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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type (Col), hda6, hda5, hda9, fld and fve mutants

ABSTRACT: The goals of this study are to compare the RNA profiling by NGS in different mutants and Genome-wide analysis of gene regulatory networks 14-day old plant of Col and each mutants were generated by deep sequencing, using Illumina HiSeq2500

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Keqiang Wu

PROVIDER: E-GEOD-78946 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-Wide Analysis of Gene Regulatory Networks of the FVE-HDA6-FLD Complex in Arabidopsis.

Yu Chun-Wei CW Chang Kao-Yuan KY Wu Keqiang K

Frontiers in plant science 20160428

FVE/MSI4 is a homolog of the mammalian RbAp48 protein. We found that FVE regulates flowering time by repressing FLC through decreasing histone H3K4 trimethylation and H3 acetylation. Furthermore, FVE interacts with the histone deacetylase HDA6 and the histone demethylase FLD, suggesting that these proteins may form a protein complex to regulate flowering time. To further investigate the function of the FVE-FLD-HDA6 complex, we compared the gene expression profiles of fve, fld, and hda6 mutant pl ...[more]

PMID: 27200029

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The 3M-bM-^@M-2-tag digital gene expression library construction and Illumina sequencing analysis of Wild Type and SPL-/- ovules with placenta Transcriptomes

Project description:To elucidate the molecular basis underlying early female reproductive development, Here, we used high-throughput tag-sequencing analysis to identify genes preferentially expressed in female meiocytes (FMs) by comparing gene expression profiles from wild type ovules undergoing megasporogenesis with those from the lacking megasporogenesis spl mutant ovules. A total of 862 genes were identified as FMs with levels that are consistently reduced in spl ovules in two biological replicates. Genes involved in biogenesis, metabolism, transporter activity and DNA binding were over-represented in female meiocytes, suggesting that female meiocytes are synthetically and metabolically more active. Total mRNA profiles of stage 10-11 old M-oM-,M-^Boral buds wild type (WT) and SPL-/- ovules with placenta were generated by deep sequencing, Repeat twice, using Illumina adaptor 2 (GEX adapter 2).

2014-03-20 | E-GEOD-51069 | biostudies-arrayexpress

Arabidopsis SUMO E3 Ligase SIZ1 Interacts with HDA6 and Negatively Regulates HDA6 Function during Flowering.

Project description:The changes in histone acetylation mediated by histone deacetylases (HDAC) play a crucial role in plant development and response to environmental changes. Mammalian HDACs are regulated by post-translational modifications (PTM), such as phosphorylation, acetylation, ubiquitination and small ubiquitin-like modifier (SUMO) modification (SUMOylation), which affect enzymatic activity and transcriptional repression. Whether PTMs of plant HDACs alter their functions are largely unknown. In this study, we demonstrated that the Arabidopsis SUMO E3 ligase SAP AND MIZ1 DOMAIN-CONTAINING LIGASE1 (SIZ1) interacts with HISTONE DEACETYLASE 6 (HDA6) both in vitro and in vivo. Biochemical analyses indicated that HDA6 is not modified by SUMO1. Overexpression of HDA6 in siz1-3 background results in a decreased level of histone H3 acetylation, indicating that the activity of HDA6 is increased in siz1-3 plants. Chromatin immunoprecipitation (ChIP) assays showed that SIZ1 represses HDA6 binding to its target genes FLOWERING LOCUS C (FLC) and MADS AFFECTING FLOWERING 4 (MAF4), resulting in the upregulation of FLC and MAF4 by increasing the level of histone H3 acetylation. Together, these findings indicate that the Arabidopsis SUMO E3 ligase SIZ1 interacts with HDA6 and negatively regulates HDA6 function.

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Project description:Whole genome bisulfite sequencing (WGBS) of the NA18507 (Yoruba) lymphoblastoid cell line high resolution methylome of one cell type

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Oviduct-Embryo Interactions in Cattle: Two-Way Traffic or a One-Way Street? [RNA-Seq]

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2015-11-04 | E-GEOD-74612 | biostudies-arrayexpress

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2016-08-05 | E-GEOD-75933 | biostudies-arrayexpress

Arabidopsis PHL2 act as the key component of the central regulatory system controlling transcriptional responses to phosphate starvation

Project description:We first compared the transcriptomes of the roots of WT seedlings grown under P+ and P- conditions. Using a 2-fold change and a FDR (false discovery rate) of <0.05 as the cut-off for selecting the differentially expressed transcripts, we found that the expression of 581 genes was induced and that the expression of 120 genes was repressed by Pi starvation. We then compared the expression levels of these 581 PSI genes in the WT and phl2. The results showed that the average expression level of these genes was 51% lower in phl2 relative to the WT. If we arbitrarily defined a 30% reduction in the expression level of PSI genes as â??a significant reductionâ??, the expression of 87.6% of PSI genes was significantly reduced in P- phl2 relative to P- WT seedlings. Thus, we conclude that PHL2 is a key component of the central regulatory system controlling transcriptional responses to Pi starvation. We performed a RNA-seq analysis on WT and phl2 plants. Total RNAs were extracted from the roots of P+ and P- WT seedlings (i.e., seedling grown on P-sufficient and P-deficient media) and of P- phl2 seedlings. The extracted RNAs were subjected to RNA deep sequencing. Our RNA-seq analyses showed that among the 581 PSI genes, the expression of 87% is significantly reduced in phl2, demonstrating that PHL2 positively regulates the transcription of a large number of PSI genes at the genomic level

2016-07-05 | E-GEOD-74972 | biostudies-arrayexpress

RNAseq analysis of NGATHA loss and gain of function alleles

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2014-07-31 | E-GEOD-56326 | biostudies-arrayexpress

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Project description:Zebularine is a non-methylable cytidine analog that is used in epigenetic and cancer research. Its application has been shown to activate several transcriptionally silenced genetic elements; however, extent of this activation and other effects on the transcriptome are unknown. Here, we show that zebularine treatment induces preferentially genes associated with DNA damage repair response and this activation is strongly ATR-dependent. The set of up- and down-regulated genes after 24 h zebularine treatment is almost fully contained in the set of genes with changed transcription in response to 24 h MMC treatment. We identified only few genes that were up-regulated in common by longer (5 days) zebularine treatment and loss of epigenetic control in ddm1 mutant. Our results suggest that zebularine does not induce global activation of targets of transcriptional gene silencing and indicate previously unanticipated DNA damaging effects associated with zebularine-treatment. Examination of transcriptional changes in response to mock, 24 h and 5 days 20 uM zebularine and 24 h 10 uM MMC treatment in Arabidopsis wild-type and/or atr-2.

2014-11-18 | E-GEOD-63355 | biostudies-arrayexpress

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2011-08-29 | E-GEOD-30795 | biostudies-arrayexpress

gene expression analysis in Pbx1; Emx1-cre mutant cortex at embryonic day 15.5

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