snakePipes: facilitating flexible, scalable and integrative epigenomic analysis

Bhardwaj, Vivek; Heyne, Steffen; Sikora, Katarzyna; Rabbani, Leily; Rauer, Michael; Kilpert, Fabian; Richter, Andreas S.; Ryan, Devon P.; Manke, Thomas

doi:10.1093/bioinformatics/btz436

Cited by 133 publications

(141 citation statements)

References 13 publications

(14 reference statements)

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“…Raw data files were mapped to GRCz11 using the bioinformatics pipeline snakePipes using the ATAC seq mode [48]. In this pipeline, fastq files are quality and adapter trimmed with Trim galore!, aligned with Bowtie2 and peaks are detected with MACS2.…”

Section: Raw Data Processing and Statistical Analysismentioning

confidence: 99%

Inhibition of methyltransferase activity of enhancer of zeste 2 leads to enhanced lipid accumulation and altered chromatin status in zebrafish

Broeder

Ballangby

Kamminga

et al. 2020

Epigenetics & Chromatin

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Background: Recent studies indicate that exposure to environmental chemicals may increase susceptibility to developing metabolic diseases. This susceptibility may in part be caused by changes to the epigenetic landscape which consequently affect gene expression and lead to changes in lipid metabolism. The epigenetic modifier enhancer of zeste 2 (Ezh2) is a histone H3K27 methyltransferase implicated to play a role in lipid metabolism and adipogenesis. In this study, we used the zebrafish (Danio rerio) to investigate the role of Ezh2 on lipid metabolism and chromatin status following developmental exposure to the Ezh1/2 inhibitor PF-06726304 acetate. We used the environmental chemical tributyltin (TBT) as a positive control, as this chemical is known to act on lipid metabolism via EZH-mediated pathways in mammals. Results:Zebrafish embryos (0-5 days post-fertilization, dpf ) exposed to non-toxic concentrations of PF-06726304 acetate (5 μM) and TBT (1 nM) exhibited increased lipid accumulation. Changes in chromatin were analyzed by the assay for transposase-accessible chromatin sequencing (ATAC-seq) at 50% epiboly (5.5 hpf ). We observed 349 altered chromatin regions, predominantly located at H3K27me3 loci and mostly more open chromatin in the exposed samples. Genes associated to these loci were linked to metabolic pathways. In addition, a selection of genes involved in lipid homeostasis, adipogenesis and genes specifically targeted by PF-06726304 acetate via altered chromatin accessibility were differentially expressed after TBT and PF-06726304 acetate exposure at 5 dpf, but not at 50% epiboly stage. One gene, cebpa, did not show a change in chromatin, but did show a change in gene expression at 5 dpf. Interestingly, underlying H3K27me3 marks were significantly decreased at this locus at 50% epiboly. Conclusions:Here, we show for the first time the applicability of ATAC-seq as a tool to investigate toxicological responses in zebrafish. Our analysis indicates that Ezh2 inhibition leads to a partial primed state of chromatin linked to metabolic pathways which results in gene expression changes later in development, leading to enhanced lipid accumulation. Although ATAC-seq seems promising, our in-depth assessment of the cebpa locus indicates that we need to consider underlying epigenetic marks as well.

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Section: Raw Data Processing and Statistical Analysismentioning

confidence: 99%

Inhibition of methyltransferase activity of enhancer of zeste 2 leads to enhanced lipid accumulation and altered chromatin status in zebrafish

Broeder

Ballangby

Kamminga

et al. 2020

Epigenetics & Chromatin

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“…Since wg-blimp only integrates published software, and exhaustive evaluation of all conceivable pipeline setups would result in combinatorial explosion, we focus here on a feature-wise comparison of pipelines, similar to (19). We compared wg-blimp to BAT (20), bicycle (21), CpG_Me/DMRichR (10,(22)(23)(24), ENCODE-DCC's WGBS pipeline (25), Methy-Pipe (26), Nextflow methylseq (two available workflows) (27), PiGx (28) and snakePipes (19). Pipelines were compared with regards to technical setup (installation, workflow management), WGBS read processing (adapter trimming, alignment, methylation calling, quality control), and post-alignment analyses (DMR detection, segmentation, annotation).…”

Section: Resultsmentioning

confidence: 99%

wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing data

Wöste

Leitão

Laurentino

et al. 2019

Preprint

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BackgroundAnalysing whole genome bisulfite sequencing datasets is a data-intensive task that requires comprehensive and reproducible workflows to generate valid results. While many algorithms have been developed for tasks such as alignment, comprehensive end-to-end pipelines are still sparse. Furthermore, previous pipelines lack features or show technical deficiencies, thus impeding analyses.ResultsWe developed wg-blimp (whole genome bisulfite sequencing methylation analysis pipeline) as an end-to-end pipeline to ease whole genome bisulfite sequencing data analysis. It integrates established algorithms for alignment, quality control, methylation calling, detection of differentially methylated regions, and methylome segmentation, requiring only a reference genome and raw sequencing data as input. Comparing wg-blimp to previous end-to-end pipelines reveals similar setups for common sequence processing tasks, but shows differences for post-alignment analyses. We improve on previous pipelines by providing a more comprehensive analysis workflow as well as an interactive user interface. To demonstrate wg-blimp’s ability to produce correct results we used it to call differentially methylated regions for two publicly available datasets. We were able to replicate 112 of 114 previously published regions, and found results to be consistent with previous findings. We further applied wg-blimp to a publicly available sample of embryonic stem cells to showcase methylome segmentation. As expected, unmethylated regions were in close proximity of transcription start sites. Segmentation results were consistent with previous analyses, despite different reference genomes and sequencing techniques.Conclusionswg-blimp provides a comprehensive analysis pipeline for whole genome bisulfite sequencing data as well as a user interface for simplified result inspection. We demonstrated its applicability by analysing multiple publicly available datasets. Thus, wg-blimp is a relevant alternative to previous analysis pipelines and may facilitate future epigenetic research.

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“…In this work we present AutoRELACS, an automated implementation of the RELACS protocol (9) that enables the automated high-throughput generation of ChIP-seq experiments. AutoRELACS natively interfaces with the computational pipelines offered by snakePipes (13), thus streamlining the generation and analysis of DNA-binding profiles at unprecedented scale.…”

Section: Discussionmentioning

confidence: 99%

“…BCL files were converted to fastq format using bcl2fastq2 (v. 2.20.0) and demultiplexed on illumina barcodes. Fastq files were used as input to snakePipes’ DNA-mapping and ChIP-seq workflows (v. 1.2.3) (13), using default parameters as listed in https://github.com/FrancescoFerrari88/AutoRELACS/tree/master/snakePipes_defaults. Mapping was performed on the genome build dm6 and hg38 for D. melanogaster and H. sapiens respectively.…”

Section: Methodsmentioning

confidence: 99%

“…6-A) Libraries are sequenced on Illumina’s sequencing devices. Upon completion of the sequencing run, bcl2 files are automatically converted to fastq format and input into the fully automated ChIP-seq workflow available as part of the snakePipes suite (13). SnakePipes’ ChIP-seq workflow performs demultiplexing of reads on RELACS custom barcodes, quality controls, mapping and filtering of duplicate reads using unique molecular identifiers (UMI), and further downstream analysis like generation of input-normalized coverage tracks and peak calling.…”

Section: Mainmentioning

confidence: 99%

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AutoRELACS: Automated Generation And Analysis Of Ultra-parallel ChIP-seq

Arrigoni

Ferrari

Weller

et al. 2020

Preprint

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11Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a method used to profile 12 protein-DNA interactions genome-wide. RELACS (Restriction Enzyme-based Labeling of 13 Chromatin in Situ) is a recently developed ChIP-seq protocol that deploys a chromatin barcoding 14 strategy to enable standardized and high-throughput generation of ChIP-seq data. The manual 15 implementation of RELACS is constrained by human processivity in both data generation and data 16 analysis. To overcome these limitations, we have developed AutoRELACS, an automated 17 implementation of the RELACS protocol using the liquid handler Biomek i7 workstation. We 18 match the unprecedented processivity in data generation allowed by AutoRELACS with the 19 automated computation pipelines offered by snakePipes. In doing so, we build a continuous 20 workflow that streamlines epigenetic profiling, from sample collection to biological interpretation. 21Here, we show that AutoRELACS successfully automates chromatin barcode integration, and is 22 able to generate high-quality ChIP-seq data comparable with the standards of the manual protocol, 23 also for limited amounts of biological samples. 24 25 2 BACKGROUND 26Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a widely used method to 27 study protein-DNA interactions genome-wide (1). Despite the enormous contribution that ChIP-28 seq has brought to our understanding of epigenetic and transcriptional control, the traditional ChIP-29 seq protocol (2,3) presents various limitations. For example, it requires substantial amounts of 30 biological input material, which is often a limiting factor in relevant clinical settings, and it is low-31 throughput, which prevents comprehensive epigenetic profiling. Furthermore, the protocol is 32 poorly standardized across cell types, resulting in a high degree of technical variability that 33 hampers biological interpretation of the data. 35Over the last ten years, much work has been devoted to address these and other shortcomings (4-36 8). In line with these efforts, we have recently developed RELACS (Restriction Enzyme-based 37 Labeling of Chromatin in Situ), a method that employs chromatin barcoding to enable high-38 throughput generation of ChIP-seq experiments (9). RELACS works reliably with low input 39 material and can be used for quantitative ChIP-seq analysis (9,10). The method is highly 40 standardized, and could potentially be scaled to profile hundreds of samples in parallel for tens of 41 DNA-binding proteins at once. Yet, the current manual implementation is limited by human 42 processivity in both data generation and data analysis. 43 44To match the ideal potential of this methodology, we have implemented an automated version of 45 the RELACS protocol, named AutoRELACS, using the liquid handler Biomek i7 automated 46 workstation (Beckman Coulter). While other automated ChIP-seq implementations already exist 47 (11,12), they still require a large amount of sample material, and they do not utilize the enormous 48 3 multiple...

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snakePipes: facilitating flexible, scalable and integrative epigenomic analysis

Cited by 133 publications

References 13 publications

Inhibition of methyltransferase activity of enhancer of zeste 2 leads to enhanced lipid accumulation and altered chromatin status in zebrafish

Inhibition of methyltransferase activity of enhancer of zeste 2 leads to enhanced lipid accumulation and altered chromatin status in zebrafish

wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing data

AutoRELACS: Automated Generation And Analysis Of Ultra-parallel ChIP-seq

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