The Holly and the I.D. – News from Epigenetics

Holly leaf shape may be due to epigenetic control – one of several recent developments in the field of epigenetics.

Epi-Deck the Halls:  National Geographic reported that the prickly outline of holly leaves appears to be an epigenetic response to predation.  The same plant can have smooth leaves and prickly leaves.  Browsing by animals sets off an epigenetic response, leading to the prickly outline, even though each leaf cell has the same genetic code.

Sex cells:  A protein named Tet that erases epigenetic markers may be responsible for turning on the meiotic genes that switch regular cells into sperm or eggs, reported Nature on Dec. 20.

Gene accessibility:  A paper in the journal Cell (Hihara et al., Dec. 13) found that local chromatin dynamics, including Brownian motion, plays a role in the accessibility of molecular machines to stretches of DNA.  “We propose that this local nucleosome fluctuation is the basis for scanning genome information,” the authors said.

Large-scale organization:  Another research article in Cell (Sandhu et al., Oct 25) discussed “Large-Scale Functional Organization of Long-Range Chromatin Interaction Networks.”   These networks play important roles in transcription regulation.  They are organized into “nonrandom spatial clustering” the authors dub”rich clubs,” communities and spokes.  This large-scale organization helps repress mutations among vital genes, and “shapes functionally compartmentalized and error-tolerant transcriptional regulation of human genome in three dimensions.”

Add another dimension: Speaking of 3-D, a paper in Science today (Dec 21) discussed alternative splicing in 4 dimensions.  Alternative splicing “leads to different patterns of splicing that represent cell type–specific alternative interpretations of the genomic information,” the authors said.  “Alternative splicing allows the shuffling of protein-coding domains or confers distinct sensitivity of the spliced mRNAs to regulatory factors.” Though evolutionary in tone, the article’s science concerned “modulating the scope of signaling, gene regulation, and protein-protein networks” that speak of organization and control.

The paper they referenced in the same issue of Science by Barbosa-Morais et al. was also evolutionary, but the actual data do not require a common ancestry interpretation, especially since it concerned “vertebrate splicing codes.”  The overall finding was that “overall organ AS [alternative splicing] profiles more strongly reflect the identity of a species than they do organ type.”  For more on alternative splicing, see a PhysOrg entry, “Alternative splicing of RNA rewires signaling in different tissues, may contribute to species differences.”

Epigenetic islands:  In Nature on Nov. 9, Dirk Schübeler discussed “Epigenetic Islands in a Genetic Ocean.”  He talked about the latest discoveries in methylation patterns: “This inheritability makes DNA methylation highly attractive as a potential means to store information in a form of epigenetic memory that regulates genes over developmental processes or in response to environmental conditions.”

Not parasites:  In a Presidential Address in Science Nov 9, Nina V. Federoff debunked the idea that transposable elements (TE) are parasites on the genome.  TE’s comprise more than half of many mammalian genomes and were thought to be junk or selfish invaders:

My purpose here is to challenge the current, somewhat pejorative, view of TEs as genomic parasites with the mounting evidence that TEs and transposition play a profoundly generative role in genome evolution. I contend that it is precisely the elaboration of epigenetic mechanisms from their prokaryotic origins as suppressors of genetic exchanges that underlies both the genome expansion and the proliferation of TEs characteristic of higher eukaryotes. This is the inverse of the prevailing view that epigenetic mechanisms evolved to control the disruptive potential of TEs. The evidence that TEs shape eukaryotic genomes is by now incontrovertible. My thesis, then, is that TEs and the transposases they encode underlie the evolvability of higher eukaryotes’ massive, messy genomes.

Systems biology meets epigenetics:  PhysOrg reported that some Swiss scientists are making progress understanding the interplay of epigenetic interactions with a systems biology approach.  Combining both approaches with a computational model is providing insights into concepts like how a stem cell differentiates into a tissue cell, or how chromatin modifications affect gene expression.

Epigenetics is proving to be a fruitful field for research, possibly as fruitful (or more so) than the discovery of the genetic code itself.  As stated earlier (8/21/2012, 9/06/2012), it involves “codes upon codes” explaining how a human being can develop from a small set of genes through regulation, alternative splicing and post-transcriptional modifications.  The proliferation of codes is inversely proportional to the credibility of Darwinism.