Genome complexity: transcription factors triple role (Introduction)

by David Turell , Wednesday, July 05, 2023, 16:40 (297 days ago) @ David Turell

Bind DNA, protein and RNA:

https://phys.org/news/2023-07-tango-reveals-transcription-factors-dna.html

"Transcription factors help to regulate gene expression—turning genes on or off and dialing up or down their level of activity—often in partnership with the proteins that they bind. They anchor themselves and their partner proteins to DNA at binding sites in genetic regulatory sequences, bringing together the components that are needed to make gene expression happen.

"Transcription factors are a well-known family of proteins, but new research from Whitehead Institute Member Richard Young and colleagues shows that the picture we have had of them is incomplete. In a paper published in Molecular Cell on July 3, Young and postdocs Ozgur Oksuz and Jonathan Henninger reveal that along with DNA and protein, many transcription factors can also bind RNA.

"The researchers found that RNA binding keeps transcription factors near their DNA binding sites for longer, helping to fine tune gene expression. This rethinking of how transcription factors work may lead to a better understanding of gene regulation, and may provide new targets for RNA-based therapeutics.

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"'We show that RNA binding by transcription factors is a general phenomenon," Oksuz says. "Individual examples in the past were thought to be exceptions to the rule. Other studies dismissed signs of RNA binding in transcription factors as an artifact—an accident of the experiment rather than a real finding. The clues have been there all along, but I think earlier work was so focused on the DNA and protein interactions that they didn't consider RNA."

"The reason that researchers had not recognized transcription factors' RNA binding region as such is because it is not a typical RNA binding domain. Typical RNA binding domains form stable structures that researchers can detect or predict with current technologies. Transcription factors do not contain such structures, and so standard searches for RNA binding domains had not identified them in transcription factors.

***

"Next, the researchers tested to see if RNA binding affected the transcription factors' function. When transcription factors had their ARMs mutated so they couldn't bind RNA, those transcription factors were less effective in finding their target sites, remaining at those sites and regulating genes. The mutations did not prevent transcription factors from functioning altogether, suggesting that RNA binding contributes to fine-tuning of gene regulation.

"Further experiments confirmed the importance of RNA binding to transcription factor function. The researchers mutated the ARM of a transcription factor important to embryonic development, and found that this led to developmental defects in zebrafish. Additionally, they looked through a list of genetic mutations known to contribute to cancer and heritable diseases, and found that a number of these occur in the RNA binding regions of transcription factors. All of these findings point to RNA binding playing an important role in transcription factors' regulation of gene expression.

"They may also provide therapeutic opportunities. The transcription factors studied by the researchers were found to bind RNA molecules that are produced in the regulatory regions of the genome where the transcription factors bind DNA. This set of transcription factors includes factors that can increase or decrease gene expression."

Comment: another layer of genome controls uncovered. Continuing evidence of purposeful design.