Transcriptomics and chromatin accessibility signatures define the cervical-thoracic boundary along the vertebrate...

Area of Science:

• Developmental Biology
• Genetics
• Molecular Biology

Background:

• Somite development is crucial for musculoskeletal system formation in vertebrate embryos.
• Regional anatomical variations in somite-derived tissues are evident along the body axis, particularly in the vertebral column.
• Understanding the genetic mechanisms driving this regionalization is essential for deciphering developmental processes.

Purpose of the Study:

• To investigate the genetic control of regionalization at the cervical to thoracic (C-T) boundary in vertebrate embryos.
• To establish molecular profiles, including chromatin landscapes and transcriptional programs, defining this anatomical transition.
• To identify candidate cis-regulatory elements (CREs) and transcription factors (TFs) involved in C-T boundary formation.

Main Methods:

• ATAC-sequencing and RNA-sequencing were employed to profile somite molecular characteristics.
• Differential analysis was used to identify candidate CREs and differentially expressed genes.
• In silico footprinting identified TF binding sites.
• In vivo electroporation of citrine reporters validated CRE activity.
• CRISPR-on experiments were used to investigate lncRNA regulation.

Main Results:

• Molecular profiles revealed chromatin landscapes and transcriptional programs defining the C-T anatomical transition.
• Candidate CREs associated with key HOX genes (HOXC6, HOXC8) were identified and validated.
• HOXC6 was implicated in regulating SOX transcription factors (SOX5, SOX6, SOX9), which are involved in chondrogenesis.
• A novel lncRNA, lncRNA-HOXC6TA, located within the HOXC cluster, was identified and suggested to be regulated by HOXC6.

Conclusions:

• The study provides valuable molecular datasets for understanding vertebrate C-T transition.
• Identified regulatory elements and transcription factors offer insights into the genetic control of regional somite development.
• Further research is needed to elucidate the function of lncRNA-HOXC6TA in thoracic region development.