Arabidopsis MPSS. An Online Resource for Quantitative Expression Analysis

Lee, David K.; Vu, Tam H.; Tej, Shivakundan Singh; Edberg, Steve B.; Matvienko, Marta; Tindell, Larry D.

doi:10.1104/pp.104.039495

Cited by 108 publications

(116 citation statements)

References 12 publications

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“…Arabidopsis massively parallel signature sequencing (MPSS) data for PLDz expression was obtained from http://mpss. udel.edu/at (Meyers et al, 2004). For PLDz1, the MPSS expression profile was in general agreement with the real-time PCR data; PLDz1 expression level in roots was 5 times higher than that in leaves (Fig.…”

Section: Pldz1 and Pldz2 Are Expressed Highly In Rootssupporting

confidence: 75%

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Double Knockouts of Phospholipases Dζ1 and Dζ2 in Arabidopsis Affect Root Elongation during Phosphate-Limited Growth But Do Not Affect Root Hair Patterning

et al. 2005

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(M.L., X.W.)Root elongation and root hair formation are important in nutrient absorption. We found that two Arabidopsis (Arabidopsis thaliana) phospholipase Ds (PLDs), PLDz1 and PLDz2, were involved in root elongation during phosphate limitation. PLDz1 and PLDz2 are structurally different from the majority of plant PLDs by having phox and pleckstrin homology domains. Both PLDzs were expressed more in roots than in other tissues. It was reported previously that inducible suppression or inducible overexpression of PLDz1 affected root hair patterning. However, gene knockouts of PLDz1, PLDz2, or the double knockout of PLDz1 and PLDz2 showed no effect on root hair formation. The expression of PLDzs increased in response to phosphate limitation. The elongation of primary roots in PLDz1 and PLDz2 double knockout mutants was slower than that of wild type and single knockout mutants. The loss of PLDz2, but not PLDz1, led to a decreased accumulation of phosphatidic acid in roots under phosphate-limited conditions. These results indicate that PLDz1 and PLDz2 play a role in regulating root development in response to nutrient limitation.

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Section: Pldz1 and Pldz2 Are Expressed Highly In Rootssupporting

confidence: 75%

“…C and D, Expression levels of PLDz1 and PLDz2 as detected by MPSS. The MPSS data were obtained from the Arabidopsis MPSS Web site (http://mpss.udel.edu/at; Meyers et al, 2004).…”

Section: Mutants Ablate the Expression Of One Or Both Pldzsmentioning

confidence: 99%

Double Knockouts of Phospholipases Dζ1 and Dζ2 in Arabidopsis Affect Root Elongation during Phosphate-Limited Growth But Do Not Affect Root Hair Patterning

et al. 2005

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“…To test this hypothesis we performed transcript profiling using the Agilent V3 oligo microarray, which contains probes for 28,500 genes from The Institute for Genomic Research's ATH1 v.5 annotation as well 10,000 probes based on Massively Parallel Signature Sequencing data (Meyers et al, 2004) and identified genes that are misexpressed in the absence of AtCAF1a and AtCAF1b. For this experiment we examined 3-week-old rosette leaves from wild-type, Atcaf1a-1, and Atcaf1b-2 plants, both before and intervals after wounding, using three independent biological replicates for each genotype and time point.…”

Section: Transcript Profiling Of Atcaf1a and Atcaf1b Mutantsmentioning

confidence: 99%

“…The Agilent Arabidopsis V3 oliogoarray chip containing 60-mer oligos probes for 28,500 genes from The Institute for Genomic Research's ATH1 v.5 annotation as well as 10,000 probes based on Massively Parallel Signature Sequencing data (Meyers et al, 2004) were utilized for transcript profiling (Agilent Technologies). Total RNA was prepared from three independent biological replicates for each genotype 3 treatment combination as described for RT-PCR.…”

Section: Microarray Analysesmentioning

confidence: 99%

Arabidopsis Deadenylases AtCAF1a and AtCAF1b Play Overlapping and Distinct Roles in Mediating Environmental Stress Responses

et al. 2009

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To maintain homeostasis in an ever-changing environment organisms have evolved mechanisms to reprogram gene expression. One central mechanism regulating gene expression is messenger RNA (mRNA) degradation, which is initiated by poly(A) tail shortening (deadenylation). The carbon catabolite repressor 4-CCR4 associated factor1 (CCR4-CAF1) complex is the major enzyme complex that catalyzes mRNA deadenylation and is conserved among eukaryotes. However, the components and functions of this global regulatory complex have not been well characterized in plants. Here we investigate the CAF1 family in Arabidopsis (Arabidopsis thaliana). We identify 11 AtCAF1 homologs and show that a subset of these genes are responsive to mechanical wounding, among them are AtCAF1a and AtCAF1b whose expression levels are rapidly and transiently induced by wounding. The differential expression profiles of the various AtCAF1s suggest that not all AtCAF1 genes are involved in stress-responsive regulation of transcript levels. Comparison of misexpressed genes identified via transcript profiling of Atcaf1a and Atcaf1b mutants at different time points before and after wounding suggests that AtCAF1a and AtCAF1b target shared and unique transcripts for deadenylation with temporal specificity. Consistent with the AtPI4Kγ3 transcript exhibiting the largest increase in abundance in Atcaf1b, AtCAF1b targets AtPI4Kγ3 mRNA for deadenylation. Stress-tolerance assays demonstrate that AtCAF1a and AtCAF1b are involved in mediating abiotic stress responses. However, AtCAF1a and AtCAF1b are not functionally redundant in all cases, nor are they essential for all environmental stresses. These findings demonstrate that these closely related proteins exhibit overlapping and distinct roles with respect to mRNA deadenylation and mediation of stress responses.

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“…Strikingly, RNA of 13 of the family members was detected predominantly or exclusively in floral tissue. The expression of the ATHB26 gene could not be detected by northerns, nor could it be detected by Massively Parallel Signature Sequencing with confidence (Meyers et al, 2004). Digital northern analyses were carried out for ATHB26 using Genevestigator (Zimmermann et al, 2004), which consolidates the data from microarray data performed on Arabidopsis.…”

Section: The Arabidopsis Zf-hd Family Members Are All Expressed In Flmentioning

confidence: 99%

The Arabidopsis Zinc Finger-Homeodomain Genes Encode Proteins with Unique Biochemical Properties That Are Coordinately Expressed during Floral Development

2006

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Arabidopsis (Arabidopsis thaliana) contains approximately 100 homeobox genes, many of which have been shown to play critical roles in various developmental processes. Here we characterize the zinc finger-homeodomain (ZF-HD) subfamily of homeobox genes, consisting of 14 members in Arabidopsis. We demonstrate that the HDs of the ZF-HD proteins share some similarities with other known HDs in Arabidopsis, but they contain distinct features that cluster them as a unique class of plant HD-containing proteins. We have carried out mutational analyses to show that the noncanonical residues present in the HDs of this family of proteins are important for function. Yeast (Saccharomyces cerevisiae) two-hybrid matrix analyses of the ZF-HD proteins reveal that these proteins both homo-and heterodimerize, which may contribute to greater selectivity in DNA binding. These assays also show that most of these proteins do not contain an intrinsic activation domain, suggesting that interactions with other factors are required for transcriptional activation. We also show that the family members are all expressed predominantly or exclusively in floral tissue, indicating a likely regulatory role during floral development. Furthermore, we have identified loss-of-function mutations for six of these genes that individually show no obvious phenotype, supporting the idea that the encoded proteins have common roles in floral development. Based on these results, we propose the ZF-HD gene family encodes a group of transcriptional regulators with unique biochemical activities that play overlapping regulatory roles in Arabidopsis floral development.

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Arabidopsis MPSS. An Online Resource for Quantitative Expression Analysis

Cited by 108 publications

References 12 publications

Double Knockouts of Phospholipases Dζ1 and Dζ2 in Arabidopsis Affect Root Elongation during Phosphate-Limited Growth But Do Not Affect Root Hair Patterning

Double Knockouts of Phospholipases Dζ1 and Dζ2 in Arabidopsis Affect Root Elongation during Phosphate-Limited Growth But Do Not Affect Root Hair Patterning

Arabidopsis Deadenylases AtCAF1a and AtCAF1b Play Overlapping and Distinct Roles in Mediating Environmental Stress Responses

The Arabidopsis Zinc Finger-Homeodomain Genes Encode Proteins with Unique Biochemical Properties That Are Coordinately Expressed during Floral Development

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