New publication: Epigenetics & Chromatin

Schmeier Research Group // Massey University

PUBLICATION

We are very happy about this one. The first paper from work led by my PhD student Elena! Congrats! Link to open access article here: https://doi.org/10.1186/s13072-017-0158-9

Abstract below:

Macrophages are sentinel cells essential for tissue homeostasis and host defence. Owing to their plasticity, macrophages acquire a range of functional phenotypes in response to microenvironmental stimuli, of which M(IFN-γ) and M(IL-4/IL-13) are well known for their opposing pro- and anti-inflammatory roles. Enhancers have emerged as regulatory DNA elements crucial for transcriptional activation of gene expression. Using cap analysis of gene expression and epigenetic data, we identify on large-scale transcribed enhancers in bone marrow-derived mouse macrophages, their time kinetics, and target protein-coding genes. We observe an increase in target gene expression, concomitant with increasing numbers of associated enhancers, and find that genes associated with many enhancers show a shift towards stronger enrichment for macrophage-specific biological processes. We infer enhancers that drive transcriptional responses of genes upon M(IFN-γ) and M(IL-4/IL-13) macrophage activation and demonstrate stimuli specificity of regulatory associations. Finally, we show that enhancer regions are enriched for binding sites of inflammation-related transcription factors, suggesting a link between stimuli response and enhancer transcriptional control. Our study provides new insights into genome-wide enhancer-mediated transcriptional control of macrophage genes, including those implicated in macrophage activation, and offers a detailed genome-wide catalogue of transcribed enhancers in bone marrow-derived mouse macrophages.

Publications // latest

Genome-wide profiling of transcribed enhancers during macrophage activation. Epigenetics & Chromatin, 2017, 10:50

Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer. Scientific Reports, 2017, 7(1):11590

Consensus molecular classification of colorectal cancer and association with the colonic microbiota. Diseases of the Colon & Rectum, 2017, 60(6):E90-E91 (In proceedings: Annual Meeting of the American Society of Colon and Rectal Surgeons)

Workshops // upcoming

[ Feb 2018 ] Software Carpentry Workshop, Massey University Auckland

Tweets // latest