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

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

PROVIDER: PRJEB38395 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR4165150_1.fastq.gz	Fastqsanger.gz
	ERR4165150_2.fastq.gz	Fastqsanger.gz
	ERR4165151_1.fastq.gz	Fastqsanger.gz
	ERR4165151_2.fastq.gz	Fastqsanger.gz
	ERR4165152_1.fastq.gz	Fastqsanger.gz

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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.

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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 of different mouse cell lines

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

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Amplicon based single molecule footprinting on ES cells and derivatives

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Massively multiplex single-molecule oligonucleosome footprinting

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Massively multiplex single-molecule oligonucleosome footprinting

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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.

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