Program predicts placement of chemical tags that control gene activity

September 21, 2014, University of California - San Diego

Biochemists working at the University of California, San Diego, have developed a program that predicts the placement of chemical marks that control the activity of genes based on sequences of DNA. They describe their analysis and report results from its application to human embryonic cells in a paper published in Nature Methods online September 21.

"All of our cells have the same blueprint, the same DNA, although they serve separate functions," said John Whitaker, lead author of the report. "Skin cells protect, send signals, and these differences emerge because different subsets of genes are active or silent within particular kinds of ."

These patterns of activity are controlled by modifications of the DNA that do not alter its sequence—chemical tags that influence which genes are read and which are skipped within a particular cell.

By comparing sequences with and without epigenomic modification, the researchers identified DNA patterns associated with the changes. They call this novel analysis pipeline Epigram and have made both the program and the DNA motifs they identified openly available to other scientists.

"The interplay between genetic and epigenomic regulation has only begun to be deciphered," said Wei Wang, professor of chemistry and biochemistry who directed the work. "This study revealed that there are specific DNA sequences that are recognized by DNA-binding proteins," which specify exactly where other enzymes place epigenomic marks.

The epigenome guides the development of complex organisms from single fertilized eggs. The researchers analyzed epigenomic patterns in human and four cell lineages derived from them to catalogue genetic elements that shape the epigenome during development.

Damage to the epigenome not only disrupts development, but can happen at any point in our lives and sometimes leads to illness. Identification of the DNA sequences that guide the placement of epigenomic could guide experimental analysis, the authors say. By editing DNA sequences that control epigenomic modifications, scientists could probe their functions and perhaps in the future mend epigenomic mistakes that cause harm. —Susan Brown

Explore further: Lessons from epigenome evolution: Exploring the epigenome's regulatory function

More information: Predicting the human epigenome from DNA motifs, Nature Methods, DOI: 10.1038/nmeth.3065

Related Stories

New technique maps life's effects on our DNA

July 20, 2014

Researchers at the BBSRC-funded Babraham Institute, in collaboration with the Wellcome Trust Sanger Institute Single Cell Genomics Centre, have developed a powerful new single-cell technique to help investigate how the environment ...

Throwing a loop to silence gene expression

September 2, 2014

All human cells contain essentially the same DNA sequence – their genetic information. How is it possible that shapes and functions of cells in the different parts of the body are so different? While every cell's DNA contains ...

Recommended for you

NASA's Mars 2020 rover is put to the test

March 20, 2019

In a little more than seven minutes in the early afternoon of Feb. 18, 2021, NASA's Mars 2020 rover will execute about 27,000 actions and calculations as it speeds through the hazardous transition from the edge of space to ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.