GLI transcriptional repression regulates tissue-specific enhancer activity in response to Hedgehog signaling

Abstract

Transcriptional repression needs to be rapidly reversible during embryonic development. This extends to the Hedgehog pathway, which primarily serves to counter GLI repression by processing GLI proteins into transcriptional activators. In investigating the mechanisms underlying GLI repression, we find that a subset of GLI binding regions, termed HH-responsive enhancers, specifically loses acetylation in the absence of HH signaling. These regions are highly enriched around HH target genes and primarily drive HH-specific transcriptional activity in the mouse limb bud. They also retain H3K27ac enrichment in limb buds devoid of GLI activator and repressor, indicating that their activity is primarily regulated by GLI repression. Furthermore, the Polycomb repression complex is not active at most of these regions, suggesting it is not a major mechanism of GLI repression. We propose a model for tissue-specific enhancer activity in which an HDAC-associated GLI repression complex regulates target genes by altering the acetylation status at enhancers.

Disruption of a Hedgehog-Foxf1-Rspo2 signaling axis leads to tracheomalacia and a loss of Sox9+ tracheal chondrocytes

“…We next examined published ChIP-seq data to examine whether Rspo2 , Notum , Wnt4 and Wnt11 were likely to be direct target genes of Gli and Foxf1 transcription factors. We used previously published Gli3-3xFlag ChIP from E10.5 limb buds and Foxf1 ChIP from E18.5 lungs ( Dharmadhikari et al, 2016 ; Lex et al, 2020 ); these datasets are the most similar to tracheal chondrocytes currently available. We also examined previously published ATAC-seq and H3K4me3 ChIP-seq performed in the E9.5 cardiopulmonary foregut progenitors to help identify active promoter and enhancer regions ( Steimle et al, 2018 ).…”

“…ChIP-Seq analysis was performed on the following published datasets: (1) Foxf1 ChIP on dissected E18.5 lung ( , Dharmadhikari et al, 2016 ); (2) Gli3-3xFlag ChIP on dissected E10.5 limb buds ( , Lex et al, 2020 ); and (3) ATAC-seq and H3K4me3 ChIP performed on E9.5 cardiopulmonary progenitors ( , Steimle et al, 2018 ). These datasets were reprocessed using CSBB, and for visualization purposes, bigwig files were generated using deepTools (BamCoverage function) ( Ramírez et al, 2016 ) from bam files.…”

Gli3 utilizes Hand2 to synergistically regulate tissue-specific transcriptional networks

“…Subsequent activation can then occur from either GliA or additional TFs. GliR function is primarily carried out by Gli3 and is indispensable for proper Hh-dependent patterning (Litingtung and Chiang 2000;Wang et al 2000;Oosterveen et al 2012;Lex et al 2020). Recent studies in the limb, which is dependent upon Gli3R for proper patterning, have shown that not all GBMs are created equal.…”

“…Recent studies in the limb, which is dependent upon Gli3R for proper patterning, have shown that not all GBMs are created equal. While some GBMs appear to be completely dependent on a Hh input, others remain 'stable' with Gli3 occupancy occurring independent of the morphogen (Lex et al 2020). However, to date, no classification system of GBM utilization in the face has been established.…”

Ciliary and extraciliary Gpr161 pools repress hedgehog signaling in a tissue-specific manner

“…Although Gli family members bind to same consensus DNA sequences, the differential roles of GliA and GliR in sculpting tissues could likely arise from context-dependent cis-regulation of targets by coactivators/repressors (Oosterveen et al, 2012). Alternatively, tissue-specific regulation of enhancer activity could regulate Gli-mediated repression (Lex et al, 2020). The effects of ciliary loss of Gpr161 are dependent on requirements of the tissues on GliR levels as follows:…”