deepTools: a flexible platform for exploring deep-sequencing data

Ramírez, Fidel; Dündar, Friederike; Diehl, Sarah; Grüning, Björn; Manke, Thomas

doi:10.1093/nar/gku365

Cited by 2,568 publications

(2,415 citation statements)

References 7 publications

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“…ChIP-Seq data were aligned to mouse genome mm9 using Bowtie 37 with n = 1 and m =3 as parameter. Normalized Bigwig files were obtained using DeepTools 38 . Bioinformatics analyses were performed via the Cistrome platform 39 or Bioconductor 40 .…”

Section: Methodsmentioning

confidence: 99%

Polycomb-like proteins link the PRC2 complex to CpG islands

Liefke

Jiang

et al. 2017

Nature

247

323

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The Polycomb repressive complex 2 (PRC2) mainly mediates transcriptional repression1,2 and plays essential roles in various biological processes including the maintenance of cell identity and proper differentiation. Polycomb-like proteins (PCLs), including PHF1, MTF2 and PHF19, are PRC2 associated factors that form sub-complexes with PRC2 core components3, and have been proposed to modulate PRC2’s enzymatic activity or its recruitment to specific genomic loci4–13. Mammalian PRC2 binding sites are enriched in CG content, which correlate with CpG islands that display a low level of DNA methylation14. However, the mechanism of PRC2 recruitment to CpG islands is not fully understood. In this study, we solved the crystal structures of the N-terminal domains of PHF1 and MTF2 with bound CpG-containing DNAs in the presence of H3K36me3-containing histone peptides. We found that the extended homologous (EH) regions of both proteins fold into a winged-helix structure, which specifically binds to the unmethylated CpG motif but in a manner completely different from the canonical winged-helix motif-DNA recognition. We further showed that the PCL EH domains are required for efficient recruitment of PRC2 to CpG island-containing promoters in mouse embryonic cells. Our research provides the first direct evidence demonstrating that PCLs are critical for PRC2 recruitment to CpG islands, thereby further clarifying their roles in transcriptional regulation in vivo.

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Section: Methodsmentioning

confidence: 99%

Polycomb-like proteins link the PRC2 complex to CpG islands

Liefke

Jiang

et al. 2017

Nature

247

323

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“…DNA methylation distribution plots and gene clustering analyses by methylation patterns were performed with deepTools 66 .…”

Section: Author Contributionsmentioning

confidence: 99%

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

et al. 2017

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Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive retrotransposon sequence that was over-represented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago. Notably, the timing of this TE burst coincided with the uplift of the Tian Shan mountains, which is thought to be the center of the location where the apple originated, suggesting that TEs and associated processes may have contributed to the diversification of the apple ancestor and possibly to its divergence from pear. Finally, genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development.

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“…The analysis was performed with deepTools (v1.5.9.1) (Ramírez et al 2014) and the 60-way phyloP (Pollard et al 2010) conservation bigWig (mm10.60way.phyloP60way. bw) available from UCSC.…”

Section: Conservation Analysismentioning

confidence: 99%

“…Alignments from multiple samples corresponding to the same tissue were merged together and transformed to bigWig format. The ChIP-seq samples were scaled by library size and Input subtracted using bigwigCompare in the deepTools package (Ramírez et al 2014). Figure 4 demonstrates the ChIP-seq scaled and Input subtracted scores for the HQ genes starting upstream of the previous annotations.…”

Section: Mouse Encode Data Processingmentioning

confidence: 99%

Improved definition of the mouse transcriptome via targeted RNA sequencing

et al. 2016

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Targeted RNA sequencing (CaptureSeq) uses oligonucleotide probes to capture RNAs for sequencing, providing enriched read coverage, accurate measurement of gene expression, and quantitative expression data. We applied CaptureSeq to refine transcript annotations in the current murine GRCm38 assembly. More than 23,000 regions corresponding to putative or annotated long noncoding RNAs (lncRNAs) and 154,281 known splicing junction sites were selected for targeted sequencing across five mouse tissues and three brain subregions. The results illustrate that the mouse transcriptome is considerably more complex than previously thought. We assemble more complete transcript isoforms than GENCODE, expand transcript boundaries, and connect interspersed islands of mapped reads. We describe a novel filtering pipeline that identifies previously unannotated but high-quality transcript isoforms. In this set, 911 GENCODE neighboring genes are condensed into 400 expanded gene models. Additionally, 594 GENCODE lncRNAs acquire an open reading frame (ORF) when their structure is extended with CaptureSeq. Finally, we validate our observations using current FANTOM and Mouse ENCODE resources.

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deepTools: a flexible platform for exploring deep-sequencing data

Cited by 2,568 publications

References 7 publications

Polycomb-like proteins link the PRC2 complex to CpG islands

Polycomb-like proteins link the PRC2 complex to CpG islands

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

Improved definition of the mouse transcriptome via targeted RNA sequencing

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