FourCSeq: analysis of 4C sequencing data

Klein, Felix A.; Pakozdi, Tibor; Anders, Simon; Ghavi-Helm, Yad; Furlong, Eileen E. M.; Huber, Wolfgang

doi:10.1093/bioinformatics/btv335

Cited by 96 publications

(85 citation statements)

References 20 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The zoom-in shows interactions in the SAMD4A TAD (gray rectangle Fig 1D). Few contacts were seen only in the absence of crosslinking (which was also confirmed by a differential analysis via "FourCSeq"; Klein et al, 2015; Appendix Fig S4). Compared to highresolution Hi-C (Rao et al, 2014) and ChIA-PET contact maps (Papantonis et al, 2012) from HUVECs, i4C showed matching interaction profiles and aligned well within TAD boundaries, while also reproducibly detecting some longer-range contacts (Appendix Fig S5A and B).…”

Section: Resultssupporting

confidence: 58%

Exploiting native forces to capture chromosome conformation in mammalian cell nuclei

Brant

Georgomanolis

Nikolić

et al. 2016

Molecular Systems Biology

View full text Add to dashboard Cite

Mammalian interphase chromosomes fold into a multitude of loops to fit the confines of cell nuclei, and looping is tightly linked to regulated function. Chromosome conformation capture (3C) technology has significantly advanced our understanding of this structure‐to‐function relationship. However, all 3C‐based methods rely on chemical cross‐linking to stabilize spatial interactions. This step remains a “black box” as regards the biases it may introduce, and some discrepancies between microscopy and 3C studies have now been reported. To address these concerns, we developed “i3C”, a novel approach for capturing spatial interactions without a need for cross‐linking. We apply i3C to intact nuclei of living cells and exploit native forces that stabilize chromatin folding. Using different cell types and loci, computational modeling, and a methylation‐based orthogonal validation method, “TALE‐iD”, we show that native interactions resemble cross‐linked ones, but display improved signal‐to‐noise ratios and are more focal on regulatory elements and CTCF sites, while strictly abiding to topologically associating domain restrictions.

show abstract

Section: Resultssupporting

confidence: 58%

Exploiting native forces to capture chromosome conformation in mammalian cell nuclei

Brant

Georgomanolis

Nikolić

et al. 2016

Molecular Systems Biology

View full text Add to dashboard Cite

show abstract

“…S8" type="url"/>) when analysed with FourCseq (Klein et al, 2015). These interactions were marginally reduced in DE.…”

Section: Resultsmentioning

confidence: 99%

Functional characterisation of cis-regulatory elements governing dynamic Eomes expression in the early mouse embryo

et al. 2017

View full text Add to dashboard Cite

The T-box transcription factor (TF) Eomes is a key regulator of cell fate decisions during early mouse development. The cis-acting regulatory elements that direct expression in the anterior visceral endoderm (AVE), primitive streak (PS) and definitive endoderm (DE) have yet to be defined. Here, we identified three gene-proximal enhancer-like sequences (PSE_a, PSE_b and VPE) that faithfully activate tissue-specific expression in transgenic embryos. However, targeted deletion experiments demonstrate that PSE_a and PSE_b are dispensable, and only VPE is required for optimal Eomes expression in vivo. Embryos lacking this enhancer display variably penetrant defects in anterior-posterior axis orientation and DE formation. Chromosome conformation capture experiments reveal VPE-promoter interactions in embryonic stem cells (ESCs), prior to gene activation. The locus resides in a large (500 kb) pre-formed compartment in ESCs and activation during DE differentiation occurs in the absence of 3D structural changes. ATAC-seq analysis reveals that VPE, PSE_a and four additional putative enhancers display increased chromatin accessibility in DE that is associated with Smad2/3 binding coincident with transcriptional activation. By contrast, activation of the Eomes target genes Foxa2 and Lhx1 is associated with higher order chromatin reorganisation. Thus, diverse regulatory mechanisms govern activation of lineage specifying TFs during early development.

show abstract

“…Sequencing reads were demultiplexed and trimmed of the primer sequence using demultiplex.py from FourCSeq package (Klein et al, 2015), aligned using bowtie2 (v2.2.5) with standard parameters and quality filter set to 1 (-q 1) and processed as described (van de Werken et al, 2012). In short, reads are mapped to a restricted human reference genome (hg19), consisting of sequences directly flanking the 4C primary restriction enzyme site (DpnII), called 4C frag-ends.…”

Section: Methods Detailsmentioning

confidence: 99%

A Genetic Variant Associated with Five Vascular Diseases Is a Distal Regulator of Endothelin-1 Gene Expression

Gupta

Hadaya

Trehan

et al. 2017

Cell

392

310

View full text Add to dashboard Cite

Summary Genome-wide association studies (GWASs) implicate the PHACTR1 locus (6p24) in risk for five vascular diseases, including coronary artery disease, migraine headache, cervical artery dissection, fibro-muscular dysplasia, and hypertension. Through genetic fine mapping, we prioritized rs9349379, a common SNP in the third intron of the PHACTR1 gene, as the putative causal variant. Epigenomic data from human tissue revealed an enhancer signature at rs9349379 exclusively in aorta, suggesting a regulatory function for this SNP in the vasculature. CRISPR-edited stem cell-derived endothelial cells demonstrate rs9349379 regulates expression of endothelin 1 (EDN1), a gene located 600 kb upstream of PHACTR1. The known physiologic effects of EDN1 on the vasculature may explain the pattern of risk for the five associated diseases. Overall, these data illustrate the integration of genetic, phenotypic, and epigenetic analysis to identify the biologic mechanism by which a common, non-coding variant can distally regulate a gene and contribute to the patho-genesis of multiple vascular diseases.

show abstract

FourCSeq: analysis of 4C sequencing data

Cited by 96 publications

References 20 publications

Exploiting native forces to capture chromosome conformation in mammalian cell nuclei

Exploiting native forces to capture chromosome conformation in mammalian cell nuclei

Functional characterisation of cis-regulatory elements governing dynamic Eomes expression in the early mouse embryo

A Genetic Variant Associated with Five Vascular Diseases Is a Distal Regulator of Endothelin-1 Gene Expression

Contact Info

Product

Resources

About