GoPeaks: histone modification peak calling for CUT&Tag
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA788483 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17218055_1.fastq.gz | Fastqsanger.gz | |||
| SRR17218055_2.fastq.gz | Fastqsanger.gz | |||
| SRR17218056_1.fastq.gz | Fastqsanger.gz | |||
| SRR17218056_2.fastq.gz | Fastqsanger.gz | |||
| SRR17218057_1.fastq.gz | Fastqsanger.gz |
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Project description:Peak calling tool for CUT&Tag histone modifications.
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Project description:Genome-wide mapping of histone modifications is critical to understanding transcriptional regulation. CUT&Tag is a new method for profiling histone modifications, offering improved sensitivity and decreased cost compared with ChIP-seq. Here, we present GoPeaks, a peak calling method specifically designed for histone modification CUT&Tag data. We compare the performance of GoPeaks against commonly used peak calling algorithms to detect histone modifications that display a range of peak profiles and are frequently used in epigenetic studies. We find that GoPeaks robustly detects genome-wide histone modifications and, notably, identifies a substantial number of H3K27ac peaks with improved sensitivity compared to other standard algorithms.
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Project description:We comprehensively benchmarked CUT&Tag for H3K27ac and H3K27me3 against published ChIP-seq profiles from ENCODE in K562 cells. Across a total of 30 new and 6 published CUT&Tag datasets we found that no experiment recovers more than 50% of known ENCODE peaks, regardless of the histone mark. We tested peak callers MACS2 and SEACR, identifying optimal peak calling parameters. Balancing both precision and recall of known ENCODE peaks, SEACR without retention of duplicates showed the best performance. We found that reducing PCR cycles during library preparation lowered duplication rates at the expense of ENCODE peak recovery. Despite the moderate ENCODE peak recovery, peaks identified by CUT&Tag represent the strongest ENCODE peaks and show the same functional and biological enrichments as ChIP-seq peaks identified by ENCODE. Our workflow systematically evaluates the merits of methodological adjustments and will facilitate future efforts to apply CUT&Tag in human tissues and single cells.
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Project description:To understand how Pou4f1 functions in RGC lineage specification and subtype formation, we performed “Cleavage Under Targets & Tagmentation” (CUT&Tag) analysis using a rabbit anti-Pou4f1 antibody and embryonic 16.5 (E16.5) retinal cells to generate barcoded PCR libraries that are enriched for Pou4f1-mediated binding. In parallel, rabbit IgG was used as a negative control for peak calling analysis, and rabbit anti-H3K9ac antibody was used to mark active enhancers and promoters.
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