HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis

David, Fabrice; Delafontaine, Julien; Carat, Solenne; Ross, Frederick J.; Lefebvre, Grégory; Jarosz, Yohan; Sinclair, Lucas; Noordermeer, Daan; Rougemont, Jacques; Leleu, Marion

doi:10.1371/journal.pone.0085879

Cited by 95 publications

(100 citation statements)

References 32 publications

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“…Experimental replicates were validated as described in Methods (Supplemental Figure 3, C and D). Sequencing alignment to the Ensembl Mouse Assembly NCBIM37 (mm9), peak detection, and peak assignment to genes was performed using the High-throughput Sequencing Data Analysis portal of the HTSstation (17). As expected, E2F1 target cell-cycle genes, including Ccne1, Ccna2, Rb1, Rbl1, Cdkn2a, Tk1, and Dhfr were found (Supplemental Figure 4).…”

Section: Introductionmentioning

confidence: 58%

“…A novel deconvolution algorithm was provided, which evaluates the shape of peaks within enriched regions found by MACS. This approach provides a more accurate estimation of binding-site locations and a lower number of false-positives (17). Using the DAVID website (http://david.abcc.ncifcrf.gov), we clustered E2F1 target genes with the general GOTERM_BP2 database.…”

Section: Discussionmentioning

confidence: 99%

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E2F1 mediates sustained lipogenesis and contributes to hepatic steatosis

Denechaud¹,

López-Mejía²,

Giralt³

et al. 2015

Journal of Clinical Investigation

113

112

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Section: Introductionmentioning

confidence: 58%

Section: Discussionmentioning

confidence: 99%

E2F1 mediates sustained lipogenesis and contributes to hepatic steatosis

Denechaud¹,

López-Mejía²,

Giralt³

et al. 2015

Journal of Clinical Investigation

113

112

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“…Reads for each individual sample/replicate were mapped to the mouse genome (mm10 assembly) using the mapping module of HTSstation (based on Bowtie2) (David et al 2014) with the option "discard PCR duplicates." Triplicates were then combined to give a total of 1.53 × 10 8 mapped reads for the asynchronous samples, 8.3 × 10 7 mapped reads for the corresponding inputs, 1.2 × 10 8 mapped reads for the mitotic samples, and 1 × 10 8 mapped reads for the corresponding inputs.…”

Section: Chip-seq Analysismentioning

confidence: 99%

A role for mitotic bookmarking of SOX2 in pluripotency and differentiation

et al. 2016

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Mitotic bookmarking transcription factors remain bound to chromosomes during mitosis and were proposed to regulate phenotypic maintenance of stem and progenitor cells at the mitosis-to-G1 (M-G1) transition. However, mitotic bookmarking remains largely unexplored in most stem cell types, and its functional relevance for cell fate decisions remains unclear. Here we screened for mitotic chromosome binding within the pluripotency network of embryonic stem (ES) cells and show that SOX2 and OCT4 remain bound to mitotic chromatin through their respective DNA-binding domains. Dynamic characterization using photobleaching-based methods and single-molecule imaging revealed quantitatively similar specific DNA interactions, but different nonspecific DNA interactions, of SOX2 and OCT4 with mitotic chromatin. Using ChIP-seq (chromatin immunoprecipitation [ChIP] combined with high-throughput sequencing) to assess the genome-wide distribution of SOX2 on mitotic chromatin, we demonstrate the bookmarking activity of SOX2 on a small set of genes. Finally, we investigated the function of SOX2 mitotic bookmarking in cell fate decisions and show that its absence at the M-G1 transition impairs pluripotency maintenance and abrogates its ability to induce neuroectodermal differentiation but does not affect reprogramming efficiency toward induced pluripotent stem cells. Our study demonstrates the mitotic bookmarking property of SOX2 and reveals its functional importance in pluripotency maintenance and ES cell differentiation.

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“…Inverse PCRs for amplification were carried out using primers for the Hoxd11 and Hoxd13 viewpoints (Noordermeer et al 2011). PCR products were multiplexed and sequenced using a HiSeq sequencer from Illumina, and post-processing (demultiplexing, mapping, and 4C analysis) was conducted on the Bioinformatics and Biostatistics Core Facility HTSstation (http://htsstation.epfl.ch) (Noordermeer et al 2011;David et al 2014). Data were plotted on University of California at Santa Cruz (UCSC) genome bioinformatics site and smoothed with a window size of 11 fragments.…”

Section: C-seqmentioning

confidence: 99%

A role for HOX13 proteins in the regulatory switch between TADs at the HoxD locus

et al. 2016

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During vertebrate limb development, Hoxd genes are regulated following a bimodal strategy involving two topologically associating domains (TADs) located on either side of the gene cluster. These regulatory landscapes alternatively control different subsets of Hoxd targets, first into the arm and subsequently into the digits. We studied the transition between these two global regulations, a switch that correlates with the positioning of the wrist, which articulates these two main limb segments. We show that the HOX13 proteins themselves help switch off the telomeric TAD, likely through a global repressive mechanism. At the same time, they directly interact with distal enhancers to sustain the activity of the centromeric TAD, thus explaining both the sequential and exclusive operating processes of these two regulatory domains. We propose a model in which the activation of Hox13 gene expression in distal limb cells both interrupts the proximal Hox gene regulation and re-enforces the distal regulation. In the absence of HOX13 proteins, a proximal limb structure grows without any sign of wrist articulation, likely related to an ancestral fish-like condition.

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HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis

Cited by 95 publications

References 32 publications

E2F1 mediates sustained lipogenesis and contributes to hepatic steatosis

E2F1 mediates sustained lipogenesis and contributes to hepatic steatosis

A role for mitotic bookmarking of SOX2 in pluripotency and differentiation

A role for HOX13 proteins in the regulatory switch between TADs at the HoxD locus

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