Featured Publications

Chromatin dynamics and the role of G9a in gene regulation and enhancer silencing during early mouse development

9 November, 2015

Zylicz JJ, Dietmann S, Günesdogan U, Hackett JA, Cougot D, Lee C, Surani MA

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 V2, Ovation Rapid Library System, Ovation 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.

Pages: e09571 doi: 10.7554/eLife.09571

Kinase Gene Fusions in Defined Subsets of Melanoma

29 January, 2017

Turner J, Couts K, Sheren J, Saichaemchan S, Ariyawutyakorn W, Avolio I, Cabral E, Glogowska M, Amato C, Robinson S, Hintzsche J, Applegate A, Seelenfreund E, Gonzalez R, Wells K, Bagby S, Tentler J, Tan AC, Wisell J, Varella-Garcia M, Robinson W

Metastatic melanoma is the most aggressive and deadly form of skin cancer, with a 5yr survival rate of < 15%. Uncovering the specific mutations and genomic rearrangements that drive this disease is vital to the development of targeted therapeutics. Using the Ovation Fusion Panel Target Enrichment system and the Ovation Fusion Target App, co-first author Kasey Couts and colleagues discovered an ARMC10-BRAF fusion that had not been previously reported in melanoma. With the help of targeted RNA sequencing, this study highlights the key role kinase fusions may play in a subset of melanomas, and suggests that screening for such mutations should become part of routine clinical practice.

Pages: 53-62 doi: 10.1111/pcmr.12560

Applying the INTACT method to purify endosperm nuclei and to generate parental-specific epigenome profiles

5 January, 2017

Moreno-Romero J, Santos-González J, Hennig L, and Köhler C

This study features a novel method for successfully isolating nuclei from Arabidopsis to investigate the epigenetic landscape of two parental accessions. Learn how the authors use Ovation Ultralow Library System and Ovation Ultralow Methyl-Seq Library System to study histone modifications via ChIP-Seq and DNA methylation patterns via Methyl-Seq, respectively. In the publication, the authors meticulously detail the protocol that they used to achieve cell-type-specific nuclei for the epigenome study.

Pages: 238-254 doi: 10.1038/nprot.2016.167

TT-seq maps the human transient transcriptome

3 June, 2016

Schwalb B, Michel M, Zacher B, Frühauf K, Demel C, Tresch A, Gagneur J, Cramer P

This study describes a new technique transient transcriptome sequencing (TT-Seq) to map transcriptionally active regions and enable estimation of RNA synthesis and degradation rates. Learn how the authors use the Ovation Universal RNA-Seq System to construct dimer-free libraries from low input fragmented RNA. The whole transcriptome approach with integrated ribosomal depletion allowed for study of non-coding RNAs that are generally rapidly degraded and have been difficult to detect and study.

Pages: 1225-8 doi: 10.1126/science.aad9841