Transcription factor trapping by RNA in gene regulatory elements

Area of Science:

• Molecular Biology
• Gene Regulation
• Epigenetics

Background:

• Transcription factors (TFs) are crucial for gene regulation by binding to specific DNA sequences.
• Regulatory elements, including promoters, produce RNA transcripts.
• Some TFs can bind to RNA, suggesting a potential role for RNA in TF function.

Purpose of the Study:

• To investigate the role of RNA transcribed from regulatory elements in maintaining transcription factor occupancy.
• To determine if RNA binding contributes to the stability of TF binding at gene regulatory sites.
• To explore the potential for a positive-feedback mechanism involving RNA and TF binding.

Main Methods:

• Genome-wide analysis of transcription factor Yin-Yang 1 (YY1) binding to DNA and RNA.
• Manipulation of transcription from regulatory elements to assess impact on YY1 occupancy.
• Experimental tethering of RNA to gene regulatory elements to observe effects on YY1 binding.

Main Results:

• The transcription factor YY1 binds to both DNA regulatory elements and associated RNA species throughout the genome.
• Decreased transcription from regulatory elements leads to reduced YY1 occupancy.
• Artificial tethering of RNA enhances YY1 occupancy at these regulatory elements.

Conclusions:

• RNA transcribed from gene regulatory elements contributes to the stable binding of certain transcription factors, like YY1.
• Transcription of regulatory elements establishes a positive-feedback loop, enhancing TF stability and promoting robust gene expression programs.