Ignoring top-down causation

Dosage compensation can buffer copy-number variation in wild yeast

Susumu Ohno proposed over 40 years ago that gene duplication could provide a major force in the evolution of new gene functions, by relaxing constraint on gene sequences and allowing one or both gene copies to evolve (Ohno, 1970). The genomic era has largely borne out that hypothesis, and many studies have characterized the outcomes of whole and partial genome amplification (Jaillon et al., 2009). The immediate consequence of duplication is assumed to be increased expression of the affected genes, and in some cases the increased expression provides a selective advantage (e.g., Sandegren and Andersson, 2009; Chang et al., 2013; Edi et al., 2014). Over longer periods, the relaxed constraint afforded by functional redundancy allows one or both gene copies to evolve (Ohno, 1970), driving sub- and neo-functionalization (Lynch and Force, 2000; Lynch et al., 2001), expression divergence (Gu et al., 2004, 2005; Li et al., 2005; Wang et al., 2012), and network rewiring (Presser et al., 2008; Freschi et al., 2011; De Smet and Van de Peer, 2012).

Local chromatin environment of a Polycomb target gene instructs its own epigenetic inheritance

Epigenetic memory can be stored in the concentrations of diffusible regulatory factors that are maintained through feedback loops (trans memory) (Novick and Weiner, 1957; Ptashne, 2004; Zacharioudakis et al., 2007 ; Xu et al., 2009). Alternatively, memory could be stored locally in the chromatin environment of individual genes (cis memory), in the form of DNA methylation or post-translational modifications of histones (Moazed, 2011). While in both trans and cis memory the chromatin state is inherited, in the former case chromatin responds to the transcriptional state defined by heritable concentrations of the trans-factors, whereas in the latter case it is the local chromatin environment that instructs its own inheritance and is, therefore, the key epigenetic memory element.
My comment: The local chromatin environment links the epigenetic landscape to the physical landscape of DNA via nutrient-dependent pheromone-controlled feedback loops in species from microbes to man.
The mechanism by which one signaling pathway regulates a second provides insight into how cells integrate multiple stimuli to produce a coordinated response.
Abstract excerpt:
These studies reveal a complex interplay between reproduction and other functions in which GnRH neurons appear to integrate information from multiple sources and modulate a variety of brain functions.

Minimally, this model can be compared to any other factual representations of epigenesis and epistasis for determination of the best scientific ‘fit’.


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