Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Gene transcription profiling of Physcomitrella patens ΔPpcmt and ΔPpmet deletion mutants compared to wild type.

ABSTRACT: 7 days old protonema of Physcomitrella patens Wildtype and two transgenic lines, ΔPpcmt line 281 (Noy-Malka et al. 2014; IMSC accession 40738) and ΔPpmet line 5 (Yaari et al. 2015; IMSC accession 40758) grown on BCDAT solid medium.

ORGANISM(S): Physcomitrella patens

SUBMITTER: Gertrud Wiedemann

PROVIDER: E-MTAB-3431 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A single CMT methyltransferase homolog is involved in CHG DNA methylation and development of Physcomitrella patens.

Noy-Malka Chen C Yaari Rafael R Itzhaki Rachel R Mosquna Assaf A Auerbach Gershovitz Nitzan N Katz Aviva A Ohad Nir N

Plant molecular biology 20131227 6

C-5 DNA methylation is an essential mechanism controlling gene expression and developmental programs in a variety of organisms. Though the role of DNA methylation has been intensively studied in mammals and Arabidopsis, little is known about the evolution of this mechanism. The chromomethylase (CMT) methyltransferase family is unique to plants and was found to be involved in DNA methylation in Arabidopsis, maize and tobacco. The moss Physcomitrella patens, a model for early terrestrial plants, h ...[more]

PMID: 24370935

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Project description:RNA-binding proteins (RBPs) are intimately involved in all aspects of RNA processing and regulation and are linked to neurodegenerative diseases and cancer. Therefore, understanding the relationship between RBPs and their RNA targets is critical for a broader understanding of post-transcriptional regulation in normal and disease processes. The majority of approaches to study RNA-protein interactions focus on single RBPs, however there are many hundreds RBPs encoded in the human genome, and each cell type expresses a different catalog of these regulatory molecules, greatly limiting the ability of these single RBP approaches to capture the global landscape of RNA-protein interactions. We and others have developed approaches to globally catalog regions of mRNAs that are bound by proteins in an unbiased manner. Here we describe a detailed protocol for performing our RNase-mediated protein footprint sequencing approach, termed protein interaction profile sequencing (PIP-seq). In this protocol, RNA-protein interactions are stabilized by cross-linking, and un-bound regions are digested with RNases, leaving only the protein-bound regions intact. To control for RNase insensitive regions, proteins are first denatured and then RNP complexes are subject to RNase treatment. After high-throughput sequencing of remaining fragments, peak calling is performed to identify protein protected sites (PPSs). We describe the application of this protocol to a human embryonic kidney cell line and perform basic quality control, reproducibility and benchmarking analyses. Finally, we describe the landscape of protein-interactions in HEK293T cells, underscoring the value of this approach. Future applications of this method to study the dynamics of RNA-protein interactions in developmental processes will help to uncover the role of RBPs in post-transcriptional regulation. Protein interaction profile sequencing (PIP-seq) in HEK293T cells. Three replicates of formaldehyde cross-linked PIP-seq are described

Dataset Information

Gene transcription profiling of Physcomitrella patens ΔPpcmt and ΔPpmet deletion mutants compared to wild type.

Publications

A single CMT methyltransferase homolog is involved in CHG DNA methylation and development of Physcomitrella patens.

Similar Datasets

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