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137 results on '"Wingett, Steven W."'

1. Intra- and interchromosomal contact mapping reveals the Igh locus has extensive conformational heterogeneity and interacts with B-lineage genes

Author

Mielczarek, Olga, Rogers, Carolyn H., Zhan, Yinxiu, Matheson, Louise S., Stubbington, Michael J.T., Schoenfelder, Stefan, Bolland, Daniel J., Javierre, Biola M., Wingett, Steven W., Várnai, Csilla, Segonds-Pichon, Anne, Conn, Simon J., Krueger, Felix, Andrews, Simon, Fraser, Peter, Giorgetti, Luca, and Corcoran, Anne E.

Published
2023
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6. Multi-omic analysis of guided and unguided forebrain organoids reveal differences in cellular composition and metabolic profiles

Author

Oehlenschlaeger, Marie S., primary, Jensen, Pia, additional, Havelund, jesper F., additional, Sutcliffe, Magdalena, additional, Elmkvist, Sofie B., additional, Criscuolo, Lucrezia, additional, Wingett, Steven W., additional, Jakobsen, Lene A., additional, Brewer, Jonathan, additional, Faergeman, Nils J, additional, Lancaster, Madeline A, additional, Larsen, Martin R, additional, and Bogetofte, Helle, additional

Published
2023
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8. Genome-scale requirements for dynein-based transport revealed by a high-content arrayed CRISPR screen.

Author

Chun Hao Wong, Wingett, Steven W., Chen Qian, Hunter, Morag Rose, Taliaferro, J. Matthew, Ross-Thriepland, Douglas, and Bullock, Simon L.

Subjects
*RNA-binding proteins, *MOLECULAR motor proteins, *CRISPRS, *DNA fingerprinting, *DYNEIN, *PEROXISOMES
Abstract

The microtubule motor dynein plays a key role in cellular organization. However, little is known about how dynein's biosynthesis, assembly, and functional diversity are orchestrated. To address this issue, we have conducted an arrayed CRISPR loss-of-function screen in human cells using the distribution of dynein-tethered peroxisomes and early endosomes as readouts. From a genome-wide gRNA library, 195 validated hits were recovered and parsed into those impacting multiple dynein cargoes and those whose effects are restricted to a subset of cargoes. Clustering of high-dimensional phenotypic fingerprints revealed co-functional proteins involved in many cellular processes, including several candidate novel regulators of core dynein functions. Further analysis of one of these factors, the RNA-binding protein SUGP1, indicates that it promotes cargo trafficking by sustaining functional expression of the dynein activator LIS1. Our data represent a rich source of new hypotheses for investigating microtubule-based transport, as well as several other aspects of cellular organization captured by our high-content imaging. [ABSTRACT FROM AUTHOR]

Published
2024
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12. Genome-wide analysis of promoter contacts identifies novel regulators of late-stage adipogenesis

Author

Sandovici, Ionel, primary, Mifsud, Borbala, additional, Emery, Amy, additional, Gulati, Pawan, additional, Kentistou, Katherine A., additional, Banu, Ayesha, additional, Campbell, Niamh, additional, Hardwick, Bryn S., additional, Crooks, Alex T., additional, Fernandez-Twinn, Denise S., additional, Mennitti, Lais V., additional, Srour, Luma, additional, Awad, Sherine, additional, Chiarugi, Davide, additional, Hamilton, Russell S., additional, Wingett, Steven W., additional, Fraser, Peter, additional, Ong, Ken K., additional, Schoenfelder, Stefan, additional, Mohammad, Farhan, additional, O’Rahilly, Stephen, additional, Perry, John R.B., additional, Venkitaraman, Ashok R., additional, Ozanne, Susan E., additional, and Constância, Miguel, additional

Published
2023
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13. The reference epigenome and regulatory chromatin landscape of chronic lymphocytic leukemia

Author

Beekman, Renée, Chapaprieta, Vicente, Russiñol, Núria, Vilarrasa-Blasi, Roser, Verdaguer-Dot, Núria, Martens, Joost H. A., Duran-Ferrer, Martí, Kulis, Marta, Serra, François, Javierre, Biola M., Wingett, Steven W., Clot, Guillem, Queirós, Ana C., Castellano, Giancarlo, Blanc, Julie, Gut, Marta, Merkel, Angelika, Heath, Simon, Vlasova, Anna, Ullrich, Sebastian, Palumbo, Emilio, Enjuanes, Anna, Martín-García, David, Beà, Sílvia, Pinyol, Magda, Aymerich, Marta, Royo, Romina, Puiggros, Montserrat, Torrents, David, Datta, Avik, Lowy, Ernesto, Kostadima, Myrto, Roller, Maša, Clarke, Laura, Flicek, Paul, Agirre, Xabier, Prosper, Felipe, Baumann, Tycho, Delgado, Julio, López-Guillermo, Armando, Fraser, Peter, Yaspo, Marie-Laure, Guigó, Roderic, Siebert, Reiner, Martí-Renom, Marc A., Puente, Xose S., López-Otín, Carlos, Gut, Ivo, Stunnenberg, Hendrik G., Campo, Elias, and Martin-Subero, Jose I.

Published
2018
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18. Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells

Author

Koohy, Hashem, Bolland, Daniel J., Matheson, Louise S., Schoenfelder, Stefan, Stellato, Claudia, Dimond, Andrew, Várnai, Csilla, Chovanec, Peter, Chessa, Tamara, Denizot, Jeremy, Manzano Garcia, Raquel, Wingett, Steven W., Freire-Pritchett, Paula, Nagano, Takashi, Hawkins, Phillip, Stephens, Len, Elderkin, Sarah, Spivakov, Mikhail, Fraser, Peter, Corcoran, Anne E., and Varga-Weisz, Patrick D.

Published
2018
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20. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans

Author

Chauve, Laetitia, primary, Hodge, Francesca, additional, Murdoch, Sharlene, additional, Masoudzadeh, Fatemeh, additional, Mann, Harry-Jack, additional, Lopez-Clavijo, Andrea F., additional, Okkenhaug, Hanneke, additional, West, Greg, additional, Sousa, Bebiana C., additional, Segonds-Pichon, Anne, additional, Li, Cheryl, additional, Wingett, Steven W., additional, Kienberger, Hermine, additional, Kleigrewe, Karin, additional, de Bono, Mario, additional, Wakelam, Michael J. O., additional, and Casanueva, Olivia, additional

Published
2021
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21. Additional file 4 of The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle

Author

Furlan-Magaril, Mayra, Ando-Kuri, Masami, Arzate-Mejía, Rodrigo G., Morf, Jörg, Cairns, Jonathan, Román-Figueroa, Abraham, Tenorio-Hernández, Luis, Poot-Hernández, A. César, Andrews, Simon, Várnai, Csilla, Virk, Boo, Wingett, Steven W., and Fraser, Peter

Abstract

Additional file 4: Figure S4. TAD structure and CTCF binding is preserved during the 24 hours. A. TADs overlap between time points. B. TADs size distribution at all time points. C. 50kb resolution Median Observed/Expected Hi-C signal around 1000 randomly selected TADs from ZT6, 12 and 18 plotted on the indicated time points. TADs were scaled to fit the five central bins. D. CTCF ChIP-seq motif analysis and peak overlap between ZT0 and 12. Genomic tracks of CTCF ChIP-seq signal at example regions harbouring circadian genes. E. Above, the same metaplots as in C but for 1000 randomly CTCF peaks found at ZT12 plotted using ZT12 and ZT0 Hi-C contacts. Below, metaplot using CTCF peaks from mESC and plotted using liver ZT0 and 12 Hi-C contacts. CTCF peaks are at the central bin of the metaplot. F. TAD and cTAD size comparison (p-value < 2.2e-16, Wilcoxon rank sum test).

Published
2021
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22. Additional file 7 of The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle

Author

Furlan-Magaril, Mayra, Ando-Kuri, Masami, Arzate-Mejía, Rodrigo G., Morf, Jörg, Cairns, Jonathan, Román-Figueroa, Abraham, Tenorio-Hernández, Luis, Poot-Hernández, A. César, Andrews, Simon, Várnai, Csilla, Virk, Boo, Wingett, Steven W., and Fraser, Peter

Abstract

Additional file 7: Figure S7. Core clock gene promoter vs output circadian genes interaction landscapes.A-D. Virtual 4C for Rorc, Npas2, Nr1d2 and Per2, core clock circadian gene promoters from P-CHi-C data at all time points during the day. The Rorc circadian gene promoter contacts Cgn circadian gene promoter and both peak in transcription at ZT18. E-F Virtual 4C for Dhrs3 and Ppp1r3c output circadian genes in the liver. Acrophases are written next to the gene names. Genomic tracks show significant contacts as arcs and chromatin features including liver H3K4me3, H3K4me1, H3K27ac, DNAseI, eRNAs and TADs. Expression profiles for all genes can be found in Figure S3. The interaction profiles of core clock genes display less contacts that dynamically change over time. The two output gene contact profiles show more saturated contacts that are mostly constant during the 24 hours.

Published
2021
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23. Additional file 3 of The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle

Author

Furlan-Magaril, Mayra, Ando-Kuri, Masami, Arzate-Mejía, Rodrigo G., Morf, Jörg, Cairns, Jonathan, Román-Figueroa, Abraham, Tenorio-Hernández, Luis, Poot-Hernández, A. César, Andrews, Simon, Várnai, Csilla, Virk, Boo, Wingett, Steven W., and Fraser, Peter

Abstract

Additional file 3: Figure S3. Expression profiles of the circadian genes displayed along the paper. RNA-seq signal tracks for circadian genes shown across the paper for the four timepoints during the circadian cycle. Arntl, Npas2, Cgn, Nr1d1, Dhrs3, Nr1d2, Per2, Ppp1r3c, Tef, Rnf125, Rorc and Aco2 circadian gene expression profiles are presented.

Published
2021
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24. Additional file 6 of The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle

Author

Furlan-Magaril, Mayra, Ando-Kuri, Masami, Arzate-Mejía, Rodrigo G., Morf, Jörg, Cairns, Jonathan, Román-Figueroa, Abraham, Tenorio-Hernández, Luis, Poot-Hernández, A. César, Andrews, Simon, Várnai, Csilla, Virk, Boo, Wingett, Steven W., and Fraser, Peter

Abstract

Additional file 6: Figure S6. Circadian gene promoter-promoter interactions. A. Promoter-promoter contact network at ZT0 with the circadian genes marked in blue. B. Above, number of edges (interactions) between circadian gene promoters at ZT0, 6, 12 and 18 hours of the day (blue line) compared to a random set of non circadian promoters. Below, z-score for circadian gene promoter contacts compared to the random sampling. C. Quantification of the read counts supporting all circadian gene promoter-promoter interactions compared to a random set of non circadian promoter-promoter interactions (*** p-value < 0.001, Mann Whitney test) D. Transcriptional phase distributions of circadian promoters in contact with diurnal or nocturnal circadian promoters (all p-values < 0.0001, Wilcoxon signed rank test) for our circadian intronic gene set. E. The same as in D for the circadian gene set detected through GRO-seq (Fang et al., 2014) (all p-values < 0.0001, Wilcoxon signed rank test) F. Virtual 4C landscape for the Tef circadian gene promoter from P-CHi-C data at all time points during the day. The acrophase of Tef is written next to the gene name. Expression profiles for both genes can be found in Figure S3. Genomic tracks show significant contacts as arcs and chromatin features including liver H3K4me3, H4K4me1, H3K27ac, DNAseI, eRNAs and TADs. Tef gene promoter contacts Aco2 gene promoter both with acrophase at ZT12.

Published
2021
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25. Additional file 1 of The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle

Author

Furlan-Magaril, Mayra, Ando-Kuri, Masami, Arzate-Mejía, Rodrigo G., Morf, Jörg, Cairns, Jonathan, Román-Figueroa, Abraham, Tenorio-Hernández, Luis, Poot-Hernández, A. César, Andrews, Simon, Várnai, Csilla, Virk, Boo, Wingett, Steven W., and Fraser, Peter

Abstract

Additional file 1: Figure S1. OCCs present fluctuations in histone modifications. A. Heatmap of PC1 values for stable compartments from the three independent Hi-C biological replicates and B, the merged Hi-C biological replicates. C. PC1 eigenvector correlations between every pair of timepoints (Kruskal-Wallis rank sum test p-value < 2e-16). D. Proportion of OCCs and constant compartments in the mouse genome. E. Barplot of the frequency of the different OCCs categories with compartments switching at different times of the 24 hours. For example AABA refers to OCCs with compartment assignment A at ZT0, A at ZT6, B at ZT12 and A at ZT18. F. Chromatin features (H3Kme4 and H3Kme1) at OCCs across time points (AABB, ABBB and ABAB OCCs are shown) (*** all p-values < 0.001 except for the H3K4me1 AABB, one way ANOVA and Tukey post hoc test).

Published
2021
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27. Additional file 2 of The global and promoter-centric 3D genome organization temporally resolved during a circadian cycle

Author

Furlan-Magaril, Mayra, Ando-Kuri, Masami, Arzate-Mejía, Rodrigo G., Morf, Jörg, Cairns, Jonathan, Román-Figueroa, Abraham, Tenorio-Hernández, Luis, Poot-Hernández, A. César, Andrews, Simon, Várnai, Csilla, Virk, Boo, Wingett, Steven W., and Fraser, Peter

Abstract

Additional file 2: Figure S2. Total RNA-seq analysis at four timepoints during the circadian cycle. A. Spearman correlation analysis of the four biological replicates from ZT0 and ZT12 (r ≥ 0.85). B. Heat map of the relative transcription (Z scores) of 1,257 oscillating genes sorted by oscillation phase. C. Individual expression profiles and genome browser tracks showing examples of the RNA-seq signal for Arntl, Per1, Nr1d1, Cry1, Ppp1r3c and Gsk3a oscillating genes (Fragments Per Kilobase of transcript per Million mapped reads, FPKM) (n=4, q-value

Published
2021
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29. Platelet function is modified by common sequence variation in megakaryocyte super enhancers

Author

Petersen, Romina, Lambourne, John J., Javierre, Biola M., Grassi, Luigi, Kreuzhuber, Roman, Ruklisa, Dace, Rosa, Isabel M., Tomé, Ana R., Elding, Heather, van Geffen, Johanna P., Jiang, Tao, Farrow, Samantha, Cairns, Jonathan, Al-Subaie, Abeer M., Ashford, Sofie, Attwood, Antony, Batista, Joana, Bouman, Heleen, Burden, Frances, Choudry, Fizzah A., Clarke, Laura, Flicek, Paul, Garner, Stephen F., Haimel, Matthias, Kempster, Carly, Ladopoulos, Vasileios, Lenaerts, An-Sofie, Materek, Paulina M., McKinney, Harriet, Meacham, Stuart, Mead, Daniel, Nagy, Magdolna, Penkett, Christopher J., Rendon, Augusto, Seyres, Denis, Sun, Benjamin, Tuna, Salih, van der Weide, Marie-Elise, Wingett, Steven W., Martens, Joost H., Stegle, Oliver, Richardson, Sylvia, Vallier, Ludovic, Roberts, David J., Freson, Kathleen, Wernisch, Lorenz, Stunnenberg, Hendrik G., Danesh, John, Fraser, Peter, Soranzo, Nicole, Butterworth, Adam S., Heemskerk, Johan W., Turro, Ernest, Spivakov, Mikhail, Ouwehand, Willem H., Astle, William J., Downes, Kate, Kostadima, Myrto, Frontini, Mattia, Lambourne, John [0000-0003-2460-0759], Grassi, Luigi [0000-0002-6308-7540], Haimel, Matthias [0000-0002-0320-0214], Rendon Restrepo, Augusto [0000-0001-8994-0039], Seyres, Denis [0000-0002-2066-6980], Sun, Ben [0000-0001-6347-2281], Tuna, Salih [0000-0003-3606-4367], Richardson, Sylvia [0000-0003-1998-492X], Vallier, Ludovic [0000-0002-3848-2602], Danesh, John [0000-0003-1158-6791], Soranzo, Nicole [0000-0003-1095-3852], Butterworth, Adam [0000-0002-6915-9015], Turro Bassols, Ernest [0000-0002-1820-6563], Ouwehand, Willem [0000-0002-7744-1790], Astle, William [0000-0001-8866-6672], Downes, Kate [0000-0003-0366-1579], Frontini, Mattia [0000-0001-8074-6299], Apollo - University of Cambridge Repository, MUMC+: MA Med Staf Artsass Interne Geneeskunde (9), RS: CARIM - R1.03 - Cell biochemistry of thrombosis and haemostasis, and Biochemie

Subjects
Blood Platelets, GENE-REGULATION, BLOOD, Erythroblasts, Science, Genetic Variation, OPEN CHROMATIN, DISEASE, Article, Chromatin, DNA-BINDING PROTEINS, THROMBUS FORMATION, GENOME, HUMAN CELL-TYPES, SEQ, Enhancer Elements, Genetic, TRAIT LOCI, Humans, Promoter Regions, Genetic, Megakaryocytes
Abstract

Linking non-coding genetic variants associated with the risk of diseases or disease-relevant traits to target genes is a crucial step to realize GWAS potential in the introduction of precision medicine. Here we set out to determine the mechanisms underpinning variant association with platelet quantitative traits using cell type-matched epigenomic data and promoter long-range interactions. We identify potential regulatory functions for 423 of 565 (75%) non-coding variants associated with platelet traits and we demonstrate, through ex vivo and proof of principle genome editing validation, that variants in super enhancers play an important role in controlling archetypical platelet functions., Numerous genetic variants, including those located in the non-coding regions of the genome, are known to be associated with blood cells traits. Here, Frontini and colleagues investigate their potential regulatory functions using epigenomic data and promoter long-range interactions.

Published
2017

30. The adjuvant GLA-SE promotes human Tfh cell expansion and emergence of public TCRβ clonotypes

Author

Hill, Danika L., primary, Pierson, Wim, additional, Bolland, Daniel J., additional, Mkindi, Catherine, additional, Carr, Edward J., additional, Wang, Jiong, additional, Houard, Sophie, additional, Wingett, Steven W., additional, Audran, Regine, additional, Wallin, Elizabeth F., additional, Jongo, Said A., additional, Kamaka, Kassim, additional, Zand, Martin, additional, Spertini, Francois, additional, Daubenberger, Claudia, additional, Corcoran, Anne E., additional, and Linterman, Michelle A., additional

Published
2019
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31. Author Correction: Promoter interactome of human embryonic stem cell-derived cardiomyocytes connects GWAS regions to cardiac gene networks (Nature Communications, (2018), 9, 1, (2526), 10.1038/s41467-018-04931-0)

Author

Choy, Mun-Kit, Javierre, Biola M, Williams, Simon G, Baross, Stephanie L, Liu, Yingjuan, Wingett, Steven W, Akbarov, Artur, Wallace, Chris, Freire-Pritchett, Paula, Rugg-Gunn, Peter J, Spivakov, Mikhail, Fraser, Peter, Keavney, Bernard D, Choy, Mun-Kit, Javierre, Biola M, Williams, Simon G, Baross, Stephanie L, Liu, Yingjuan, Wingett, Steven W, Akbarov, Artur, Wallace, Chris, Freire-Pritchett, Paula, Rugg-Gunn, Peter J, Spivakov, Mikhail, Fraser, Peter, and Keavney, Bernard D

Abstract

In the original version of the Article, the gene symbol for tissue factor pathway inhibitor was inadvertently given as ‘TFP1’ instead of ‘TFPI’. This has now been corrected in both the PDF and HTML versions of the Article.

Published
2018

34. Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition

Author

Novo, Clara Lopes, primary, Javierre, Biola-Maria, additional, Cairns, Jonathan, additional, Segonds-Pichon, Anne, additional, Wingett, Steven W., additional, Freire-Pritchett, Paula, additional, Furlan-Magaril, Mayra, additional, Schoenfelder, Stefan, additional, Fraser, Peter, additional, and Rugg-Gunn, Peter J., additional

Published
2018
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36. Chromosome contacts in activated T cells identify autoimmune disease candidate genes

Author

Burren, Oliver S., primary, Rubio García, Arcadio, additional, Javierre, Biola-Maria, additional, Rainbow, Daniel B., additional, Cairns, Jonathan, additional, Cooper, Nicholas J., additional, Lambourne, John J., additional, Schofield, Ellen, additional, Castro Dopico, Xaquin, additional, Ferreira, Ricardo C., additional, Coulson, Richard, additional, Burden, Frances, additional, Rowlston, Sophia P., additional, Downes, Kate, additional, Wingett, Steven W., additional, Frontini, Mattia, additional, Ouwehand, Willem H., additional, Fraser, Peter, additional, Spivakov, Mikhail, additional, Todd, John A., additional, Wicker, Linda S., additional, Cutler, Antony J., additional, and Wallace, Chris, additional

Published
2017
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37. Lineage-specific dynamic and pre-established enhancer–promoter contacts cooperate in terminal differentiation

Author

Rubin, Adam J, primary, Barajas, Brook C, additional, Furlan-Magaril, Mayra, additional, Lopez-Pajares, Vanessa, additional, Mumbach, Maxwell R, additional, Howard, Imani, additional, Kim, Daniel S, additional, Boxer, Lisa D, additional, Cairns, Jonathan, additional, Spivakov, Mikhail, additional, Wingett, Steven W, additional, Shi, Minyi, additional, Zhao, Zhixin, additional, Greenleaf, William J, additional, Kundaje, Anshul, additional, Snyder, Michael, additional, Chang, Howard Y, additional, Fraser, Peter, additional, and Khavari, Paul A, additional

Published
2017
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38. Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells

Author

Freire-Pritchett, Paula, primary, Schoenfelder, Stefan, additional, Várnai, Csilla, additional, Wingett, Steven W, additional, Cairns, Jonathan, additional, Collier, Amanda J, additional, García-Vílchez, Raquel, additional, Furlan-Magaril, Mayra, additional, Osborne, Cameron S, additional, Fraser, Peter, additional, Rugg-Gunn, Peter J, additional, and Spivakov, Mikhail, additional

Published
2017
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39. Chromosome contacts in activated T cells identify autoimmune disease candidate genes

Author

Burren, Oliver S, primary, García, Arcadio Rubio, additional, Javierre, Biola-Maria, additional, Rainbow, Daniel B, additional, Cairns, Jonathan, additional, Cooper, Nicholas J, additional, Lambourne, John J, additional, Schofield, Ellen, additional, Dopico, Xaquin Castro, additional, Ferreira, Ricardo C, additional, Coulson, Richard, additional, Burden, Frances, additional, Rowlston, Sophia P, additional, Downes, Kate, additional, Wingett, Steven W, additional, Frontini, Mattia, additional, Ouwehand, Willem H, additional, Fraser, Peter, additional, Spivakov, Mikhail, additional, Todd, John A, additional, Wicker, Linda S, additional, Cutler, Antony J, additional, and Wallace, Chris, additional

Published
2017
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40. Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

Author

Javierre, Biola M., primary, Burren, Oliver S., additional, Wilder, Steven P., additional, Kreuzhuber, Roman, additional, Hill, Steven M., additional, Sewitz, Sven, additional, Cairns, Jonathan, additional, Wingett, Steven W., additional, Várnai, Csilla, additional, Thiecke, Michiel J., additional, Burden, Frances, additional, Farrow, Samantha, additional, Cutler, Antony J., additional, Rehnström, Karola, additional, Downes, Kate, additional, Grassi, Luigi, additional, Kostadima, Myrto, additional, Freire-Pritchett, Paula, additional, Wang, Fan, additional, Stunnenberg, Hendrik G., additional, Todd, John A., additional, Zerbino, Daniel R., additional, Stegle, Oliver, additional, Ouwehand, Willem H., additional, Frontini, Mattia, additional, Wallace, Chris, additional, Spivakov, Mikhail, additional, Fraser, Peter, additional, Martens, Joost H., additional, Kim, Bowon, additional, Sharifi, Nilofar, additional, Janssen-Megens, Eva M., additional, Yaspo, Marie-Laure, additional, Linser, Matthias, additional, Kovacsovics, Alexander, additional, Clarke, Laura, additional, Richardson, David, additional, Datta, Avik, additional, and Flicek, Paul, additional

Published
2016
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41. CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data

Author

Cairns, Jonathan, primary, Freire-Pritchett, Paula, additional, Wingett, Steven W., additional, Várnai, Csilla, additional, Dimond, Andrew, additional, Plagnol, Vincent, additional, Zerbino, Daniel, additional, Schoenfelder, Stefan, additional, Javierre, Biola-Maria, additional, Osborne, Cameron, additional, Fraser, Peter, additional, and Spivakov, Mikhail, additional

Published
2016
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42. Promoter interactome of human embryonic stem cell-derived cardiomyocytes connects GWAS regions to cardiac gene networks.

Author

Mun-Kit Choy, Javierre, Biola M., Williams, Simon G., Baross, Stephanie L., Yingjuan Liu, Wingett, Steven W., Akbarov, Artur, Wallace, Chris, Freire-Pritchett, Paula, Rugg-Gunn, Peter J., Spivakov, Mikhail, Fraser, Peter, and Keavney, Bernard D.

Abstract

Long-range chromosomal interactions bring distal regulatory elements and promoters together to regulate gene expression in biological processes. By performing promoter capture Hi-C (PCHi-C) on human embryonic stem cell-derived cardiomyocytes (hESC-CMs), we show that such promoter interactions are a key mechanism by which enhancers contact their target genes after hESC-CM differentiation from hESCs. We also show that the promoter interactome of hESC-CMs is associated with expression quantitative trait loci (eQTLs) in cardiac left ventricular tissue; captures the dynamic process of genome reorganisation after hESC-CM differentiation; overlaps genome-wide association study (GWAS) regions associated with heart rate; and identifies new candidate genes in such regions. These findings indicate that regulatory elements in hESC-CMs identified by our approach control gene expression involved in ventricular conduction and rhythm of the heart. The study of promoter interactions in other hESC-derived cell types may be of utility in functional investigation of GWAS-associated regions. [ABSTRACT FROM AUTHOR]

Published
2018
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43. Intra- and interchromosomal contact mapping reveals the Ighlocus has extensive conformational heterogeneity and interacts with B-lineage genes

Author

Mielczarek, Olga, Rogers, Carolyn H., Zhan, Yinxiu, Matheson, Louise S., Stubbington, Michael J.T., Schoenfelder, Stefan, Bolland, Daniel J., Javierre, Biola M., Wingett, Steven W., Várnai, Csilla, Segonds-Pichon, Anne, Conn, Simon J., Krueger, Felix, Andrews, Simon, Fraser, Peter, Giorgetti, Luca, and Corcoran, Anne E.

Abstract

To produce a diverse antibody repertoire, immunoglobulin heavy-chain (Igh) loci undergo large-scale alterations in structure to facilitate juxtaposition and recombination of spatially separated variable (VH), diversity (DH), and joining (JH) genes. These chromosomal alterations are poorly understood. Uncovering their patterns shows how chromosome dynamics underpins antibody diversity. Using tiled Capture Hi-C, we produce a comprehensive map of chromatin interactions throughout the 2.8-Mb Ighlocus in progenitor B cells. We find that the Ighlocus folds into semi-rigid subdomains and undergoes flexible looping of the VHgenes to its 3′ end, reconciling two views of locus organization. Deconvolution of single Ighlocus conformations using polymer simulations identifies thousands of different structures. This heterogeneity may underpin the diversity of V(D)J recombination events. All three immunoglobulin loci also participate in a highly specific, developmentally regulated network of interchromosomal interactions with genes encoding B cell-lineage factors. This suggests a model of interchromosomal coordination of B cell development.

Published
2023
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46. CHiCAGO: Robust Detection of DNA Looping Interactions in Capture Hi-C data

Author

Cairns, Jonathan, primary, Freire-Pritchett, Paula, additional, Wingett, Steven W., additional, Várnai, Csilla, additional, Dimond, Andrew, additional, Plagnol, Vincent, additional, Zerbino, Daniel, additional, Schoenfelder, Stefan, additional, Javierre, Biola-Maria, additional, Osborne, Cameron, additional, Fraser, Peter, additional, and Spivakov, Mikhail, additional

Published
2015
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47. Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome

Author

Schoenfelder, Stefan, primary, Sugar, Robert, additional, Dimond, Andrew, additional, Javierre, Biola-Maria, additional, Armstrong, Harry, additional, Mifsud, Borbala, additional, Dimitrova, Emilia, additional, Matheson, Louise, additional, Tavares-Cadete, Filipe, additional, Furlan-Magaril, Mayra, additional, Segonds-Pichon, Anne, additional, Jurkowski, Wiktor, additional, Wingett, Steven W, additional, Tabbada, Kristina, additional, Andrews, Simon, additional, Herman, Bram, additional, LeProust, Emily, additional, Osborne, Cameron S, additional, Koseki, Haruhiko, additional, Fraser, Peter, additional, Luscombe, Nicholas M, additional, and Elderkin, Sarah, additional

Published
2015
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49. Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

Author

Mifsud, Borbala, primary, Tavares-Cadete, Filipe, additional, Young, Alice N, additional, Sugar, Robert, additional, Schoenfelder, Stefan, additional, Ferreira, Lauren, additional, Wingett, Steven W, additional, Andrews, Simon, additional, Grey, William, additional, Ewels, Philip A, additional, Herman, Bram, additional, Happe, Scott, additional, Higgs, Andy, additional, LeProust, Emily, additional, Follows, George A, additional, Fraser, Peter, additional, Luscombe, Nicholas M, additional, and Osborne, Cameron S, additional

Published
2015
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50. The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements

Author

Schoenfelder, Stefan, primary, Furlan-Magaril, Mayra, additional, Mifsud, Borbala, additional, Tavares-Cadete, Filipe, additional, Sugar, Robert, additional, Javierre, Biola-Maria, additional, Nagano, Takashi, additional, Katsman, Yulia, additional, Sakthidevi, Moorthy, additional, Wingett, Steven W., additional, Dimitrova, Emilia, additional, Dimond, Andrew, additional, Edelman, Lucas B., additional, Elderkin, Sarah, additional, Tabbada, Kristina, additional, Darbo, Elodie, additional, Andrews, Simon, additional, Herman, Bram, additional, Higgs, Andy, additional, LeProust, Emily, additional, Osborne, Cameron S., additional, Mitchell, Jennifer A., additional, Luscombe, Nicholas M., additional, and Fraser, Peter, additional

Published
2015
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