Principles of ChIP-seq Data Analysis Illustrated with Examples

Ambrosini, Giovanna; Dreos, René; Bücher, Philipp

doi:10.18547/gcb.2015.vol1.iss1.e22

Cited by 5 publications

(7 citation statements)

References 22 publications

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“…We will also use a control data set from a ChIP-seq experiment done with unstimulated HeLa cells, were the STAT1 protein is supposed to reside in the cytoplasm and thus unable to bind to its target sites in the genome. The example we present is partly based on a tutorial presented elsewhere [46]. …”

Section: Resultsmentioning

confidence: 99%

The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data

et al. 2016

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BackgroundChIP-seq and related high-throughput chromatin profilig assays generate ever increasing volumes of highly valuable biological data. To make sense out of it, biologists need versatile, efficient and user-friendly tools for access, visualization and itegrative analysis of such data.ResultsHere we present the ChIP-Seq command line tools and web server, implementing basic algorithms for ChIP-seq data analysis starting with a read alignment file. The tools are optimized for memory-efficiency and speed thus allowing for processing of large data volumes on inexpensive hardware. The web interface provides access to a large database of public data. The ChIP-Seq tools have a modular and interoperable design in that the output from one application can serve as input to another one. Complex and innovative tasks can thus be achieved by running several tools in a cascade.ConclusionsThe various ChIP-Seq command line tools and web services either complement or compare favorably to related bioinformatics resources in terms of computational efficiency, ease of access to public data and interoperability with other web-based tools. The ChIP-Seq server is accessible at http://ccg.vital-it.ch/chipseq/.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3288-8) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data

et al. 2016

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“…( B ) Distribution of nucleosomes around S. cerevisiae, H. sapiens and D. rerio promoters. The Figure is based on MNase-seq data from (13–15) and has been made with the ChIP-Cor tool from the ChIP-Seq server (5). The MNase-seq data are stored in the MGA repository and are directly accessible via a pull-down menu from the ChIP-Cor input form.…”

Section: Recent Developmentsmentioning

confidence: 99%

“…EPDnew is tightly integrated with two accessory bioinformatics resources, the Signal Search Analysis (SSA) (4) and ChIP-Seq servers (5). The former offers tools for DNA motif-oriented analysis, the latter for exploring and downloading promoter-associated functional genomics data.…”

Section: Introductionmentioning

confidence: 99%

The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms

et al. 2016

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We present an update of the Eukaryotic Promoter Database EPD (http://epd.vital-it.ch), more specifically on the EPDnew division, which contains comprehensive organisms-specific transcription start site (TSS) collections automatically derived from next generation sequencing (NGS) data. Thanks to the abundant release of new high-throughput transcript mapping data (CAGE, TSS-seq, GRO-cap) the database could be extended to plant and fungal species. We further report on the expansion of the mass genome annotation (MGA) repository containing promoter-relevant chromatin profiling data and on improvements for the EPD entry viewers. Finally, we present a new data access tool, ChIP-Extract, which enables computational biologists to extract diverse types of promoter-associated data in numerical table formats that are readily imported into statistical analysis platforms such as R.

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“…CAGE data from different samples belonging to the same species were first merged into one file. TSS profiles were then extracted for promoter regions extending from -103 to +104 relative to the dominant TSS using the ChIP-Extract tool from the ChIP-Seq web server [64]. The resulting integer arrays were then converted into binary "micro-peak" arrays.…”

Section: Periodicity Analysis Of Pol-ii Initiation Patternsmentioning

confidence: 99%

“…Nucleosome distributions for promoter subsets were computed from nucleosome mapping data using the ChIP-Cor program from the ChIP-Seq web server [64]. MNase-or ChIP-seq tags were centered by 70 bp to account for the estimated fragment size of about 140 bp (centering parameter of the ChIP-Seq server).…”

Section: Nucleosome Distribution Around Promotersmentioning

confidence: 99%

Influence of rotational nucleosome positioning on transcription start site selection in animals promoters

Dreos

Ambrosini

Bücher

2016

Preprint

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The recruitment of RNA-Pol-II to the transcription start site (TSS) is an important step in gene regulation in all organisms. Core promoter elements (CPE) are conserved sequence motifs that guide Pol-II to the TSS by interacting with specific transcription factors (TFs). However, only a minority of animal promoters contains CPEs. It is still unknown how Pol-II selects the TSS in their absence. Here we present a comparative analysis of promoters' sequence composition and chromatin architecture in five eukaryotic model organisms, which shows the presence of common and unique DNA-encoded features used to organize chromatin. Analysis of Pol-II initiation patterns uncovers that, in the absence of certain CPEs, there is a strong correlation between the spread of initiation and the intensity of the 10 bp periodic signal in the nearest downstream nucleosome. Moreover, promoters' primary and secondary initiation sites show a characteristic 10 bp periodicity in the absence of CPEs.We also show that DNA natural variants in the region immediately downstream the TSS are able to affect both the nucleosome-DNA affinity and Pol-II initiation pattern. These findings support the notion that, in addition to CPEs mediated selection, sequence-induced nucleosome positioning could be a common and conserved mechanism of TSS selection in animals.Gene transcription is a complex process that starts with the recruitment and positioning of Pol-II enzyme at the transcription start site (TSS). Specific promoter sequences, known as core promoter elements (CPEs) facilitate this process. Surprisingly, only a fraction of promoters contain them. It is still unknown how Pol-II choses the start site in their absence. A recently proposed alternative mechanism implicates positioned nucleosomes in the TSS selection. Here, we provide new evidence of the existence of such mechanism with a comparative analysis of promoter's features across the animal kingdom. We analysed the promoter's DNA sequence composition in 5 organisms and found conserved and unique consensus sequences used to organize chromatin in the region of the first nucleosome downstream the TSS (N+1). Moreover, we found that all organisms show a strong correlation between the spread of Pol-II initiation and the strength of the DNA-encoded signal in the 2 N+1 region. A detailed analysis of Pol-II initiation sites reveals also the presence of a 10 bp periodicity that is correlated with the intensity of the DNA signal in the N+1 region. Importantly, we report that genetic variants that alter the DNA-nucleosome affinity in that region alter Pol-II initiation spread as well.

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Principles of ChIP-seq Data Analysis Illustrated with Examples

Cited by 5 publications

References 22 publications

The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data

The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data

The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms

Influence of rotational nucleosome positioning on transcription start site selection in animals promoters

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