Functional landscape of non-canonical open reading frames in coordinating cell fate

Area of Science:

• Genomics
• Molecular Biology
• Developmental Biology

Background:

• Thousands of unannotated short open reading frames (sORFs) in the human genome may encode microproteins with unknown functions.
• Understanding the roles of these sORF-encoded microproteins is crucial for exploring the full functional capacity of the genome.

Purpose of the Study:

• To develop a functional screening method to identify microproteins encoded by sORFs that regulate cellular differentiation.
• To investigate the specific roles and mechanisms of newly discovered microproteins in cell fate determination and early development.

Main Methods:

• Development of sORF-seq, a functional screening platform to identify sORF-encoded microproteins.
• Characterization of lncPRESS1's dual function in both nuclear and cytoplasmic compartments.
• Analysis of lncPRESS1's role in SWI/SNF complex recruitment, gene expression, Sonic hedgehog (SHH) signaling, and primary cilium interaction.

Main Results:

• Identification of hundreds of sORF-encoded microproteins involved in regulating cellular differentiation.
• Discovery of lncPRESS1 as a key regulator of cell fate with bifunctional activity.
• Demonstration of lncPRESS1's nuclear function as an lncRNA orchestrating gene expression and cytoplasmic function as a microprotein directing lineage commitment via SHH signaling.

Conclusions:

• lncPRESS1 coordinates nuclear and cytoplasmic regulatory networks, highlighting a novel mechanism for shaping early embryogenesis and human brain development.
• The findings reveal a paradigm of non-canonical ORFs in orchestrating complex biological pathways, expanding the understanding of the functional genome.
• This study underscores the importance of exploring sORFs and their encoded microproteins for a comprehensive view of genetic regulation and function.