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Items: 24

1.

RNA proximity sequencing reveals the spatial organization of the transcriptome in the nucleus.

Morf J, Wingett SW, Farabella I, Cairns J, Furlan-Magaril M, Jiménez-García LF, Liu X, Craig FF, Walker S, Segonds-Pichon A, Andrews S, Marti-Renom MA, Fraser P.

Nat Biotechnol. 2019 Jul;37(7):793-802. doi: 10.1038/s41587-019-0166-3. Epub 2019 Jul 1.

PMID:
31267103
2.

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

Hill DL, Pierson W, Bolland DJ, Mkindi C, Carr EJ, Wang J, Houard S, Wingett SW, Audran R, Wallin EF, Jongo SA, Kamaka K, Zand M, Spertini F, Daubenberger C, Corcoran AE, Linterman MA.

J Exp Med. 2019 Aug 5;216(8):1857-1873. doi: 10.1084/jem.20190301. Epub 2019 Jun 7.

3.

Author Correction: Promoter interactome of human embryonic stem cell-derived cardiomyocytes connects GWAS regions to cardiac gene networks.

Choy MK, Javierre BM, Williams SG, Baross SL, Liu Y, Wingett SW, Akbarov A, Wallace C, Freire-Pritchett P, Rugg-Gunn PJ, Spivakov M, Fraser P, Keavney BD.

Nat Commun. 2018 Nov 12;9(1):4792. doi: 10.1038/s41467-018-07399-0.

4.

FastQ Screen: A tool for multi-genome mapping and quality control.

Wingett SW, Andrews S.

Version 2. F1000Res. 2018 Aug 24 [revised 2018 Jan 1];7:1338. doi: 10.12688/f1000research.15931.2. eCollection 2018.

5.

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

Koohy H, Bolland DJ, Matheson LS, Schoenfelder S, Stellato C, Dimond A, Várnai C, Chovanec P, Chessa T, Denizot J, Manzano Garcia R, Wingett SW, Freire-Pritchett P, Nagano T, Hawkins P, Stephens L, Elderkin S, Spivakov M, Fraser P, Corcoran AE, Varga-Weisz PD.

Genome Biol. 2018 Sep 5;19(1):126. doi: 10.1186/s13059-018-1489-y.

6.

Promoter Capture Hi-C: High-resolution, Genome-wide Profiling of Promoter Interactions.

Schoenfelder S, Javierre BM, Furlan-Magaril M, Wingett SW, Fraser P.

J Vis Exp. 2018 Jun 28;(136). doi: 10.3791/57320.

7.

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

Choy MK, Javierre BM, Williams SG, Baross SL, Liu Y, Wingett SW, Akbarov A, Wallace C, Freire-Pritchett P, Rugg-Gunn PJ, Spivakov M, Fraser P, Keavney BD.

Nat Commun. 2018 Jun 28;9(1):2526. doi: 10.1038/s41467-018-04931-0. Erratum in: Nat Commun. 2018 Nov 12;9(1):4792.

8.

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

Beekman R, Chapaprieta V, Russiñol N, Vilarrasa-Blasi R, Verdaguer-Dot N, Martens JHA, Duran-Ferrer M, Kulis M, Serra F, Javierre BM, Wingett SW, Clot G, Queirós AC, Castellano G, Blanc J, Gut M, Merkel A, Heath S, Vlasova A, Ullrich S, Palumbo E, Enjuanes A, Martín-García D, Beà S, Pinyol M, Aymerich M, Royo R, Puiggros M, Torrents D, Datta A, Lowy E, Kostadima M, Roller M, Clarke L, Flicek P, Agirre X, Prosper F, Baumann T, Delgado J, López-Guillermo A, Fraser P, Yaspo ML, Guigó R, Siebert R, Martí-Renom MA, Puente XS, López-Otín C, Gut I, Stunnenberg HG, Campo E, Martin-Subero JI.

Nat Med. 2018 Jun;24(6):868-880. doi: 10.1038/s41591-018-0028-4. Epub 2018 May 21.

9.

Capture Hi-C identifies putative target genes at 33 breast cancer risk loci.

Baxter JS, Leavy OC, Dryden NH, Maguire S, Johnson N, Fedele V, Simigdala N, Martin LA, Andrews S, Wingett SW, Assiotis I, Fenwick K, Chauhan R, Rust AG, Orr N, Dudbridge F, Haider S, Fletcher O.

Nat Commun. 2018 Mar 12;9(1):1028. doi: 10.1038/s41467-018-03411-9.

10.

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

Novo CL, Javierre BM, Cairns J, Segonds-Pichon A, Wingett SW, Freire-Pritchett P, Furlan-Magaril M, Schoenfelder S, Fraser P, Rugg-Gunn PJ.

Cell Rep. 2018 Mar 6;22(10):2615-2627. doi: 10.1016/j.celrep.2018.02.040.

11.

Capturing Three-Dimensional Genome Organization in Individual Cells by Single-Cell Hi-C.

Nagano T, Wingett SW, Fraser P.

Methods Mol Biol. 2017;1654:79-97. doi: 10.1007/978-1-4939-7231-9_6.

PMID:
28986784
12.

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

Burren OS, Rubio García A, Javierre BM, Rainbow DB, Cairns J, Cooper NJ, Lambourne JJ, Schofield E, Castro Dopico X, Ferreira RC, Coulson R, Burden F, Rowlston SP, Downes K, Wingett SW, Frontini M, Ouwehand WH, Fraser P, Spivakov M, Todd JA, Wicker LS, Cutler AJ, Wallace C.

Genome Biol. 2017 Sep 4;18(1):165. doi: 10.1186/s13059-017-1285-0.

13.

Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation.

Rubin AJ, Barajas BC, Furlan-Magaril M, Lopez-Pajares V, Mumbach MR, Howard I, Kim DS, Boxer LD, Cairns J, Spivakov M, Wingett SW, Shi M, Zhao Z, Greenleaf WJ, Kundaje A, Snyder M, Chang HY, Fraser P, Khavari PA.

Nat Genet. 2017 Oct;49(10):1522-1528. doi: 10.1038/ng.3935. Epub 2017 Aug 14.

14.

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

Petersen R, Lambourne JJ, Javierre BM, Grassi L, Kreuzhuber R, Ruklisa D, Rosa IM, Tomé AR, Elding H, van Geffen JP, Jiang T, Farrow S, Cairns J, Al-Subaie AM, Ashford S, Attwood A, Batista J, Bouman H, Burden F, Choudry FA, Clarke L, Flicek P, Garner SF, Haimel M, Kempster C, Ladopoulos V, Lenaerts AS, Materek PM, McKinney H, Meacham S, Mead D, Nagy M, Penkett CJ, Rendon A, Seyres D, Sun B, Tuna S, van der Weide ME, Wingett SW, Martens JH, Stegle O, Richardson S, Vallier L, Roberts DJ, Freson K, Wernisch L, Stunnenberg HG, Danesh J, Fraser P, Soranzo N, Butterworth AS, Heemskerk JW, Turro E, Spivakov M, Ouwehand WH, Astle WJ, Downes K, Kostadima M, Frontini M.

Nat Commun. 2017 Jul 13;8:16058. doi: 10.1038/ncomms16058.

15.

Dynamic Rewiring of Promoter-Anchored Chromatin Loops during Adipocyte Differentiation.

Siersbæk R, Madsen JGS, Javierre BM, Nielsen R, Bagge EK, Cairns J, Wingett SW, Traynor S, Spivakov M, Fraser P, Mandrup S.

Mol Cell. 2017 May 4;66(3):420-435.e5. doi: 10.1016/j.molcel.2017.04.010.

16.

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

Freire-Pritchett P, Schoenfelder S, Várnai C, Wingett SW, Cairns J, Collier AJ, García-Vílchez R, Furlan-Magaril M, Osborne CS, Fraser P, Rugg-Gunn PJ, Spivakov M.

Elife. 2017 Mar 23;6. pii: e21926. doi: 10.7554/eLife.21926.

17.

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

Javierre BM, Burren OS, Wilder SP, Kreuzhuber R, Hill SM, Sewitz S, Cairns J, Wingett SW, Várnai C, Thiecke MJ, Burden F, Farrow S, Cutler AJ, Rehnström K, Downes K, Grassi L, Kostadima M, Freire-Pritchett P, Wang F; BLUEPRINT Consortium, Stunnenberg HG, Todd JA, Zerbino DR, Stegle O, Ouwehand WH, Frontini M, Wallace C, Spivakov M, Fraser P.

Cell. 2016 Nov 17;167(5):1369-1384.e19. doi: 10.1016/j.cell.2016.09.037.

18.

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

Cairns J, Freire-Pritchett P, Wingett SW, Várnai C, Dimond A, Plagnol V, Zerbino D, Schoenfelder S, Javierre BM, Osborne C, Fraser P, Spivakov M.

Genome Biol. 2016 Jun 15;17(1):127. doi: 10.1186/s13059-016-0992-2.

19.

Single-cell Hi-C for genome-wide detection of chromatin interactions that occur simultaneously in a single cell.

Nagano T, Lubling Y, Yaffe E, Wingett SW, Dean W, Tanay A, Fraser P.

Nat Protoc. 2015 Dec;10(12):1986-2003. doi: 10.1038/nprot.2015.127. Epub 2015 Nov 5.

PMID:
26540590
20.

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

Schoenfelder S, Sugar R, Dimond A, Javierre BM, Armstrong H, Mifsud B, Dimitrova E, Matheson L, Tavares-Cadete F, Furlan-Magaril M, Segonds-Pichon A, Jurkowski W, Wingett SW, Tabbada K, Andrews S, Herman B, LeProust E, Osborne CS, Koseki H, Fraser P, Luscombe NM, Elderkin S.

Nat Genet. 2015 Oct;47(10):1179-1186. doi: 10.1038/ng.3393. Epub 2015 Aug 31.

21.

Comparison of Hi-C results using in-solution versus in-nucleus ligation.

Nagano T, Várnai C, Schoenfelder S, Javierre BM, Wingett SW, Fraser P.

Genome Biol. 2015 Aug 26;16:175. doi: 10.1186/s13059-015-0753-7.

22.

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

Mifsud B, Tavares-Cadete F, Young AN, Sugar R, Schoenfelder S, Ferreira L, Wingett SW, Andrews S, Grey W, Ewels PA, Herman B, Happe S, Higgs A, LeProust E, Follows GA, Fraser P, Luscombe NM, Osborne CS.

Nat Genet. 2015 Jun;47(6):598-606. doi: 10.1038/ng.3286. Epub 2015 May 4.

PMID:
25938943
23.

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

Schoenfelder S, Furlan-Magaril M, Mifsud B, Tavares-Cadete F, Sugar R, Javierre BM, Nagano T, Katsman Y, Sakthidevi M, Wingett SW, Dimitrova E, Dimond A, Edelman LB, Elderkin S, Tabbada K, Darbo E, Andrews S, Herman B, Higgs A, LeProust E, Osborne CS, Mitchell JA, Luscombe NM, Fraser P.

Genome Res. 2015 Apr;25(4):582-97. doi: 10.1101/gr.185272.114. Epub 2015 Mar 9.

24.

Global reorganization of the nuclear landscape in senescent cells.

Chandra T, Ewels PA, Schoenfelder S, Furlan-Magaril M, Wingett SW, Kirschner K, Thuret JY, Andrews S, Fraser P, Reik W.

Cell Rep. 2015 Feb 3;10(4):471-83. doi: 10.1016/j.celrep.2014.12.055. Epub 2015 Jan 29.

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