Deciphering Cis-Regulatory Principles of Transcriptional regulation: Combining large-scale genetics and genomics to dissect functional principles of genome regulation during embryonic development

Publications

CTCF, BEAF-32, and CP190 are not required for the establishment of TADs in early Drosophila embryos but have locus-specific roles

Auteurs: Cavalheiro GR, Girardot C, Viales RR, Pollex T, Cao TBN, Lacour P, Feng S, Rabinowitz A, Furlong EEM
Publié dans: Science Advances, Numéro 9(5):eade1085, 2023, ISSN 2375-2548
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/sciadv.ade1085

Simultaneous cellular and molecular phenotyping of embryonic mutants using single-cell regulatory trajectories

Auteurs: Secchia S, Forneris M, Heinen T, Stegle O, Furlong EEM
Publié dans: Developmental Cell, Numéro 57/4, 2022, ISSN 1534-5807
Éditeur: Cell Press
DOI: 10.1016/j.devcel.2022.01.016

Lineage-Resolved Enhancer and Promoter Usage during a Time Course of Embryogenesis

Auteurs: Reddington JP, Garfield DA, Sigalova OM, Karabacak Calviello A, Marco-Ferreres R, Girardot C, Viales RR, Degner JF, Ohler U, Furlong EEM
Publié dans: Developmental Cell, Numéro 09 Nov 2020, 55(5), 2020, Page(s) 648-664.e9, ISSN 1534-5807
Éditeur: Cell Press
DOI: 10.1016/j.devcel.2020.10.009

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

Auteurs: Yad Ghavi-Helm, Aleksander Jankowski, Sascha Meiers, Rebecca R. Viales, Jan O. Korbel, Eileen E. M. Furlong
Publié dans: Nature Genetics, Numéro 51/8, 2019, Page(s) 1272-1282, ISSN 1061-4036
Éditeur: Nature Publishing Group
DOI: 10.1038/s41588-019-0462-3

Regulating specificity in enhancer-promoter communication

Auteurs: Galouzis CC, Furlong EEM
Publié dans: Cell Biology, Numéro 75/102065, 2022, ISSN 0955-0674
Éditeur: Elsevier BV
DOI: 10.1016/j.ceb.2022.01.010

Cis -acting variation is common across regulatory layers but is often buffered during embryonic development

Auteurs: Swann Floc'hlay, Emily S. Wong, Bingqing Zhao, Rebecca R. Viales, Morgane Thomas-Chollier, Denis Thieffry, David A. Garfield, Eileen E.M. Furlong
Publié dans: Genome Research, Numéro 31/2, 2021, Page(s) 211-224, ISSN 1088-9051
Éditeur: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.266338.120

Enhancers have more cofactor specificity than we think: A potential new way to classify enhancers based on their functional cofactor requirements

Auteurs: Pijuan-Sala B, Furlong EEM
Publié dans: Molecular Cell, Numéro 82/16, 2022, ISSN 1097-2765
Éditeur: Cell Press
DOI: 10.1016/j.molcel.2022.07.015

Extremely rapid and reversible optogenetic perturbation of nuclear proteins in living embryos

Auteurs: Kögler AC, Kherdjemil Y, Bender K,Rabinowitz A, Marco-Ferreres R, Furlong EEM
Publié dans: Developmental Cell, Numéro 06 Aug 2021, 56(16), 2021, Page(s) 2348-2363.e8, ISSN 1534-5807
Éditeur: Cell Press
DOI: 10.1016/j.devcel.2021.07.011

The continuum of Drosophila embryonic development at single-cell resolution

Auteurs: Calderon D, Blecher-Gonen R, Huang X, Secchia S, Kentro J, Daza RM, Martin B, Dulja A, Schaub C, Trapnell C, Larschan E, O'Connor-Giles KM, Furlong EEM, Shendure J
Publié dans: Science, Numéro 6606/377, 2022, ISSN 0036-8075
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/science.abn5800

Chromatin topology, condensates and gene regulation: shifting paradigms or just a phase?

Auteurs: Mustafa Mir, Wendy Bickmore, Eileen E. M. Furlong, Geeta Narlikar
Publié dans: Development, Numéro 146/19, 2019, Page(s) dev182766, ISSN 0950-1991
Éditeur: The Company of Biologists Ltd.
DOI: 10.1242/dev.182766

scDALI: modeling allelic heterogeneity in single cells reveals context-specific genetic regulation

Auteurs: Heinen T, Secchia S, Reddington JP, Zhao B, Furlong EEM, Stegle O
Publié dans: Genome Biology, Numéro 23/1, 2022, ISSN 1474-760X
Éditeur: BMC part of Springer Nature
DOI: 10.1186/s13059-021-02593-8

The role of transcription in shaping the spatial organization of the genome

Auteurs: Bas van Steensel, Eileen E. M. Furlong
Publié dans: Nature Reviews Molecular Cell Biology, 2019, ISSN 1471-0072
Éditeur: Nature Publishing Group
DOI: 10.1038/s41580-019-0114-6

The road ahead in genetics and genomics

Auteurs: 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
Publié dans: Nature reviews. Genetics, Numéro 24 Aug 2020, 21(10), 2020, Page(s) 581-596, ISSN 1471-0064
Éditeur: Springer Nature Limited
DOI: 10.1038/s41576-020-0272-6

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