The role of site accessibility in microRNA target recognition

Currently, most microRNA predictors perform so poorly that it was easy to assume that secondary structure formation has a more important role in target recognition, instead of relying in sequence complementarity alone. To further evaluate this hypothesis, this group previously reported the development of a quantitative (luminiscent) assay for measuring repression by microRNAs, and here they employed this methodology over a selection of targets that were engineered for specific sequence mutations. These in vitro (cell culture) observations were used to train an in silico model, which they implemented into a new predictor, available from their website.

[...] Our results show that site accessibility is as important as sequence match in the seed for determining the efficacy of microRNA- mediated translational repression, and they suggest that effective microRNA binding also requires unpairing of the local region flanking the target. We introduce a parameter-free thermodynamic model that explains these effects and shows that preferential positioning of microRNA target sites in regions of high accessibility is a conserved feature in genomes. Our findings thus indicate that the thermodynamics of intra- and intermolecular base pairing account for a significant portion of the microRNA- target interaction, consistent with observations for siRNA- target interactions. However, our model does not explain the entire variance in our experiments. This may be in part due to limitations of RNA structure prediction algorithms and their inability to account for the effects that RNA binding proteins have on secondary structures. Moreover, microRNAs bind as part of the RISC complex, [... and] RISC proteins are likely to constrain base-pairing interactions between microRNA and target site and otherwise influence the mechanics of the duplex formation.

Kertesz M. et al. 2007. Nat Genet 39:1278-84

epigenetics


More comments can be found in the same issue of Nature Genetics.

Periodic epi-organization of the yeast genome revealed by the distribution of promoter sites

Some studies of the chromatin structure have revealed that particular chromosome regions are compartmentalized in some areas of the nucleus, as is the case for nucleoli; other similar phenomena of regional specialization is the case of the centrosomal and nucleolar polarity, and it is very likely that these spatial arrangements must have an influence over gene expression regulation. In this paper, Kepes analyzed the transcriptional organization of Saccharomyces and found periodicity between the location of protein binding sites. He used ChIP data from several transcription factors, like Rap1p, and noticed regularities in distances between the targets from the same chromosome; for example, in the chromosome IX, Rap1p targets were spaced by ~31 kb. Data used from different ChIP experiments in different labs showed the same regularity. Other proteins analyzed showed also specificity in their preferred periods, different for each chromosome. To validate these model and to evaluate if this results have an impact on other cellular processes, Kepes analyzed the distribution of the ARS sequences -and these were distributed in a regular manner for each independent chromosome as well. Periodicity was not an artifact of the ChIP experiments, because lowering the stringency only produced loss of signal. These results not only provide a way to discriminate ChIP results, using spacing distances from the same chromosome, but also establish a link between spatial arrangement and expression regulation:

Relative positions of clusters of coregulated genes (Kepes/JMB)

[..] This concept also accounts for the optimization of gene control by several regulators, despite combinatorial intricacy, through target assignment to a cluster positioned for the correct set of regulators. It solves the paradox of the high efficiency of DNA-related processes despite extreme DNA compaction, as compaction now appears to be partly achieved by a dynamic epi-organization that actually increases transcriptional, replicational and perhaps recombinational efficiencies. Finally, it provides a framework to understand why yeast “heterochromatin barriers” that block the spread of transcriptionally silent chromatin consist of multiple binding sites for various regulators

Dr.Kepes recently gave a conference here at the MPI entitled "The solenoidal model of chromosomes", which motivated to read more about his work.

Kepes, F. 2003. J Mol Biol 329(5):859-65

epigenetics