Conservation of RET regulatory function from human to zebrafish without sequence similarity

Area of Science:

• Genomics
• Developmental Biology
• Evolutionary Biology

Background:

• Evolutionary sequence conservation is a common method for identifying functional noncoding regulatory elements.
• The RET proto-oncogene plays crucial roles in neural crest development and is implicated in various cancers.

Purpose of the Study:

• To investigate the functional capacity of teleost and mammalian noncoding sequences at the ret/RET locus using a transgenic assay.
• To determine if sequence similarity approaches adequately capture all functional regulatory elements.

Main Methods:

• Utilized a transposon-based transgenic assay in zebrafish.
• Assessed the regulatory activity of conserved noncoding sequences from zebrafish (teleost) and human (mammalian) RET loci.
• Monitored reporter gene expression to evaluate locus-specific regulation.

Main Results:

• Most teleost noncoding sequences from the ret locus drove reporter gene expression specifically in zebrafish.
• Many teleost sequences exhibited overlapping regulatory control, indicating complex regulatory networks.
• A majority of human RET noncoding sequences also directed ret-specific expression in zebrafish.
• Functional regulatory elements were detected even in regions with low sequence similarity.

Conclusions:

• Transgenic assays reveal significant functional noncoding sequence information not detectable by sequence similarity alone.
• Conserved noncoding elements across vertebrates can retain conserved regulatory functions.
• Current reliance on sequence conservation may underestimate the extent of functional noncoding DNA, particularly for genes like RET.