Eileen Furlong

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Eileen E.M. Furlong
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NationalityIrish
Alma materUniversity College Dublin, Stanford University
Known forEnhancers, Chromatin, Development, Genomics, Single cells, 3D genomes
AwardsMember of the Academia Europaea, EMBO Membership
Scientific career
FieldsTranscription/Chromatin biology, Developmental Biology and Genomics
InstitutionsEuropean Molecular Biology Laboratory (Heidelberg)
Websitehttp://furlonglab.embl.de

Eileen Furlong is an Irish scientist (molecular biologist) in the fields Transcription/Chromatin, Developmental Biology and Genomics.[1][2] She is noted for her work in understanding how the genome is regulated, in particular to how developmental enhancers function, how they interact within three dimensional chromatin topologies and how they drive cell fate decisions during embryogenesis.[3][4][5] She is Head of the Department of Genome Biology at the European Molecular Biology Laboratory (EMBL). Eileen is an elected member of EMBO (2013),[6][7] the Academia Europaea (2016),[8] and to EMBO’s research council (2018).[9]

Education

Eileen Furlong obtained a B.Sc (Hons) at University College Dublin, and a Ph.D. at the Conway institute at UCD, studying transcriptional regulation of immediate early response genes in the lab of Prof. Finian Martin. She performed her postdoctoral studies in the Dept. of Developmental Biology at Stanford University, in Prof. Matt Scott’s lab, developing genomics tools to functionally dissect developmental programmes during embryogenesis.

Academic career and research

Furlong started her independent lab at EMBL in 2002,[10] and became Head of Dept. (Genome Biology) in 2009. Her research integrates genomics, genetics and Computational biology|computational approaches to functionally dissect the role of non-coding cis-regulatory elements in the regulation of gene expression.[11][12] In particular, using mesoderm specification into different muscle primordia as a model system. Her group’s research has uncovered a number of properties of Enhancer (genetics)|enhancers[13][14][15][16] and enhancer-Promoter_(genetics)|promoter communication, including pre-formed enhancer-promoter ‘Nuclear_organization#DNA_looping|loops’[17][18] and the ability of many enhancer’s to function even when larger Topologically_associating_domain |chromatin topologies are perturbed,[19][20][21] in addition to mechanisms that allow enhancers to withstand the effects of genetic variation, including collective transcription factor recruitment,[22][23] genetic epistasis within enhancers[24] and promoters,[25] and extensive redundancy[26], which together contribute to Canalisation_(genetics)|canalization in developmental patterning.

Furlong’s work was instrumental in the development and application of genomic approaches to understand embryonic development,[27] including the development of Drosophila microarrays,[28][29] an automatic transgenic embryo sorter,[30][31] ChIP in embryos,[32][33][34] tissue specific[35][36][37] and single cell approaches[38] - which combined with genetic manipulations provided some of the first insights into developmental programmes during embryogenesis at a genome-wide scale.[39][40]

Furlong is a member of the editorial board of the Journals Developmental Cell,[41] Development,[42] Molecular Systems Biology,[43] Current Opinion in Genetics Develop.,[44] Current Opinion in Cell Biol.,[45] an ERC panel member[46][47] and a main organisers of the international Conferences “From Functional Genomics to Systems Biology”, “EMBL Transcription and Chromatin” meeting, and a keynote speaker of a number of conferences.[48][49][50][51][52][53][54]

References

  1. ↑ "Furlong EE - Search Results - PubMed". PubMed.
  2. ↑ "Eileen Furlong (0000-0002-9544-8339)". orcid.org.
  3. ↑ "Eileen E Furlong". scholar.google.com.
  4. ↑ "Deciphering the regulatory code". EMBL. 4 November 2009.
  5. ↑ Niemitz, Emily (February 2014). "Synthetic modeling of developmental enhancers". Nature Genetics. 46 (2): 99–99. doi:10.1038/ng.2888. ISSN 1546-1718.
  6. ↑ "EMBO facts figures 2013" (PDF). embo.org.
  7. ↑ "Find people in the EMBO Communities". people.embo.org.
  8. ↑ "Academy of Europe: Furlong Eileen". www.ae-info.org.
  9. ↑ "Council". EMBO.
  10. ↑ "Furlong Group - Genome regulation and topology during embryonic development - EMBL". www.embl.de.
  11. ↑ Furlong, EEM; Levine, M (28 September 2018). "Developmental enhancers and chromosome topology". Science. 361 (6409): 1341–1345. doi:10.1126/science.aau0320. PMID 30262496.
  12. ↑ Spitz, F; Furlong, EE (September 2012). "Transcription factors: from enhancer binding to developmental control". Nature reviews. Genetics. 13 (9): 613–26. doi:10.1038/nrg3207. PMID 22868264.
  13. ↑ Zinzen, RP; Girardot, C; Gagneur, J; Braun, M; Furlong, EE (5 November 2009). "Combinatorial binding predicts spatio-temporal cis-regulatory activity". Nature. 462 (7269): 65–70. doi:10.1038/nature08531. PMID 19890324.
  14. ↑ He, Xin; Sinha, Saurabh (February 2010). "ChIPs and regulatory bits". Nature Biotechnology. 28 (2): 142–143. doi:10.1038/nbt0210-142. ISSN 1546-1696.
  15. ↑ Stark, Alexander (1 January 2009). "Learning the transcriptional regulatory code". Molecular Systems Biology. 5 (1): 329. doi:10.1038/msb.2009.88. ISSN 1744-4292.
  16. ↑ Rister, Jens; Desplan, Claude (2010). "Deciphering the genome's regulatory code: The many languages of DNA". BioEssays. 32 (5): 381–384. doi:10.1002/bies.200900197. ISSN 1521-1878.
  17. ↑ Ghavi-Helm, Y; Klein, FA; Pakozdi, T; Ciglar, L; Noordermeer, D; Huber, W; Furlong, EE (7 August 2014). "Enhancer loops appear stable during development and are associated with paused polymerase". Nature. 512 (7512): 96–100. doi:10.1038/nature13417. PMID 25043061.
  18. ↑ "Unexpected stability and complexity in transcriptional enhancers' interactions". phys.org.
  19. ↑ Ghavi-Helm, Y; Jankowski, A; Meiers, S; Viales, RR; Korbel, JO; Furlong, EEM (August 2019). "Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression". Nature genetics. 51 (8): 1272–1282. doi:10.1038/s41588-019-0462-3. PMID 31308546.
  20. ↑ Finn, Elizabeth H.; Misteli, Tom (August 2019). "A genome disconnect". Nature Genetics. 51 (8): 1205–1206. doi:10.1038/s41588-019-0476-x. ISSN 1546-1718.
  21. ↑ Koch, Linda (October 2019). "Toppling TAD tenets". Nature Reviews Genetics. 20 (10): 565–565. doi:10.1038/s41576-019-0164-9. ISSN 1471-0064.
  22. ↑ Junion, G; Spivakov, M; Girardot, C; Braun, M; Gustafson, EH; Birney, E; Furlong, EE (3 February 2012). "A transcription factor collective defines cardiac cell fate and reflects lineage history". Cell. 148 (3): 473–86. doi:10.1016/j.cell.2012.01.030. PMID 22304916.
  23. ↑ Khoueiry, P; Girardot, C; Ciglar, L; Peng, PC; Gustafson, EH; Sinha, S; Furlong, EE (9 August 2017). "Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity". eLife. 6. doi:10.7554/eLife.28440. PMID 28792889.
  24. ↑ Cannavò, E; Koelling, N; Harnett, D; Garfield, D; Casale, FP; Ciglar, L; Gustafson, HE; Viales, RR; Marco-Ferreres, R; Degner, JF; Zhao, B; Stegle, O; Birney, E; Furlong, EE (19 January 2017). "Genetic variants regulating expression levels and isoform diversity during embryogenesis". Nature. 541 (7637): 402–406. doi:10.1038/nature20802. PMID 28024300.
  25. ↑ Schor, IE; Degner, JF; Harnett, D; Cannavò, E; Casale, FP; Shim, H; Garfield, DA; Birney, E; Stephens, M; Stegle, O; Furlong, EE (April 2017). "Promoter shape varies across populations and affects promoter evolution and expression noise". Nature genetics. 49 (4): 550–558. doi:10.1038/ng.3791. PMID 28191888.
  26. ↑ Cannavò, E; Khoueiry, P; Garfield, DA; Geeleher, P; Zichner, T; Gustafson, EH; Ciglar, L; Korbel, JO; Furlong, EE (11 January 2016). "Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks". Current biology : CB. 26 (1): 38–51. doi:10.1016/j.cub.2015.11.034. PMID 26687625.
  27. ↑ Flintoft, Louisa (February 2013). "Predictions across space and time". Nature Reviews Genetics. 14 (2): 78–79. doi:10.1038/nrg3411. ISSN 1471-0064.
  28. ↑ Arbeitman, MN; Furlong, EE; Imam, F; Johnson, E; Null, BH; Baker, BS; Krasnow, MA; Scott, MP; Davis, RW; White, KP (27 September 2002). "Gene expression during the life cycle of Drosophila melanogaster". Science. 297 (5590): 2270–5. doi:10.1126/science.1072152. PMID 12351791.
  29. ↑ Science, American Association for the Advancement of (27 September 2002). "This Week in Science: Editor summaries of this week's papers". Science. 297 (5590): 2165. ISSN 0036-8075.
  30. ↑ Furlong, EE; Profitt, D; Scott, MP (February 2001). "Automated sorting of live transgenic embryos". Nature biotechnology. 19 (2): 153–6. doi:10.1038/84422. PMID 11175730.
  31. ↑ "Biological particle sorter". Google Patents. 21 March 2001.
  32. ↑ Sandmann, T; Jensen, LJ; Jakobsen, JS; Karzynski, MM; Eichenlaub, MP; Bork, P; Furlong, EE (June 2006). "A temporal map of transcription factor activity: mef2 directly regulates target genes at all stages of muscle development". Developmental cell. 10 (6): 797–807. doi:10.1016/j.devcel.2006.04.009. PMID 16740481.
  33. ↑ Sandmann, T; Girardot, C; Brehme, M; Tongprasit, W; Stolc, V; Furlong, EE (15 February 2007). "A core transcriptional network for early mesoderm development in Drosophila melanogaster". Genes & development. 21 (4): 436–49. doi:10.1101/gad.1509007. PMID 17322403.
  34. ↑ Skipper, Magdalena (April 2007). "Chipping away at developmental networks". Nature Reviews Genetics. 8 (4): 249–249. doi:10.1038/nrg2077. ISSN 1471-0064.
  35. ↑ Bonn, S; Zinzen, RP; Girardot, C; Gustafson, EH; Perez-Gonzalez, A; Delhomme, N; Ghavi-Helm, Y; Wilczyński, B; Riddell, A; Furlong, EE (8 January 2012). "Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development". Nature genetics. 44 (2): 148–56. doi:10.1038/ng.1064. PMID 22231485.
  36. ↑ Bonn, S; Zinzen, RP; Perez-Gonzalez, A; Riddell, A; Gavin, AC; Furlong, EE (26 April 2012). "Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP". Nature protocols. 7 (5): 978–94. doi:10.1038/nprot.2012.049. PMID 22538849.
  37. ↑ Reddington, JP; Garfield, DA; Sigalova, OM; Karabacak Calviello, A; Marco-Ferreres, R; Girardot, C; Viales, RR; Degner, JF; Ohler, U; Furlong, EEM (7 December 2020). "Lineage-Resolved Enhancer and Promoter Usage during a Time Course of Embryogenesis". Developmental cell. 55 (5): 648-664.e9. doi:10.1016/j.devcel.2020.10.009.
  38. ↑ Cusanovich, DA; Reddington, JP; Garfield, DA; Daza, RM; Aghamirzaie, D; Marco-Ferreres, R; Pliner, HA; Christiansen, L; Qiu, X; Steemers, FJ; Trapnell, C; Shendure, J; Furlong, EEM (22 March 2018). "The cis-regulatory dynamics of embryonic development at single-cell resolution". Nature. 555 (7697): 538–542. doi:10.1038/nature25981. PMID 29539636.
  39. ↑ Furlong, EE; Andersen, EC; Null, B; White, KP; Scott, MP (31 August 2001). "Patterns of gene expression during Drosophila mesoderm development". Science. 293 (5535): 1629–33. doi:10.1126/science.1062660. PMID 11486054.
  40. ↑ Science, American Association for the Advancement of (31 August 2001). "This Week in Science: Research in Science journals". Science. 293 (5535): 1553. ISSN 0036-8075.
  41. ↑ "Editorial Board: Developmental Cell". www.cell.com.
  42. ↑ "Editors and Board | Development". dev.biologists.org.
  43. ↑ "Editors & Board | Molecular Systems Biology". www.embopress.org.
  44. ↑ "Current Opinion in Genetics & Development Editorial Board".
  45. ↑ "Current Opinion in Cell Biology Editorial Board".
  46. ↑ "ERC Investigators - EMBL". www.embl.de.
  47. ↑ "Futures: Genome regulation - ERC grantee Eileen Furlong". EMBL. 13 March 2017.
  48. ↑ "Evolutionary Systems Biology". Wellcome Connecting Science Courses and Conferences.
  49. ↑ "CSH Asia 2020 Conference Systems Biology of Gene Regulation and Genome Editing". cshl.csh-asia.org.
  50. ↑ "Flyer Online Symposium Minerva-Gentner Symposium 2020" (PDF).
  51. ↑ "Speaker - Cell Symposia: Transcriptional Regulation". www.cell-symposia.com.
  52. ↑ "Eileen Furlong". www.iscb.org.
  53. ↑ "EMBL professor Eileen Furlong: keynote on Genome Regulation". UBC. 4 October 2017.
  54. ↑ Pathology, Research Institute of Molecular. "Eileen Furlong to give Max Birnstiel Lecture". The Research Institute of Molecular Pathology.

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