ArticleMethods (San Diego, Calif.)2018
5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design.
Article in Methods (San Diego, Calif.), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Persistent chromatin loops shape gene expression plasticity upon stimulation and restimulation of human neurons.bioRxiv : the preprint server for biology · 2025Article
- Learning induces persistent chromatin loops underlying robust gene expression during memory recall.bioRxiv : the preprint server for biology · 2025Article
- Mosaic H3K9me3 at BREACHes predicts synaptic gene expression associated with fragile X syndrome cognitive severity.bioRxiv : the preprint server for biology · 2025Article
- 3D epigenomics and 3D epigenopathies.BMB reports · 2024Review
- Targeting the chromatin structural changes of antitumor immunity.Journal of pharmaceutical analysis · 2024Review
- Spatially coordinated heterochromatinization of long synaptic genes in fragile X syndrome.Cell · 2023Article
- Article
- Neuronal Yin Yang1 in the prefrontal cortex regulates transcriptional and behavioral responses to chronic stress in mice.Nature communications · 2022Article
- The macro and micro of chromosome conformation capture.Wiley interdisciplinary reviews. Developmental biology · 2021Review
- 3DeFDR: statistical methods for identifying cell type-specific looping interactions in 5C and Hi-C data.Genome biology · 2020Article
- Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression.Nature neuroscience · 2020Article
- Methods for mapping 3D chromosome architecture.Nature reviews. Genetics · 2020Review
- A subset of topologically associating domains fold into mesoscale core-periphery networks.Scientific reports · 2019Article
- LADL: light-activated dynamic looping for endogenous gene expression control.Nature methods · 2019Article
- Systematic Evaluation of Statistical Methods for Identifying Looping Interactions in 5C Data.Cell systems · 2019Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs, and looping interactions. Currently, there is a great need to evaluate the link between chromatin topology and genome function across many biological conditions and genetic perturbations. Hi-C can generate genome-wide maps of looping interactions but is intractable for high-throughput comparison of loops across multiple conditions due to the enormous number of reads (>6 Billion) required per library. Here, we describe 5C-ID, a new version of Chromosome-Conformation-Capture-Carbon-Copy (5C) with restriction digest and ligation performed in the nucleus (in situ Chromosome-Conformation-Capture (3C)) and ligation-mediated amplification performed with a double alternating primer design. We demonstrate that 5C-ID produces higher-resolution 3D genome folding maps with reduced spatial noise using markedly lower cell numbers than canonical 5C. 5C-ID enables the creation of high-resolution, high-coverage maps of chromatin loops in up to a 30 Megabase subset of the genome at a fraction of the cost of Hi-C.
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Registered trials
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.