Robust detection of chromosomal contacts from small cell numbers using low-input Capture-C
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE99257 | GEO | 2017/11/20
SECONDARY ACCESSION(S): PRJNA387734
REPOSITORIES: GEO
Shared Molecules
Only show the datasets with similarity scores above: 0.5
Threshold
0.5
Similar Datasets
Project description:Development of MAP-C (mutation analysis in pools by chromosome conformation capture), which involves performing 3C on a pool of mutants (generated by programmed oligonucleotide pools, error-prone PCR, or existing mutant collections), followed by amplification of 3C DNA using primers specific to a chromosomal contact of interest (with the mutagenized or barcode region included), and as a control, amplifying the mutagenized or barcode region regardless of ligation. The 3C and genomic libraries are amplified with primers that add sequencing and flowcell adapters, and then deep sequenced to quantify the abundance of each mutant/barcode. The ratio of abundance in the 3C compared to the genomic library reflects the extent to which each sequence variant participates in the chromosomal contact of interest.
2018-08-05 | GSE118118 | GEO
Project description:This study evaluates the number of lymph nodes dissected in specimens following fixation with 10% neutral buffered formaldehyde or Carnoy’s solution. Specimens were randomized for fixation in each solution.
| 2204199 | ecrin-mdr-crc
Project description:We report the distribution of interactive sites with the sequence close from Meis2 promoter within the genome of mouse embryonic forebrain. We prepared the chromatin from 11 dpc embryonic forebrain and made 3C (chromosomal conformation capture) library. High-throughput sequencing applied for the 3C analysis revealed the distribution of modified interactive sites within developing forebrain. 4C-seq analysis of mouse 11 dpc embryonic forebrain with the sequence close from Meis2 promoter. Forebrain isolated and disected from 11 dpc embryos are fixed by 1% formaldehyde. After conventional 3C reaction, 3C library for highthroughput sequence is prepared by combination of adaptor ligation and nesting PCR reactions.
2014-01-15 | E-GEOD-52281 | biostudies-arrayexpress
Project description:Chromosome conformation capture (3C) techniques are crucial to understanding tissue-specific regulation of gene expression, but current methods generally require large numbers of cells. This hampers the investigation of chromatin architecture in rare cell populations. We present a new low-input Capture-C approach that can generate high-quality 3C interaction profiles from 10 000-20 000 cells, depending on the resolution used for analysis. We also present a PCR-free, sequencing-free 3C technique based on NanoString technology called C-String. By comparing C-String and Capture-C interaction profiles we show that the latter are not skewed by PCR amplification. Furthermore, we demonstrate that chromatin interactions detected by Capture-C do not depend on the degree of cross-linking by performing experiments with varying formaldehyde concentrations.
| S-EPMC5728395 | biostudies-literature
Project description:Though important for gene regulation most studies of genome organisation use either fluorescence in situ hybridisation (FISH) or chromosome conformation capture (3C) methods. FISH directly visualises the spatial relationship of sequences, but is usually applied to a few loci at a time. The frequency at which sequences are ligated together by formaldehyde crosslinking can be measured genome-wide by 3C methods, with higher frequencies thought to reflect shorter distances. FISH and 3C should therefore give the same views of genome organisation, but this has not been tested extensively. We investigate the murine HoxD locus with 5C and FISH in different developmental and activity states, and in the presence or absence of epigenetic regulators. We identify situations where the two datasets are concordant, but find other conditions where chromatin topographies extrapolated from 5C or FISH data are not compatible. We conclude that products captured by 3C do not always reflect spatial proximity, with ligation occurring between sequences located hundreds of nanometers apart – influenced by nuclear environment and chromatin composition. We conclude that results obtained at high-resolution with either 3C methods or by FISH alone must be interpreted with caution and that conclusions about genome organisation should be validated by independent methods. 5C oligonucleotides were designed around EcoRI restriction sites following an alternative scheme
2015-01-02 | E-GEOD-61814 | biostudies-arrayexpress
Project description:Though important for gene regulation most studies of genome organisation use either fluorescence in situ hybridisation (FISH) or chromosome conformation capture (3C) methods. FISH directly visualises the spatial relationship of sequences, but is usually applied to a few loci at a time. The frequency at which sequences are ligated together by formaldehyde crosslinking can be measured genome-wide by 3C methods, with higher frequencies thought to reflect shorter distances. FISH and 3C should therefore give the same views of genome organisation, but this has not been tested extensively. We investigate the murine HoxD locus with 5C and FISH in different developmental and activity states, and in the presence or absence of epigenetic regulators. We identify situations where the two datasets are concordant, but find other conditions where chromatin topographies extrapolated from 5C or FISH data are not compatible. We conclude that products captured by 3C do not always reflect spatial proximity, with ligation occurring between sequences located hundreds of nanometers apart – influenced by nuclear environment and chromatin composition. We conclude that results obtained at high-resolution with either 3C methods or by FISH alone must be interpreted with caution and that conclusions about genome organisation should be validated by independent methods.
2015-01-02 | GSE61814 | GEO
Project description:Chromosome Conformation Capture (3 C) methods, including Hi-C (a high-throughput variation of 3 C), detect pairwise interactions between DNA regions, enabling the reconstruction of chromatin architecture in the nucleus. HiChIP is a modification of the Hi-C experiment that includes a chromatin immunoprecipitation (ChIP) step, allowing genome-wide identification of chromatin contacts mediated by a protein of interest. In mammalian cells, cohesin protein complex is one of the major players in the establishment of chromatin loops. We present an improved cohesin HiChIP experimental protocol. Using comprehensive bioinformatic analysis, we show that a dual chromatin fixation method compared to the standard formaldehyde-only method, results in a substantially better signal-to-noise ratio, increased ChIP efficiency and improved detection of chromatin loops and architectural stripes. Additionally, we propose an automated pipeline called nf-HiChIP (https://github.com/SFGLab/hichip-nf-pipeline) for processing HiChIP samples starting from raw sequencing reads data and ending with a set of significant chromatin interactions (loops), which allows efficient and timely analysis of multiple samples in parallel, without requiring additional ChIP-seq experiments. Finally, using advanced approaches for biophysical modelling and stripe calling we generate accurate loop extrusion polymer models for a region of interest and provide a detailed picture of architectural stripes, respectively.
2025-03-14 | GSE266640 | GEO
Project description:Background: DNA in the nucleus of a living cell carries out its functions in the context of a complex, three-dimensional chromatin architecture. Several recently developed methods, each an extension of the chromatin conformation capture (3C) assay, have enabled the genome-wide profiling of chromatin contacts between pairs of loci in yeast, fruit fly, human and mouse. Especially in complex eukaryotes, data generated by these methods, coupled with other genome-wide datasets, demonstrated that non-random chromatin folding correlates strongly with cellular processes such as gene expression and DNA replication. Here we describe a novel assay to map genome-wide chromatin contacts, tethered multiple 3C (TM3C), that involves a simple protocol of restriction enzyme digestion and religation of fragments upon agarose gel beads followed by deep DNA paired-end sequencing. In addition to identifying contacts between pairs of loci, TM3C enables identification of contacts among more than two loci simultaneously. Results: We use TM3C to assay the genome architectures of two human cell lines: KBM7, a near-haploid chronic leukemia cell line, and NHEK, a normal diploid human epidermal keratinocyte cell line. We confirm that the contact frequency maps produced by TM3C exhibit features characteristic of existing genome architecture datasets, including the expected scaling of contact probabilities with genomic distance, as well as a low noise-to-signal ratio between inter- and intrachromosomal contacts. We also confirm that TM3C captures several known cell type-specific contacts, ploidy shifts and translocations, such as Ph+ formation in KBM7. Furthermore, we develop a two-phase mapping strategy that separately maps chimeric subsequences within a single read, allowing us to identify contacts involving three or four loci simultaneously, potentially corresponding to combinatorial regulation events. This mapping strategy also greatly increases the number of distinct binary contacts identified and, therefore, the coverage obtained for a fixed number of mapped reads. We confirm a subset of the triplet contacts involving the IGF2-H19 imprinting control region (ICR) using PCR analysis for KBM7 cells. Assaying the genome architecture of a near-haploid cell line allows us to create 3D models of a human cell line without averaging signal from two homologous copies of a chromosome. Our 3D models of KBM7 show clustering of small chromosomes with each other and large chromosomes with each other, consistent with previous studies of the genome architectures of other human cell lines. Conclusion: TM3C is a simple protocol for ascertaining genome architecture and can be used to identify simultaneous contacts among three or four loci. Application of TM3C to a near-haploid human cell line revealed large-scale features of chromosomal organization and complex chromatin loops that may play a role in regulating reciprocal expression of the IGF2 and H19 genes. Analysis of the spatial organization of two human cell lines (KBM7, a near-haploid chronic leukemia cell line, and NHEK, a normal diploid human epidermal keratinocyte cell line) using tethered multiple 3C (TM3C), a novel and simple protocol for ascertaining genome architecture which can be used to identify simultaneous contacts among three or four loci in addition to binary contacts that can be identified using traditional chromosome conformation capture coupled with next generation sequencing (Hi-C).
2015-04-29 | E-GEOD-60623 | biostudies-arrayexpress
Project description:Chromosome conformation capture (3C) provides an adaptable tool through which to study diverse biological questions. Currently, 3C techniques provide either low-resolution interaction profiles across the entire genome, e.g. HiC, or high-resolution interaction profiles at up to several hundred loci, e.g. NG Capture-C and 4C-seq. Generation of high-resolution, genome-wide interaction profiles can feasibly be achieved through efficiency improvements to current high-resolution methods. To this end we systematically tested and removed areas inefficiency in NG Capture-C to develop a new method Nuclear Capture-C, which provides a 300% increase in informative sequencing content. Using Nuclear Capture-C we target 8,026 erythroid promoters in triplicate, showing that this method can achieve high-resolution genome-wide 3C interaction profiles at scale.
2020-10-28 | GSE160229 | GEO
Project description:NG Capture-C provides high resolution chromatin conformation capture (3C) interaction maps. NG Capture-C was carried out in erythroid and hESC cells at the Hba, Hbb, Myc, and Slc25a37 locus to generate sequence libraries for analytical software testing.
2020-11-02 | GSE129378 | GEO