Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the early Drosophila embryo

Genome Research
Katharine N SchulzMelissa M. Harrison

Abstract

The transition from a specified germ cell to a population of pluripotent cells occurs rapidly following fertilization. During this developmental transition, the zygotic genome is largely transcriptionally quiescent and undergoes significant chromatin remodeling. In Drosophila, the DNA-binding protein Zelda (also known as Vielfaltig) is required for this transition and for transcriptional activation of the zygotic genome. Open chromatin is associated with Zelda-bound loci, as well as more generally with regions of active transcription. Nonetheless, the extent to which Zelda influences chromatin accessibility across the genome is largely unknown. Here we used formaldehyde-assisted isolation of regulatory elements to determine the role of Zelda in regulating regions of open chromatin in the early embryo. We demonstrate that Zelda is essential for hundreds of regions of open chromatin. This Zelda-mediated chromatin accessibility facilitates transcription-factor recruitment and early gene expression. Thus, Zelda possesses some key characteristics of a pioneer factor. Unexpectedly, chromatin at a large subset of Zelda-bound regions remains open even in the absence of Zelda. The GAGA factor-binding motif and embryonic GAGA factor bind...Continue Reading

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Citations

Jul 22, 2016·Proceedings of the National Academy of Sciences of the United States of America·Ann Boija, Mattias Mannervik
Nov 6, 2018·Development·Jumana Alhaj AbedRichard S Jones
Jun 14, 2019·Development·Nadine L VastenhouwHoward D Lipshitz
May 23, 2019·Genome Biology and Evolution·Pei-Chen PengSaurabh Sinha
Oct 7, 2017·Genes & Development·Mustafa MirXavier Darzacq
Nov 11, 2017·Development·Ana Fernandez-Nicolas, Xavier Belles
Jul 4, 2017·PLoS Genetics·Lupis RibeiroRodrigo Nunes da Fonseca
Sep 28, 2018·The Journal of Cell Biology·Sabrina Ladstätter, Kikuë Tachibana
Jan 25, 2019·Nature Reviews. Genetics·Sandy L KlemmWilliam J Greenleaf
Jan 1, 2019·Genome Biology and Evolution·Jasmin D KurafeiskiErich Bornberg-Bauer
Sep 4, 2020·Genetics·Stephen Small, David N Arnosti
Jun 2, 2016·Development·Makiko Iwafuchi-Doi, Kenneth S Zaret
Aug 2, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Xuelei LaiChloe Zubieta
Mar 7, 2018·The Journal of Biological Chemistry·Alexandre Mayran, Jacques Drouin
Jan 18, 2018·PLoS Genetics·Yi Xie, J Todd Blankenship
Mar 2, 2018·PLoS Genetics·Rodrigo Nunes da Fonseca, Thiago M Venancio
Apr 18, 2019·The FEBS Journal·Alba Ventos-AlfonsoXavier Belles
Dec 5, 2019·Briefings in Functional Genomics·Charlotte MorettiYad Ghavi-Helm
Jan 23, 2020·International Journal of Molecular Sciences·Mario Zurita, Juan Manuel Murillo-Maldonado
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May 19, 2019·Nature Communications·Shunmin HeDahua Chen
May 26, 2017·Genes & Development·Christopher M UyeharaDaniel J McKay

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