Food, toxins, and stress can all have enormous effects on the epigenome, but pinning down the true epigenetic mechanisms at work is the tricky part. While it’s been difficult to determine mechanisms of action in standard animal models, new ones have been developed using Tetracyline-induced systems, that make it much simpler to tease out how specific heritable epigenetic changes behave.

Dr. Tian Chi and his colleagues at Yale established “a unique animal model where heritable epigenetic changes can be introduced into specific target genes using a tetracycline-controlled gene regulatory system.” This enabled them “to dissect various parameters potentially affecting the inheritability of environmentally induced epigenetic changes” by being able to epigenetically modify any gene at any developmental stage.

“Conventional animal models of environmental epigenetics involve natural environmental factors that have pleiotropic effects on the epigenome, which hampers mechanistic studies. Thus, if a gene is found, for example, to be heritably methylated following an acute exposure, it would be unclear” what the true mechanisms of inheritance are, says Chi.

As Chi explains, the confusion is in part because “there are two types of signals that direct epigenetic inheritance. The cis-signals are based on self-perpetuating chromatin marks, while trans-signals are based on self-perpetuating diffusible molecules such as transcription activators capable of self-sustaining expression through feedback loops”. It is thus unclear if the inheritance of the above-mentioned DNA methylation is due to a self-templating effect of CpG methylation (a cis-signal), the self-sustaining overexpression of a DNA methylase (a trans-signal), or both.

The Yale scientists deployed their new model and chose to focus on the cis-acting mechanism. Here’s what they found:

“Chromatin lesions introduced at the right time during fetal development tend to persist into adulthood (at least in the tissues examined), regardless of the DNA sequence or location of the target genes, or the nature of the chromatin modifications.” Chi elaborated, “Thus, it seems that you can induce mitotically heritable chromatin lesions of any type anywhere in the fetal epigenome, as long as the lesion is introduced at the right time during embryogenesis. The data demonstrate that the fetal epigenome is far more malleable than previously assumed. In contrast, the adult epigenome is much more resilient.”

Chi elaborated, “Thus, it seems that you can induce mitotically heritable chromatin lesions of any type anywhere in the fetal epigenome, as long as the lesion is introduced at the right time during embryogenesis. The data demonstrate that the fetal epigenome is far more malleable than previously assumed. In contrast, the adult epigenome is much more resilient.” “It is well known that when transgenes are integrated into heterochromatic loci, they can get silenced through DNA methylation, and in some cases, the silencing is transgenerationally heritable.” Chi noted his team’s surprise “that when transgenes are integrated into the Col1a1 locus, they do not get silenced (or activated), but chromatin lesions at the transgenes, induced by tetracycline during embryogenesis, are heritable transgenerationally. Importantly, not only is DNA methylation heritable, but also are activating histone modifications. Such a locus has never been reported before, which suggests a novel mechanism of epigenetic inheritance.”

In terms of the big picture, Chi feels that “Our data show the tetracycline-based system can generate mechanistic insights difficult to obtain with conventional models of epigenetic inheritance. The limitation here is that you have to engineer DNA binding sites into target genes, which is tedious. Now, with the Cas9-based system, (currently being developed for future studies), we can manipulate the epigenetic states of endogenous genes using small guide RNAs without genetically modifying the genes, making it possible to apply our basic strategy at a much larger scale.”

Chi and team conclude, “Thus, in our inducible animal models, mitotic inheritance of epigenetic perturbation seems critically dependent on the timing of the perturbation, whereas transgenerational inheritance additionally depends on the location of the perturbation. In contrast, other parameters examined, particularly the chromatin modification pattern and DNA sequence appear irrelevant.” Moving forward, Chi further expands, “We have used the tetracycline system to probe the mode of action of the cis-signals, but the system is also applicable to trans-signals, which we are working on.”

Check out the epigenetic mechanisms of your inner child over at Development, October 2013.