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WSU Researcher Gets NSF Grant To Study Gene Looping

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Athar Ansari, assistant professor of biological sciences in the College of Liberal Arts and Sciences, has won a $718,000 grant from the National Science Foundation to study gene looping, a mechanism that regulates transcription of a number of genes including HIV proviral gene and BRCA1 gene linked to breast cancer.

Fifty years ago, it was proposed that the genetic information within cells flows from DNA to RNA to protein. This concept was dubbed the central dogma of molecular biology. Transmission of genetic information from DNA to RNA is called transcription, the primary step at which gene expression is regulated. The process of transcription is regulated in a number of ways in different cell types.

In 2005, Ansari was one of the first researchers to show that genes exist in a looped conformation and gene looping could be an important transcription regulatory mechanism in eukaryotic cells.

During transcription, RNA blueprints are made using DNA strands as templates. RNA polymerase II is the molecular tool that carries out the transcription, from template to blueprint, in eukaryotic cells.

Ansari found that RNA polymerase II transcribes a looped, rather than a linear, DNA template in certain eukaryotic cells. Using the Chromosome Conformation Capture approach developed at Harvard and uniquely modified by Ansari for his experiments, he observed that during transcription DNA elements located at the two ends of a gene — called the promoter and terminator — physically interact to form a loop. When a loop forms, transcription efficiency increases exponentially.

“After publicizing these findings, others found that the HIV gene forms a gene loop, and the gene loop is important for its transcription,” said Ansari. Gene looping was also observed during transcriptional of BRCA1, the gene that’s often mutated in breast cancer cell lines.

But Ansari’s most recent and unexpected finding is that an initiation factor called TFIIB, which facilitates gene looping, occurs in a complex with a number of termination factors, called a holo-TFIIB complex. “No one was expecting that, so we had to do a lot of experiments and use different approaches, and all gave us the same result,” said Ansari.

This finding has shaped the focus of Ansari’s current round of research, in which he’s looking to reveal the role of other factors that are either unidentified or whose role in transcription is unknown. More specifically, he and his team will use mass spectrometry to identify the proteins that are present in holo-TFIIB complexes and study how they facilitate gene looping.

Ansari will also work to determine the scope of gene looping on a genome-wide scale. He intends to ascertain what types of genes are looping, “if a certain gene is looping or not, and if it’s looping, whether there’s any correlation with transcription efficiency,” said Ansari.

“Right now we’re studying the significance of gene looping in yeast cells, and later on we can extend these findings in understanding the role of gene looping in cell differentiation in higher eukaryotes, which is important in terms of development and disease,” said Ansari. “That will be very interesting.”

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