Comprehensive analysis of chromatin landscape in filamentous fungus Aspergillus nidulans

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	Comprehensive analysis of chromatin landscape in filamentous fungus Aspergillus nidulans
	Djordjevic, D.; Deshpande, V.; Wong, K. H.; Ho, W. K.
	2014-12-04
Source Publication	Australian Pathogen Bioinformatics Symposium
Publication Place	Canberra
Abstract	Eukaryotic genome consists of chromatin, which includes DNA and various histone and non-histone proteins. Chromatin organisation, such as the deposition of active or repressive histone modifications, plays an important role in regulating gene expression. Advances in Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) and associated bioinformatics analytical techniques have enabled genome-wide analysis of many histone modifications. The chromatin landscape of human, mouse, and several model organisms have been widely studied, but other medically and biotechnologically important species, including many fungal species, are not yet fully studied. Here we present a genome-wide chromatin landscape of an important filamentous fungal model organism, Aspergillus nidulans.Using ChIP-seq, we generated genome-wide profiles of H3, H3K4me3, H3K4me1, H3K27ac, H3K9me3, H3K9ac, and PolII in A. nidulans in the presence or absence of NH4. All sequences were mapped to the reference genome, and processed using the standard ChIP-seq analysis pipeline SPP. We used a recently developed hierarchically linked infinite hidden Markov model (hiHMM [1]) to systematically discover and characterise the most prevalent combination of histone modifications, i.e., chromatin state.Our analysis revealed an interesting new chromatin state that consists of both H3K9me3 and H3K27ac, and is associated with gene repression. This state is covering 15-20% of the genome, and is located most prevalently in sub-telomeric regions, covering secondary metabolism and transmembrane transport genes. In addition, 10-20% of the genome are marked by classical enhancer chromatin marks, suggesting that these previously uncharacterised non-coding regions may have potential regulatory functions.Our work represents a valuable resource in A. nidulansthat opens new avenues for investigation of the dynamic chromatin organisation and gene regulation in various fungal species.
Keyword	Chromatin Fungus Aspergillus Nidulans
Language	英語English
The Source to Article	PB_Publication
PUB ID	13864
Document Type	Conference paper
Collection	DEPARTMENT OF BIOMEDICAL SCIENCES Faculty of Health Sciences
Corresponding Author	Wong, K. H.; Ho, W. K.
Recommended Citation GB/T 7714	Djordjevic, D.,Deshpande, V.,Wong, K. H.,et al. Comprehensive analysis of chromatin landscape in filamentous fungus Aspergillus nidulans[C], Canberra, 2014.
APA	Djordjevic, D.., Deshpande, V.., Wong, K. H.., & Ho, W. K. (2014). Comprehensive analysis of chromatin landscape in filamentous fungus Aspergillus nidulans. Australian Pathogen Bioinformatics Symposium.

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