An essential role for PTIP in mediating Hox gene regulation along PcG and trxG pathways
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ABSTRACT:
PROVIDER: PRJNA841579 | ENA |
REPOSITORIES: ENA
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Project description:During Drosophila development, Polycomb-group and Trithorax-group proteins function to ensure correct maintenance of transcription patterns by epigenetically repressing or activating target gene expression. To get a deep insight into the PcG and trxG pathways, we investigated a BRCT domain-containing protein called PTIP, which was generally identified as a transcriptional coactivator and belongs to the TRR complex. At the genome scale, we sorted given PTIP binding peaks into two groups: PTIP/TRR-cobound and PTIP/PC-cobound peaks. In particular, we found that PTIP mediates the molecular switch between H3K4me3/H3K27ac and H3K27me3 histone modifications at TRR or PC occupied regions. Thus, we suggest that PTIP is a mediator rather than a dedicated co-activator along PcG and trxG pathways. Our hypothesis is further supported by the genetic assay: PTIP interacts genetically with either PcG or TrxG in a dosage-dependent manner, suggesting that PTIP functions as a co-factor of PcG/TrxG proteins. In addition, in accordance with the analysis of ChIP-seq, these genetic interactions correlate with modified ectopic HOX protein levels in imaginal discs, which reveals an essential role for PTIP in PcG-mediated Hox gene repression. Hence, we reveal a novel role for PTIP in the epigenetic regulation of gene expression along PcG and trxG pathways.
2022-05-23 | GSE203601 | GEO
Project description:Purpose: The goals of this study are to find out CtBP and PcG coregulated targets through transcriptome profiling (RNA-seq). Methods: Kc cell mRNA profiles of 7-day Ctrl and CtBP and ph-p+E(z) RNAi were generated by deep sequencing, in triplicate, using Illumina HiSeqTM 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: hyper-geometric test and the Benjamini Hochberg FDR correction method and TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the drosophila genome (build dm6) and identified 11,282 transcripts in the 9 samples, among which 381 PcG targets were selected for further analysis. Hierarchical clustering of differentially expressed genes divided these targets into three groups named CtBP co-activated genes,CtBP unaffected genes and CtBP co-repressed genes respectivly. RNA-seq data confirmed CtBP co-activated genes contain 22 known homeobox genes, and 4 of these were validated with qRT–PCR. These results suggest that CtBP is selectively required for the activation of PcG-repressed genes, especially the homeobox transcription factors including Hox genes.Conclusions: Our study represents the first detailed analysis of CtBP and PcG coregulated targets.
2022-05-17 | GSE88807 | GEO
Project description:The microarray reported here is part of a study aimed to investigate whether the gene expression profile of Polycomb, Trithorax and interacting molecules (collectively referred to PcG/TrxG genes) might be related to different states of differentiative potential. In particular , this microarray profiles the expression of PcG/TrxG genes in adipose-derived mesenchymal stem cells isolated from the inguinal fat depot of mice of different age.
2010-11-30 | GSE25068 | GEO
Project description:The microarray reported here is part of a study aimed to investigate whether the gene expression profile of Polycomb, Trithorax and interacting molecules (collectively referred to PcG/TrxG genes) might be related to different states of differentiative potential. In particular , this microarray profiles the expression of PcG/TrxG genes in adipose-derived mesenchymal stem cells isolated from the inguinal fat depot of mice of different age. MSC have been isolated from the inguinal fat pad of FVB mice aged 1, 3, 6, 12 or 24 months.
2010-11-30 | E-GEOD-25068 | biostudies-arrayexpress
Project description:We used ChIP on chip assays to determine the genome wide distribution of a large set of PcG and trxG proteins, their associated histone marks and four candidate DNA-binding factors for PcG protein recruitment.
2008-07-26 | E-MEXP-1708 | biostudies-arrayexpress
Project description:We used ChIP on chip assays to determine the genome wide distribution of a large set of PcG and trxG proteins, their associated histone marks and four candidate DNA-binding factors for PcG protein recruitment.
2008-07-26 | E-MTAB-45 | biostudies-arrayexpress
Project description:PcG and TrxG are important epigenetic regulators of genome expression. Here we have determined genomic distributions of PC, E(Z), H3K27me3, TRX, ASH1, RNA Pol II, H3K4me3, H3K27ac in cultured Drosophila ML-DmD23-c4 cells by hybridization of ChIP products with tiling microarrays
2010-01-08 | GSE18177 | GEO
Project description:PcG and TrxG are important epigenetic regulators of genome expression. Here we have determined genomic distributions of PC, E(Z), H3K27me3, TRX, ASH1, RNA Pol II, H3K4me3, H3K27ac in cultured Drosophila ML-DmBG3-c2 cells by hybridization of ChIP products with tiling microarrays.
2010-01-08 | GSE18100 | GEO
Project description:[original Title] Rapid and synchronous clearance of PcG histone modifications from Hox genes anticipates motor neuron differentiation. Hox genes are expressed in patterns that are spatially and temporally collinear with their chromosomal organization. This feature is an evolutionarily conserved hallmark of embryonic development, and in vertebrates it is critical, among others, for the specification of motor neuron subtypes and the wiring of sensory-motor circuits. We show here that the differentiation of motor neurons from stem cells is accompanied by a synchronous, domain-wide clearance of “repressive” Polycomb (PcG)-dependent histone methylation from Hox gene chromatin domains. These findings argue against the idea, advanced recently, that the collinear dynamics of Hox gene expression invariably reflects the progressive clearance of repressive chromatin modifications. The rapid establishment of stable chromatin domains in response to a transient patterning signal likely serves as a molecular correlate of enduring rostro-caudal neural identity, which underlies the specification of postmitotic motor neuron subtype diversity and neuronal circuit assembly.
2013-07-04 | GSE19447 | GEO
Project description:[original Title] Rapid and synchronous clearance of PcG histone modifications from Hox genes anticipates motor neuron differentiation. Hox genes are expressed in patterns that are spatially and temporally collinear with their chromosomal organization. This feature is an evolutionarily conserved hallmark of embryonic development, and in vertebrates it is critical, among others, for the specification of motor neuron subtypes and the wiring of sensory-motor circuits. We show here that the differentiation of motor neurons from stem cells is accompanied by a synchronous, domain-wide clearance of M-bM-^@M-^\repressiveM-bM-^@M-^] Polycomb (PcG)-dependent histone methylation from Hox gene chromatin domains. These findings argue against the idea, advanced recently, that the collinear dynamics of Hox gene expression invariably reflects the progressive clearance of repressive chromatin modifications. The rapid establishment of stable chromatin domains in response to a transient patterning signal likely serves as a molecular correlate of enduring rostro-caudal neural identity, which underlies the specification of postmitotic motor neuron subtype diversity and neuronal circuit assembly. The differentiation of ventral motor neurons is induced by treating embryonic stem cell cultures with retinoic acid and hedgehog agonist. Here, ChIP-chip using a custom Agilent array is used to profile the occupancy of H3K27me3, H3K4me3, and H3K79me2 at various defined stages during the differentiation process.
2013-07-04 | E-GEOD-19447 | biostudies-arrayexpress