Caenorhabditis elegans
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA203768 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR863647.fastq.gz | Fastqsanger.gz | |||
| SRR863648.fastq.gz | Fastqsanger.gz | |||
| SRR863649.fastq.gz | Fastqsanger.gz | |||
| SRR863650.fastq.gz | Fastqsanger.gz |
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Project description:Inhibition of transcriptional elongation plays an important role in gene regulation in metazoans, including C. elegans, which lacks Negative Elongation Factor homologs. Here we combine genomic and biochemical approaches to dissect a novel role of C. elegans AF10 homolog, ZFP-1, in transcriptional control. We show that ZFP-1 and its interacting partner DOT-1.1 have a global role in negatively modulating the level of Pol II transcription on essential widely expressed genes. Moreover,the ZFP-1/DOT-1.1 complex contributes to progressive Pol II stalling on essential genes during development and to rapid Pol II stalling during stress response. The slowing down of Pol II transcription by ZFP-1/DOT-1.1 is associated with an increase in H3K79 methylation and a decrease in H2B monoubiquitination, which promotes transcription. We propose a model where recruitment of ZFP-1/DOT-1.1 and deposition of H3K79 methylation at highly expressed genes initiates a negative feedback mechanism for modulation of their expression. GRO-seq (Global Run-On sequening) for nascent transcript detectiong on WT and zfp-1(ok554) mutant nematode (C. elegans) larvae in L3 stage, performed in duplicate per condition (4 samples total).
2013-07-05 | E-GEOD-47132 | biostudies-arrayexpress
Project description:Inhibition of transcriptional elongation plays an important role in gene regulation in metazoans, including C. elegans, which lacks Negative Elongation Factor homologs. Here we combine genomic and biochemical approaches to dissect a novel role of C. elegans AF10 homolog, ZFP-1, in transcriptional control. We show that ZFP-1 and its interacting partner DOT-1.1 have a global role in negatively modulating the level of Pol II transcription on essential widely expressed genes. Moreover,the ZFP-1/DOT-1.1 complex contributes to progressive Pol II stalling on essential genes during development and to rapid Pol II stalling during stress response. The slowing down of Pol II transcription by ZFP-1/DOT-1.1 is associated with an increase in H3K79 methylation and a decrease in H2B monoubiquitination, which promotes transcription. We propose a model where recruitment of ZFP-1/DOT-1.1 and deposition of H3K79 methylation at highly expressed genes initiates a negative feedback mechanism for modulation of their expression.
2013-07-05 | GSE47132 | GEO
Project description:Transcriptional control is mediated by interactions of transcription factors with their cognate DNA elements, as well as by epigenetic modifications to chromatin catalyzed by a variety of enzymes. Thus, understanding the crosstalk between transcription factors and epigenetic modifiers is of prime importance. The Dot1-like protein (DOT1L) is an evolutionary conserved methyltransferase with catalytic specificity towards histone 3 lysine 79 (H3K79). DOT1L is essential for mammalian development and has been studied mostly in the context of aggressive leukemias. Recent observations suggest that the role of DOT1L in malignant transformation can be generalized to contexts beyond leukemia. For instance, DOT1L has been implicated in breast cancer progression, and this has been attributed to its cooperation with c-Myc. However, the mechanistic details underlying this association are unknown. Previous work in our lab has shown that DOT-1.1, the C. elegans DOT1L homologue, is recruited to chromatin by ZFP-1 (similarly to DOT1L recruitment by AF10 in mammals), and this complex negatively modulates transcription. Interestingly, promoters of ZFP-1/DOT-1.1 target genes are enriched in E-boxes, the consensus binding motif for c-Myc. Prompted by the exciting hypothesis that DOT-1.1 and MML-1, the C. elegans c-Myc homologue, cooperate genome-wide, we profiled gene expression in wild-type worms and dot-1.1(gk105059), zfp-1(ok554), and mml-1(gk402844) loss-of-function mutants by microarray. We found significant overlaps between genes upregulated in the three mutants, and the same was observed for downregulated genes. A significant global increase of non-coding transcripts was observed in either mutant compared with wild-type. Therefore, ZFP-1/DOT-1.1 and MML-1 co-regulate both coding and non-coding genes and globally inhibit non-coding transcription. Further investigation is underway to uncover the mechanism of cooperation of ZFP-1/DOT-1.1 and MML-1. Profiling of gene expression in wild-type third larval stage (L3) larvae and zfp-1(ok554), dot-1.1(gk105059) and mml-1(gk402844) mutant worms.
2021-09-09 | GSE115677 | GEO
Project description:Histone modification marks such as H3K4me1 and H3K27ac have been used to map putative enhancers, but these marks represent only a fraction of the full repertoire of histone modifications decorating these regulatory regions. In mammals, methylation of histone H3 on lysine 79 (H3K79me), deposited by the methyltransferase DOT1L, is present at enhancers. In C. elegans, putative enhancers have been predicted based on chromatin modifications and regions of chromatin accessibility. Our own overlap analysis has revealed that both DOT-1.1, the C. elegans DOT1L homologue, and its major interacting partner, the chromatin-binding factor ZFP-1 (AF10 in mammals), are enriched at both distal and intragenic enhancers. Previous work has shown that Dot1 proteins prevent encroachment of heterochromatin to actively transcribed regions in yeast and in MLL-rearranged leukemias. Here we find that, in C. elegans, loss of DOT-1.1 is accompanied by ectopic H3K9me2, a hallmark of heterochromatin, at distal and intragenic enhancers. This observation suggests a new role for DOT1L in the control of heterochromatin formation at enhancers, which may partake on the control of developmentally regulated genes.
2024-06-07 | GSE115551 | GEO
Project description:Histone modification marks such as H3K4me1 and H3K27ac have been used to map putative enhancers, but these marks represent only a fraction of the full repertoire of histone modifications decorating these regulatory regions. In mammals, methylation of histone H3 on lysine 79 (H3K79me), deposited by the methyltransferase DOT1L, is present at enhancers. In C. elegans, putative enhancers have been predicted based on chromatin modifications and regions of chromatin accessibility. Our own overlap analysis has revealed that both DOT-1.1, the C. elegans DOT1L homologue, and its major interacting partner, the chromatin-binding factor ZFP-1 (AF10 in mammals), are enriched at both distal and intragenic enhancers. Previous work has shown that Dot1 proteins prevent encroachment of heterochromatin to actively transcribed regions in yeast and in MLL-rearranged leukemias. Here we find that, in C. elegans, loss of DOT-1.1 is accompanied by ectopic H3K9me2, a hallmark of heterochromatin, at distal and intragenic enhancers. This observation suggests a new role for DOT1L in the control of heterochromatin formation at enhancers, which may partake on the control of developmentally regulated genes.
2020-09-08 | GSE150407 | GEO
Project description:Integral nuclear pore proteins bind to Pol III genes and are required for Pol III transcript processing in C. elegans [array]
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Project description:Integral nuclear pore proteins bind to Pol III genes and are required for Pol III transcript processing in C. elegans [seq]
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Project description:Strome Pol II, H3K36me3 and CENP-A in met-1 EEMB
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Project description:Genome-wide RNA Pol II-CTD occupancy in wild type and mutant worms
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Project description:The Mediator complex orchestrates multiple transcription factors with the Pol II apparatus for precise transcriptional control. However, its interplay with the surrounding chromatin remains poorly understood. Here, we analyze differential histone modifications between WT and MED23-/- (KO) cells and identify H2B mono-ubiquitination at lysine 120 (H2Bub) as a MED23-dependent histone modification. Using tandem affinity purification and mass spectrometry, we find that MED23 associates with the RNF20/40 complex, the enzyme for H2Bub, and show that this association is critical for the recruitment of RNF20/40 to chromatin. In a cell-free system, Mediator directly and substantially increases H2Bub on recombinant chromatin through its cooperation with RNF20/40 and the PAF complex. Integrative genome-wide analyses show that MED23 depletion specifically reduces H2Bub on a subset of MED23-contolled genes. Importantly, MED23-coupled H2Bub levels are oppositely regulated during myogenesis and lung carcinogenesis. In sum, these results establish a mechanistic link between the Mediator complex and a critical chromatin modification in coordinating transcription with cell growth and differentiation. To examine the enrichment of H2B ubiquitination, Pol II, H3K4me3, H3K79me3 in WT and KO MED23 MEF cells, we performed H2Bub ChIP-seq, Pol II ChIP-seq, H3K4me3 ChIP-seq and H3K79me3 ChIP-seq assays. 10 high-throughput sequencing data were deposited and WT, KO input data were controls for peak calling.
2015-09-16 | E-GEOD-59518 | biostudies-arrayexpress