Despite high levels of homology, transcription coactivators p300 and CREB binding protein (CBP) are both indispensable during embryogenesis. They are largely known to regulate the same genes. To... Show moreDespite high levels of homology, transcription coactivators p300 and CREB binding protein (CBP) are both indispensable during embryogenesis. They are largely known to regulate the same genes. To identify genes preferentially regulated by p300 or CBP, we performed an extensive genome-wide survey using the ChIP-seq on cell-cycle synchronized cells. We found that 57% of the tags were within genes or proximal promoters, with an overall preference for binding to transcription start and end sites. The heterogeneous binding patterns possibly reflect the divergent roles of CBP and p300 in transcriptional regulation. Most of the 16 103 genes were bound by both CBP and p300. However, after stimulation 89 and 1944 genes were preferentially bound by CBP or p300, respectively. Target genes were found to be primarily involved in the regulation of metabolic and developmental processes, and transcription, with CBP showing a stronger preference than p300 for genes active in negative regulation of transcription. Analysis of transcription factor binding sites suggest that CBP and p300 have many partners in common, but AP-1 and Serum Response Factor (SRF) appear to be more prominent in CBP-specific sequences, whereas AP-2 and SP1 are enriched in p300-specific targets. Taken together, our findings further elucidate the distinct roles of coactivators p300 and CBP in transcriptional regulation. Show less
Antisense-mediated exon skipping is currently the most promising therapeutic approach for Duchenne muscular dystrophy (DMD). The rationale is to use antisense oligonucleotides (AONs) to hide exons... Show moreAntisense-mediated exon skipping is currently the most promising therapeutic approach for Duchenne muscular dystrophy (DMD). The rationale is to use antisense oligonucleotides (AONs) to hide exons from the splicing machinery, causing them to be skipped from the mature mRNA. Thus, the mutated, out-of-frame dystrophin transcripts as seen in DMD are reframed, allowing the generation of internally deleted, partly functional dystrophin proteins, rather than prematurely truncated, nonfunctional ones. This approach is mutation specific, so multiple AONs targeting all internal DMD exons have been designed and tested. Here, we have retrospectively compared our own set of 156 exon-internal AONs and 256 AONs as present in patents and publications from Dr. Wilton (Australia), which includes exon-internal as well as splice site-targeting AONs. Effective AONs are significantly more often exon-internal and, as anticipated, have better thermodynamic properties. Comparison of splice site and exon-internal AONs revealed that exon-internal AONs are more efficient and target more predicted exonic splicing enhancer and less predicted exon splicing silencer sites, but also have better thermodynamic properties. This suggests that exons may be better AON targets than introns per se, because of their higher GC content, which generally will result in improved AON binding. Show less
Ommen, G.J.B. van; Aartsma-Rus, A.; Putten, M. van; Thoen, P.B.; Verbeek, S.; Yilmaz, S.; ... ; Deutekom, J. van 2010
Neuromuscular disorders are a frequent cause of chronic disability in man. They often result from mutations in single genes and are thus, in principle, well suited for gene therapy. However, the... Show moreNeuromuscular disorders are a frequent cause of chronic disability in man. They often result from mutations in single genes and are thus, in principle, well suited for gene therapy. However, the tissues involved (muscle and the central nervous system) are post-mitotic, which poses a challenge for most viral vectors. In some cases, alternative approaches may use small molecules, for example, antisense oligonucleotides (AONs). These do not deliver a new gene, but rather modulate existing gene products or alter the utilization of pathways. For Duchenne muscular dystrophy, this approach is in early phase clinical trials, and for two other common neuromuscular disorders (spinal muscular atrophy and myotonic dystrophy), significant preclinical advances have recently been made. Show less
The two therapeutic approaches currently most advanced in clinical trials for Duchenne muscular dystrophy are antisense-mediated exon skipping and forced read-through of premature stop codons.... Show moreThe two therapeutic approaches currently most advanced in clinical trials for Duchenne muscular dystrophy are antisense-mediated exon skipping and forced read-through of premature stop codons. Interestingly, these approaches target the gene product rather than the gene itself. This review will explain the rationale and current state of affairs of these approaches and will then discuss how these gene-derived therapies might also be applicable to other diseases. Show less
