Click here to sign in with or

by Patricia Waldron, Cornell University

A new Cornell study, published in Nature Genetics, sheds light on a controversial debate in epigenetics—the set of molecular changes occurring on top of the genome that regulate how genes are turned on and off, but without changing a cell's DNA sequence.

The discovery may streamline the interpretation of new genomes from less-studied animals, researchers said.

Scientists studying epigenetics have long argued over the role of histone marks—little chemical tags hitched onto histones, the spool-like proteins that DNA wraps around inside the nucleus. Some researchers believe histone marks play a role in activating genes and kicking off transcription—the process of copying DNA into RNA to make proteins or for other cellular functions. The new study, however, finds that histone marks are laid down during the transcription process and don't play a regulatory role.

"This potentially has big implications for the way that we interpret genomes," said Charles Danko, the Robert N. Noyce Associate Professor in Life Science and Technology at the Baker Institute in the College of Veterinary Medicine and corresponding author of the study. "We would like to apply these same technologies to interpret the genome function in horse, dog and other veterinary species where there is not as much funding for research."

Zhong Wang, formerly of the Danko lab, and now a professor at Dalian University in China, is a co-lead author on the study, "Prediction of Histone Post-Translational Modification Patterns Based on Nascent Transcription Data," which published March 10 in Nature Genetics.

Wang used publicly available data sets of transcription in mice and humans to develop a computer program that predicts where histone marks occur in the genome. The program, called dHIT, takes data from a single experiment showing where transcription is actively occurring on the chromosomes. Researchers can use a technique called ChRO-seq, which was developed in the Danko lab, or a related technique called PRO-seq, developed at Cornell, to generate the transcription data.

Danko's group used this approach successfully to predict histone locations in mouse, human and horse cells. They showed dHIT works almost as well as biological experiments that directly measure the location of each mark.

Dr. Doug Antczak, the Dorothy Havemeyer McConville Professor of Equine Medicine at Baker, and colleagues from the Functional Annotation of Animal Genomes (FAANG) project contributed data and samples from horses for these experiments.

Alexandra Chivu, a doctoral student in the Danko lab and co-lead author, used dHIT in combination with experimental techniques measuring histone marks to find out what happens when transcription is blocked in a cell. She showed that without transcription, histone marks disappear, confirming that their intricate patterns often depend on transcription.

Before the development of dHIT, entire scientific consortia of researchers would work together on a single genome from a model organism to identify the location of histone marks. These new tools greatly simplify that process.

Next, Danko plans to tease out the actual role of histone marks by removing them and measuring the impact on transcription. "If we accept that these marks are parts of the machinery of transcription, then a really interesting question is, what parts of that machinery are they involved in?" he said. "What is their role if it's not regulation?" Explore further Identification of a unique 'switch' for blood vessel generation More information: Zhong Wang et al, Prediction of histone post-translational modification patterns based on nascent transcription data, Nature Genetics (2022). DOI: 10.1038/s41588-022-01026-x Journal information: Nature Genetics

More from Physics Forums | Science Articles, Homework Help, Discussion

Use this form if you have come across a typo, inaccuracy or would like to send an edit request for the content on this page. For general inquiries, please use our contact form. For general feedback, use the public comments section below (please adhere to guidelines).

Please select the most appropriate category to facilitate processing of your request

Thank you for taking time to provide your feedback to the editors.

Your feedback is important to us. However, we do not guarantee individual replies due to the high volume of messages.

Your email address is used only to let the recipient know who sent the email. Neither your address nor the recipient's address will be used for any other purpose. The information you enter will appear in your e-mail message and is not retained by Phys.org in any form.

Get weekly and/or daily updates delivered to your inbox. You can unsubscribe at any time and we'll never share your details to third parties.

Medical research advances and health news

The latest engineering, electronics and technology advances

The most comprehensive sci-tech news coverage on the web

This site uses cookies to assist with navigation, analyse your use of our services, collect data for ads personalisation and provide content from third parties. By using our site, you acknowledge that you have read and understand our Privacy Policy and Terms of Use.