A new integrated genetic and transcriptomic approach for investigating DUX4 and DUX4C

Area of Science:

• Genomics
• Molecular Biology
• Human Genetics

Background:

• The double homeobox 4 gene (DUX4) and its paralogue DUX4C are located in chromosome 4's subtelomeric region.
• These genes are linked to facioscapulohumeral muscular dystrophy (FSHD) and various cancers.
• High sequence similarity and numerous paralogues complicate accurate genotyping and expression analysis with short-read sequencing.

Purpose of the Study:

• To clarify the genetic architecture and disease associations of DUX4 and DUX4C.
• To develop advanced genomic resources for studying these genes.
• To enable precise expression profiling and haplotype analysis.

Main Methods:

• Identification of two distinct DUX4C haplotypes (DUX4C-4qα and DUX4C-4qβ).
• Generation of a comprehensive reference genome (D4Ref-T2T) using long-read sequencing, integrating DUX4 and DUX4C haplotypes.
• Characterization of full-length DUX4C mRNA isoforms and creation of a transcriptome reference.

Main Results:

• Strong linkage disequilibrium observed between DUX4C and DUX4 haplotypes (r² = 0.86).
• DUX4 expression detected in both breast tumor and FSHD tissues.
• DUX4C expression was specific to breast tumors, linked to pathways of leukocyte differentiation and cell migration.

Conclusions:

• The developed D4Ref-T2T reference genome and transcriptome resources facilitate accurate DUX4 and DUX4C analysis.
• DUX4 and DUX4C exhibit distinct expression patterns in disease contexts.
• DUX4C expression in tumors suggests a role in immune cell processes and tumor progression.