August 21, 2012 | David F. Coppedge

Epigenetics Leads the Genetics News

More and more studies are revealing systems that regulate DNA.  Here are some recent samples.

Stress responsePhysOrg headlined, “Study finds stress triggers widespread epigenetic changes that aid in disease resistance reported.”  A study by the Salk Institute made it clear that epigenetics involves a code: “The scientists found that exposure to a pathogenic bacteria caused widespread changes in a plant’s epigenetic code, an extra layer of biochemical instructions in DNA that help control gene expression. The epigenetic changes were linked to the activity of genes responsible for coordinating a plant’s response to stress, suggesting that the epigenome may help organisms develop resistance to pathogens and other environmental stressors.

A primer on PLoS Biology, similarly, emphasized the role of chromatin in stress response (Smith & Workman, “Chromatin: Key Responders to Stress,” PLoS Biology, July 31, 2012).

Developmental switches in lampreysScience Daily reported on a study that shows that lampreys have a way of sequestering genes after their use in development to prevent re-expression.  “In effect, by undergoing programmed genome rearrangement and gene loss during embryogenesis, the sea lamprey “seals” the genes away in the small germline compartment so they cannot be misexpressed and thereby create untoward problems (such as development of cancer, for example).”  This mechanism differs from epigenetic switching in mammals.  “The strategy removes the possibility that the genes will be expressed in deleterious ways,” the article stated.  “Humans, on the other hand, must contain these genes through other ‘epigenetic’ mechanisms that are not fool-proof.”  The authors probably did not intend to convey the notion that evolution is going downhill.

Caste system:  Epigenetics may be responsible for converting ants that have the same genetic code into workers and queens – the castes in an ant colony.  “The first ant methylomes uncover the relationship between DNA methylation and caste differentiation,” PhysOrg reported.  Methylation is one epigenetic mechanism whereby genes are tagged for repression by the addition of a methyl tag.

Mobile protectionScience reported on August 3 (Vol. 337 no. 6094 pp. 529-530, DOI: 10.1126/science.1227095) that exposure to trasnposons (foreign mobile elements in DNA) triggers a response by “Piwi” proteins and piRNAs to mount an “enhanced response” to “actively repress transposons to safeguard the genetic information.”  The immediate response triggers another response by small RNAs to preserve the memory of the invasion for future generations, a kind of inheritance of acquired characteristics.  The complexity of this epigenetic response is coming to light, along with possible new functions for “junk DNA”:

Once piRNAs have managed the immediate threat of a foreign element, 22G-RNAs establish an epigenetic memory that mediates transgenerational repression. Although initiated by piRNAs, permanent silencing soon becomes independent of the Piwi pathway and is stable for generations. Consistent with an impact on transcription, the repressed target region becomes packaged with silent histone (heterochromatic) marks. Genetic screens and candidate approaches identify nuclear WAGOs, chromodomain protein, and putative histone methyltransferases, among others, as key components of the machinery required to maintain this repression over generations. The studies by Bagijn et al. and others provide a global view on how foreign elements are silenced—from the initial trigger by piRNAs, to a heritable state via 22G-RNAs. Like worm piRNAs, some mammalian Piwi proteins are invested with millions of uniquely mapping piRNAs, but with no known function. It can be envisaged that with relaxed engagement rules, these might also participate in genome surveillance.

Stem cell stemness:  Epigenetics may also play a role in keeping stem cells from differentiating until the time is right.  “In a finding that could be important to the use of all kinds of stem cells in treating disease, scientists have discovered the crucial role of a protein called Mof in preserving the ‘stem-ness’ of stem cells, and priming them to become specialized cells in mice,” PhysOrg wrote of a study at University of Michigan.  “It plays a key role in the “epigenetics” of stem cells — that is, helping stem cells read and use their DNA.”

Genome stability:  A new open-access paper in PNAS suggests that epigenetic processes contribute to stabilize the genome (Birchler and Veitia, “Gene balance hypothesis: Connecting issues of dosage sensitivity across biological disciplines,” PNAS, Aug 20, 2012, 3/pnas.1207726109).  Specialists may wish to explore the implications for evolution of the “Gene Balance Hypothesis” by Birchler and Veitia.  For example, “with a greater number of protein–protein interactions involved with macromolecular complexes, there are increasing negative fitness consequences of single gene duplication, which manifests as a stoichiometric imbalance.”

Another codePhysOrg reported (without much detail) about an “exceptional breakthrough” by an interdisciplinary team that rivals the discovery of the base-pairing genetic code of Watson and Crick: a code that determines the recognition of RNA transcripts of DNA.  It involves pentatricopeptide repeat (PPR) proteins.  “The new paper in PLOS Genetics describes for the first time how PPR proteins recognise their RNA targets via an easy-to-understand code,” the article claimed, without describing the code itself.  “This mechanism mimics the simplicity and predictability of the pairing between DNA strands described by Watson and Crick 60 years ago, but at a protein/RNA interface.”  Because of the lack of detail in this article, the claims may require further analysis; nevertheless, the word “code” clearly dominated the story.

For more on the increasing awareness of the importance of epigenetics, see our July 4, 2012 entry, “Epigenetics: the 21st Century Scientific Revolution.”

We recommend again the popular-level introduction to the subject, The Mysterious Epigenome: What Lies Beyond DNA by Woodward & Gills.

It’s interesting that few of these articles mentioned evolution.  No wonder; the discovery of regulatory codes above the already-challenging genetic code would scare any Darwinist needing to account for them.  Darwin was known to have stomach aches most of his life.  One can imagine how sick he would be to hear about the genetic code.  It would be downright cruel to then tell him about epigenetic codes.  Codes are not conducive to a healthy GI tract for those committed to unguided, materialist theories.

 

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