Stripe Transcription Factors Improve Chromatin Accessibility for Gene Expression Regulation

July 26, 2022

The “Non-Coding” Genome

It’s becoming increasingly clear that the majority of disease-causing genetic variants fall within the non-coding portion of the genome. With this line of evidence, ‘non-coding’ may not be the most useful term anymore, but essentially it refers to the portion of the genome that does not code for mRNA and proteins.

So what is the function of the majority of the genome? The current evidence points to regulation of the expression of protein-coding genes as the main role. Within this regulation, there are cis-regulatory elements, like promoters, that act on nearby genes, and trans-regulatory elements, like enhancers, which act on distant genes.

Cis-Regulatory Elements of the Genome

Cis-regulatory elements are of particular interest because these are typically the elements that interact with transcription factors (TFs), proteins which bind to DNA and regulate gene expression. To better understand this cis-regulatory “code” of genomic elements and TFs, Zhao et. al. uncovered that TFs need to work together for effective gene expression regulation.

Published in Molecular Cell last week, the authors’ study combined chromatin accessibility data (ATAC-seq), transcriptomics (RNA-seq), TF ChIP-seq, and more to uncover that there are families of TFs that co-localize with other TFs to facilitate their functions. These families are called Stripe TFs because of the distinct appearance of ‘stripes’ in their locations in the authors’ data visualization.

Stripe TFs: A Partner in Gene Expression Regulation

This ‘partner’ function of Stripe TFs is critical: Stripe TFs recognize and bind to specific sequences in the mammalian genome that increase chromatin accessibility, allowing other TFs to access their binding sites. This work further elucidates how the cis-regulatory code functions, and the role(s) played by the majority of the genome.

Outsourcing Bioinformatics Analysis

The varied types of sophisticated data analysis needed for a study like this highlights the importance of having skilled bioinformaticians as a part of your research team. Our experts at Bridge Informatics provide bioinformatics-as-a-service (BaaS), where you can outsource your bioinformatics needs to us. Book a free discovery call to discuss your project needs.

Jane Cook, Journalist & Content Writer, Bridge Informatics

Jane is a Content Writer at Bridge Informatics, a professional services firm that helps biotech customers implement advanced techniques in management and analysis of genomic data. Bridge Informatics focuses on data mining, machine learning, and various bioinformatic techniques to discover biomarkers and companion diagnostics. If you’re interested in reaching out, please email or


pcr tubes prepared for amplification and genomic analysis

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