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About the Authors:
Daniel Antony Pass
Contributed equally to this work with: Daniel Antony Pass, Emily Sornay
Roles Formal analysis, Investigation, Methodology, Software, Visualization, Writing - original draft, Writing - review & editing
* E-mail: [email protected]
Affiliation: Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
ORCID http://orcid.org/0000-0003-2799-8432
Emily Sornay
Contributed equally to this work with: Daniel Antony Pass, Emily Sornay
Roles Investigation, Methodology, Validation, Writing - original draft, Writing - review & editing
Affiliation: Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
ORCID http://orcid.org/0000-0003-0720-2660
Angela Marchbank
Roles Investigation, Methodology, Supervision, Validation
Affiliation: Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
Margaret R. Crawford
Roles Investigation, Methodology, Validation
Affiliation: Genome Centre, University of Sussex, Sussex House, Falmer, Brighton, United Kingdom
ORCID http://orcid.org/0000-0001-8369-3508
Konrad Paszkiewicz
Roles Investigation, Methodology, Validation
Affiliation: Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter, United Kingdom
Nicholas A. Kent
Roles Conceptualization, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Supervision, Validation, Visualization, Writing - review & editing
Affiliation: Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
James A. H. Murray
Roles Conceptualization, Funding acquisition, Investigation, Methodology, Project administration, Resources, Supervision, Writing - review & editing
Affiliation: Cardiff School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
ORCID http://orcid.org/0000-0002-2282-3839Abstract
All eukaryotic genomes are packaged as chromatin, with DNA interlaced with both regularly patterned nucleosomes and sub-nucleosomal-sized protein structures such as mobile and labile transcription factors (TF) and initiation complexes, together forming a dynamic chromatin landscape. Whilst details of nucleosome position in Arabidopsis have been previously analysed, there is less understanding of their relationship to more dynamic sub-nucleosomal particles (subNSPs) defined as protected regions shorter than the ~150bp typical of nucleosomes. The genome-wide profile of these subNSPs has not been previously analysed in plants and this study investigates the relationship of dynamic bound particles with transcriptional control. Here we combine differential micrococcal nuclease (MNase) digestion and a modified paired-end sequencing protocol to reveal the chromatin structure landscape of Arabidopsis cells across a wide particle size range. Linking this data to RNAseq expression analysis provides detailed insight into the relationship of identified DNA-bound particles with transcriptional activity. The use of differential digestion reveals sensitive positions, including a labile -1 nucleosome positioned upstream of the transcription start...