Next-gen genetics: exploring the epigenome

19 December 2016

Research into genetics and DNA has progressed dramatically with the conclusion of the Human Genome Project in 2003. The project spanned 13 years and cost $2.7 billion but was successful in finding the complete sequence of the human genome. It has lead to the discovery of more than 1,800 disease-associated gene variants so far.

In 2006, genetics researchers then started working on the next generation of sequencing technologies and it has now become possible to find the DNA blueprint of individuals in a day or two with a cost as low as $1,000 dollars. As a result, there are massive amounts of data generated each year enabling rapid discoveries in various areas from human health, agriculture, animal science, and forensic sciences to animal conservation.

“Because of our increasing knowledge in the genome and epigenome, genetic engineering techniques such as TALENS and CRISPR/Cas9 technologies are able to change the actual DNA sequence or chromatin states,” explains Dr Manching Ku, a next-generation sequencing and chromatin dynamics specialist based in San Diego.

In molecular biology, TALEN (Transcription Activator-Like Effector Nucleases) and CRISPR (Clustered Regulatory Interspaced Short Palindromic Repeats)/Cas9 are genome editing tools which researchers can use to make specific changes at targeted genomic sites and are used for applications like correction of gene defects, gene knockout, developing potential therapeutic strategies for inherited diseases, and for epigenome studies.

The epigenome is the multitude of chemical compounds added to DNA that modify the genome without altering the underlying DNA sequence. An active area of research in genetics, the epigenome’s implications during cell fate transition in the context of regenerative medicine and cancer is being investigated.


ChIP (Chromatin-immunoprecipitation) is a method to interrogate any histone modifications or DNA-binding proteins that combine or associate with DNA. Using Chromatin-immunoprecipitation coupled with next-generation sequencing (ChIP-Seq), Ku has worked on enabling the interrogation of various biological systems including embryonic stem cells, induced pluripotent stem cells (iPS), solid tumours, tissues, and cancer cells.

iPS cells reprogram somatic cells into an embryonic state by over-expression of transcription factors (or more recently using small molecules). The DNA sequence is the same, but the transcription and epigenetic states of somatic vs. embryonic states are different. Each cell state has its own unique transcription programs (a subset of genes that are active and another subset of genes that are inactive, some call it transcription or epigenetic signatures). The unique transcription programs in each state give the identity and function of these cells.

Epigenome and epigenetic mechanisms

Ku was a part of the U.S. NIH ENCODE consortium which aimed to understand the histone modification landscape in various human cell types and epigenetic mechanisms like DNA methylation, chromatin accessibility, non-coding RNA, etc.

“By understanding epigenetic mechanisms and identifying important players in cancer, aging and neurological disorders, it’ll help us narrow down future therapeutic targets,” says Ku.

One epigenomic protein is the bromodomain protein, which was found to be a key player in cancer biology. Bromodomain proteins can recognise and bind to acetylated histones. This binding is important for activating other oncogenes in certain types of myeloma and leukemia. Researchers later developed a compound called JQ1, a potent inhibitor of bromodomain proteins, which was shown to prevent many kinds of cancer in mouse models.

In an age where people are living longer but not necessarily healthier, neurodegenerative diseases have become a major challenge, with a large portion of the world’s population suffering from different forms of memory disorders as they grow older.

“There has been enormous efforts in neuroscience to study the underlying genetic mechanisms of these diseases, but we still lack a clear picture,” says Ku.

However, a better understanding of the epigenome and epigenetic mechanisms also have implications for the treatment of disorders caused by old age or diseases such as Alzheimer’s, depression, schizophrenia, autism, and drug addiction, among others.

“Many researchers have turned to epigenetics aspects of these diseases because it’s likely to be multi-factorial and multi-genic,” she adds.

Epigenetics in oncology

There are lots of unknowns regarding new emerging diseases and epigenetics play an important role in many cellular processes, and cancer is one of them.

“One active area of research in cancer epigenetics is how cancer cells evade drug treatments by becoming resistant,” says Ku.

Epigenetic research is also equally exciting because of the possibility of isolating the cause of some cancers at not just the genetic but also the molecular level. Cancer is heterogeneous and there is a possibility that there are many different cell states or cell types in just one tumour. Recently, single cell analyses in cancer have been developed to be more specific in targeting cancers.

“So, instead of cutting a tumour and analysing its epigenetics and transcription mechanisms, scientists are developing newer and more sensitive methods to study cancer cells one by one,” adds Ku.

Regenerative medicine and possibilities of epigenetic editing tools

Epigenetics also has applications in regenerative medicine by, for instance, modelling human diseases using iPS cells.

“Using patient skin cells to recapitulate the cellular state by reprogramming can help us understand disease progression,” says Ku. “It is quite important to study the actual epigenetic state and compare the model to original cell types.”

In the longer term, genetic engineering tools can also be used to change epigenetic states. Instead of changing DNA sequences, scientists have used the same tools to tether different epigenetic modifiers to target specific DNA methylation patterns and/or chromatin environment.

Says Ku, “If we understand the underlying genetic and epigenetic causes in diseases, we may be able to use these epigenetic editing tools to correct disease-causing mutations.”

Dr Manching Ku obtained her Bachelor of Science (Summa Cum Laude) in Biochemistry from the University of Massachusetts and completed her Ph.D in Biochemistry at Tufts University. She received her postdoctoral training at the Harvard Medical School and the Broad Institute of Harvard and MIT. Currently, she is the director of next-generation sequencing core at Salk Institute for Biological Studies in San Diego, California. Ku received a Croucher Fellowship in 2007 for her study at Harvard University.

To view Ku’s personal Croucher profile, please click here.