The Complex Interplay of Epigenetics and Alternative Splicing in Development

The Complex Interplay of Epigenetics and Alternative Splicing in Development

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How are multiple proteins with distinct functions made from one gene, and what controls this “alternative splicing” process? In a recent paper, researchers discovered a significant correlation between differential exon usage across human developmental stages and the presence of different epigenetic marks around these exons. These chemical “tags” instruct the cell how to use a certain part of the DNA. Many of the genes that were regulated in this epigenetic manner have roles connected to development and metabolism.

How Does Epigenetics Regulate Alternative Splicing?

Alternative usage of exons, the protein-coding regions of genes, has long been observed in mammalian genomes. This process, called alternative splicing, allows a single gene to effectively encode many proteins with distinct functions. While studies have identified much of the molecular “machinery” involved in alternative splicing, the instructions for which exons get used or excised are less clear.

In a recent study published in Scientific Reports, researchers used data from the Human Epigenome Atlas, covering 11 adult human tissues and 8 cultured cell lines that resemble early developmental stages, to study the epigenetic mechanisms involved in exon usage. Our understanding of epigenetics (information external to the DNA sequence that regulates gene expression) is constantly evolving, uncovering new layers to the function and regulation of the genome.

Differential Regulation Across Developmental Stages

Diving deep into their data, the research team correlated differential exon usage with the presence of different epigenetic marks at the exon boundaries. They found a global enrichment of differential exon usage and differential epigenetic marks for different subgroups of genes, particularly those involved in cell signaling and developmental processes. Notably, a stronger correlation was observed in cell lines that represented early developmental stages, while mature tissues had fewer overlaps.

This study uncovers an underappreciated, yet significant role of epigenetic marks at the boundaries of protein-coding regions of genes. These marks do not merely define which exons will be used to make proteins but also regulate the abundance of the various exon combinations used in different tissues. 

Broader Context and Potential Impact

The findings highlight the intertwined relationship between epigenetics and alternative splicing, particularly in the dynamic realms of embryonic development and cellular signaling. The discoveries also shed light on the intricate molecular mechanisms underlying human development and growth, offering insights that could be invaluable in therapeutic contexts.

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Lauren Dembeck, Ph.D., Geneticist & Science Writer, Bridge Informatics

Lauren Dembeck, Ph.D., is an experienced science and medical writer. During her doctoral research at North Carolina State University, she conducted genome-wide association studies to identify genetic variants contributing to natural variation in complex traits and used a combination of classical and molecular genetics approaches in validation studies. Lauren was a postdoctoral fellow at the Okinawa Institute of Science and Technology in Japan. During her postdoc, she used fluorescence-activated cell sorting paired with high-throughput sequencing approaches to study the formation and regulation of neuronal circuits. 

She is part of our team of expert content writers at Bridge Informatics, bringing our readers and customers everything they need to know at the cutting edge of bioinformatics research. If you’re interested in reaching out, please email [email protected] or [email protected].

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