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ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements

ABSTRACT: ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements

PROVIDER: PRJNA946792 | ENA |

REPOSITORIES: ENA

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ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements

Project description:Gene expression is controlled by dynamic localization of thousands of regulatory proteins to precise genomic regions. Understanding this cell-type specific process has been a longstanding goal yet remains challenging because DNA-protein mapping methods generally study one protein at a time. To address this, we developed ChIP-DIP (ChIP Done In Parallel) to generate genome-wide maps of hundreds of diverse regulatory proteins in a single experiment. ChIP-DIP produces highly accurate maps within large pools (>160 proteins), for all classes of DNA-associated proteins, including histone modifications, chromatin regulators, and transcription factors, and across multiple conditions simultaneously. First, we used ChIP-DIP to measure temporal chromatin dynamics in primary dendritic cells following stimulation. Next, we explored quantitative histone combinations that define distinct classes of regulatory elements and characterized their functional activity in human and mouse cell lines. Overall, ChIP-DIP generates context-specific, protein localization maps at consortium scale within any molecular biology lab and experimental system.

2024-11-26 | GSE227773 | GEO

Single-cell chromatin conformation capture of diploid cells by Dip-C (analyzed with the dip-c package)

Project description:To reconstruct the 3D genomes of single diploid human and mouse cells, we performed single-cell chromatin conformation capture by a novel method, Dip-C, on human cells, and re-analyzed published data on mouse cells by the Dip-C algorithm.

2018-08-15 | GSE117109 | GEO

DIP-chip: Rapid and accurate determination of DNA-binding specificity

Project description:Validation of DNA ImmunoPrecipitation with microarray analysis (DIP-chip) technique using the Leu3 DNA binding domain. Keywords: DIP-chip, Leu3

2006-10-13 | GSE6016 | GEO

Gene expression profiling in Dip G-treated HL-60 cells

Project description:To understand the function of the small molecule Dip G, the gene expression profiles of HL-60 cells treated with Dip G were analyzed using the microarray.

2017-07-31 | GSE84652 | GEO

Investigation of Drosophila fruitless neurons that express Dpr/DIP cell adhesion molecules

Project description:Drosophila reproductive behaviors are directed by fruitless neurons. A reanalysis of genomic studies shows that genes encoding dpr and DIP Immunoglobulin superfamily (IgSF) members are expressed in fru P1 neurons. We find that each fru P1 and dpr/DIP (fru P1 ∩ dpr/DIP) overlapping expression pattern is similar in both sexes, but there are dimorphisms in neuronal morphology and cell number. Behavioral studies of fru P1 ∩ dpr/DIP perturbation genotypes indicates that the mushroom body functions together with the lateral protocerebral complex to direct courtship behavior. A single-cell RNA-seq analysis of fru P1 neurons shows that many DIPs have high expression in a small set of neurons, whereas the dprs are often expressed in a larger set of neurons at intermediate levels, with a myriad of dpr/DIP expression combinations. Functionally, we find that perturbations of sex hierarchy genes and of DIP-ε change the sex-specific morphologies of fru P1 ∩ DIP-α neurons.

2021-02-23 | GSE162098 | GEO

Staphylococcus aureus strain:DIP

Project description:Genome assembly of Staphylococcus aureus strain DIP

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Simultaneous Detection of DNA Adenine and Cytosine Methylation using NT-seq [series2: 6mA DIP enrichment]

Project description:DNA methylation plays important roles in foreign DNA defense, mismatch repair, and gene regulation in prokaryotic genomes. Existing methods for DNA methylation detection using next-generation sequencing (NGS) are incapable of simultaneously detecting multiple types of DNA methylation. Here, we present nitrite treatment followed by sequencing (NT-seq), a sequencing method to simultaneously detect adenine and cytosine methylation. We demonstrated that NT-seq reliably detects three types of methylation motifs in E. coli and H. pylori genomes. We further applied NT-seq to a microbial community standard for de novo methylation motif discovery. Finally, by coupling methyl DNA immunoprecipitation and NT-seq (DIP-NT-seq), we showed that 6mA could be accurately mapped at single-base resolution in the bacterial and eukaryotic genomes. NT-seq thus provides a simple and reliable solution for detecting multiple types of DNA methylations.

2022-05-12 | GSE184373 | GEO

Computer Assisted Early Detection of Liver Metastases From fMRI Maps

Project description:The purpose of this protocol is to develop a detailed MRI technique and haemodynamic maps enabling early detection of colorectal metastases in the liver.

| 2037102 | ecrin-mdr-crc

Coop-seq: quantitative measurement of cooperative binding between transcription factors to hundreds of variants simultaneously

Project description:Cooperative binding of transcription factors is known to be important in the regulation of many promoters and enhancers, but current methods to measure cooperativity parameters have been laborious and therefore limited to studying only a few sequence variants at a time. Coop-seq (cooperativity by sequencing) is capable of efficiently and accurately determining the cooperativity parameters for hundreds of different DNA sequences in a single experiment, which we demonstrate using members of the Sox and POU families of transcription factors. Spec-seq directly measures specificity by sequencing. We run an EMSA experiment on TF of interest with a library of DNA targets. Then we extract and sequence the bound and unbound portion of the DNA separately. Finally we count the occurences of each variant in the library and calculate the ratio and the relative binding energy.

2016-12-05 | GSE85122 | GEO

Transneuronal Dpr12/DIP-δ interactions facilitate compartmentalized dopaminergic innervation of Drosophila mushroom body axons

Project description:The mechanisms controlling wiring of neuronal networks are not completely understood. The stereotypic architecture of the Drosophila mushroom-body (MB) offers a unique system to study circuit assembly. The adult medial MB γ-lobe is comprised of a long bundle of axons that wires with specific modulatory and output neurons in a tiled manner defining five distinct zones. We found that the immunoglobulin superfamily protein Dpr12 is cell-autonomously required in γ-neurons for their developmental regrowth into the distal γ4/5 zones, where both Dpr12 and its interacting protein, DIP-δ, are enriched. DIP-δ functions in a subset of dopaminergic neurons that wire with γ-neurons within the γ4/5 zone. During metamorphosis, these dopaminergic projections arrive to the γ4/5 zone prior to γ-axons, suggesting that γ-axons extend through a prepatterned region. Thus, Dpr12/DIP-δ transneuronal interaction is required for γ4/5 zone formation. Our study sheds light onto molecular and cellular mechanisms underlying circuit formation within subcellular resolution.

2021-04-13 | GSE165896 | GEO

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