RNA-Seq of Drosophila melanogaster Cdk12-null mutants versus control
Ontology highlight
ABSTRACT:
INSTRUMENT(S): NextSeq 500
ORGANISM(S): Drosophila melanogaster
SUBMITTER: Hannah Clarke
PROVIDER: E-MTAB-12090 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We describe the epigenetic profiling of the H3K9me2 and HP1a in Drosophila third instar larvae before and after CDK12 depletion by RNA interference (RNAi). Here we show that CDK12 regulates heterochromatin dynamics in Drosophila chromosomes. Depletion of CDK12 induces the increased HP1a and H3K9me2 binding profile on the coding region of euchromatic genes, with the X chromosome being the most affected. These results are consistent with the polytene chromosome immunostaining pattern of HP1a and H3K9me2 after CDK12 knockdown in our initial cytological observations, which show that CDK12 depletion induce heterochromatin spreading on euchromatic arms, especially on the X chromosome. This study describes a novel role of the CDK12 complex in controlling the epigenetic transition between euchromatin and heterochromatin. Examination of the genome-wide H3K9me2 and HP1a binding profile in wildtype larvae (WT) and CDK12-depleted larvae (CDK12-KD). Examination of the genome-wide CDK12 binding profile in wildtype larvae (WT). Twelve independent immunoprecipitations were conducted for each antibody. Two biological replicates were performed.
2015-11-02 | E-GEOD-63011 | biostudies-arrayexpress
Project description:Immunocytochemical studies revealed that dG9a moves into nucleus after cycle 8 and appears to regulate gene expression by di-methylating H3K9 from cycle 8 to cycle 11. To determine which genes are regulated by dG9a during cycles 8-11, we examined mRNA levels by performing RNA-sequence analysis using early embryos (0-2 h after egg laying) of dG9a null mutant and wild type as a control mRNA profiles of about 0-2h-old embryos of wild type (CantonS) and dG9a-depleted (dG9aRG5) strain
2015-08-01 | E-GEOD-56665 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE40894: The Oscillating miRNA 959-964 cluster impacts Drosophila feeding time and other circadian outputs [expression]. GSE40943: The Oscillating miRNA 959-964 cluster impacts Drosophila feeding time and other circadian outputs [miRNA-seq]. Refer to individual Series
2012-11-02 | E-GEOD-40981 | biostudies-arrayexpress
Project description:We sequenced mRNA extracted from heads of a D. melanogaster population that was sedated with a stream of ethanol saturated vapor, 30 minutes before RNA extraction; and from an age-matched untreated control group. Differential gene expression between the two groups was calculated and reported. Examination of mRNA levels in heads of D. melanogaster adult females after ethanol exposure was performed using next generation sequencing (NGS) technology.
2016-02-11 | E-GEOD-77792 | biostudies-arrayexpress
Project description:Using high throughput sequencing of Drosophila head RNA, a small set of miRNAs that undergo robust circadian oscillations in levels were discovered. We concentrated on a cluster of six miRNAs, mir-959-964, all of which peak at about ZT12 or lights-off. The data indicate that the cluster pri-miRNA is transcribed under bona fide circadian transcriptional control and that all 6 mature miRNAs have short half-lives, a requirement for oscillating. Manipulation of food intake dramatically affects the levels and timing of cluster miRNA transcription with no more than minor effects on the core circadian oscillator. This indicates that the central clock regulates feeding, which in turn regulates proper levels and cycling of the cluster miRNAs. Viable Gal4 knock-in as well as cluster knock-out and over-expression strains were used to localize cluster miRNA expression as well as explore their functions. The adult head fat body is a major site of expression, and feeding behavior, innate immunity, metabolism, and perhaps stress responses are under cluster miRNA regulation. The feeding behavior results indicate that there is a feedback circuit between feeding time and cluster miRNA function as well as a surprising role of post-transcriptional regulation in these behaviors and physiology. Six samples of small RNA libraries (RNA size 19 to 29 nucleotides long) were prepared from Drosophila heads, each collected at one circadian time point during a light-dark cycle (ZT0, ZT4, ZT8, ZT12, ZT16, ZT20).
2012-11-02 | E-GEOD-40943 | biostudies-arrayexpress
Project description:The subcellular localization and translation of messenger RNA (mRNA) supports functional differentiation between cellular compartments. In neuronal dendrites, local translation of mRNA provides a rapid and specific mechanism for synaptic plasticity and memory formation, and might be involved in the pathophysiology of certain brain disorders. Despite the importance of dendritic mRNA translation, little is known about which mRNAs can be translated in dendrites in vivo and when their translation occurs. Here we collect ribosome-bound mRNA from the dendrites of CA1 pyramidal neurons in the adult mouse hippocampus. We find that dendritic mRNA rapidly associates with ribosomes following a novel experience consisting of a contextual fear conditioning trial. High throughput RNA sequencing followed by machine learning classification reveals an unexpected breadth of ribosome-bound dendritic mRNAs, including mRNAs expected to be entirely somatic. Our findings are in agreement with a mechanism of synaptic plasticity that engages the acute local translation of functionally diverse dendritic mRNAs. RNA-Seq of ribosome-bound mRNA immunoprecipitated from dendrites and soma of CA1 pyramidal neurons in the mouse hippocampus
2014-07-30 | E-GEOD-58343 | biostudies-arrayexpress
Project description:Yorkshire pigs were divergently selected for residual feed intake (RFI) for 8 generations. Pigs with low RFI have reduced feed intake. Based on the resource allocation theory, we hypothesize that these low RFI pigs might have compromised immune response to immune stimulation. To test this hypothesis, twenty eight gilts of initial body weight (BW) of 63 4 kg from pigs selected for low RFI and high RFI were randomly selected for the ISU RFI selection project and utilized in two replicates (14 pigs/replicate) for this study. All pigs were housed in individual metabolism pens, had free access to water and were fed a corn-soy-based diet twice daily, and feed restricted (1.5 kg/day) as previously described. After a 9-day adaptation period pigs were randomly assigned within line to either a control (n = 6, three pigs per line) or lipopolysaccharide (LPS) challenge (n = 8, 4 pigs per line) group. Pigs in the challenge group were then repeatedly challenged with an intramuscular injection of 30, 36, 39, and 42 g/kg BW of LPS from E. coli O5:B5 (sigma-Aldrich, St. Louis, MO) dissolved in saline solution at time points 0, 48, 96, and 144 hours post initial injection (hpi) to compensate for LPS tolerance after initial injection, respectively, while animals in the control group were injected with an equivalent volume of saline solution at the equivalent time points. Rectal temperatures of individual pigs were measured immediately before the initial injection (serving as baseline, called 0 hpi for convenience), and 2, 4, 6, and 24 hpi, and 0, 4, 24 hours after each subsequent injection for all pigs. Blood samples were collected from the jugular vein into TempusTM Blood RNA tubes (Life Technologies, Grand Island, NY) for long-term storage at -80 C, EDTA tubes (BD, Franklin Lakes, NJ) for CBC tests and serum tubes for cytokine assays at 0, 2, 6, 24 and 168 hpi. At 168 hpi, all pigs were euthanized via barbiturate overdose, exsanguinated and tissue samples including the longissimus dorsi muscle, liver, spleen, and ileum were isolated, cleaned an frozen for later use. This study only focused on samples and data collected for the first 24 hours. Total RNA was extracted from the 32 blood samples of the treatment group in Replicate 2, collected at 0, 2, 6, and 24 hpi, by using preserved blood RNA purification kit I (Norgen Biotek Corp, Thorold, Ontario) per manufacturers instruction. On-column DNA digestion was performed as described using DNase I (Qiagen, Valencia, CA). Globin transcripts (HBB and HBA) were depleted by following an RNase H-mediated method. The quantity and integrity of the RNA were monitored by using Nanodrop 2000 (Thermo Scientific, Waltham, MA) and Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) before and after globin depletion. The efficiency of globin depletion of each sample was checked by conventional RT-qPCR with -actin and GAPDH as the internal controls. Globin depletion efficiencies for all RNA samples were above 85%.
2017-03-24 | E-MTAB-5606 | biostudies-arrayexpress
Project description:Zfp800 was identified by Gene Co-expression Network analysis to be an interesting candidate gene involved in endocrine specification and β-cell maturation. We found that Zfp800 null mice exhibited early post-natal lethality, and at E18.5 their pancreata exhibited a reduced number of pancreatic endocrine cells, alterations in exocrine cell morphology, and marked changes in genes involved in protein translation, hormone secretion, and developmental pathways in the pancreas.
2021-03-02 | E-MTAB-9538 | biostudies-arrayexpress
Project description:Biallelic loss of cyclin-dependent kinase 12 (CDK12) defines a unique molecular subtype of metastatic castration resistant prostate cancer (mCRPC). It remains unclear, however, whether CDK12 loss per se is sufficient to drive prostate cancer development—either alone, or in the context of other genetic alterations—and whether CDK12-mutant tumors exhibit sensitivity to specific pharmacotherapies. Here, we demonstrate that tissue-specific Cdk12 ablation is sufficient to induce preneoplastic lesions in the mouse prostate. Allograft-based CRISPR screening demonstrated that Cdk12 loss is positively associated with p53 inactivation, but negatively associated with Pten inactivation—similar to what is seen in human mCRPC. Consistent with this, ablation of Cdk12 in prostate organoids with concurrent p53 loss promotes their proliferation and ability to form tumors in mice, while Cdk12 knockout in the Pten-null prostate cancer mouse model abrogates tumor growth. Bigenic CDK12 and p53 loss allografts represent a new syngeneic model for the study of prostate cancer. Cdk12-null organoids (either with or without p53 co-ablation) and patient-derived xenografts from tumors with CDK12 inactivation are highly sensitive to inhibition or degradation of its paralog kinase, CDK13. Together, these data identify CDK12 as a bona fide tumor suppressor gene with impact on tumor progression and paralog-based synthetic lethality is a promising strategy for treating CDK12 mutant mCRPC.
2024-04-17 | GSE254387 | GEO
Project description:Biallelic loss of cyclin-dependent kinase 12 (CDK12) defines a unique molecular subtype of metastatic castration resistant prostate cancer (mCRPC). It remains unclear, however, whether CDK12 loss per se is sufficient to drive prostate cancer development—either alone, or in the context of other genetic alterations—and whether CDK12-mutant tumors exhibit sensitivity to specific pharmacotherapies. Here, we demonstrate that tissue-specific Cdk12 ablation is sufficient to induce preneoplastic lesions in the mouse prostate. Allograft-based CRISPR screening demonstrated that Cdk12 loss is positively associated with p53 inactivation, but negatively associated with Pten inactivation—similar to what is seen in human mCRPC. Consistent with this, ablation of Cdk12 in prostate organoids with concurrent p53 loss promotes their proliferation and ability to form tumors in mice, while Cdk12 knockout in the Pten-null prostate cancer mouse model abrogates tumor growth. Bigenic CDK12 and p53 loss allografts represent a new syngeneic model for the study of prostate cancer. Cdk12-null organoids (either with or without p53 co-ablation) and patient-derived xenografts from tumors with CDK12 inactivation are highly sensitive to inhibition or degradation of its paralog kinase, CDK13. Together, these data identify CDK12 as a bona fide tumor suppressor gene with impact on tumor progression and paralog-based synthetic lethality is a promising strategy for treating CDK12 mutant mCRPC.
2024-04-17 | GSE254388 | GEO