DNA methylation is involved in many key cellular processes and is an important component in gene expression. Likewise, errors in methylation can be linked to a variety of human diseases. While genomic sequencing tools are effective at pinpointing polymorphisms that may cause a disease, those same methods are unable to capture the effects of methylation because the individual genes still look the same. Specifically, there has been considerable effort to study DNA methylation on N6-adenine (6mA) in eukaryotic cells, which include human cells, but while genomic data is available, the role of methylation in these cells remains elusive.
“Previously, methods that had been developed to identify these methylation sites in the genome were very conservative and could only look at certain nucleotide lengths at a given time so a large number of methylation sites were missed,” said Dr. Hakon Hakonarson, director of the Center for Applied Genomics (CAG) at CHOP and one of the senior co-authors of the study. “We needed to develop a better way of identifying and predicting methylation sites with a tool that could identify these motifs throughout the genome that may have a robust functional impact that are potentially disease causing.”
In order to address this issue plaguing the research community, CAG and its partners at NJIT turned to deep learning. Zhi Wei, professor of computer science at NJIT and a senior co-author of the study, worked with Hakonarson and his team to develop a deep learning algorithm that could predict where these sites of methylation happened, which would then help researchers determine the effect they might have on certain nearby genes.
Wei calls his software Deep6mA. To predict where these methylation sites might be found, Wei led the development of a neural network, which is a machine learning model that attempts to learn in similar ways to a brain. Neural networks have been utilized in cellular research before, but this is its first application to study DNA methylation sites on natural multicellular organisms.
Wei cited four advantages of the new method: automation of the sequence feature representation of different levels of detail; integration of a broad spectrum of methylation sequences flanking genes of interest; enabling of the potential visualization of inherent sequence motifs for interpretation; and facilitation of model development and prediction in large-scale genomic data.
The study team applied this algorithm to three different types of representative organisms: A. thaliana, D. melanogaster, and E.coli, the first two being eukaryotic. Deep6mA was able to identify 6mA methylation sites down to the resolution of a single nucleotide, or basic unit of DNA. Even in this initial confirmation study, the researchers were able to visualize regulatory patterns that they had been unable to observe using previously existing methods.
"One limitation is that our proposed prediction is purely based on sequence information," Wei said in his discussion statement of the study. “Whether a candidate is a 6mA site or not will also depend on many other factors. Methylation, including 6mA, is a dynamic process, which will change with cellular context. In the future, we would like to take other factors into consideration [such as] gene expression. We hope to predict 6mA across cellular context by integrating other data."
“We already know that a number of genes have a disease-causing mechanism brought about by methylation, and while this study was not done in human cells, the eukaryotic cell models were very comparable,” Hakonarson said. “Genomic scientists looking to translate their findings into clinical applications would find this tool very useful, and the level of precision could eventually lead to the discovery of specific cells or targets that are candidates for therapeutic intervention.”
This study was supported by The Children’s Hospital of Philadelphia Endowed Chair in Genomic Research and an Institutional Development Award to the Center for Applied Genomics from Children’s Hospital of Philadelphia. This work was also supported by Extreme Science and Engineering Discovery Environment (XSEDE) through allocation CIE160021 and CIE170034 supported by National Science Foundation grant ACI-1548562.
Open-source software used in this research included Keras v2+, Tensorflow 1.12 and the Python3 programming language.
Tan et al, “Elucidation of DNA methylation on N6-adenine with deep learning.” Nat Mach Intell, online August 3, 2020. DOI: 10.1038/s42256-020-0211-4.
About Children’s Hospital of Philadelphia: Children’s Hospital of Philadelphia was founded in 1855 as the nation’s first pediatric hospital. Through its long-standing commitment to providing exceptional patient care, training new generations of pediatric healthcare professionals, and pioneering major research initiatives, Children’s Hospital has fostered many discoveries that have benefited children worldwide. Its pediatric research program is among the largest in the country. In addition, its unique family-centered care and public service programs have brought the 564-bed hospital recognition as a leading advocate for children and adolescents. For more information, visit http://www.chop.edu.
About New Jersey Institute of Technology: One of only 32 polytechnic universities in the United States, New Jersey Institute of Technology (NJIT) prepares students to become leaders in the technology-dependent economy of the 21st century. NJIT’s multidisciplinary curriculum and computing-intensive approach to education provide technological proficiency, business acumen and leadership skills. NJIT is rated an “R1” research university by the Carnegie Classification®, which indicates the highest level of research activity. NJIT conducts approximately $161 million in research activity each year and has a $2.8 billion annual economic impact on the State of New Jersey. NJIT is ranked #1 nationally by Forbes for the upward economic mobility of its lowest-income students and is among the top 2 percent of public colleges and universities in return on educational investment, according to PayScale.com. NJIT also is ranked by U.S. News and World Report as one of the top 50 public national universities.
Deric Raymond, NJIT
Ben Leach, CHOP