Transcriptional and epigenetic analyses of the DMD locus reveal novel cis ‑acting DNA elements that govern muscle dystrophin expression

Abstract

The dystrophin gene (DMD) is the largest gene in the human genome, mapping on the Xp21 chromosome locus. It spans 2.2Mb and accounts for approximately 0,1% of the entire human genome. Mutations in this gene cause Duchenne and Becker Muscular Dystrophy, X-linked Dilated Cardiomyopathy, and other milder muscle phenotypes. Beside the remarkable number of reports describing dystrophin gene expression and the pathogenic consequences of the gene mutations in dystrophinopathies, the full scenario of the DMD transcription dynamics remains however, poorly understood. Considering that the full transcription of the DMD gene requires about 16h, we have investigated the activity of RNA Polymerase II along the entire DMD locus within the context of specific chromatin modifications using a variety of chromatin-based techniques. Our results unveil a surprisingly powerful processivity of the RNA polymerase II along the entire 2.2Mb of the DMD locus with just one site of pausing around intron 52. We also discovered epigenetic marks highlighting the existence of four novel cis‑DNA elements, two of which, located within intron 34 and exon 45, appear to govern the architecture of the DMD chromatin with implications on the expression levels of the muscle dystrophin mRNA. Overall, our findings provide a global view on how the entire DMD locus is dynamically transcribed by the RNA pol II and shed light on the mechanisms involved in dystrophin gene expression control, which can positively impact on the optimization of the novel ongoing therapeutic strategies for dystrophinopathies.

A novel member of Prame family, Gm12794c, counteracts retinoic acid differentiation through the methyltransferase activity of PRC2

“…inhibitor GSK126 [49] abolished Gm12794c repressive effects demonstrating that functional PRC2 complex is required for the Gm12794c-mediated p21/Cdkn1A transcriptional repression (Fig. 5c).…”

mRNA in situ hybridization exhibits unbalanced nuclear/cytoplasmic dystrophin transcript repartition in Duchenne myogenic cells and skeletal muscle biopsies

“…RNA pol II can enter a paused or stalled status immediately downstream of the transcription start site before productive elongation occurs. Therefore, we suggested that this region is crucial for dystrophin transcriptional dynamics 23 .…”

“…Interestingly, we found differences in DMD cells depending on mutations. DMD patients’ cells carrying a deletion which includes exon 52 showed a very reduced DMD transcript, possibly related to the role of intron 52 regions in the chromatin shape which regulates DMD transcription 23 . Indeed, we previously reported a unique pausing site of RNA pol II in intron 52, which is almost invariably the site of breakpoint in exon 52 deletions.…”

249th ENMC International Workshop: The role of brain dystrophin in muscular dystrophy: Implications for clinical care and translational research, Hoofddorp, The Netherlands, November 29th–December 1st 2019

“…Very little is known about DMD locus epigenetics. A few studies demonstrated the presence of regions of open chromatin structures, which may have still unravelled regulatory roles [15] . Finally, it should not be forgotten that the DMD gene is an onco-suppressor gene, acting either in myogenic cancers but also in brain cancer types [16] .…”