Mapping SET1B Chromatin Interactions with DamID using DamMapper, a Comprehensive Snakemake Workflow
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PROVIDER: PRJNA1262346 | ENA |
REPOSITORIES: ENA
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Project description:Background DNA adenine methyltransferase identification followed by sequencing (DamID-seq) is a powerful method used to map genome-wide chromatin-protein interactions. However, the bioinformatic analysis of DamID-seq data presents significant challenges due to the inherent complexities of the data and a notable lack of comprehensive software solutions for data-processing and downstream analysis. Results To address these challenges, we present a comprehensive bioinformatic workflow for DamID-seq data analysis, DamMapper, using the Snakemake workflow management system. Key features include straightforward processing of multiple biological replicates, visualisation of quality control figures, such as a correlation heatmaps and principal component analysis (PCA) plotting, and robust code quality maintained through continuous integration (CI). Reproducibility is ensured across diverse computational environments, including cloud computing and high-performance computing (HPC) clusters, through the implementation of software environments (Conda) and containerisation (Docker/Apptainer). We validated this workflow using a previously published DamID-seq dataset and Furthermore, we apply it to analyse novel datasets for proteins involved in the hypoxia response, specifically the transcription factor HIF-1α and the histone methyltransferase SET1B. This application reveals a strong concordance between our HIF-1α DamID-seq results and ChIP-seq data, and importantly, provides the first genome-wide DNA binding map for SET1B. Conclusions This work provides a validated, reproducible, and feature-rich workflow that overcomes common hurdles in DamID-seq data analysis. By streamlining the processing and ensuring robustness, DamMapper facilitates reliable analysis and enables new biological discoveries, as demonstrated by the characterization of SET1B binding sites. The workflow is available under the MIT license at: https://github.com/niekwit/damid-seq.
2025-08-21 | GSE296995 | GEO
Project description:Hypoxia-inducible transcription factors (HIFs) are fundamental to the cellular adaptation to low oxygen levels but how they interact with chromatin and efficiently activate their target genes is unclear. Using genome-wide mutagenesis in human cancer cells, we define genes required for HIF transcriptional activation, and identify a requirement for the Histone 3 lysine 4 (H3K4) methyltransferase SET1B. Loss of SET1B leads to a selective reduction in HIF transcriptional activity in hypoxia, with SET1B driving expression of genes involved in angiogenesis rather than glycolysis, resulting in impaired tumour establishment in SET1B deficient xenografts. Mechanistically, we show that SET1B is itself oxygen regulated, accumulates on chromatin in hypoxia, and is recruited to HIF target genes through HIF-1a. Accordingly, we show that the hypoxic induction of H3K4me3 at specific HIF targets is both HIF and SET1B dependent, and when impaired, decreases promotor acetylation and gene expression. Together, these findings reveal SET1B as a determinant of site-specific histone methylation and provide insight into how HIF target genes are differentially regulated.
2021-05-04 | GSE169087 | GEO
Project description:Hypoxia-inducible transcription factors (HIFs) are fundamental to the cellular adaptation to low oxygen levels but how they interact with chromatin and efficiently activate their target genes is unclear. Using genome-wide mutagenesis in human cancer cells, we define genes required for HIF transcriptional activation, and identify a requirement for the Histone 3 lysine 4 (H3K4) methyltransferase SET1B. Loss of SET1B leads to a selective reduction in HIF transcriptional activity in hypoxia, with SET1B driving expression of genes involved in angiogenesis rather than glycolysis, resulting in impaired tumour establishment in SET1B deficient xenografts. Mechanistically, we show that SET1B is itself oxygen regulated, accumulates on chromatin in hypoxia, and is recruited to HIF target genes through HIF-1a. Accordingly, we show that the hypoxic induction of H3K4me3 at specific HIF targets is both HIF and SET1B dependent, and when impaired, decreases promotor acetylation and gene expression. Together, these findings reveal SET1B as a determinant of site-specific histone methylation and provide insight into how HIF target genes are differentially regulated.
2021-04-30 | GSE169040 | GEO
Project description:Hypoxia-inducible transcription factors (HIFs) are fundamental to the cellular adaptation to low oxygen levels but how they interact with chromatin and efficiently activate their target genes is unclear. Using genome-wide mutagenesis in human cancer cells, we define genes required for HIF transcriptional activation, and identify a requirement for the Histone 3 lysine 4 (H3K4) methyltransferase SET1B. Loss of SET1B leads to a selective reduction in HIF transcriptional activity in hypoxia, with SET1B driving expression of genes involved in angiogenesis rather than glycolysis, resulting in impaired tumour establishment in SET1B deficient xenografts. Mechanistically, we show that SET1B is itself oxygen regulated, accumulates on chromatin in hypoxia, and is recruited to HIF target genes through HIF-1a. Accordingly, we show that the hypoxic induction of H3K4me3 at specific HIF targets is both HIF and SET1B dependent, and when impaired, decreases promotor acetylation and gene expression. Together, these findings reveal SET1B as a determinant of site-specific histone methylation and provide insight into how HIF target genes are differentially regulated.
2021-04-30 | GSE159128 | GEO
Project description:Regulatory transcription factors control many important biological processes including cellular differentiation, responses to environmental perturbations and stresses, and host-pathogen interactions. Determining the genome-wide binding of regulatory transcription factors to DNA is essential to understanding the function of transcription factors in these often complex biological processes. Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is a modern method for genome-wide mapping of in vivo protein-DNA binding interactions that is an attractive alternative to the traditional and widely used chromatin immunoprecipitation followed by sequencing (ChIP-seq) method. CUT&RUN is amenable to a higher throughput experimental setup and has a substantially higher dynamic range with lower per-sample sequencing costs compared to ChIP-seq. Here, we describe a comprehensive CUT&RUN protocol and accompanying data analysis workflow that is tailored for genome-wide analysis of transcription factor-DNA binding interactions in the human fungal pathogen Candida albicans. This detailed protocol describes all necessary experimental procedures, from epitope tagging of transcription factor coding genes, to library preparation for sequencing; additionally, it includes our customized computational workflow for CUT&RUN data analysis.
2022-07-15 | GSE193803 | GEO
Project description:Dam identification (DamID) is a powerful technique to generate genome-wide maps of chromatin protein binding. Due to its high sensitivity it is particularly suited to study the genome interactions of chromatin proteins in small tissue samples in model organisms such as Drosophila. Here we report an intein-based approach to tune the expression level of Dam and Dam-fusion proteins in Drosophila by addition of a ligand to fly food. This helps to suppress toxic effects of Dam. In addition we describe a strategy for genetically controlled expression of Dam in a specific cell type in complex tissues. We demonstrate the utility of the latter by generating a glia-specific map of Polycomb in small samples of brain tissue. We determined DamID scores for Polycomb, normalized by Dam only control, for Drosophila larval central brain, larval fat bodies and repo+ glial cells of larval central brain. All samples were performed with 2 biological replicates. In case of Dam only control for larval central brain, each biological replicate was performed with 3 technical replicates.
2016-03-17 | E-GEOD-75831 | biostudies-arrayexpress
Project description:We present Nanopore-DamID, a method to simultaneously detect cytosine methylation and DNA-protein interactions from single molecules, via selective sequencing of adenine-labelled DNA. Assaying LaminB1 and CTCF binding with Nanopore-DamID, we identify escape from LAD-associated repression of hypomethylated promoters amidst generalised hypermethylation of LaminB1-associated regulatory elements. We detect novel CTCF binding sites in highly repetitive regions, and allele-specific CTCF binding to imprinted genes and the active X chromosome. Nanopore-DamID highlights the importance of DNA methylation to transcription factor activity.
2025-05-15 | GSE203109 | GEO
Project description:We used DamID to map nucleolus interactions in human cells using a 4x tandem repeat of the nucleolar targeting sequence of AP3D1 (Scott, 2010) ("4xAP3"). These interactions are mapped in various human cell lines, including human K562 cells
2020-12-18 | GSE148609 | GEO
Project description:We performed DamID-seq assay in WT and MATR3-depleted AML12 cells to investigate the Lamina-associated-domains (LADs) affected by loss of MATR3.
2025-03-14 | GSE200242 | GEO
Project description:Dam identification (DamID) is a powerful technique to generate genome-wide maps of chromatin protein binding. Due to its high sensitivity it is particularly suited to study the genome interactions of chromatin proteins in small tissue samples in model organisms such as Drosophila. Here we report an intein-based approach to tune the expression level of Dam and Dam-fusion proteins in Drosophila by addition of a ligand to fly food. This helps to suppress toxic effects of Dam. In addition we describe a strategy for genetically controlled expression of Dam in a specific cell type in complex tissues. We demonstrate the utility of the latter by generating a glia-specific map of Polycomb in small samples of brain tissue.
2016-03-17 | GSE75831 | GEO