Epigenetics

Epigenetics is the study of chemical modifications or physical structure changes to chromatin in the absence of DNA sequence alterations. These modifications modulate gene expression to enable cell differentiation and identity. Disruption of the epigenome from environmental factors can have a significant impact on growth, development and disease.

NuGEN solutions enable both the characterization of epigenetic changes in the DNA and the elucidation of the impact of those alterations on gene expression. Our Methyl-Seq Systems allow investigation of direct methylation of DNA via bisulfite sequencing while our Ovation Ultralow Library Systems enable fast library construction for ChIP-Seq, FAIRE-Seq, Hi-C and more. Used in conjunction with our RNA-Seq library systems, researchers can probe both epigenetic modifications of interest and their associated gene expression changes.

Researchers have found evidence that suggests different cytosine modifications are functionally distinct and thus should be studied independently to better understand their biological impact. To distinguish cytosine DNA modifications, NuGEN has partnered with CEGX to combine our Methyl-Seq NGS library prep kits with CEGX's TrueMethyl® to enable accurate quantification of 5mC and 5hmC in parallel at single-base resolution.

Learn more about distinguishing DNA modifications here.
Learn more about 5-methylcytosine here.
Learn more about 5-hydroxymethylcytosine here.

Maintenance of parent-of-origin-specific gene expression by ZFP57

Genetic imprinting is a phenomenon by which the maternal or paternal allele is 'marked' epigenetically to control gene expression. Riso, et al., describe the role of ZFP57 in the maintenance of these epigenetic markers in mouse stem cells using Ovation Ultralow System V2 and Ovation Ultralow Methyl-Seq. The authors conclude that ZFP57 plays a key role in maintaining the methylation state of Imprinting control regions that regulate imprinted gene expression.

Mapping Hydroxymethylation Patterns in Neurodegenerative Disease

Dr. Mill is a Professor of Epigenetics at the University of Exeter Medical School in the United Kingdom where he is interested in understanding the causes and consequences of genomic variation in the brain, and the role this plays in neuropsychiatric and neurodegenerative disease. To better understand how DNA methylation and hydroxymethylation play a role in neurobiology, Dr. Mill's research has taken advantage of the TrueMethyl oxBS technology to quantify the 'true' levels of these DNA modifications and to better determine how gene regulation is affected in specific neural cell populations.

Dynamic changes in chromatin modifications observed during early mouse development

Development is very dynamic process that is intimately regulated by changes in chromatin modifications. In this study, Zylicz and colleagues investigated how epigenetics influences the genome during early embryonic development. Zylicz, et al. performed a comprehensive analysis utilizing Ovation RNA-Seq System V2Ovation Rapid Library SystemOvation Ultralow Library System, and Ovation Ultralow Methyl-Seq Library System to understand how epigenetics influences transcriptional regulation and chromosomal modifications. Their findings identify two enzymes (EZH2 and G9a) that dramatically affect histone methylation and thus impact cell fate decisions during development.

Methylated Biomarkers: A new tool for liquid biopsy

Legendre and Gooden et. al. analyze cell free DNA in breast cancer patients and healthy individuals. Using the Ovation® Ultralow Methyl-Seq Library System, the authors define tumor-specific signatures by identifying 21 hypermethylation hotspots associated with metastatic breast cancer.

Epigenetics as a read-out for inherited traits

Dr. Moreno-Romero's studies focus on the identification of epigenetic modifications that occur during early stages of endosperm development. Methyl-seq libraries were prepared using the Ovation® Ultralow Methyl-Seq Library System and ChIP-seq libraries were prepared with Ovation Ultralow Library System V2 using very small amounts of starting material.

ChIPping to an answer: Gene dysregulation in disease development

Dr. Mannini and co-workers investigate the role of the cohesion complex in gene transcription. The scientists use multiple orthogonal methods including ChIP-sequencing with the Ovation® Ultralow Library System V2 to uncover the impact of gene dysregulation as an underlying mechanism for Cornelia de Lange syndrome.