Genome-wide identification of MYB3R3-bound genes
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE60554 | GEO | 2015/06/01
SECONDARY ACCESSION(S): PRJNA258532
REPOSITORIES: GEO
Similar Datasets
Project description:R1R2R3-Myb proteins represent an evolutionarily conserved class of Myb family proteins important for cell cycle regulation and differentiation in eukaryotic cells. In plants, this class of Myb proteins are believed to play important roles in cell cycle regulation through transcriptional regulation of G2/M phase-specific genes by binding to common cis-elements, called MSA elements. In Arabidopsis thaliana, MYB3R1 and MYB3R4 act as transcriptional activators and positively regulate cytokinesis by activating transcription of KNOLLE, which encodes a cytokinesis-specific syntaxin. Here, we show that the double mutation myb3r1 myb3r4 causes pleiotropic developmental defects, some of which are due to deficiency of KNOLLE whereas other are not, suggesting multiple target genes are involved. Consistently, microarray analysis of the double mutant revealed altered expression of many genes, among which G2/M-specific genes showed significant overrepresentation of the MSA motif and a strong tendency to be down-regulated by the double mutation. Our results demonstrate, on a genome-wide level, the importance of the MYB3R-MSA pathway for regulating G2/M-specific transcription. In addition, MYB3R1 and MYB3R4 may have diverse roles during plant development by regulating G2/M-specific genes with various functions, as well as genes possibly unrelated to the cell cycle. Comparison between the myb3r1 myb3r4 double mutant and wild type in three paired replicates.
2011-09-06 | E-GEOD-29433 | biostudies-arrayexpress
Project description:R1R2R3-Myb proteins represent an evolutionarily conserved class of Myb family proteins important for cell cycle regulation and differentiation in eukaryotic cells. In plants, this class of Myb proteins are believed to play important roles in cell cycle regulation through transcriptional regulation of G2/M phase-specific genes by binding to common cis-elements, called MSA elements. In Arabidopsis thaliana, MYB3R1 and MYB3R4 act as transcriptional activators and positively regulate cytokinesis by activating transcription of KNOLLE, which encodes a cytokinesis-specific syntaxin. Here, we show that the double mutation myb3r1 myb3r4 causes pleiotropic developmental defects, some of which are due to deficiency of KNOLLE whereas other are not, suggesting multiple target genes are involved. Consistently, microarray analysis of the double mutant revealed altered expression of many genes, among which G2/M-specific genes showed significant overrepresentation of the MSA motif and a strong tendency to be down-regulated by the double mutation. Our results demonstrate, on a genome-wide level, the importance of the MYB3R-MSA pathway for regulating G2/M-specific transcription. In addition, MYB3R1 and MYB3R4 may have diverse roles during plant development by regulating G2/M-specific genes with various functions, as well as genes possibly unrelated to the cell cycle.
2011-09-07 | GSE29433 | GEO
Project description:Promoters of many G2/M phase-specific genes in plants contain mitosis-specific activator (MSA) elements, which act as G2/M phase-specific enhancers and bind with R1R2R3-Myb transcription factors. A least three R1R2R3-Myb proteins are expressed in tobacco (Nicotiana tabacum). To examine the genome-wide effects of NtmybA2 overexpression, we constructed transgenic tobacco BY-2 cell lines overexpressing full-length NtmybA2 protein. In addition, we generated transgenic BY-2 cell lines that overexpress truncated hyperactive form of NtmybA2 (NtmybA2âC) lacking its C-terminal region which negatively regulates its own activity for transcriptional activation. We used a custom-made 16K cDNA microarray for comparative transcriptome analysis of these transgenic tobacco BY-2 cell lines. As control sample, BY-2 cells transformed with empty vector pPZP-35S were used. The transgenic cell lines were analyzed during stationary phase (i.e. day 7-8 after subculture into fresh media). Keywords: Genetic modification 1. pPZP-35S vector control, 2. NtmybA2 overexpressor, 3. C-truncated NtmybA2 (NtmyA2âC) overexpressor
2010-05-22 | E-GEOD-14251 | biostudies-arrayexpress
Project description:Promoters of many G2/M phase-specific genes in plants contain mitosis-specific activator (MSA) elements, which act as G2/M phase-specific enhancers and bind with R1R2R3-Myb transcription factors. A least three R1R2R3-Myb proteins are expressed in tobacco (Nicotiana tabacum). To examine the genome-wide effects of NtmybA2 overexpression, we constructed transgenic tobacco BY-2 cell lines overexpressing full-length NtmybA2 protein. In addition, we generated transgenic BY-2 cell lines that overexpress truncated hyperactive form of NtmybA2 (NtmybA2∆C) lacking its C-terminal region which negatively regulates its own activity for transcriptional activation. We used a custom-made 16K cDNA microarray for comparative transcriptome analysis of these transgenic tobacco BY-2 cell lines. As control sample, BY-2 cells transformed with empty vector pPZP-35S were used. The transgenic cell lines were analyzed during stationary phase (i.e. day 7-8 after subculture into fresh media). Keywords: Genetic modification
2009-02-28 | GSE14251 | GEO
Project description:Temporal and spatial regulation of cell division is central for generating multicellular organs with predictable sizes and shapes. However, it remains largely unclear how genes with mitotic functions are transcriptionally regulated during organogenesis in plants. Here, we showed that a group of R1R2R3-Myb transcription factors are responsible for developmentally controlled downregulation of variety of mitotic genes in Arabidopsis. Loss of their functions resulted in elevated expression of mitotic genes in quiescent cells including those underwent terminal differentiation. Concomitantly, their mutations enhanced cell division activities in various aspects of plant development, generating organs with increased sizes and irregular architectures. In addition, we showed that this type of R1R2R3-Myb proteins are required for oscillated expression of G2/M-specfiic genes, most likely by inhibiting transcription outside of G2/M in the cell cycle. Our finding uncovered a novel plant-specific mechanism in which scheduled expression of G2/M-specific genes may require their global repression both in the cell cycle and during development.
2015-03-31 | GSE52298 | GEO
Project description:Temporal and spatial regulation of cell division is central for generating multicellular organs with predictable sizes and shapes. However, it remains largely unclear how genes with mitotic functions are transcriptionally regulated during organogenesis in plants. Here, we showed that a group of R1R2R3-Myb transcription factors are responsible for developmentally controlled downregulation of variety of mitotic genes in Arabidopsis. Loss of their functions resulted in elevated expression of mitotic genes in quiescent cells including those underwent terminal differentiation. Concomitantly, their mutations enhanced cell division activities in various aspects of plant development, generating organs with increased sizes and irregular architectures. In addition, we showed that this type of R1R2R3-Myb proteins are required for oscillated expression of G2/M-specfiic genes, most likely by inhibiting transcription outside of G2/M in the cell cycle. Our finding uncovered a novel plant-specific mechanism in which scheduled expression of G2/M-specific genes may require their global repression both in the cell cycle and during development. Seedlings (9d-old) or leaves (5d or 15d-old) of the wild type or myb3r mutants were sampled for RNA extraction and hybridization on Affymetrix microarrays.
2015-03-31 | E-GEOD-52298 | biostudies-arrayexpress
Project description:Most E2F-binding sites repress transcription through the recruitment of Retinoblasoma (RB) family members until the end of the G1 cell-cycle phase. Although the MYB promoter contains an E2F-binding site, its transcription is activated shortly after the exit from quiescence, before RB family members inactivation, by unknown mechanisms. We had previously uncovered a nuclear factor distinct from E2F, Myb-sp, whose DNA-binding site overlapped the E2F element and had hypothesized that this factor might overcome the transcriptional repression of MYB by E2F-RB family members. We have purified Myb-sp and discovered that Myc-associated zinc finger proteins (MAZ) are major components. We show that various MAZ isoforms are present in Myb-sp and activate transcription via the MYB-E2F element. Moreover, while forced RB or p130 expression repressed the activity of a luciferase reporter driven by the MYB-E2F element, co-expression of MAZ proteins not only reverted repression, but also activated transcription. Finally, we show that MAZ binds the MYB promoter in vivo, that its binding site is critical for MYB transactivation, and that MAZ knockdown inhibits MYB expression during the exit from quiescence. Together, these data indicate that MAZ is essential to bypass MYB promoter repression by RB family members and to induce MYB expression.
2017-10-04 | PXD006857 | Pride
Project description:To identify genomic regions bound by B-Myb and LIN9 (a subunit of the MuvB complex), we performed ChIP-Sequencing (ChIP-Seq) using chromatin from proliferating HeLa cells in which we can detect a robust association between B-Myb and subunits of the MuvB complex. This analysis allowed us identify late cell cycle or G2/M expressed genes as specific targets of the B-Myb-MuvB complex. Examination of B-Myb and LIN9 binding in asynchronously growing HeLa cells
2012-01-25 | E-GEOD-27030 | biostudies-arrayexpress
Project description:To identify genomic regions bound by B-Myb and LIN9 (a subunit of the MuvB complex), we performed ChIP-Sequencing (ChIP-Seq) using chromatin from proliferating HeLa cells in which we can detect a robust association between B-Myb and subunits of the MuvB complex. This analysis allowed us identify late cell cycle or G2/M expressed genes as specific targets of the B-Myb-MuvB complex.
2012-01-25 | GSE27030 | GEO
Project description:YAP, a major downstream effector of the Hippo signaling pathway, is an important regulator of cell proliferation. Previous studies have shown that YAP cooperates with the two transcription factors E2F and MYC to mediate G1 to S transition by regulating early cell cycle gene expression. On the other hand, the ability of YAP to regulate G2/M gene expression is dependent on the Myb-MuvB (MMB) complex, consisting of the evolutionary MuvB core complex of five proteins and the facultative subunit B-MYB, a transcription factor. We now carried out interaction studies and found that YAP directly binds to the B-MYB subunit of MMB. Disruption of the YAP/B-MYB interaction by overexpression of the YAP binding domain of B-MYB results in errors in cell division. We also show that YAP and MMB interact in vivo in the developing heart. Genome wide expression and binding studies revealed that YAP and MMB regulate an overlapping set of cell cycle genes in cardiomyocytes. Cardiac specific deletion of the LIN9 subunit of MMB prevents the upregulation of cell cycle genes and the increased proliferation of cardiomyocytes lacking the hippo-signaling component SAV1. Similarly, we find that proliferation of postnatal cardiomyocytes induced by constitutive active YAP depends on MMB. Our findings provide new insights in the mechanisms of cell cycle regulation by the Hippo pathway in cardiomyocytes and suggests that YAP and MMB interact to induce genes critical for cell cycle regulation.
2020-05-07 | GSE137132 | GEO