Integration of 3D genome topology and local chromatin features uncovers enhancers underlying craniofacial-specific cartilage defects

Abstract

Aberrations in tissue-specific enhancers underlie many developmental defects. Disrupting a noncoding region distal from the human SOX9 gene causes the Pierre Robin sequence (PRS) characterized by the undersized lower jaw. Such a craniofacial-specific defect has been previously linked to enhancers transiently active in cranial neural crest cells (CNCCs). We demonstrate that the PRS region also strongly regulates Sox9 in CNCC-derived Meckel’s cartilage (MC), but not in limb cartilages, even after decommissioning of CNCC enhancers. Such an MC-specific regulatory effect correlates with the MC-specific chromatin contacts between the PRS region and Sox9 , highlighting the importance of lineage-dependent chromatin topology in instructing enhancer usage. By integrating the enhancer signatures and chromatin topology, we uncovered >10,000 enhancers that function differentially between MC and limb cartilages and demonstrated their association with human diseases. Our findings provide critical insights for understanding the choreography of gene regulation during development and interpreting the genetic basis of craniofacial pathologies.

Ultrasound-triggered in situ gelation with ROS-controlled drug release for cartilage repair

“…ROS-sensitive TK was fabricated and embedded between mPEG and DSPE as the intermediate connector. The chemical structure of TK was identified by 1 H NMR (AVANCE, 500 HMZ) in deuterated chloroform (CDCl 3 ) (Fig. S1a, ESI †).…”

“…TK-mPEG was successfully synthesized by conjugating the carboxyl of TK and the amine of PEG under the catalyst (EDC/NHS). The chemical structure of TK-mPEG was also identified by 1 H NMR in CDCl 3 (Fig. S1b, ESI †).…”

“…5 mg TK and 1 ml H 2 O 2 (100 mM) were co-incubated for 1 h in the dark. Then, the product was freeze-dried and monitored by 1 H NMR.…”

“…Cartilage, a transparent and resilient tissue, plays an essential role in the motor system. [1][2][3][4] Cartilage defects caused by trauma, osteoarthritis and other degenerative diseases create a substantial socioeconomic burden. [5][6][7][8] Currently, the regeneration of cartilage is compromised due to the deficiency of blood vessels and the limitation of innate self-proliferation ability.…”

Cis-Regulatory Elements in Mammals

“…However, the openness is significantly reduced after cranial neural crest cells differentiate into chondrocytes, suggesting that these enhancers may regulate the early growth and differentiation of the neural crest and no longer function in cartilage [ 101 ]. When clusters of these enhancers were knocked out in mice, the expression levels of Sox9 were significantly decreased and the animals showed significant jaw hypoplasia, but there was no effect in the development of the forelimb cartilage and no significant change in the expression level of Sox9 [ 102 ]. This suggests that there is tissue specificity of enhancers in regulating the development of traits.…”