HDAC9 structural variants disrupting TWIST1 transcriptional regulation lead to craniofacial and limb malformations.
Naama HirschIdit DahanEva D'haeneMatan AvniSarah VergultMarta Vidal-GarcíaPamela MaginiClaudio GrazianoGiulia SeveriElena BonoraAnna Maria NardoneFrancesco BrancatiAlberto Fernández JaénOlson J RoryBenedikt HallgrimssonRamon Y BirnbaumPublished in: Genome research (2022)
Structural variants (SVs) can affect protein-coding sequences as well as gene regulatory elements. However, SVs disrupting protein-coding sequences that also function as cis -regulatory elements remain largely uncharacterized. Here, we show that craniosynostosis patients with SVs containing the histone deacetylase 9 (HDAC9 ) protein-coding sequence are associated with disruption of TWIST1 regulatory elements that reside within the HDAC9 sequence. Based on SVs within the HDAC9 - TWIST1 locus, we defined the 3'- HDAC9 sequence as a critical TWIST1 regulatory region, encompassing craniofacial TWIST1 enhancers and CTCF sites. Deletions of either Twist1 enhancers (eTw5-7 Δ/Δ ) or CTCF site (CTCF-5 Δ/Δ ) within the Hdac9 protein-coding sequence led to decreased Twist1 expression and altered anterior/posterior limb expression patterns of SHH pathway genes. This decreased Twist1 expression results in a smaller sized and asymmetric skull and polydactyly that resembles Twist1 +/- mouse phenotype. Chromatin conformation analysis revealed that the Twist1 promoter interacts with Hdac9 sequences that encompass Twist1 enhancers and a CTCF site, and that interactions depended on the presence of both regulatory regions. Finally, a large inversion of the entire Hdac9 sequence ( Hdac9 INV/+ ) in mice that does not disrupt Hdac9 expression but repositions Twist1 regulatory elements showed decreased Twist1 expression and led to a craniosynostosis-like phenotype and polydactyly. Thus, our study elucidates essential components of TWIST1 transcriptional machinery that reside within the HDAC9 sequence. It suggests that SVs encompassing protein-coding sequences could lead to a phenotype that is not attributed to its protein function but rather to a disruption of the transcriptional regulation of a nearby gene.
Keyphrases
- histone deacetylase
- epithelial mesenchymal transition
- binding protein
- poor prognosis
- transcription factor
- amino acid
- protein protein
- gene expression
- dna methylation
- genome wide
- signaling pathway
- magnetic resonance imaging
- type diabetes
- adipose tissue
- magnetic resonance
- molecular dynamics simulations
- skeletal muscle
- wild type
- contrast enhanced