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ABSTRACT:
PROVIDER: PRJNA732422 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Aromatic dimer dehydrogenases from Novosphingobium aromaticivorans reduce aromatic diketones
| PRJNA731907 | ENA
Project description:Aromatic diketones are a major product of formic acid lignin depolymerization. Novosphingobium aromaticivorans can degrade these diketones, but the enzymes used in this process were unknown. We used RNA-Seq to identify aromatic dimer dehydrogenases as potential candidates for the initial reduction of the aromatic G-diketone, then verified this using in vitro enzyme assays.
2021-05-22 | GSE174697 | GEO
Project description:Aromatic compounds are an important renewable source of commodity chemicals traditionally produced from fossil fuels. Aromatics derived from plant lignin can potentially be converted into commodity chemicals through depolymerization followed by microbial funneling of monomers and low molecular weight oligomers. This study investigates the catabolism of the b-5 linked aromatic dimer dehydrodiconiferyl alcohol (DC-A) by the bacterium Novosphingobium aromaticivorans. We used genome wide screens to identify candidate genes involved in DC-A catabolism. Subsequent in vivo and in vitro analyses of these candidates elucidated a catabolic pathway composed of four required gene products and several partially redundant dehydrogenases that convert DC-A to aromatic monomers that can be funneled into the central aromatic metabolic pathway of N. aromaticivorans. Specifically, a newly identified γ-formaldehyde lyase, PcfL, opens the phenylcoumaran ring to form a stilbene and formaldehyde. A lignostilbene dioxygenase, LsdD, then cleaves the stilbene to generate the aromatic monomers, vanillin and 5-formylferulate (5-FF). We also show that an aldehyde dehydrogenase FerD oxidizes 5-FF before it is decarboxylated by LigW, yielding ferulic acid. We found that some enzymes involved in b-5 catabolism pathway can act on multiple substrates and that some steps in the pathway can be mediated by multiple enzymes, providing new insights into the robust flexibility of aromatic catabolism in N. aromaticivorans. We performed a comparative genomic analysis to predict that key enzymes in the newly discovered b-5 aromatic catabolic pathway are common among Sphingomonads.
2024-02-29 | GSE259365 | GEO
Project description:Microrchidia (MORC) proteins are GHKL ATPases that function in gene silencing in multiple organisms. Animal MORCs also contain CW-type zinc finger domains, which are known to bind to modified histones. We identified mouse MORC3 in a mutant screen for factors required for transgene silencing. We also found that MORC3 localizes to promoters marked by H3K4 trimethylation (H3K4me3) throughout the genome, consistent with its binding to H3K4me3 in vitro. We solved the crystal structure of the MORC3 ATPase-CW domain bound to the nucleotide analog AMPPNP and in complex with a H3K4me3 peptide. The CW domain uses an aromatic cage to bind trimethylated Lys4 and forms extensive hydrogen bonds with the H3 tail. We used native mass spectrometry to show that this region forms ATP dependent dimers, and that dimer formation is enhanced in the presence of non-hydrolyzable ATP analogs. Our work sheds light on aspects of the molecular function of MORC3 and suggests a counterintuitive role of MORC3 in both binding to active promoters and regulating gene silencing.
2016-08-15 | GSE78258 | GEO
Project description:We report ChIP-seq and ChIP-exo data for GR in liver tissue isolated from WT and GRdim mice. Comparison of the mouse models reveals that GR interacts with the genome as both a monomer and dimer. Examination of GR, RNAPII and CEBPb binding in WT and GRdim mice on a genome-wide scale
2015-04-14 | E-GEOD-59752 | biostudies-arrayexpress
Project description:All histone-DNA contacts in a nucleosome must be disrupted for RNA polymerase II (RNAPII) to transcribe through chromatin. However, the structural transitions of the nucleosome during transcription in vivo are unknown. To identify nucleosomal intermediates formed during transcription in vivo, we mapped subnucleosomal protections in Drosophila cells using Micrococcal Nuclease followed by deep sequencing. At the first nucleosome position downstream of the transcription start site, we identified hexasomes lacking an H2A/H2B dimer. Inhibiting topoisomerases or depleting histone chaperones increased dimer loss, whereas inhibiting release of paused RNAPII or reducing RNAPII elongation decreased dimer loss. Our results suggest that positive torsion generated by elongating RNAPII evicts the distal H2A/H2B dimer in vivo. We also identified diagnostic subnucleosomal particle remnants in cell-free human DNA data as a relic of transcribed genes from the tissue-of-origin. Thus the identification of subnucleosomal particle fragments from nuclease protection data represents a general strategy for structural epigenomics.
2017-12-22 | GSE98351 | GEO
Project description:NOTCH/RBPJ/MAML ternary transcriptional complex binds to regulatory element and drives gene expression. The complex can function as monomer and dimer. How dimeric complexes regulate gene expression in human cancer is not well studied. Here, we integrate genomic data sets and analyze Notch dimeric complexes-regulated transcriptome and cis-regulatory elements. A subset of coding and non-coding RNA is Notch dimeric complexes-associated. Dimeric complexes recognition sequence enriched in functional dynamic Notch sites and majority of dimer recognition sequence located in (super-)enhancers. Using CRISPR-Cas9-mediated genome editing, we evaluated the function of one dimer-responsive element located in the promoter region of a noncoding RNA NDANR1 and 5' end 16kb away from HES5. Mutation of SPS in this element reduced expression of HES5 and NDANR1. This finding indicates that dimer-responsive elements can function as enhancer for HES5 and at the same time can function as promoter for noncoding RNA NDANR1. Our study reveals the pervasive role of Notch dimeric complexes in transcriptional regulation in human cancer genome.
2017-08-23 | GSE72175 | GEO
Project description:The purpose of this study is to evaluate the use of a D-dimer based protocol to screen for thrombotic events in colorectal surgical patients. This study is unique because of the multistage screening process for DVT’s using a standardized D-dimer testing methodology and ultrasound that will take place throughout the preoperative, perioperative, and postoperative processes. The data collected from this screening study will help establish the baseline DVT rates in UTMB’s colorectal surgical patients before and after surgery. Additionally, the data from this study can help determine if a D-dimer blood test has predictive value in UTMB’s colorectal surgical patient population. This study may also provide preliminary evidence for further research regarding the adjustment of D-dimer cutoff values. Specifically for patient subsets such as surgical colorectal patients with a moderate pretest probability and clinical conditions associated with low test specificity
| 2405227 | ecrin-mdr-crc
Project description:We provided an improved SELEX-Seq strategy for characterizing DNA-binding specificity of transcription factor. We valided the strategy by characterzing the DNA-binding specificty of NF-M-NM-:B p50 dimer. Proteins of the Nf-kappab family were bound to DNA oligonucleotides containing a degenerate region. The protein-DNA complexes were selected after one or multiple rounds of SELEX and the DNA molecules were deep sequenced.
2014-05-05 | E-GEOD-48660 | biostudies-arrayexpress
Project description:The objective of this study was to analyze AHR activation through aromatic amino acid metabolism. To this end, glioblastoma cells were exposed to aromatic amino acid derived metabolites and their ability to activate AHR was analysed. In addition, AHR activation was evaluated in glioblastoma cells expressing IL4I1, an aromatic amino acid degrading enzyme, with or without shRNA mediated knockdown of AHR.
2020-08-19 | GSE129977 | GEO