Transcriptomics

Dataset Information

5

Genome-wide RNA polymerase II recruitment study during the intraerythrocytic life cycle of Plasmodium falciparum.


ABSTRACT: We exploited the phosphorylation state of the RNAPII CTD to assess the transcriptional status of most P. falciparum genes across the IDC. We raised highly specific monoclonal antibodies against three forms of the parasite CTD, namely unphosphorylated, Ser5-P and Ser2/5-P, and used these in ChIP-on-chip type experiments to map the genome-wide recruitment and activity of RNAPII. We raised and used 3 different anti-RNAPII antibodies in ChIP-on-chip analysis to map the position and status of RNAPII across the entire P. falciparum genome over the 48 h of the IDC at 8 h intervals resulting in TP1-6. Total 4 antibodies were used for ChIP-chip analysis for six time points each done in triplicates, except one antibody 8WG16 which was done in duplicate. We also used 8WG16, commercial RNAPII antibody in similar study done in duplicates.

ORGANISM(S): Plasmodium falciparum  

SUBMITTER: Haifen Chen   Zbynek Bozdech  Mark Featherstone  Archana P Gupta  Mark Stephen Featherstone  Lei Zhu  Ragini Rai  Christiane Ruedl  Jie Zheng 

PROVIDER: E-GEOD-57748 | ArrayExpress | 2014-11-19

SECONDARY ACCESSION(S): GSE57748PRJNA247990

REPOSITORIES: GEO, ArrayExpress

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Publications

Genome-wide analysis in Plasmodium falciparum reveals early and late phases of RNA polymerase II occupancy during the infectious cycle.

Rai Ragini R   Zhu Lei L   Chen Haifen H   Gupta Archana Patkar AP   Sze Siu Kwan SK   Zheng Jie J   Ruedl Christiane C   Bozdech Zbynek Z   Featherstone Mark M  

BMC genomics 20141106


BACKGROUND: Over the course of its intraerythrocytic developmental cycle (IDC), the malaria parasite Plasmodium falciparum tightly orchestrates the rise and fall of transcript levels for hundreds of genes. Considerable debate has focused on the relative importance of transcriptional versus post-transcriptional processes in the regulation of transcript levels. Enzymatically active forms of RNAPII in other organisms have been associated with phosphorylation on the serines at positions 2 and 5 of t  ...[more]

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