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Amplicon based single molecule footprinting on ES cells and derivatives

ABSTRACT: Amplicon based single molecule footprinting on ES cells and derivatives

PROVIDER: PRJEB38056 | ENA |

REPOSITORIES: ENA

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Amplicon based single molecule footprinting on ES cells and derivatives

Project description:Single Molecule Footprinting (SMF) data from Sonmezer et al., 2020. SMF data is obtained by treating isolated nuclei with methyltransferases, where binding of proteins on DNA, e.g. nucleosomes and TFs, leave behind unmethylated cytosines as footprints. Data in this experiment comprises SMF data obtained from ES cells and various derivatives of ES cells, such DNMT-null, REST-knockout ES cells, neural progenitors and ES cells treated with NRF1 sirNA.

2020-12-26 | E-MTAB-9033 | biostudies-arrayexpress

Bait-capture based single molecule footprinting on ES cells and derivatives

Project description:Bait-capture based single molecule footprinting on ES cells and derivatives

| PRJEB38395 | ENA

Bait-capture based single molecule footprinting on ES cells and derivatives

Project description:Bait-capture based Single Molecule Footprinting (SMF) data from Sonmezer et al., 2020. SMF data is obtained by treating isolated nuclei with methyltransferases, where binding of proteins on DNA, e.g. nucleosomes and TFs, leave behind unmethylated cytosines as footprints. Data in this experiment comprises SMF data obtained from ES, DNMT-TKO, and neural progenitor (NP) cells. These data were generated by employing Agilent Sure-Select Mouse Methyl-Seq kit, enriching the sample for regulatory regions of mouse genome prior to library preparation. Thus, these data contain high coverage accessibility information at regulatory loci in different cell types.

2021-05-04 | E-MTAB-9123 | biostudies-arrayexpress

Bait-capture based single molecule footprinting of different mouse cell lines

Project description:Bait-capture based Single Molecule Footprinting (SMF) data from Kreibich et al., 2022. SMF data is obtained by treating extracted nuclei with a GpC methyltransferase, where binding of proteins on DNA, e.g. nucleosomes and transcription factors (TFs), leave behind unmethylated GpCs as footprints. Data in this experiment comprises SMF data obtained from WT embryonic stem cells (ES), DNMT TKO ES, TET TKO ES, F1 hybrid ES (129/CAST), neural progenitor (NP),�myoblast (C2C12) and�murine erythroleukemia (MEL)�cells. These data were generated by employing Agilent Sure-Select Mouse Methyl-Seq kit, enriching the sample for cis-regulatory regions of the mouse genome prior to library preparation. Thus, these data contain high coverage accessibility information at regulatory loci in different cell types. The SMF procedure maintains the endogenous DNA methtylation in CpG context, allowing the simultaneous detection of chromatin accessibility, TF binding and endogenous DNA methylation.

2023-02-06 | E-MTAB-11700 | biostudies-arrayexpress

Massively multiplex single-molecule oligonucleosome footprinting

Project description:Massively multiplex single-molecule oligonucleosome footprinting

| PRJNA681807 | ENA

Massively multiplex single-molecule oligonucleosome footprinting

Project description:SAMOSA is a single-molecule oligonucleosome footprinting technology, which can be employed to reveal nucleosome patterns (nucleosome positioning, nucleosome repeat length) at transcription factor binding sites and epigenomic domains.

2020-12-02 | GSE162410 | GEO

High-Throughput Single-Molecule R-loop Footprinting Reveals Principles of R-loop Formation

Project description:High-Throughput Single-Molecule R-loop Footprinting Reveals Principles of R-loop Formation

| PRJNA541182 | ENA

Genome-wide single molecule footprinting reveals high RNA polymerase II turnover at paused promoters

Project description:Transcription initiation entails chromatin opening followed by pre-initiation complex formation and RNA Polymerase II recruitment. Subsequent polymerase elongation requires additional signals, resulting in increased residence time downstream of the start site, a phenomenon referred to as pausing. Here we harnessed single molecule footprinting to quantify distinct steps of initiation in vivo throughout the drosophila genome. This identifies the impact of promoter structure on initiation dynamics in relation to nucleosomal occupancy. Additionally, perturbation of transcriptional initiation reveals an unexpected high turnover of polymerases at paused promoters--an observation confirmed at the level of nascent RNAs. These observations argue that absence of elongation is largely caused by premature termination rather than stable polymerase stalling. In support of this non-processive model, we observe that induction of the paused heat-shock promoter depends on continuous initiation. Our study provides a framework to quantify protein binding at single molecule resolution and refines concepts of transcriptional pausing.

2017-06-23 | GSE77369 | GEO

Carbene Footprinting Accurately Maps Binding Sites in Protein-Ligand and Protein-Protein Interactions

Project description:Specific interactions between proteins and their binding partners are fundamental to life processes. Differential protein footprinting using a new and efficient, photo-activated aryltrifluromethylcarbene probe together with mass spectrometry has been employed to identify protein-ligand and protein-protein interaction sites. In a model protein-small molecule system, the location of a penta-N-acetylchitopentaose carbohydrate substrate was accurately mapped to the binding cleft of lysozyme. As a fine detail, footprinting revealed disruption of an intramolecular hydrogen-bond network within lysozyme, which is known to be associated with substrate binding. In a more complex example, the interactions between a 100 kDa, multi-domain deubiquitinating enzyme, USP5, and a diubiquitin substrate were located to different functional domains thus clarifying uncertainties from an X-ray crystal structure of USP5. The much improved properties of this bespoke diazirine probe make differential carbene footprinting a viable method for rapid and accurate identification of protein binding sites utilizing benign, near-UV photoactivation.

2016-12-19 | PXD004971 | Pride

Chem-Seq of chemical derivatives in MM1S cells

Project description:An ability to map the global interactions of a chemical entity with chromatin genome-wide could provide new insights into the mechanisms by which a small molecule perturbs cellular functions. we developed a method that uses chemical derivatives and massively parallel DNA sequencing (Chem-Seq) to identify the sites bound by small chemical molecules throughout the human genome.

2013-12-13 | GSE44098 | GEO

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