Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA298050 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2571450.fastq.gz | Fastqsanger.gz | |||
| SRR2571460.fastq.gz | Fastqsanger.gz | |||
| SRR2571470.fastq.gz | Fastqsanger.gz | |||
| SRR2571480.fastq.gz | Fastqsanger.gz | |||
| SRR2571451.fastq.gz | Fastqsanger.gz |
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Project description:Protein post-translational modification regulates near every aspect of cellular processes in eukaryotes. However, the identification of new protein post-translational modification is very challenging. Here, using genetically encoded unnatural amino acids as chemical probes, we report the identification and validation of a previously unreported form of protein post-translational modification, aminoacylated lysine ubiquitination, in which the modification occurs on the α-amine group of aminoacylated lysine. We identify more than two thousands of unique aminoacylated lysine ubiquitination sites on all 20 aminoacylated lysines in two human cell lines. The aminoacylated lysine ubiquitination modifications can mediate rapid protein degradation, complementing the canonical lysine ubiquitination-mediated proteome degradation. Furthermore, we demonstrate that the ubiquitin conjugating enzyme UBE2W acts as a writer of aminoacylated lysine ubiquitination and facilitates the ubiquitination of internal α-amine groups on proteins using an unexpected enzymatic activity. More broadly, the discovery and validation of aminoacylated lysine ubiquitination paves the way for the identification and verification of new protein post-translation modifications with the genetic code expansion strategy.
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Project description:A generalizable strategy with programmable site-specificity for in situ profiling of histone modifications on unperturbed chromatin remains highly desirable but challenging. We herein developed a Single-site-resolved multi-omics (SiTomics) strategy for systematic mapping of dynamic modifications, and subsequent profiling of chromatinized proteome and genome defined by specific chromatin acylations in living cells. By leveraging the genetic code expansion strategy, our SiTomics toolkit revealed distinct crotonylation (e.g., H3K56cr) and β-hydroxybutyrylation (e.g., H3K56bhb) upon short chain fatty acids stimulation, and established linkages for chromatin acylation mark-defined proteome, genome and functions. This led to the identification of GLYR1 as a distinct interacting protein in modulating H3K56cr’s gene body localization as well as the discovery of an elevated super-enhancer repertoire underlying bhb-mediated chromatin modulations. SiTomics offers a platform technology for elucidating the “metabolites-modification-regulation” axis, which is widely applicable for multi-omics profiling and functional dissection of modifications beyond acylations and proteins beyond histones.
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Project description:A generalizable strategy with programmable site-specificity for in situ profiling of histone modifications on unperturbed chromatin remains highly desirable but challenging. We herein developed a Single-site-resolved multi-omics (SiTomics) strategy for systematic mapping of dynamic modifications, and subsequent profiling of chromatinized proteome and genome defined by specific chromatin acylations in living cells. By leveraging the genetic code expansion strategy, our SiTomics toolkit revealed distinct crotonylation (e.g., H3K56cr) and β-hydroxybutyrylation (e.g., H3K56bhb) upon short chain fatty acids stimulation, and established linkages for chromatin acylation mark-defined proteome, genome and functions. This led to the identification of GLYR1 as a distinct interacting protein in modulating H3K56cr’s gene body localization as well as the discovery of an elevated super-enhancer repertoire underlying bhb-mediated chromatin modulations. SiTomics offers a platform technology for elucidating the “metabolites-modification-regulation” axis, which is widely applicable for multi-omics profiling and functional dissection of modifications beyond acylations and proteins beyond histones.
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Project description:Genetically encoded unnatural amino acids provide powerful strategies for modulating the molecular functions of proteins in mammalian cells. However this approach has not been coupled to genome-wide measurements, because efficient unnatural amino acid incorporation is limited to readily transfectable cells and leads to very heterogeneous expression. We demonstrate that rapid piggybac integration of the orthogonal pyrrolysyl-tRNA synthetase (PylS)/tRNAPyl CUA pair (and its derivatives) into the mammalian genome enables efficient, homogeneous unnatural amino acid incorporation into target proteins in diverse cells, and we reveal the distinct transcriptional responses of ES cells and MEFs to amber suppression. Genetically encoding Nε-acetyl-lysine in place of six lysine residues in histone H3, that are known to be post-translationally acetylated, enables deposition of pre-acetylated histones into cellular chromatin, via a synthetic pathway that is orthogonal to enzymatic modification, allowing us to determine the consequences of acetylation at specific amino acids in histones on gene expression. mRNA was sequenced using polyA-enrichment and Truseq library preparation protocol. Two biological replicates were sequences for each cell line and condition
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