Genome-wide chromatin localization profiling of transcription factor MML-1
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PROVIDER: PRJNA508616 | ENA |
REPOSITORIES: ENA
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Project description:MML-1 (Myc and Mondo-Like) encodes a Myc superfamily protein which, together with its partner MXL-2 (Max-like), regulates lifespan via distinct gene sets important for longevity. It is also required for normal migration of ray precursor cells in the male tail and for proper epidermal expression of extracellular matrix component genes. MML-1 binds to MXL-2, required for its protein stability. The MML-1/MXL-2 complex activate transcription mostly via E-box elements.
2024-06-07 | GSE123393 | GEO
Project description:modENCODE_submission_2943 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP198(official name : OP198 genotype : unc-119(ed3); wgIs198(mml-1::TY1 EGFP FLAG C; unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The MML-1::EGFP fusion protein is expressed in the correct mml-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the MML-1 transcription factor. made_by : R Waterston ); Developmental Stage: L3; Genotype: unc-119(ed3); wgIs198(mml-1::TY1 EGFP FLAG C; unc-119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene mml-1; Strain OP198(official name : OP198 genotype : unc-119(ed3); wgIs198(mml-1::TY1 EGFP FLAG C; unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The MML-1::EGFP fusion protein is expressed in the correct mml-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the MML-1 transcription factor. made_by : R Waterston ); temp (temperature) 20 degree celsius
2013-07-11 | E-GEOD-48688 | biostudies-arrayexpress
Project description:Accumulating evidence has demonstrated the presence of inter-tissue communication regulating systemic aging, but the underlying molecular network has not been fully explored. We and others previously showed that two basic helix-loop-helix transcription factors, MML-1 and HLH-30, are required for lifespan extension in several longevity paradigms, including germline-less Caenorhabditis elegans. However, it is unknown what tissues these factors target to promote longevity. Here, using tissue-specific knockdown experiments, we found that MML-1 and its heterodimer partners MXL-2 and HLH-30 act primarily in neurons to extend longevity in germline-less animals. Neuronal functions of MML-1/MXL-2 and HLH-30 are also essential to prevent aging in non-neuronal tissues, including muscle and the intestine. Interestingly, however, both the temporal requirement and the downstream function of MML-1 in neurons were distinct from those of HLH-30. MML-1 was active early, while HLH-30 functioned later in life to sustain longevity in germline-less animals. Moreover, neuronal RNA interference (RNAi)-based transcriptome analysis revealed that the glutamate transporter GLT-5 is a novel downstream target of MML-1 but not HLH-30. Furthermore, the MML-1–GTL-5 axis in neurons is critical to prevent an age-dependent collapse of proteostasis and increased oxidative stress through autophagy and peroxidase MLT-7, respectively, in long-lived animals. Collectively, our study revealed that systemic aging is regulated by a novel molecular network involving neuronal MML-1 function in both neural and peripheral tissues.
2023-09-18 | GSE234429 | GEO
Project description:Accumulating evidence has demonstrated the presence of inter-tissue communication regulating systemic aging, but the underlying molecular network has not been fully explored. We and others previously showed that two basic helix-loop-helix transcription factors, MML-1 and HLH-30, are required for lifespan extension in several longevity paradigms, including germline-less Caenorhabditis elegans. However, it is unknown what tissues these factors target to promote longevity. Here, using tissue-specific knockdown experiments, we found that MML-1 and its heterodimer partners MXL-2 and HLH-30 act primarily in neurons to extend longevity in germline-less animals. Neuronal functions of MML-1/MXL-2 and HLH-30 are also essential to prevent aging in non-neuronal tissues, including muscle and the intestine. Interestingly, however, both the temporal requirement and the downstream function of MML-1 in neurons were distinct from those of HLH-30. MML-1 was active early, while HLH-30 functioned later in life to sustain longevity in germline-less animals. Moreover, neuronal RNA interference (RNAi)-based transcriptome analysis revealed that the glutamate transporter GLT-5 is a novel downstream target of MML-1 but not HLH-30. Furthermore, the MML-1–GTL-5 axis in neurons is critical to prevent an age-dependent collapse of proteostasis and increased oxidative stress through autophagy and peroxidase MLT-7, respectively, in long-lived animals. Collectively, our study revealed that systemic aging is regulated by a novel molecular network involving neuronal MML-1 function in both neural and peripheral tissues.
2023-09-18 | GSE234430 | GEO
Project description:We analyzed the genome wide localization of H3K4me3, H3K27me3 and the NUP98-PHF23 (with V5 tag) fusion protein which binds H3K4me3 via its PHD finger, using ChIP-seq. Results correlated with gene expression profiles. NUP98-PHF23 bound only 1.6% of H3K4me3 marks including Hoxa/b + Meis1. Assess H3K4me3 and H3K27me3 histone marks, and correlate these marks with chromatin binding of the NP23 fusion protein using lymphoblast and myeloblast cell lines derived from NP23 leukemias.
2014-03-06 | E-GEOD-54786 | biostudies-arrayexpress
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:PurposeHighly accelerated B 1 + -mapping based on the Bloch-Siegert shift to allow 3D acquisitions even within a brief period of a single breath-hold.Theory and methodsThe B 1 + dependent Bloch-Siegert phase shift is measured within a highly subsampled 3D-volume and reconstructed using a two-step variational approach, exploiting the different spatial distribution of morphology and B 1 + -field. By appropriate variable substitution the basic non-convex optimization problem is transformed in a sequential solution of two convex optimization problems with a total generalized variation (TGV) regularization for the morphology part and a smoothness constraint for the B 1 + -field. The method is evaluated on 3D in vivo data with retro- and prospective subsampling. The reconstructed B 1 + -maps are compared to a zero-padded low resolution reconstruction and a fully sampled reference.ResultsThe reconstructed B 1 + -field maps are in high accordance to the reference for all measurements with a mean error below 1% and a maximum of about 4% for acceleration factors up to 100. The minimal error for different sampling patterns was achieved by sampling a dense region in k-space center with acquisition times of around 10-12 s for 3D-acquistions.ConclusionsThe proposed variational approach enables highly accelerated 3D acquisitions of Bloch-Siegert data and thus full liver coverage in a single breath hold.
| S-EPMC6491998 | biostudies-literature
Project description:BANC-seq (Binding Affinities to Native Chromatin by sequencing) allows determination of absolute apparent binding affinites of transcription factors to native chromatin in a genome-wide manner. In this study, we establish the method and show that chromatin and DNA sequence define binding affinites of FOXA1, SP1, YY1 and MYC/MAX complex. To relate the identified binding affinities to the actual transcriptional levels of these transcription factors in the cells used in this study, and to confirm that the nuclear isolation protocol used in the study does not lead to loss of nuclear proteins, we have generated whole proteomes including proteomics standards for absolute quantification of proteins. In addition, to validate some of the findings of the study, we have performed PAQMAN (Protein-nucleic acid affinity quantification by MAss spectrometry in nuclear extracts), as well as DNA pulldowns followed by mass spec.
2023-02-09 | PXD038502 | Pride
Project description:modENCODE_submission_2943 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
2013-07-11 | GSE48688 | GEO
Project description:Genome wide localization of SUMO1 and SUMO2/3 proteins revealed an asscociation of SUMO proetins with active chromatin. SUMO proteins are enriched at super enhancers and enhancers and SUMOylation regulates a subset of these super enhancers. Super enhancers regulated by SUMOylation were enriched for transcription factor TFAP2C and SUMOylation negatively regulates TFAP2C localization to enhancers and super enhancers. Proteomics and ChIP-PCR at MYC SE suggests that chromatin bound TFAP2C recruits histone deacetylation complexes that increases upon SAE2 knockdown. Conversely, SUMOylation promoted TFAP2C asscociation with pre-mRNA splicing machinery components. Taken together, our study revealed a critical role of SUMOylation in chromatin modification through an AP-2 family of transcription factor, TFAP2C and a potential role of TFAP2C in pre-mRNA splicing.
2024-04-13 | GSE171804 | GEO