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TranscriptomicsDegradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica)
MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) regulate gene expression in eukaryotes. Plant miRNAs modulate their targets mainly via messenger RNA (mRNA) cleavage. Small RNA targets have been extensively investigated in Arabidopsis using computational prediction, experimental validation, an...
ORGANISM(S): Oryza sativa Indica Group 
2010-01-01 | E-GEOD-19050 | biostudies-arrayexpress
TranscriptomicsRNase ZS1-mediated UbL40 mRNA decay controls thermo-sensitive genic male sterility in rice.
Male sterility is an important trait in hybrid crop breeding. Thermo-sensitive genic male sterility (TGMS) lines, which are male-sterile at restrictive (high) temperatures but convert to male-fertile at permissive (low) temperatures, have been widely utilized in two-line hybrid rice breeding3. Howev...
ORGANISM(S): Oryza sativa Indica Group 
2014-09-11 | E-GEOD-42314 | biostudies-arrayexpress
TranscriptomicsControl of agricultural traits by hc-siRNA associated MITEs in rice
Transposable elements (TEs) and repetitive sequences comprise over 40% of rice genome. Different TEs are tightly regulated by distinct epigenetic mechanisms. For example, the activities of LTR retrotransposon Tos17 and non-LTR retrotransposon LINE element Karma are uniquely regulated by histone H3K9...
ORGANISM(S): Oryza sativa Japonica Group 
2014-02-04 | E-GEOD-50778 | biostudies-arrayexpress
TranscriptomicsIntegrative genome-wide analysis reveals HLP1, a novel RNA-binding protein? regulates plant flowering by targeted alternative polyadenylation
Alternative polyadenylation (APA) is a widespread mechanism for gene regulation and has been implicated in flowering, but the molecular basis governing the choice of a specific poly(A) site during the vegetative-to-reproductive growth transition remains unclear. Here we characterize HLP1, an hnRNP A...
ORGANISM(S): Arabidopsis thaliana 
2015-06-30 | E-GEOD-39051 | biostudies-arrayexpress
TranscriptomicsProtein arginine methyltransferase AtPRMT5 is involved in pre-mRNA splicing in Arabidopsis thaliana
In this study, we analyzed the Arabidopsis homologue of PRMT5, AtPRMT5M-bM-^@M-^Ys function in RNA processing. RNA-seq analyses revealed that AtPRMT5 is involved in a subset of pre-mRNA splicing. Several RNA processing factors involved in regulating flowering time were validated that the correspondi...
ORGANISM(S): Arabidopsis thaliana 
2010-10-07 | E-GEOD-21323 | biostudies-arrayexpress
TranscriptomicsmRNA-seq data of 14 days old Arabidopsis seedlings in Col-0 and At rz-1b At rz-1c double mutant
Nuclear-localized RNA binding proteins are involved in various aspects of RNA metabolism, which in turn modulates gene expression. However, the functions of nuclear-localized RNA binding proteins in plants are poorly understood. Here we report the functions of two proteins containing RNA recognition...
ORGANISM(S): Arabidopsis thaliana 
2015-12-15 | E-GEOD-75959 | biostudies-arrayexpress
GenomicsREF6 recognizes specific DNA sequence to regulate H3K27me3 demethylation and organ boundary formation
RELATIVE OF EARLY FLOWERING 6 (REF6, also known as JMJ12) counteracts Polycomb mediated gene silencing through demethylating histone H3 lysine 27 trimethylation (H3K27me3) in Arabidopsis. Genome-wide analysis has demonstrated that REF6 dependent H3K37me3 demethylation occurs on hundreds of genes. Ho...
ORGANISM(S): Arabidopsis thaliana 
2016-03-22 | E-GEOD-65329 | biostudies-arrayexpress
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