Eileen Furlong

Eileen E. M. Furlong FRS MAE is an Irish molecular biologist working in the fields of transcription, chromatin biology, developmental biology and genomics.[3] She is known 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.[1][4][5] She is Head of the Department of Genome Biology at the European Molecular Biology Laboratory (EMBL). Furlong was elected a member of the European Molecular Biology Organization (EMBO) in 2013,[6] the Academia Europaea in 2016[7] and to EMBO’s research council in 2018.[8]

Eileen Furlong

FRS MAE
Furlong in 2017
Born
Eileen E.M. Furlong
NationalityIrish
Alma materUniversity College Dublin (BSc, PhD)
AwardsMember of the Academia Europaea (2016)
EMBO Membership (2013)
Scientific career
FieldsEnhancers
Chromatin topology
Embryonic development
Single cell genomics
Transcription factors[1]
InstitutionsEuropean Molecular Biology Laboratory
Stanford University
ThesisTissue-specific regulation of gene expression by the transcription factors Ying-Yang 1 and nuclear factor 1 (1996)
Doctoral advisorFinian Martin[2]
Websitefurlonglab.embl.de

Education

Eileen Furlong obtained a Bachelor of Science degree at University College Dublin, and a PhD at the Conway institute at UCD, studying transcriptional regulation of immediate early response genes in the lab of Finian Martin.[2]

Career and research

After her PhD, Furlong was a postdoctoral researcher at Stanford University, in Matthew P. Scott's lab,[9] developing genomics tools to functionally dissect developmental programmes during embryogenesis. Furlong started her independent lab at EMBL in 2002,[10] and was appointed head of department [11] in 2009. Her research integrates genomics, genetics and computational biology approaches to functionally dissect the role of non-coding cis-regulatory elements in the regulation of gene expression.[12][13] In particular, using mesoderm specification into different muscle primordia as a model system. Her group’s research has uncovered a number of properties of enhancers[14][15][16][17] and enhancer-promoter communication, including pre-formed enhancer-promoter ‘loops’[18][19] and the ability of many enhancer’s to function even when larger chromatin topologies are perturbed,[20][21][22] in addition to mechanisms that allow enhancers to withstand the effects of genetic variation, including collective transcription factor recruitment,[23][24] genetic epistasis within enhancers[25] and promoters,[26] and extensive redundancy,[27] which together contribute to canalization in developmental patterning.

Furlong’s work was credited in the development and application of genomic approaches to understand embryonic development,[28][29] including the development of Drosophila microarrays,[30][31] an automatic transgenic embryo sorter,[32][33] Chromatin immunoprecipitation (ChIP) in embryos,[34][35][36] tissue specific[37][38][39] and single cell approaches[40] - which combined with genetic manipulations provided insight into developmental programmes during embryogenesis at a genome-wide scale.[41][42]

Furlong serves on the editorial boards of the scientific journals Developmental Cell,[43] Development,[44] Molecular Systems Biology,[45] Current Opinion in Genetics Development,[46] Current Opinion in Cell Biology,[47][48] a European Research Council (ERC) panel member[49][50] and an organiser of the international Conferences From Functional Genomics to Systems Biology,[51] EMBL Transcription and Chromatin[52] meeting, and a keynote speaker at national and international conferences including Intelligent Systems for Molecular Biology (ISMB).[53][54][55][56][57][58][59]

Awards and honors

Furlong was elected a member of the European Molecular Biology Organization (EMBO) in 2013,[6] and a Member of the Academia Europaea (MAE) in 2016.[7] Furlong was awarded ERC advanced investigator funding CisRegVar 2013-2018[60] and DeCRypT 2019-2023.[61] She was elected a Fellow of the Royal Society in May 2022.[62]

References
  1. Eileen Furlong publications indexed by Google Scholar
  2. Furlong, Eileen E. M. (1996). Tissue-specific regulation of gene expression by the transcription factors Ying-Yang 1 and nuclear factor 1 (PhD thesis). OCLC 605563938. ProQuest 301522152.
  3. Eileen Furlong publications from Europe PubMed Central
  4. "Deciphering the regulatory code". EMBL. 4 November 2009.
  5. Niemitz, Emily (2014). "Synthetic modeling of developmental enhancers". Nature Genetics. 46 (2): 99. doi:10.1038/ng.2888. ISSN 1546-1718. S2CID 38520086.
  6. "Find people in the EMBO Communities". people.embo.org.
  7. "Academy of Europe: Furlong Eileen". ae-info.org.
  8. "Council". EMBO. 22 March 2021.
  9. Furlong, Eileen E.M.; Profitt, David; Scott, Matthew P. (2001). "Automated sorting of live transgenic embryos". Nature Biotechnology. 19 (2): 153–156. doi:10.1038/84422. ISSN 1087-0156. PMID 11175730. S2CID 14228050.
  10. "Furlong Group - Genome regulation and topology during embryonic development - EMBL". embl.de.
  11. "Genome Biology".
  12. Furlong, EEM; Levine, M (28 September 2018). "Developmental enhancers and chromosome topology". Science. 361 (6409): 1341–1345. Bibcode:2018Sci...361.1341F. doi:10.1126/science.aau0320. PMC 6986801. PMID 30262496.
  13. 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. S2CID 205485256.
  14. 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. Bibcode:2009Natur.462...65Z. doi:10.1038/nature08531. PMID 19890324. S2CID 4320071.
  15. He, Xin; Sinha, Saurabh (February 2010). "ChIPs and regulatory bits". Nature Biotechnology. 28 (2): 142–143. doi:10.1038/nbt0210-142. ISSN 1546-1696. PMID 20139950. S2CID 30471127.
  16. 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. PMC 2795480. PMID 19920814.
  17. 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. PMC 3024831. PMID 20394065.
  18. 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. Bibcode:2014Natur.512...96G. doi:10.1038/nature13417. PMID 25043061. S2CID 4464054.
  19. "Unexpected stability and complexity in transcriptional enhancers' interactions". phys.org.
  20. 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. PMC 7116017. PMID 31308546.
  21. 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. PMC 7418859. PMID 31332379.
  22. Koch, Linda (October 2019). "Toppling TAD tenets". Nature Reviews Genetics. 20 (10): 565. doi:10.1038/s41576-019-0164-9. ISSN 1471-0064. PMID 31367009. S2CID 199056689.
  23. 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. S2CID 7990140.
  24. 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. PMC 5550276. PMID 28792889.
  25. 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. Bibcode:2017Natur.541..402C. doi:10.1038/nature20802. PMID 28024300. S2CID 205252947.
  26. 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. S2CID 3331476.
  27. 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. 26 (1): 38–51. doi:10.1016/j.cub.2015.11.034. PMC 4712172. PMID 26687625.
  28. McGuire, AL; Gabriel, S; Tishkoff, SA; Wonkam, A; Chakravarti, A; Furlong, EEM; Treutlein, B; Meissner, A; Chang, HY; López-Bigas, N; Segal, E; Kim, JS (October 2020). "The road ahead in genetics and genomics". Nature Reviews. Genetics. 21 (10): 581–596. doi:10.1038/s41576-020-0272-6. PMC 7444682. PMID 32839576.
  29. Flintoft, Louisa (February 2013). "Predictions across space and time". Nature Reviews Genetics. 14 (2): 78–79. doi:10.1038/nrg3411. ISSN 1471-0064. PMID 23269464. S2CID 41780530.
  30. Arbeitman, MN; Furlong, EE; Imam, F; Johnson, E; Null, BH; Baker, BS; Krasnow, MA; Scott, MP; Davis, RW; White, KP (2002). "Gene expression during the life cycle of Drosophila melanogaster". Science. 297 (5590): 2270–5. Bibcode:2002Sci...297.2270A. doi:10.1126/science.1072152. PMID 12351791. S2CID 15639586.
  31. 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. doi:10.1126/science.2002.297.5590.twis. ISSN 0036-8075. S2CID 239597164.
  32. 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. S2CID 14228050.
  33. "Biological particle sorter". Google Patents. 21 March 2001.
  34. 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.
  35. 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. PMC 1804332. PMID 17322403.
  36. Skipper, Magdalena (April 2007). "Chipping away at developmental networks". Nature Reviews Genetics. 8 (4): 249. doi:10.1038/nrg2077. ISSN 1471-0064. S2CID 38908110.
  37. 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. S2CID 143727.
  38. 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. S2CID 20098167.
  39. 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. PMID 33171098. S2CID 226302320.
  40. 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 (2018). "The cis-regulatory dynamics of embryonic development at single-cell resolution". Nature. 555 (7697): 538–542. Bibcode:2018Natur.555..538C. doi:10.1038/nature25981. PMC 5866720. PMID 29539636.
  41. 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. Bibcode:2001Sci...293.1629F. doi:10.1126/science.1062660. PMID 11486054. S2CID 13826608.
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  60. "ERC grant CisRegVar".
  61. "ERC grant DeCRypT".
  62. "Outstanding scientists elected as Fellows and Foreign Members of the Royal Society". Royal Society. 10 May 2022. Retrieved 11 May 2022.
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