ArticleMolecular cell2022
HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization.
Article in Molecular cell, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed, 83 citations in OpenAlex.
- Spatial chromatin architecture and accessibility co-profiling of mammalian tissues.Nature methods · 2026Article
- A thioredoxin-Serinc2-lipid signaling axis modulates mood-related behaviors in mice.Molecular psychiatry · 2026Article
- Foundation model reveals the shared organization of transcription and topologically associating domains.Cell systems · 2026Article
- 3D chromatin organisation contributes to the regulatory logic in differentiating lymphatic endothelium.EMBO reports · 2026Article
- Mapping 3D genome organization at nucleosome-scale with Micro-C and Region Capture Micro-C (RCMC).Nature protocols · 2026Review
- Transcriptional plasticity of ventral tegmental area neurons induced after cessation of chronic cocaine exposure is required for incubation of cocaine seeking.bioRxiv : the preprint server for biology · 2026Article
- Segmentally Duplicated Regulatory Elements Undergo Human-Specific Rewiring.Molecular biology and evolution · 2026Article
- PATTY corrects open-chromatin bias for improved bulk and single-cell CUT&Tag profiling.Nature communications · 2026Article
- GraphLooper: predicting chromatin loops based on hierarchical multi-view graph pooling method.Briefings in bioinformatics · 2026Article
- Signal control during tissue regeneration in adult animals.Nature reviews. Molecular cell biology · 2026Review
- Trimodal single-cell profiling of transcriptome, epigenome and 3D genome in complex tissues with scHiCAR.Nature biotechnology · 2026Article
- HiChIA-Rep quantifies the similarity between enrichment-based chromatin interactions datasets.bioRxiv : the preprint server for biology · 2026Article
- An integrated multi-omics and network analysis of neutrophil differentiation from initial- to late-stage.Genome biology · 2026Article
- CHAMP1 is an essential regulator for human myoblast fusion and muscle development.Nature communications · 2026Article
- Elucidation of chromatin loops among regulatory regions using Hi-TrAC.Frontiers in epigenetics and epigenomics · 2026Article
- Segmentally duplicated regulatory elements undergo human-specific rewiring.bioRxiv : the preprint server for biology · 2025Article
- Visualizing genetic information flow in space and time.Science China. Life sciences · 2025Review
- A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress.Genome research · 2025Article
- A subset of transposable elements as mechano-response enhancer elements in controlling human embryonic stem cell fate.Nature cell biology · 2025Article
- PATTY corrects open-chromatin bias for improved bulk and single-cell CUT&Tag profiling.Research square · 2025Article
Corrections and comments
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Authors and funding
12 authors at 4 institutions in 1 country.
Funding
Abstract
The long-range interactions of cis-regulatory elements (cREs) play a central role in gene regulation. cREs can be characterized as accessible chromatin sequences. However, it remains technically challenging to comprehensively identify their spatial interactions. Here, we report a new method HiCAR (Hi-C on accessible regulatory DNA), which utilizes Tn5 transposase and chromatin proximity ligation, for the analysis of open-chromatin-anchored interactions with low-input cells. By applying HiCAR in human embryonic stem cells and lymphoblastoid cells, we demonstrate that HiCAR identifies high-resolution chromatin contacts with an efficiency comparable with that of in situ Hi-C over all distance ranges. Interestingly, we found that the "poised" gene promoters exhibit silencer-like function to repress the expression of distal genes via promoter-promoter interactions. Lastly, we applied HiCAR to 30,000 primary human muscle stem cells and demonstrated that HiCAR is capable of analyzing chromatin accessibility and looping using low-input primary cells and clinical samples.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.