 80 percent will go to 100 percent.”4 Another senior ENCODE researcher noted that “almost every nucleotide is associated with a function.”5 A headline in Science declared, “ENCODE project writes eulogy for junk DNA.”6,,, Evolutionists Strike Back Darwin defenders weren’t going to take ENCODE’s data sitting down.,,, How could they possibly oppose such empirically based conclusions? The same way they always defend their theory: by assuming an evolutionary viewpoint is correct and reinterpreting the data in light of their paradigm–and by personally attacking, (i.e. ad hominem), those who challenge their position.,,, http://www.evolutionnews.org/2015/07/the_encode_embr097561.html Toppling Another Evolutionary Icon, ENCODE Suggests Endogenous Retroviruses Are Functional – Casey Luskin – September 7, 2015 Excerpt: ENCODE didn’t merely study the genome to determine which DNA elements are biochemically active and making RNA. It also studied patterns of biochemical activity, uncovering highly non-random patterns of RNA production–patterns which indicate that these vast quantities of RNA transcripts aren’t junk…. 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. 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.” http://www.evolutionnews.org/2015/09/toppling_anothe099111.html
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