Multiplexed analysis of chromosome conformation at vastly improved sensitivity
Open accessAbstract
Methods for analyzing chromosome conformation in mammalian cells are either low resolution or low throughput and are technically challenging. In next-generation (NG) Capture-C, we have redesigned the Capture-C method to achieve unprecedented levels of sensitivity and reproducibility. NG Capture-C can be used to analyze many genetic loci and samples simultaneously. High-resolution data can be produced with as few as 100,000 cells, and single-nucleotide polymorphisms can be used to generate allele-specific tracks. The method is straightforward to perform and should greatly facilitate the investigation of many questions related to gene regulation as well as the functional dissection of traits examined in genome-wide association studies.
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The α-globin genes are regulated by four conserved erythroid-specific enhancers (R1-R4) and a mouse specific element (Rm) located 14-38 kb upstream of the promoters.
“We have shown that the α-globin genes are regulated by four conserved erythroid-specific enhancers (R1-R4) and a mouse specific element (Rm) located 14-38 kb upstream of the promoters15–17.”
From Tissue-specific CTCF-cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo (2017) · cites this paper as [17]
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“, 2016), next-generation (NG) Capture-C for high-resolution and high-throughput chromosome conformation analysis (Davies et al., 2016), and live imaging of transgenic mice to capture a brainwide view of neural activity (Wekselblatt et al.”
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“We initially used Capture-C [28,29], a targeted 3C method based on DpnII digestion, to evaluate changes in chromatin interactions with the promoters of”
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“Capture-C After cell fixation with 1% formaldehyde for 10min and cell sorting as described above, Capture-C was performed with a double-capture procedure (Davies et al. 2016).”
MethodPromoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions
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peakC: a flexible, non-parametric peak calling package for 4C and Capture-C data
Geeven, G., Teunissen, H., de Laat, W. L., & de Wit, E. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky443 · Cited by 102 · see citing works
“Capture-C data was taken from (10) and (21) and was downloaded from GEO (accession GSE67959 and GSE97867, respectively).”
The Ftx Noncoding Locus Controls X Chromosome Inactivation Independently of Its RNA Products
Furlan, G., Hernandez, N. G., Huret, C., Galupa, R., van Bemmel, J. G., Romito, A., Heard, É., Morey, C., & Rougeulle, C. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.03.024 · Cited by 106 · see citing works
Mettananda, S., Fisher, C. A., Hay, D., Badat, M., Quek, L. S., Clark, K., Hublitz, P., Downes, D. J., Kerry, J., Gosden, M. E., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-00479-7 · Cited by 104 · see citing works
Self-citationUMI-4C for quantitative and targeted chromosomal contact profiling
Schwartzman, O., Mukamel, Z., Elkayam, N. O., Olivares‐Chauvet, P., Lubling, Y., Landan, G., Izraeli, S., & Tanay, A. (2016) · Nature Methods · doi:10.1038/nmeth.3922 · Cited by 94 · see citing works
“K562 cells were further validated by fluorescence in situ hybridization (FISH) for the genomic translocation t(9;22) BCR-ABL.”
Background3C and 3C-based techniques: the powerful tools for spatial genome organization deciphering
Han, J., Zhang, Z., & Wang, K. (2018) · Molecular Cytogenetics · doi:10.1186/s13039-018-0368-2 · Cited by 97 · see citing works
“re-designed the Capture-C protocol and developed another method, called next generation (NG) Capture-C [117].”
MethodInfluentialTrac-looping measures genome structure and chromatin accessibility
Lai, B., Tang, Q., Jin, W., Hu, G., Wangsa, D., Cui, K., Stanton, B. Z., Ren, G., Ding, Y., Zhao, M., et al. (2018) · Nature Methods · doi:10.1038/s41592-018-0107-y · Cited by 85 · see citing works
Oudelaar, A. M., Harrold, C. L., Hanssen, L. L. P., Telenius, J. M., Higgs, D. R., & Hughes, J. R. (2019) · Nature Communications · doi:10.1038/s41467-019-13404-x · Cited by 80 · see citing works
“Capture-C – experimental procedure We performed Capture-C experiments in 3 biological replicates of primary erythroid cells derived from WT and D3839 mice following the Next-Generation Capture-C protocol (Davies et al., 2015).”
MethodInfluentialSelf-citationGrampp, S., Platt, J. L., Lauer, V., Salama, R. A., Kranz, F., Neumann, V. K., Wach, S., Stöhr, C., Hartmann, A., Eckardt, K., et al. (2016) · Nature Communications · doi:10.1038/ncomms13183 · Cited by 86 · see citing works
Epigenetic reprogramming of immune cells in injury, repair, and resolution
Placek, K., Schultze, J. L., & Aschenbrenner, A. C. (2019) · Journal of Clinical Investigation · doi:10.1172/jci124619 · Cited by 83 · see citing works
Mining the Unknown: Assigning Function to Noncoding Single Nucleotide Polymorphisms
Nishizaki, S. S., & Boyle, A. P. (2016) · Trends in Genetics · doi:10.1016/j.tig.2016.10.008 · Cited by 84 · see citing works
Transcriptional enhancers and their communication with gene promoters
Ray-Jones, H., & Spivakov, M. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-03903-w · Cited by 81 · see citing works
Spatial Genome Re-organization between Fetal and Adult Hematopoietic Stem Cells
Chen, C.-Y., Yu, W.-B., Tober, J., Gao, P., He, B., Lee, K., Trieu, T., Blobel, G., Speck, N., & Tan, K. (2019) · bioRxiv · doi:10.1016/j.celrep.2019.11.065 · Cited by 65 · see citing works
HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization
Wei, X., Yu, X., Peters, D., Marius, C., Sun, T., Shan, R., Ou, J., Lin, X., Yue, F., Li, W., et al. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.01.023 · Cited by 83 · see citing works
van Bemmel, J. G., Galupa, R., Gard, C., Servant, N., Picard, C., Davies, J. O. J., Szempruch, A. J., Zhan, Y., Żylicz, J. J., Nora, E. P., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0412-0 · Cited by 76 · see citing works
“Capture-C was performed as described in 41.”
Self-citationEpigenetic and Transcriptional Networks Underlying Atrial Fibrillation
van Ouwerkerk, A. F., Hall, A. W., Kadow, Z. A., Lazarevic, S., Reyat, J. S., Tucker, N. R., Nadadur, R. D., Bosada, F. M., Bianchi, V., Ellinor, P. T., et al. (2020) · Circulation Research · doi:10.1161/circresaha.120.316574 · Cited by 78 · see citing works
Three-dimensional genome architecture and emerging technologies: looping in disease
Mishra, A., & Hawkins, R. D. (2017) · Genome Medicine · doi:10.1186/s13073-017-0477-2 · Cited by 77 · see citing works
Huang, P., Peslak, S. A., Lan, X., Khandros, E., Yano, J. A., Sharma, M., Keller, C. A., Giardine, B. M., Qin, K., Abdulmalik, O. Y., et al. (2020) · Blood · doi:10.1182/blood.2020005301 · Cited by 77 · see citing works
Brown, J. M., Roberts, N. A., Graham, B., Waithe, D., Lagerholm, C., Telenius, J. M., De Ornellas, S., Oudelaar, A. M., Scott, C., Szczerbal, I., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06248-4 · Cited by 72 · see citing works
Capture‐C reveals preformed chromatin interactions between HIF‐binding sites and distant promoters
Platt, J. L., Salama, R. A., Smythies, J., Choudhry, H., Davies, J. O. J., Hughes, J. R., Ratcliffe, P. J., & Mole, D. R. (2016) · EMBO Reports · doi:10.15252/embr.201642198 · Cited by 71 · see citing works
“To address these, and related questions as to the number and range of interactions made by HIF-binding sequences under different inducing conditions, we deployed a recently developed multiplexed assay of chromatin conformation [16,17] in normoxic and hypoxic cells, and in renal cancer cells in which HIF is activated i…”
InfluentialSelf-citationActivation of γ-globin expression by hypoxia-inducible factor 1α
Feng, R., Mayuranathan, T., Huang, P., Doerfler, P. A., Li, Y., Yao, Y., Zhang, J., Palmer, L. E., Mayberry, K. D., Christakopoulos, G. E., et al. (2022) · Nature · doi:10.1038/s41586-022-05312-w · Cited by 69 · see citing works
Approaches and advances in the genetic causes of autoimmune disease and their implications
Inshaw, J. R. J., Cutler, A. J., Burren, O. S., Stefana, M. I., & Todd, J. A. (2018) · Nature Immunology · doi:10.1038/s41590-018-0129-8 · Cited by 70 · see citing works
Transcription factors: building hubs in the 3D space
Giammartino, D. C. D., Polyzos, A., & Apostolou, E. (2020) · Cell Cycle · doi:10.1080/15384101.2020.1805238 · Cited by 66 · see citing works
“Recent technological advances that combine Hi-C with antibody-based or oligo-based enrichment steps, such as ChIA-PET [34], PLAC-seq [35], HiChIP [36] and Capture Hi-C [37] have drastically improved the resolution and the discovery rate of promoter–enhancer interactionss.”
BackgroundThe impact of DNA methylation on CTCF-mediated 3D genome organization
Monteagudo, A., Noordermeer, D., & Greenberg, M. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-024-01241-6 · Cited by 66 · see citing works
“Recent refinements of 3C techniques, such as Hi-ChIP 98,99 , Capture-C and Capture Hi-C 100,101 and (Capture) Micro-C 102,103 , have vastly increased both resolutive powers and signal-to-noise ratios.”
Galupa, R., Nora, E. P., Worsley-Hunt, R., Picard, C., Gard, C., van Bemmel, J. G., Servant, N., Zhan, Y., Marjou, F. E., Johanneau, C., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.10.030 · Cited by 63 · see citing works
“Capture-C Capture-C was performed as described in (Davies et al., 2016) with some modifications.”
MethodGodfrey, L., Crump, N. T., O’Byrne, S., Lau, I., Rice, S., Harman, J. R., Jackson, T., Elliott, N., Buck, G., Connor, C., et al. (2020) · Leukemia · doi:10.1038/s41375-020-0808-y · Cited by 65 · see citing works
“Data analysis was performed using an in-house pipeline (https://github.com/Hughes-Genome-Group/CCseqBasicF/ releases; Davies 2016) and statistical analysis was performed as described [18].”
MethodZhu, Y., Tazearslan, C., & Suh, Y. (2017) · Experimental Biology and Medicine · doi:10.1177/1535370217713750 · Cited by 64 · see citing works
Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture
Downes, D. J., Smith, A., Karpińska, M. A., Velychko, T., Rue-Albrecht, K., Sims, D., Milne, T. A., Davies, J. O. J., Oudelaar, A. M., & Hughes, J. R. (2022) · Nature Protocols · doi:10.1038/s41596-021-00651-w · Cited by 59 · see citing works
Self-citationEssential role of Cp190 in physical and regulatory boundary formation
Kaushal, A., Dorier, J., Wang, B., Mohana, G., Taschner, M., Cousin, P., Waridel, P., Iseli, C., Semenova, A., Restrepo, S., et al. (2022) · Science Advances · doi:10.1126/sciadv.abl8834 · Cited by 61 · see citing works
Determining chromatin architecture with Micro Capture-C
Hamley, J. C., Li, H., Denny, N., Downes, D. J., & Davies, J. O. J. (2023) · Nature Protocols · doi:10.1038/s41596-023-00817-8 · Cited by 59 · see citing works
Self-citationRaffield, L. M., Ulirsch, J. C., Naik, R. P. P., Lessard, S., Handsaker, R. E., Jain, D., Kang, H. M., Pankratz, N., Auer, P. L., Bao, E. L., et al. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007293 · Cited by 63 · see citing works
“Furthermore, in the highly homologous mouse locus, elegant chromatin confirmation assays have demonstrated that the MCS-R2 element interacts strongly with both α-globin gene promoters[23], and targeted genomic deletions of this element result in altered α-globin transcription[24].”
BackgroundHIC2 controls developmental hemoglobin switching by repressing BCL11A transcription
Huang, P., Peslak, S. A., Ren, R., Khandros, E., Qin, K., Keller, C. A., Giardine, B. M., Bell, H. W., Lan, X., Sharma, M., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01152-6 · Cited by 57 · see citing works
Gentsch, G. E., Spruce, T., Owens, N. D. L., & Smith, J. C. (2019) · Nature Communications · doi:10.1038/s41467-019-12263-w · Cited by 57 · see citing works
Reactivation of a developmentally silenced embryonic globin gene
King, A. J., Songdej, D., Downes, D. J., Beagrie, R. A., Liu, S., Buckley, M., Peng, H., Suciu, M., Oudelaar, A. M., Hanssen, L. L. P., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24402-3 · Cited by 53 · see citing works
Self-citationVertebrate centromeres in mitosis are functionally bipartite structures stabilized by cohesin
Sacristán, C., Samejima, K., Ruiz, L. A., Deb, M., Lambers, M. L. A., Buckle, A., Brackley, C. A., Robertson, D., Hori, T., Webb, S., et al. (2024) · Cell · doi:10.1016/j.cell.2024.04.014 · Cited by 53 · see citing works
“32 We visualized the data by plotting relative directionality of interactions over a range of distances from each genomic viewpoint.”
The stochastic nature of genome organization and function
Sood, V., & Misteli, T. (2021) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2021.10.004 · Cited by 56 · see citing works
Zhong, J., Niu, L., Lin, Z., Bai, X., Chen, Y., Luo, F., Hou, C., & Xiao, C. (2023) · Nature Communications · doi:10.1038/s41467-023-36899-x · Cited by 57 · see citing works
Raviram, R., Rocha, P. P., Luo, V. M., Swanzey, E., Miraldi, E. R., Chuong, E. B., Feschotte, C., Bonneau, R., & Skok, J. A. (2018) · Genome biology · doi:10.1186/s13059-018-1598-7 · Cited by 51 · see citing works
Lauer, V., Grampp, S., Platt, J. L., Lafleur, V. N., Lombardi, O., Choudhry, H., Kranz, F., Hartmann, A., Wullich, B., Yamamoto, A., et al. (2019) · Journal of Biological Chemistry · doi:10.1074/jbc.ra119.009827 · Cited by 50 · see citing works
“Experiments were performed as described previously (29, 30).”
MethodTruch, J., Downes, D., Scott, C., Gür, E., Telenius, J., Repapi, E., Schwessinger, R., Gosden, M., Brown, J. M., Taylor, S., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31194-7 · Cited by 48 · see citing works
Self-citationAlteration of genome folding via contact domain boundary insertion
Zhang, D., Huang, P., Sharma, M., Keller, C. A., Giardine, B. M., Zhang, H., Gilgenast, T. G., Phillips‐Cremins, J. E., Hardison, R. C., & Blobel, G. A. (2020) · Nature Genetics · doi:10.1038/s41588-020-0680-8 · Cited by 48 · see citing works
Single-cell Hi-C data analysis: safety in numbers
Galitsyna, A. A., & Gelfand, M. S. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab316 · Cited by 49 · see citing works
“Target enrichment for a genomic region is already well developed for bulk chromosome capture approaches [20, 25, 35].”
BackgroundEnhancers predominantly regulate gene expression during differentiation via transcription initiation
Larke, M., Schweßinger, R., Telenius, J., Telenius, J. M., Beagrie, R. A., Downes, D. J., Oudelaar, A. M., Truch, J., Graham, B., Oudelaar, A. M., et al. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.01.002 · Cited by 49 · see citing works
“3C libraries were prepared using DpnII, as in (Davies et al., 2015), with the following modifications: no douncing was performed, all spins were performed at 300g, an additional centrifugation step (300g, 15 min, 4°C) was performed to pellet nuclei after ligation before resuspending in 300 μL 1x T.”
MethodSelf-citationQi, Q., Li, C., Tang, X., He, Y., Li, Y., Yee, T., Shrestha, D., Feng, R., Xu, P., Zhou, X., et al. (2020) · Blood · doi:10.1182/blood.2020005780 · Cited by 44 · see citing works
The macro and micro of chromosome conformation capture
Goel, V. Y., & Hansen, A. S. (2020) · Wiley Interdisciplinary Reviews Developmental Biology · doi:10.1002/wdev.395 · Cited by 46 · see citing works
“…reliance upon oligonucleotides synthesized on microarrays yielded high costs per sample for small experimental designs and that the Capture-C method was not sensitive enough to detect weak interactions, researchers developed next-generation (NG) Capture-C as a solution (Davies et al., 2016).”
Chromatin gene-gene loops support the cross-regulation of genes with related function
Pollex, T., Marco-Ferreres, R., Ciglar, L., Ghavi-Helm, Y., Rabinowitz, A. H., Viales, R. R., Schaub, C., Jankowski, A., Girardot, C., & Furlong, E. E. M. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.12.023 · Cited by 45 · see citing works
Impaired DNA demethylation of C/EBP sites causes premature agingPreprint
Schäfer, A., Mekker, B., Mallick, M., Vastolo, V., Karaulanov, E., Sebastian, D., von der Lippen, C., Epe, B., Downes, D. J., Scholz, C., et al. (2018) · Genes & Development · doi:10.1101/gad.311969.118 · Cited by 42 · see citing works
“(Bottom) NG Capture-C-seq (next-generation Capture-C combined with sequencing) interaction profile of a representative wild-type and double-knockoutMEF line in a 450-kb genomic region on chromosome 5.”
MethodInfluentialChromatin interactome mapping at 139 independent breast cancer risk signals
Beesley, J., Sivakumaran, H., Marjaneh, M. M., Lima, L. G., Hillman, K. M., Kaufmann, S., Tuano, N., Hussein, N., Ham, S., Mukhopadhyay, P., et al. (2020) · Genome biology · doi:10.1186/s13059-019-1877-y · Cited by 43 · see citing works
Qian, Y., Zhang, L., Cai, M., Li, H., Xu, H., Yang, H., Zhao, Z., Rhie, S. K., Farnham, P., Shi, J., et al. (2019) · Science Advances · doi:10.1126/sciadv.aaw6710 · Cited by 42 · see citing works
A Dynamic Folded Hairpin Conformation Is Associated with α-Globin Activation in Erythroid Cells
Chiariello, A. M., Bianco, S., Oudelaar, A. M., Esposito, A., Annunziatella, C., Fiorillo, L., Conte, M., Corrado, A., Prisco, A., Larke, M., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.01.044 · Cited by 41 · see citing works
“2126 Cell Reports 30, 2125–2135, February 18, 2020 Overall, the 3D conformations derived by our study are compatible with previous experimental observations (Anguita et al., 2004; Davies et al., 2016; Hay et al., 2016; Hughes et al., 2014) and recapitulate them under a unique, simple structural rationale.”
ResultSelf-citationPioneer activity distinguishes activating from non‐activating SOX2 binding sites
Maresca, M., van den Brand, T., Li, H., Teunissen, H., Davies, J. O. J., & de Wit, E. (2023) · The EMBO Journal · doi:10.15252/embj.2022113150 · Cited by 35 · see citing works
“We used the “matchRanges” function in the nullranges package (Davis et al , 2023) with the ATACseq and ChIPseq heights as the covariates, in addition to using the “method = ‘stratified’” argument.”
Self-citationBejjani, F., Tolza, C., Boulanger, M., Downes, D. J., Romero, R., Maqbool, M. A., Aabidine, A. Z. E., Andrau, J., Lèbre, S., Bréhélin, L., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab053 · Cited by 42 · see citing works
“The experiments were performed as previously described in (43).”
MethodSelf-citationTranscription modulates chromatin dynamics and locus configuration sampling
Forte, G., Buckle, A., Boyle, S., Marenduzzo, D., Gilbert, N., & Brackley, C. A. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01059-8 · Cited by 40 · see citing works
Issuree, P. D. A., Day, K. R., Au, C., Raviram, R., Zappile, P., Skok, J. A., Xue, H., Myers, R., & Littman, D. R. (2018) · Nature Communications · doi:10.1038/s41467-018-05834-w · Cited by 40 · see citing works
Downes, D. J., Beagrie, R. A., Gosden, M. E., Telenius, J. M., Carpenter, S. J., Nußbaum, L., Ornellas, S. D., Sergeant, M. J., Eijsbouts, C. Q., Schweßinger, R., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20809-6 · Cited by 43 · see citing works
Self-citationMultiple renal cancer susceptibility polymorphisms modulate the HIF pathway
Grampp, S., Schmid, V., Salama, R. A., Lauer, V., Kranz, F., Platt, J. L., Smythies, J., Choudhry, H., Goppelt‐Struebe, M., Ratcliffe, P. J., et al. (2017) · PLoS Genetics · doi:10.1371/journal.pgen.1006872 · Cited by 38 · see citing works
“1 locus, we first used a chromatin conformation assay (Capture-C, [9,22]) to examine for physical interaction between this region and distant gene promoters (Fig 2A).”
MicroRNA-196a is regulated by ER and is a prognostic biomarker in ER+ breast cancer
Milevskiy, M. J. G., Gujral, U., Marques, C., Stone, A. M., Northwood, K. S., Burke, L. J., Gee, J. M. W., Nephew, K. P., Clark, S. J., & Brown, M. A. (2019) · British Journal of Cancer · doi:10.1038/s41416-019-0395-8 · Cited by 38 · see citing works
“To explore this hypothesis a high resolution chromatin interaction analysis of this region in breast cancer cells would be required, such as 5C (32) or NG Capture-C (33), coupled with ERα ChIP-Seq and ChIA-PET (34).”
MethodPredicting Genome Architecture: Challenges and Solutions
Belokopytova, P., & Fishman, V. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2020.617202 · Cited by 38 · see citing works
Zhang, L., He, A., Chen, B., Bi, J., Chen, J., Guo, D., Qian, Y., Wang, W., Shi, T., Zhao, Z., et al. (2020) · Genome Research · doi:10.1101/gr.251058.119 · Cited by 38 · see citing works
“Capture Hi-C and Hi-C data were analyzed based on a pipeline proposed in previous studies (Supplemental Table S2; Servant et al. 2015; Davies et al. 2016; Belaghzal et al. 2017).”
MethodSimon, C. S., Downes, D. J., Gosden, M. E., Telenius, J. M., Higgs, D. R., Hughes, J. R., Costello, I., Bikoff, E. K., & Robertson, E. J. (2017) · Development · doi:10.1242/dev.147322 · Cited by 35 · see citing works
“NG Capture-C was performed as described previously (Davies et al., 2016) on single cell suspensions of ESC, DE or erythrocytes.”
MethodInfluentialSelf-citationRevisiting 3D chromatin architecture in cancer development and progression
Feng, Y., & Pauklin, S. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa747 · Cited by 36 · see citing works
“In addition, Douglas Higgs/Jim Hughes labs further refined their previously developed Capture-C approach (113) and presented a new next-generation (NG) Capture-C protocol (114).”
BackgroundSpecies-specific regulation ofXISTby theJPX/FTXorthologs
Rosspopoff, O., Cazottes, E., Huret, C., Loda, A., Collier, A. J., Casanova, M., Rugg‐Gunn, P. J., Heard, É., Ouimette, J., & Rougeulle, C. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad029 · Cited by 35 · see citing works
“In situ Capture HiC was performed as previously published (27) with the following modifications.”
MethodVermeulen, C., Allahyar, A., Bouwman, B. A. M., Krijger, P. H. L., Verstegen, M. J. A. M., Geeven, G., Valdes‐Quezada, C., Renkens, I., Straver, R., Kloosterman, W. P., et al. (2020) · Nature Protocols · doi:10.1038/s41596-019-0242-7 · Cited by 35 · see citing works
Exploration of Coding and Non-coding Variants in Cancer Using GenomePaint
Zhou, X., Wang, J., Patel, J. N., Valentine, M. B., Shao, Y., Newman, S., Sioson, E., Tian, L., Liu, Y., Brady, S. W., et al. (2021) · Cancer Cell · doi:10.1016/j.ccell.2020.12.011 · Cited by 35 · see citing works
- Authors
- Davies, J. O. J., Telenius, J. M., McGowan, S. J., Roberts, N. A., Taylor, S., Higgs, D. R., & Hughes, J. R.
- Affiliations
- University of Oxford (GB)
- Corresponding author
- Hughes, Jim R
- ORCID
- Venue
- Nature Methods
- Published
- 2015-11-23
- Volume
- 13
- Issue
- 1
- Pages
- 74-80
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC4724891
- OpenAlex
- W2173155483
- Cited by
- 268
- References
- 35
- Citations by year
- 2026: 11 · 2025: 11 · 2024: 24 · 2023: 25 · 2022: 26 · 2021: 29 · 2020: 41 · 2019: 37 · 2018: 29 · 2017: 19 · 2016: 15 · 2015: 1
- FWCI
- 9.27
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Wellcome Trust (098931/Z/12/Z, 106130/Z/14/Z, 106130)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- chromosome conformation, 3C, single nucleotide polymorphisms, gene expression regulation, genome-wide association study
- MeSH terms
- Chromosomes, Human, Humans, Regulatory Sequences, Nucleic Acid, Reproducibility of Results, Polymorphism, Single Nucleotide
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