HiChIP-Peaks: A HiChIP peak calling algorithm

Shi, Chenfu; Rattray, Magnus; Orozco, Gisela

doi:10.1101/682781

Cited by 3 publications

(5 citation statements)

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“…For example, HiChIP has been used to delineate promoter-enhancer interactions in keratinocytes and CD8+ T-cell lines exploring psoriasis and psoriatic arthritis disease-associated SNPs and similar methods could be explored in AS. (38,39) Additionally, targeted RUNX3 enhancer element genomic editing strategies are also needed to elucidate the effects on RUNX3 expression and downstream cellular signaling.…”

Section: Discussion (685 Words)mentioning

confidence: 99%

Disruption of c-MYC binding and chromosomal looping involving genetic variants associated with ankylosing spondylitis upstream of RUNX3 promoter

Cohen

Davidson

Selmi

et al. 2021

Preprint

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BackgroundAnkylosing Spondylitis (AS) is a common form of inflammatory spinal arthritis with a complex aetiology and high heritability, involving more than 100 genetic associations. These include several AS-associated single nucleotide polymorphisms (SNPs) upstream of RUNX3, which encodes the multifunctional RUNT-related transcription factor (TF) 3. The lead associated SNP rs6600247 (p= 2.6 x 10-15) lies ~13kb upstream of the RUNX3 promoter adjacent to a c-MYC TF binding-site. The effect of rs6600247 genotype on DNA binding and chromosome looping were investigated by electrophoretic mobility gel shift assays (EMSA), Western blotting-EMSA (WEMSA) and Chromosome Conformation Capture (3C).ResultsInterrogation of ENCODE published data showed open chromatin in the region overlapping rs6600247 in primary human CD14+ monocytes in contrast to Jurkat T cell line or primary T-cells. The rs6600247 AS-risk allele is predicted to specifically disrupt a c-MYC binding-site. Using a 50bp DNA probe spanning rs6600247 there was consistently less binding to the AS-risk “C” allele of both purified c-MYC protein and nuclear extracts (NE) from monocyte-like U937 cells. WEMSA on U937 NE and purified c-MYC protein confirmed these differences (n=2; p<0.05). 3C experiments demonstrated negligible interaction between the region encompassing rs6600247 and the RUNX3 promoter. A stronger interaction frequency was demonstrated between the RUNX3 promoter and the previously characterised AS-associated SNP rs4648889.ConclusionsThe lead SNP rs6600247, located in an enhancer-like region upstream of the RUNX3 promoter, modulates c-MYC binding. However, the region encompassing rs6600247 has rather limited physical interaction with the promoter of RUNX3. In contrast a clear chromatin looping event between the region encompassing rs4648889 and the RUNX3 promoter was observed. These data provide further evidence for complexity in the regulatory elements upstream of the RUNX3 promoter and the involvement of RUNX3 transcriptional regulation in AS.

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Section: Discussion (685 Words)mentioning

confidence: 99%

Disruption of c-MYC binding and chromosomal looping involving genetic variants associated with ankylosing spondylitis upstream of RUNX3 promoter

Cohen

Davidson

Selmi

et al. 2021

Preprint

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“…Interaction matrices were then generated with the same software. To generate anchor points for downstream looping analysis, outputs from HiC-Pro were used as inputs for peak calling in HiChIP-Peaks [85]. To ensure loops were called from similar background enhancers, peaks from HiChIP-Peaks were concatenated into a single file and used as anchor point inputs for loop calling via hichipper [86].…”

Section: Hichip Protocol Processing and Analysismentioning

confidence: 99%

High Enhancer Activity is an Epigenetic Feature of HPV Negative Atypical Head and Neck Squamous Cell Carcinoma

Callahan

Kochat

Liu

et al. 2021

Preprint

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Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous disease with significant morbidity and mortality and frequent recurrence. Pre-NGS efforts to transcriptionally classify HNSCC into groups of varying prognosis have identified four accepted molecular subtypes of disease: Atypical (AT), Basal (BA), Classical (CL), and Mesenchymal (MS). Here, we investigated the active enhancer landscapes of these subtypes using representative HNSCC cell lines and identified samples belonging to the AT subtype as having increased enhancer activity compared to the other 3 HNSCC subtypes. Cell lines belonging to atypical subtype were more resistant to bromodomain inhibitors (BETi). PRO-Seq experiments that both TCGA tumors and AT cell lines showed higher eRNA transcripts for enhancers controlling BETi resistance pathways, such as lipid metabolism and MAPK signaling. Additionally, HiChIP experiments suggested higher enhancer-promoter (E-P) contacts in the AT subtype, including on genes identified in the eRNA analysis. Consistently, known BETi resistance pathways were upregulated upon exposure to these inhibitors. Together, our results identify that the AT subtype of HNSCC is associated with high enhancer activity, resistance to BET inhibition, and signaling pathways that could serve as future targets for sensitizing HNSCC to BET inhibition.

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“…We wanted to test the assumption that GWAS results from various diseases would enrich for regulatory elements that are active in cell types relevant to their disease mechanism. To do so we used the H3K27ac signal collected from our HiChIP data using our recently developed tool, HiChIP-Peaks (Shi, Rattray and Orozco 2019), to estimate an enrichment score of these SNPs over a background ( figure 3B). As expected, SNPs associated with psoriasis, PsA, atopic dermatitis, melanoma and SSc show significant enrichment for the activity marker H3K27ac in the cell lines studied.…”

Section: Gwas Variants Are Significantly Enriched In the Cell Types Smentioning

confidence: 99%

“…The reads were then mapped to the GRCh38 genome with Hi-C Pro v2.11.0 (Servant et al 2015), using default settings. Enriched regions (H3K27ac peaks) where identified using HiChIP-peaks v 0.1.1 (Shi, Rattray and Orozco 2019) with default settings and FDR<0.01. Loops were identified using FitHiChIP (Bhattacharyya et al 2019) using the following settings: Coverage normalization, stringent background with merging enabled, peaks generated from HiChIP-peaks and 5kb bin size.…”

Section: Hichip Library Generation and Processingmentioning

confidence: 99%

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An active chromatin interactome in relevant cell lines elucidates biological mechanisms at genetic risk loci for dermatological traits

Shi

Ray-Jones

Ding

et al. 2020

Preprint

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In the last 15 years Genome wide association studies (GWAS) have uncovered the genetic factors that contribute to disease risk for many disorders, yet the biological significance of many of these associations remain unclear. This is because about 90% of these variants are predicted to affect regulatory elements that are highly cell-type specific and can affect distal genes through chromatin interaction mechanisms and, therefore, understanding their role in disease is challenging.Previous studies have attempted to use chromatin conformation methods to describe the functional mechanism in disease associated loci. However, the majority of these studies have focused on cell lines derived from blood, which might not be the most relevant cell lines for dermatological conditions.Here, we generated HiChIP for H3K27ac, Hi-C and RNA-seq datasets from a keratinocyte and a skinplaque derived CD8+ T cell line. We studied their active chromatin conformation with the aim to identify biological mechanisms that could be affected by variants associated with skin related diseases: psoriasis (Ps), psoriatic arthritis (PsA), systemic sclerosis (SSc), melanoma and atopic dermatitis.In our analysis we show that HiChIP interactions provide functional evidence for gene regulation by showing that enhancers linked to genes that respond to IFN-γ stimulation are strongly enriched for motifs for TFs related to the stimulation. We also show that by using chromatin conformation we can recall 53% of eQTLs identified by GTEx in skin.In addition to our datasets, we integrated public datasets for a B cell-like lymphoblastoid cell line and primary CD4+ T cells to expand our analysis to include GWAS variants associated with the aforementioned diseases likely to be mediated specifically by B cells and CD4+ T cells (such as in systemic sclerosis and melanoma). We then identified the numerous genes that interact with GWAS variants associated and show that these genes strongly enrich for pathways that are related to the trait studied. For example, the top enriched pathways for autoimmune conditions such as PsA and psoriasis included responses to cytokines and T cell regulation, whereas for melanoma they were related to replicative senescence.We show examples of how our analysis can inform changes in the current description of a few psoriasis associated risk loci. For example, the variant rs10794648, which had previously been assigned to IFNLR1, was linked to GRHL3 in our dataset, a gene essential in skin repair and development. This can indicate a renewed importance of skin related factors in the risk of disease.In conclusion, this study allows us to further characterize disease risk loci by using novel chromatin conformation techniques, which can help identify the genes that are putatively involved in disease and has the potential to identify therapeutic targets.

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HiChIP-Peaks: A HiChIP peak calling algorithm

Cited by 3 publications

References 23 publications

Disruption of c-MYC binding and chromosomal looping involving genetic variants associated with ankylosing spondylitis upstream of RUNX3 promoter

Disruption of c-MYC binding and chromosomal looping involving genetic variants associated with ankylosing spondylitis upstream of RUNX3 promoter

High Enhancer Activity is an Epigenetic Feature of HPV Negative Atypical Head and Neck Squamous Cell Carcinoma

An active chromatin interactome in relevant cell lines elucidates biological mechanisms at genetic risk loci for dermatological traits

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