Towards annotating the plant epigenome: the Arabidopsis thaliana small RNA locus map.


Type
Article
Change log
Authors
Hardcastle, Thomas J 
Müller, Sebastian Y  ORCID logo  https://orcid.org/0000-0002-0148-7020
Abstract

Based on 98 public and internal small RNA high throughput sequencing libraries, we mapped small RNAs to the genome of the model organism Arabidopsis thaliana and defined loci based on their expression using an empirical Bayesian approach. The resulting loci were subsequently classified based on their genetic and epigenetic context as well as their expression properties. We present the results of this classification, which broadly conforms to previously reported divisions between transcriptional and post-transcriptional gene silencing small RNAs, and to PolIV and PolV dependencies. However, we are able to demonstrate the existence of further subdivisions in the small RNA population of functional significance. Moreover, we present a framework for similar analyses of small RNA populations in all species.

Description
Keywords
Arabidopsis, Arabidopsis Proteins, Bayes Theorem, Epigenesis, Genetic, Epigenomics, Gene Expression Regulation, Plant, Genome, Plant, High-Throughput Nucleotide Sequencing, RNA Interference, RNA, Plant, RNA, Small Interfering
Journal Title
Sci Rep
Conference Name
Journal ISSN
2045-2322
2045-2322
Volume Title
8
Publisher
Springer Science and Business Media LLC
Sponsorship
European Research Council (340642)