@article{454979ac2a1c428eaa9318d6c58003a1,
title = "XPaused Pol II coordinates tissue morphogenesis in the drosophila embryo",
abstract = "Paused RNA polymerase (Pol II) is a pervasive feature of Drosophila embryos and mammalian stem cells, but its role in development is uncertain. Here, we demonstrate that a spectrum of paused Pol II determines the {"}time to synchrony{"} - the time required to achieve coordinated gene expression across the cells of a tissue. To determine whether synchronous patterns of gene activation are significant in development, we manipulated the timing of snail expression, which controls the coordinated invagination of ∼1,000 mesoderm cells during gastrulation. Replacement of the strongly paused snail promoter with moderately paused or nonpaused promoters causes stochastic activation of snail expression and increased variability of mesoderm invagination. Computational modeling of the dorsal-ventral patterning network recapitulates these variable and bistable gastrulation profiles and emphasizes the importance of timing of gene activation in development. We conclude that paused Pol II and transcriptional synchrony are essential for coordinating cell behavior during morphogenesis.",
author = "Mounia Lagha and Bothma, {Jacques P.} and Emilia Esposito and Samuel Ng and Laura Stefanik and Chiahao Tsui and Jeffrey Johnston and Kai Chen and Gilmour, {David S.} and Julia Zeitlinger and Levine, {Michael S.}",
note = "Funding Information: The authors are grateful to Alistair Boettiger for sharing his ideas about Snail autoregulation. We also thank Mike Perry and Valerie Hilgers for their insightful discussions, Didier Rocancourt for help with artwork, and Lily Mirels and Eileen Wagner for comments on the manuscript. M.L. is the recipient of a Human Frontier fellowship. This work was funded by grants from the NIH, GM46638 to M.S.L. and GM47477 to D.S.G. M.L. and J.P.B. initiated efforts to create a stochastic pattern of snail activation. They also worked closely to determine activation profiles of both endogenous genes and transgenes containing minimal promoter sequences. J.P.B. conceived the use of esg as a means for identifying sna − /sna − mutant embryos. M.L. worked with L.S. and D.S.G. to document the sufficiency of minimal promoter sequences in establishing paused RNA polymerase II via permanganate protection assays. She also worked with E.E., K.C., J.J., and J.Z. to document the spectrum of Pol II binding at different promoters via whole-genome ChIP-seq assays. J.P.B. performed the imaging and developed the segmentation algorithms needed to determine t50 activation profiles. He also performed imaging to count mRNAs and analyzed the models exploring the relationship between timing and levels of gene expression. J.P.B. modeled the dynamics of Snail protein expression. M.L. and E.E. designed and created minigenes and BAC transgenes. M.L. performed the genetic crosses. C.T. injected all the plasmid transgenes, and BestGene injected all the BAC transgenes. S.N. helped M.L. and J.P.B. to collect and stain embryos. M.L., J.P.B., and M.S.L wrote the manuscript. ",
year = "2013",
month = may,
day = "23",
doi = "10.1016/j.cell.2013.04.045",
language = "English (US)",
volume = "153",
pages = "976",
journal = "Cell",
issn = "0092-8674",
publisher = "Cell Press",
number = "5",
}