Transcriptomic regulation during meiosis
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
SUBMITTER: Nicolas Robine
PROVIDER: E-GEOD-10944 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE10836: Meiotic time course of Histone H3 occupancy GSE10837: Meiotic time course of the trimethylation of the Lysine 4 of Histone H3 (H3K4me3) in a mutant Spo11F GSE10838: Meiotic time course of Histone H3 occupancy in a mutant Spo11F GSE10839: Meiotic time course of the trimethylation of the Lysine 4 of Histone H3 (H3K4me3) in a mutant clb5Delta-clb6Delta GSE10840: Meiotic time course of the trimethylation of the Lysine 4 of Histone H3 (H3K4me3) GSE10944: Transcriptomic regulation during meiosis GSE10947: Transcriptomic regulation during meiosis (Spo11Y135F mutant) GSE10948: Transcriptomic regulation during meiosis (Clb5Delta-Clb6Delta mutant) GSE12879: Meiotic DNA double strand breaks in wild-type and set1 cells Keywords: SuperSeries Refer to individual Series
2008-10-31 | E-GEOD-11004 | biostudies-arrayexpress
Project description:We studied the meiotic regulation of transcription in the mutant Spo11Y135F (deficient for the formation of meiotic double-strand breaks), by comparing the mRNA level at time t=1h to t=8h after meiosis induction, to the mRNA level at time t=0h. Keywords: yeast meiotic time course, transcriptome For each time point, we measured the level of mRNA extracted at the time point to a mRNA meiotic mix composed of mRNA extracted at each time point. We normalize this ratio to the ratio measured at time t=0h and transform into log2ratios. The experiment is carried out in duplicates, from two independant cultures.
2008-10-31 | E-GEOD-10947 | biostudies-arrayexpress
Project description:Nemaline myopathy (NM) is a congenital myopathy that can result in lethal muscle dysfunction and is thought to be a disease of the sarcomere thin filament. Recently, several proteins of unknown function have been implicated in NM, and their role in the disease remains unresolved. Here, we demonstrate that loss of a muscle-specific protein, Klhl40, results in a nemaline-like myopathy in mice that closely phenocopies the muscle abnormalities observed KLHL40 deficient patients. We show that Klhl40 dynamically localizes to the sarcomere I-band and A-band and binds to Nebulin (Neb), a protein frequently implicated in NM, as well as a putative thin filament protein, Lmod3. Klhl40 belongs to the BTB-BACK-Kelch (BBK) family of proteins, some of which have been previously shown to promote degradation of their substrates. In contrast, we find that Klhl40 promotes stability of Neb and Lmod3 and blocks Lmod3 ubiquitination. Accordingly, loss of Klhl40 reduces Neb and Lmod3 protein in skeletal muscle of mice and KLHL40 deficient patients. Because loss of sarcomere thin filament proteins is a frequent cause of NM, our data establishes a possible molecular basis for NM in KLHL40 deficient patients by establishing a novel pro-stability function of Klhl40 for Neb and Lmod3. Total RNA was harvested from quadriceps muscle of three Klhl40 WT (control) and three Klhl40 KO mice. Each KO mouse was sacrificed with a corresponding WT littermate. Tissues were also taken at 0 days of age to minimize confounding gene changes occurring due to malnourishment as the phenotype worsens.
2014-04-08 | E-GEOD-56570 | biostudies-arrayexpress
Project description:Comparison of L. lactis NZ9000 ?lmrR versus L. lactis NZ9000 wild type Keywords: Transcription profiling Comparison between strain lacking transcriptional regulator LmrR of major Lactococcal mdr transporter LmrCD, and wild type parental strain.
2007-10-04 | E-GEOD-9168 | biostudies-arrayexpress
Project description:We studied the meiotic regulation of transcription in the mutant Clb5Delta-Clb6Delta (deficient for the meiotic replication), by comparing the mRNA level at time t=1h to t=8h after meiosis induction, to the mRNA level at time t=0h. Keywords: yeast meiotic time course, transcriptome For each time point, we measured the level of mRNA extracted at the time point to a mRNA meiotic mix composed of mRNA extracted at each time point. We normalize this ratio to the ratio measured at time t=0h and transform into log2ratios.
2008-10-31 | E-GEOD-10948 | biostudies-arrayexpress
Project description:To study the meiotic dynamic of the methylation of H3K4, in relation with the transcriptomic regulation, we determine the meiotic time-course of H3K4me3 by ChIP-chip. Keywords: ChIP-chip, meiotic time course, histone modification Strain ORD7339 meiotic time-course from 0 to 6h. Immunoprecipitation with rabbit polyclonal anti-triMe H3K4 (Abcam #Ab8580).
2010-05-17 | E-GEOD-10840 | biostudies-arrayexpress
Project description:Spinal Muscular Atrophy (SMA) is a devastating neuromuscular disease caused by hypomorphic loss of function in the Survival Motor Neuron (SMN) protein. SMA presents across broad spectrum of disease severity. Unfortunately, vertebrate models of intermediate SMA have been difficult to generate and are thus unable to address key aspects of disease etiology. To address these issues, we developed a Drosophila model system that recapitulates the full range of SMA severity, allowing studies of pre-onset biology as well as late-stage disease processes. In this study, TMT-based quantitative proteomic profiling was performed on mild and intermediate Drosophila models of SMA to elucidate proteins and pathways that contribute to the disease. Using this approach, we elaborated a role for the SMN complex in the regulation of innate immune signaling.
2024-04-11 | PXD046801 | Pride
Project description:Three types of phenotypic expression of M-CM-^_-lactam resistance has been reported in MRSA: heterogeneous-, homogeneous-, and Eagle-type resistance. Heterogeneous to homogeneous (hetero-to-homo) conversion of M-CM-^_-lactam resistance is postulated to be caused by a chromosomal mutation (chr*) together with mecA-gene expression. The Eagle-type resistance is a special pattern of chr* expression in the pre-MRSA strain N315 under the strong mecI-gene mediated repression of mecA gene transcription. Here, for the identification of chr*, experiments were conducted using an in-vitro derived homogeneously imipenem-resistant MRSA strain N315M-bM-^HM-^FIPH5 (M-bM-^HM-^FIPH5). The strain was selected with imipenem 8 mg/L from the heterogeneously imipenem-resistant MRSA strain N315M-bM-^HM-^FIP (M-bM-^HM-^FIP). The whole genome sequencing of M-bM-^HM-^FIPH5 revealed the presence of a unique mutation in the rpoB gene, rpoB(N967I), causing the amino-acid (AA) substitution of Asp by Ile at the 967th AA position of the RNA polymerase M-CM-^_ subunit. The effect of the mutation on the phenotypic change was confirmed by constructing and studying the phenotype of the strains H5rpoB(I967N), a M-bM-^HM-^FIPH5-derived strain cured of the rpoB mutation, and N315rpoB(N967I), a N315-derived strain introduced with the mutated rpoB gene. H5rpoB(I967N) regained the hetero-MRSA phenotype, and the mutant strain N315rpoB(N967I) showed an Eagle-type phenotype similar to that of N315h4. Furthermore, subsequent whole genome sequencing revealed that N315h4 also had a missense mutation in the rpoB gene rpoB(R644H). The rpoB mutations caused decreased autolysis, prolonged doubling-time, and tolerance to bactericidal concentrations of methicillin. We concluded that the certain rpoB mutations are chr* responsible for the hetero-to-homo phenotypic conversion of MRSA. We compared the gene expression profiles of the wild-type strain and rpoB mutant (N967I) using a 60mer oligo array.
2013-08-27 | E-GEOD-42218 | biostudies-arrayexpress
Project description:Myocardin-related transcription factors (MRTFs) play a central role in the regulation of actin expression and cytoskeletal dynamics. Stimuli that promote actin polymerization allow for shuttling of MRTFs to the nucleus where they activate serum response factor (SRF), a regulator of actin and other cytoskeletal protein genes. SRF is an essential regulator of skeletal muscle differentiation and numerous components of the muscle sarcomere, but the potential involvement of MRTFs in skeletal muscle development has not been examined. We explored the role of MRTFs in muscle development in vivo by generating mutant mice harboring a skeletal muscle-specific deletion of MRTF-B and a global deletion of MRTF-A. These double knockout (dKO) mice were able to form sarcomeres during embryogenesis. However, the sarcomeres were abnormally small and disorganized, causing skeletal muscle hypoplasia and perinatal lethality. Transcriptome analysis demonstrated dramatic dysregulation of actin genes in MRTF dKO mice, highlighting the importance of MRTFs in actin cycling and myofibrillogenesis. MRTFs were also necessary for the survival of skeletal myoblasts and for the efficient formation of intact myotubes. Our findings reveal a central role for MRTFs in sarcomere formation during skeletal muscle development and point to the potential involvement of these transcriptional coactivators in skeletal myopathies. Gene expression profile was generated comparing wild type (WT) and HSA-Cre, MRTF-A/B double knockout mice, by deep seqencing, with three biological replicates, using Illumina HiSeq 2500.
2016-08-02 | E-GEOD-84063 | biostudies-arrayexpress
Project description:ChIP-chip was performed to identify the genomic binding locations for the termination factors Nrd1, and Rtt103, and for RNA polymerase (Pol) II phosphorylated at the tyrosine 1 and threonine 4 position of its C-terminal domain (CTD). In different phases of the transcription cycle, Pol II recruits different factors via its CTD, which consists of heptapeptide repeats with the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. Here we show that the CTD of transcribing yeast Pol II is phosphorylated at Tyr1, and that this impairs recruitment of termination factors. Tyr1 phosphorylation levels rise downstream of the transcription start site (TSS), and decrease before the polyadenylation (pA) site. Tyr1-phosphorylated gene bodies are depleted of CTD-binding termination factors Nrd1, Pcf11, and Rtt103. Tyr1 phosphorylation blocks CTD binding by these termination factors, but stimulates binding of elongation factor Spt6. These results show that CTD modifications can not only stimulate but also block factor recruitment, and lead to an extended CTD code for transcription cycle coordination.
2012-06-29 | E-MTAB-1060 | biostudies-arrayexpress