A new study published online this week in Nature Genetics reports that a certain class of genes, those with expression restricted to a specific developmental time point, follow a different set of rules than the rest of the genome.
The modifications to histones in promoter and enhancer regions are generally predictive of gene expression. For example, when a promoter is highly methylated at lysine 4 on histone H3 (H3K4me3), its associated gene is generally highly transcribed. Other marks may also be associated with activation, while different marks are associated with gene repression.
Developmentally regulated genes show similar H3K4me3 levels to silent genes, even though they are highly expressed during development.{credit}Pérez-Lluch et al. Nat. Genet. doi: 10.1038/ng.3381{/credit}
SÍlvia Pérez-Lluch et al. examined the expression levels and histone modifications for all genes in the Drosophila modENCODE data set and identified a surprising pattern. Genes that were restricted in their expression to a specific developmental timepoint (called “developmentally regulated genes”) lacked epigenetic marks of active transcription, even when they were highly expressed. The authors confirmed the same pattern using modENCODE data for the netmatode C. elegans.
Developmentally regulated genes showed expression levels during their actively transcribed period that were similar to those of genes that are expressed stably throughout development. Another pattern identified by the authors was that strong histone marking is also associated with transcriptional stability. Comparable expression and chromatin modification data to that of the fly and worm aren’t yet available for mammals across multiple developmental timepoints. However, using data from ENCODE, the authors were able to show that mammalian cells showed a similar trend with regards to transcriptional stability.
We asked the lead authors of the study, SÍlvia Pérez-Lluch, Montserrat Corominas and Roderic Guigo to give us a little insight into the history of this study and where they see this research going in the future:
When you began this study, what were your expectations? Did you expect to find that active chromatin marks were missing from so many actively transcribed genes?
We did not. Actually, our initial aim was not to investigate the relationship between chromatin marking and transcription, but the role of histone modifications in the regulation of splicing. We designed our initial experiments to compare levels of histone modifications in exons that were differentially included between Eye-antenna and Wing imaginal discs (EID and WID)—our hypothesis at that time being that the levels of some histone modifications would correlate with differential exon inclusion between these two tissues. But the results were quite frustrating, since we did find, in general, very low levels of marking in exons that were differentially included between WID and EID. This was initially very disappointing to us. However, we also found, more generally, that many genes that were differentially expressed between WID and EID had also very low levels of a number of histone modifications typically associated to active transcription—even genes with very high expression levels. Since many such genes are likely to be regulated during development, this led us to hypothesize that lack of active histone modifications could be a general feature of developmentally regulated genes. This seemed an implausible hypothesis, going against the current models of the relationship between chromatin marking and transcription. Nevertheless, we turned to modENCODE data to further test it. The results were so strikingly consistent with our model that we “forgot” about our initial aim, and we focused our efforts instead into gathering additional supporting evidence. Understandably, our results were initially met with skepticism—the concern being that lack of chromatin marking could be a technical artifact derived from developmentally regulated genes having restricted expression patterns, and therefore making histone modifications difficult to detect using current technologies. Thus, a substantial amount of our work has been directed to address this concern.
Why do you think this pattern had not been observed before?
We are actually not the first to observe transcription with apparent lack of histone modifications. There have been a few reports of genes being transcribed in the absence of some histone modifications. Our main contribution is to show that this phenomenon is more widespread that generally assumed, and that it characterizes specifically genes that are regulated during development (at least in fly and worm). Why has this not been observed before? Mostly because data containing estimates of gene expression and histone modification along a sufficiently large number of developmental time points were not available before the modENCODE project. Then, we used a very simple, but effective measure to identify genes regulated during development, the coefficient of variation of gene expression. In summary, to make this observation you need both the data and the right approach to look at it
Your study showed that the link with transcriptional stability is also present in mammalian cells. If the association between chromatin marks and developmental regulation also holds in mammals, what, if any, do you think are the implications for biomedical research?
This is difficult to answer. Our initial results suggest that the model could be also applicable to mammals, but the data to test it are not yet available. Here we need to emphasize the importance of well-designed large-scale data production projects that monitor genome activity (transcription, chromatin structure, 3-dimensional genome organization, transcription factor binding, etc.) in a systematic and consistent way. We also want to emphasize that, at this point, our research is very basic. However, one could speculate that if our model holds in mammals, it could contribute to design better-informed approaches to manipulate/modulate expression levels of genes. Extrapolated to mammals, our results suggest that transcription factors play a comparatively more important role than histone modifications in the regulation of tissue specific genes. It has been shown that, in humans, tissue specific genes are more likely to be involved in diseases.
Are you able to speculate as to why developmentally regulated genes use a different epigenetic program compared to other genes?
What we call developmentally regulated genes correspond to genes with variable expression along time, which are often expressed only at a particular time point. Since development is a continuous process, one could speculate that rapid activation and de-activation of genes that are specific to a particular time point is more likely to occur without the need of modifying histone residues in chromatin.
What do you see as the most important next steps in this area?
Maybe the most important issue is to further challenge the model by investigating additional systems—in particular, mammalian systems—including differentiation processes, and additional histone modifications. The ultimate test of the model would come, however, from single-cell analysis, that is, from monitoring whether gene transcription does occur without histone modifications within the same cell. This is currently not possible given available technologies, but it may be feasible in the near future. It would be also important to investigate the role of distal enhancers, and of 3D chromatin structure, in the expression of developmentally regulated genes. Furthermore, we need to dig into the mechanism, by analyzing, for instance, how different classes of genes respond to perturbations of histone modification systems.
