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ChIPmentation for high-quality and fast ChIP-seq library preparation

Meet our grant program winners

Katarina Kouter, PhD student at the Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Slovenia

Our lab group focuses on biological basis of suicidal behavior which is sadly very prevalent in Slovenia. Despite vast knowledge on suicidality complete mechanism and factors leading to suicide are unknown. However there is an indication between changes in epigenetic profile and suicidal behavior. Currently our work focuses on changes in DNA methylation pattern. We hope our genome-wide methylation studies may offer novel insights into altered methylation pattern in suicide victims.

Suicidal behavior is a multifactorial, polygenic state that affects millions worldwide and is a result of interplay between hereditary and environmental factors, tied together by epigenetics. Our results of DNA methylation analysis using RRBS suggest that there are differences in methylation status of suicide victims that can also influence gene expression. Our results have shown several differences in methylation level between suicide victims and controls in both brain regions, with gene ontology pointing towards cell structural integrity and nervous system regulation. Additional gene expression analysis identified changes in two genes, ZNF714 and NRIP3. Subtle methylation abnormalities in many genes, working together with genetic predisposition and environment seem to influence suicidal behavior.

Still, complex processes are involved in suicidal behavior development so additional studies on a broader level would be informative. While DNA methylation is important and informative regarding the cell state, additional epigenetics regulations such as chromatin modification play an equally important role. Information on histone modification and suicidal behavior is scarce. Combining our data of DNA methylation with new knowledge of chromatin modification would characterize our study group and provide new data, help improve understanding and hopefully reduce the risk for onset of suicidal behavior.

Matias Hepp, Researcher at Universidad Catolica de la Santisima Concepcion, Chile

Our lab works on finding new cancer dual therapies that involve immunotherapy and HDACs inhibitors in different cancers, mainly colorectal. We use specific HDAC inhibitors to increase the response of the immunotherapy in that type of cancer. We will analyze the enrichment of acetyl histone modification in the promoter region of some co-stimulatory genes involved in immune response. We believe that dual treatment will increase and improve the response to immunotherapy against tumor cells in this type of cancer.

Currently we are using ChIP-qPCR to study these enrichments but we will expand our assay by using ChIP-seq with our model and with different treatments. If the treatment reduces the number of cells in each treatment,we will have poor immunoprecipitation. The new ChIPmentation technology from Diagenode will allow us to get the robust data we need, independent of the number of cells.

Juber Herrera Uribe, Post-doctoral Researcher at Iowa State University, US

As a postdoc at Iowa State University, I am working in the Pig Functional Annotation Project. The long-term goal of this project is to create a resource for understanding the expression and regulatory function of each segment of the porcine genome across and within diverse biological states (immune cells, tissues, and fetal tissues). We will perform several assays (histone mark ChIP-seq, DNA methylation, ATAC-seq, RNA-seq, ISO-seq and RAMPAGE) on ~18 tissues, 4 tissues at day 30 and 70 of gestation, the major blood cell types, as well as the alveolar macrophage stimulated with LPS and Poly (I:C).

As I mentioned before, we have to perform 6 different techniques (histone mark ChIP-seq, DNA methylation, ATAC-seq, RNA-seq, ISO-seq and RAMPAGE) on the same sample, some of them need a high number of cells to be performed. To date, we are working on different rare populations of immune cells and fetal tissues. The main characteristic of both samples is the low number of cells that we can recover for all assays that we have to perform, for that reason is crucial for us the use of techniques with ultra-low input cells as ChIPmentation. ChIPmentation is a fundamental and useful technique for us to identify the dynamic regulation of histone marks in the low cell population at the epigenetic level.

Diagenode’s ChIPmentation technology, based on tagmentation, enables the integration of library preparation during ChIP itself using transposase and sequencing-compatible adaptors. Unlike standard library preparation techniques that require multi-step ligation, ChIPmentation incorporates an easier and shorter protocol. ChIPmentation ensures high quality data and allows users to enjoy an easy protocol that can save a whole day compared to standard protocols.

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