Profiling Genome-wide Chromatin Methylation with Engineered Posttranslation Apparatus within Living Cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE42792 | GEO | 2013/03/04
SECONDARY ACCESSION(S): PRJNA183346
REPOSITORIES: GEO
Similar Datasets
Project description:We have engineered the chromatin-modifying apparatus and formulated a novel technology, termed Clickable Chromatin Enrichment with parallel DNA sequencing (CliEn-seq), to probe genome-wide chromatin modification within living cells. Examine (E)-hex-2-en-5-ynylation mediated by engineered G9a Y1154A and GLP1 Y1211A in HEK293T cells.
2013-03-04 | E-GEOD-42792 | biostudies-arrayexpress
Project description:Protein methyltransferases (PMTs) have emerged as important epigenetic regulators in myriad biological processes in both normal physiology and disease conditions. However, elucidating PMT-regulated epigenetic processes has been hampered by ambiguous knowledge about in vivo activities of individual PMTs particularly because of their overlapping but nonredundant functions. To address limitations of conventional approaches in mapping chromatin modification of specific PMTs, we have engineered the chromatin-modifying apparatus and formulated a novel technology, termed clickable chromatin enrichment with parallel DNA sequencing (CliEn-seq), to probe genome-wide chromatin modification within living cells. The three-step approach of CliEn-seq involves in vivo synthesis of S-adenosyl-L-methionine (SAM) analogues from cell-permeable methionine analogues by engineered SAM synthetase (methionine adenosyltransferase or MAT), in situ chromatin modification by engineered PMTs, subsequent enrichment and sequencing of the uniquely modified chromatins. Given critical roles of the chromatin-modifying enzymes in epigenetics and structural similarity among many PMTs, we envision that the CliEn-seq technology is generally applicable in deciphering chromatin methylation events of individual PMTs in diverse biological settings.
| S-EPMC3582175 | biostudies-literature
Project description:G-quadruplex (G4) structures exist in single-stranded DNA of chromatins and regulate genome function. However, the native chromatin G4 landscape in living cells has yet to be fully characterized. Herein, we fused BG4 antibody and GFP-tag to construct a live-cell G4 identifier (LiveG4ID). We first displayed its function as a high-specificity chromatin G4 probe in living cells by Dox-induced expression LiveG4ID in HEK293T cells and detecting its cellular localization, biocompatibility and G4-binding specificity. By coupling LiveG4ID with CUT&Tag technology, we established LiveG4ID-seq, a method for mapping native chromatin G4 landscape in living cells. LiveG4ID-seq can identify more chromatin G4 motifs than traditional CUT&Tag and ChIP-seq methods. Using LiveG4ID-seq, we profiled the dynamic landscape of chromatin G4 structures during the cell cycle. These data demonstrate the capacity of LiveG4ID-seq to profile a more accurate G4 landscape in living cells and promote future study on chromatin G4 structures.
2022-01-15 | GSE193496 | GEO
Project description:Methods for direct capturing global substrates of protein-modifying enzymes in living cells are with many challenges, and yet largely unexplored. Here, we report a strategy to directly capture substrates of protein-modifying enzymes via PTM-acceptor residue crosslinking in living cells, enabling global profiling of substrates of PTM-enzymes and validation of PTM-sites in a straightforward manner.
2023-02-22 | PXD040318 |
Project description:Profiling Genome-wide Chromatin Methylation with Engineered Posttranslation Apparatus within Living Cells
| PRJNA183346 | ENA
Project description:G-quadruplex (G4) structures formed by guanine-rich nucleic acids are implicated in essential physiological and pathological processes and serve as important drug targets. The genome-wide detection of G4s in living cells is important for exploring the functional role of G4s but has not yet been achieved due to the lack of a suitable G4 probe. Here we report an artificial 6.7 kDa G4 probe (G4P) protein that binds G4s with high affinity and specificity. We used it to capture G4s in living human, mouse, and chicken cells with the ChIP-Seq technique, yielding genome-wide landscape as well as details on the positions, frequencies, and sequence identities of G4 formation in these cells. Our results indicate that transcription is accompanied by a robust formation of G4s in genes. In human cells, we detected up to >123,000 G4P peaks, of which >1/3 had a fold increase of ≥5 and were present in >60% promoters and ~70% genes. Being much smaller than a scFv antibody (27 kDa) or even a nanobody (12-15 kDa), we expect that the G4P may find diverse applications in biology, medicine, and molecular devices as a G4 affinity agent.
2020-10-13 | GSE133379 | GEO
Project description:Eukaryotic genomes are packaged into chromatin, which is composed of condensed filaments of regularly spaced nucleosomes, resembling beads on a string. The nucleosome contains ~147 bp of DNA wrapped almost twice around a central core histone octamer. The packaging of DNA into chromatin represents a challenge to transcription factors and other proteins requiring access to their binding sites. Consequently, control of DNA accessibility is thought to play a key role in gene regulation. Here, we measure DNA accessibility genome-wide in living budding yeast cells by inducible expression of DNA methyltransferases. We find that the yeast genome is globally accessible to the methylase in living cells, unlike in nuclei, where DNA accessibility is severely limited. Gene bodies are methylated at only slightly slower rates than promoters, indicating that yeast chromatin is highly dynamic in vivo. In contrast, centromeres are strongly protected in vivo. Global shifts in nucleosome positions occur in cells as they are depleted of RSC, or ISW1 and CHD1, indicating that global nucleosome dynamics are at least partly attributable to ATP-dependent chromatin remodelers. We propose that virtually all yeast chromatin is in a state of continuous flux in living cells, but static in nuclei, suggesting that chromatin packaging is not generally repressive.
2024-03-22 | GSE230306 | GEO
Project description:Eukaryotic genomes are packaged into chromatin, which is composed of condensed filaments of regularly spaced nucleosomes, resembling beads on a string. The nucleosome contains ~147 bp of DNA wrapped almost twice around a central core histone octamer. The packaging of DNA into chromatin represents a challenge to transcription factors and other proteins requiring access to their binding sites. Consequently, control of DNA accessibility is thought to play a key role in gene regulation. Here, we measure DNA accessibility genome-wide in living budding yeast cells by inducible expression of DNA methyltransferases. We find that the yeast genome is globally accessible to the methylase in living cells, unlike in nuclei, where DNA accessibility is severely limited. Gene bodies are methylated at only slightly slower rates than promoters, indicating that yeast chromatin is highly dynamic in vivo. In contrast, centromeres are strongly protected in vivo. Global shifts in nucleosome positions occur in cells as they are depleted of RSC, or ISW1 and CHD1, indicating that global nucleosome dynamics are at least partly attributable to ATP-dependent chromatin remodelers. We propose that virtually all yeast chromatin is in a state of continuous flux in living cells, but static in nuclei, suggesting that chromatin packaging is not generally repressive.
2024-03-22 | GSE229797 | GEO
Project description:As a sextual behavior, competence or natural transformation mediates lateral gene transfer, and thereby promotes exchange of antibiotic resistance and virulence traits among bacteria. Competence is assoicated with activation of many genes, rapid build-up of membrane-bound DNA uptake apparatus, and transient growth arrest. It is completely unknown how transformable bacteria recover from the competence-associated status. This work reveals that the membrane-associated HtrA protease enables the pneumococcus (an important human pathogen) to recover from the competence-associated status by breaking down the DNA uptake apparatus. This is achieved by selective degradation of ComEA and ComEC, the major components of the DNA uptake apparatus. Deleting htrA and/or over-expressing comEA-EC led to dramatic delay in competence termination. Based on high conservation of HtrA and DNA uptake proteins among transformable bacterial, the HtrA protease may serve as a general regulator of bacteria recovery from the competence-associated status.
2018-03-22 | GSE112169 | GEO