The epigenetic signature of CFTR expression is co-ordinated via chromatin acetylation through a complex intronic element

Abstract

The CFTR (cystic fibrosis transmembrane conductance regulator) gene is a tightly regulated and differentially expressed transcript in many mucosal epithelial cell types. It appears that DNA sequence variations alone do not explain CFTR-related gastrointestinal disease patterns and that epigenetic modifiers influence CFTR expression. Our aim was to characterize the native chromatin environment in cultured cells for intestinal CFTR expression by determining the relationship between histone acetylation and occupation of CFTR by multiple transcription factors, through a common regulatory element. We used HDAC (histone deacetylase) inhibition and ChIP (chromatin immunoprecipitation) analyses to define regions associated with acute acetylation of histone at the CFTR locus. We identified a region within the first intron associated with acute acetylation of histone H4 as an epigenetic signature corresponding to an intestinespecific enhancer element for CFTR. DHS (DNase I-hypersensitivity) assays and ChIP were used to specify control elements and occupation by regulatory factors. Quantitative ChIP procedures indicate that HNF1α (hepatic nuclear factor 1α) and Cdx2 (caudal homeobox protein 2) occupy and regulate through a novel intronic enhancer element of CFTR and that Tcf4 (T-cell factor 4) overlaps the same DNA element. RNAi (RNA interference) of Tcf4 and HNF1α decreased intestinal cell CFTR expression, identifying these as positive regulatory factors and CFTR as a target for Wnt signalling. We have linked the acetylation signature of nucleosomal histones to active intestinal CFTR expression and occupation by transcription factors HNF1α, Cdx2 and Tcf4 which converge to modify chromatin architecture. These studies suggest the therapeutic potential of histone modification strategies, such as inhibition of HDAC activity, to treat CFTR-associated disease by selectively enhancing CFTR expression.

Histone Deacetylase: A Potential Therapeutic Target for Fibrotic Disorders

“…Mechanistic studies have shown that the activation of intestinal CFTR by histone acetylation was mediated by transcription factors hepatic nuclear factor 1␣, Cdx2, and Tcf4, which converge to modify chromatin architecture. These studies suggest a therapeutic potential for inhibition of HDAC activity in increasing CFTR expression (Paul et al, 2007).…”

A balance between activating and repressive histone modifications regulatescystic fibrosis transmembrane conductance regulator (CFTR) expression in vivo

“…3,7,18 Conversely, CFTR transcription was suppressed by repressors that were associated with HDAC activities. 18 The present work shows that similar dynamic changes of histone acetylation occur in regulatory sequences of CFTR in human tissues.…”

“…2). [7][8][9][10][11] We analyzed whole blood cells and tissue samples from pancreas, colon, and lung. Samples were collected in three healthy adult donors.…”

“…[15][16][17] Moreover, most of the factors that either activate or repress CFTR transcription are associated with HATs (Histone acetyltransferases) and HDACs (Histone deacetylases), respectively. 7,18 Since epigenetic modifications are profoundly altered by cell culture, we addressed the regulation of CFTR in a physiological context by analyzing human tissues from non-cystic fibrosis donors. To detect developmental changes, we compared fetal and adult tissues.…”

“…2,3 Critical sequences have been identified in the promoter of CFTR, such as CArG-like and CCAATlike elements and a variant AMPc response element (CRE). [4][5][6][7] Promoter regulatory sequences bind ubiquitously-expressed factors that either activate or repress transcription. 2 Long-distance cis-regulatory sequences interact with the CFTR promoter via a looping mechanism and bind trans-activating factors that are expressed in a restricted number of tissues.…”