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Transcriptome changes caused by RBP-P mutations in rice seed

ABSTRACT: Two RBP-P mutants, P1MH and P3MH, carrying G401S and A252T point mutations, respectively, were obtained by TILLING studies (http://www.shigen.nig.ac.jp/rice/oryzabase). The A252T mutation site in P3MH lies within the linker sequence between the two RRM domains while the G401S substitutions in P1MH is located in the glycine-rich C-terminal region. Those mutations results in varying degrees of reduced RNA binding and/or protein-protein interactive properties of RBP-P. Transcriptome analysis on the dehulled 10-14 days old developing seeds from wild type, P1MH and P3MH mutants indicates that partial loss of RBP-P function caused the differential expression of storage protein genes and relevant genes involved in several essential biological processes during rice development.

ORGANISM(S): Oryza sativa

PROVIDER: GSE117150 | GEO | 2019/05/22

REPOSITORIES: GEO

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Project description:Interaction of the Kaposi’s sarcoma-associated herpesvirus (KSHV) Rta protein with the cellular Notch signaling effector, Recombination Signaling Protein (RBP)-Jk (aka CSL and CBF-1), is essential for viral reactivation from latency. We previously showed that Rta binds to a DNA motif repeated in the viral Mta promoter (called “CANT” or Rta-c) to stimulate RBP-Jk DNA binding, and distinguished Rta from the activated Notch-1 protein. To determine whether Rta’s mechanism would apply generally to other viral promoters, we employed chromatin immunoprecipitation/deep sequencing (ChIP/Seq) to identify Rta and RBP-Jk binding sites across the KSHV genome. We show that RBP-Jk binds nearly exclusively to unique genome sites during latency and reactivation. Many, but not all, reactivation-specific RBP-Jk peaks were associated with Rta bound to single Rta-c motifs. Other motifs that were over-represented with stimulated RBP-Jk DNA binding including those for the cellular DNA binding proteins BCL11A, MNT, MAF B, and TCF12. Four of the top seven motifs that were most over-represented with inhibition of RBP-Jk DNA binding were putative binding sites for the Pit/Oct/Unc (POU) family of proteins, including POU3F3 (Oct-8) and POU5F1 (Oct-4). Interestingly, two other POU motifs, including one for the POU2F1 (Oct-1) protein, are associated with inhibition of RBP-Jk DNA binding unless Rta bound to a nearby Rta-c motif. The relative distances between the Rta-c, POU, and RBP-Jk motifs were conserved at reactivation-specific RBP-Jk peaks in three promoters that Rta transactivated, and the Rta-c and Oct-1 motifs overlapped in two of those. The proximity of the Rta-c/Oct-1 motif to an RBP-Jk motif is critical for Rta transactivation of the ORF50AS/KbZIP promoter, and knockdown of Oct-1 protein debilitated reactivation and production of infectious virus. Our data suggest a broad role for POU proteins in regulating DNA binding of RBP-Jk and its associated transactivators.

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Transcriptome changes caused by RBP-P mutations in rice seed

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