R11: a cis-regulatory node of the sea urchin embryo gene network that controls early expression of SpDelta in micromeres - PubMed (original) (raw)
. 2004 Oct 15;274(2):438-51.
doi: 10.1016/j.ydbio.2004.07.008.
Collaborators, Affiliations
- PMID: 15385170
- DOI: 10.1016/j.ydbio.2004.07.008
Free article
R11: a cis-regulatory node of the sea urchin embryo gene network that controls early expression of SpDelta in micromeres
Roger Revilla-i-Domingo et al. Dev Biol. 2004.
Free article
Abstract
A gene regulatory network (GRN) controls the process by which the endomesoderm of the sea urchin embryo is specified. In this GRN, the program of gene expression unique to the skeletogenic micromere lineage is set in train by activation of the pmar1 gene. Through a double repression system, this gene is responsible for localization of expression of downstream regulatory and signaling genes to cells of this lineage. One of these genes, delta, encodes a Notch ligand, and its expression in the right place and time is crucial to the specification of the endomesoderm. Here we report a cis-regulatory element R11 that is responsible for localizing the expression of delta by means of its response to the pmar1 repression system. R11 was identified as an evolutionarily conserved genomic sequence located about 13 kb downstream of the last exon of the delta gene. We demonstrate here that this cis-regulatory element is able to drive the expression of a reporter gene in the same cells and at the same time that the endogenous delta gene is expressed, and that temporally, spatially, and quantitatively it responds to the pmar1 repression system just as predicted for the delta gene in the endomesoderm GRN. This work illustrates the application of cis-regulatory analysis to the validation of predictions of the GRN model. In addition, we introduce new methodological tools for quantitative measurement of the output of expression constructs that promise to be of general value for cis-regulatory analysis in sea urchin embryos.
Similar articles
- A regulatory gene network that directs micromere specification in the sea urchin embryo.
Oliveri P, Carrick DM, Davidson EH. Oliveri P, et al. Dev Biol. 2002 Jun 1;246(1):209-28. doi: 10.1006/dbio.2002.0627. Dev Biol. 2002. PMID: 12027443 - An otx cis-regulatory module: a key node in the sea urchin endomesoderm gene regulatory network.
Yuh CH, Dorman ER, Howard ML, Davidson EH. Yuh CH, et al. Dev Biol. 2004 May 15;269(2):536-51. doi: 10.1016/j.ydbio.2004.02.025. Dev Biol. 2004. PMID: 15110718 - Gene regulatory networks and developmental plasticity in the early sea urchin embryo: alternative deployment of the skeletogenic gene regulatory network.
Ettensohn CA, Kitazawa C, Cheers MS, Leonard JD, Sharma T. Ettensohn CA, et al. Development. 2007 Sep;134(17):3077-87. doi: 10.1242/dev.009092. Epub 2007 Aug 1. Development. 2007. PMID: 17670786 - Developmental gene network analysis.
Revilla-i-Domingo R, Davidson EH. Revilla-i-Domingo R, et al. Int J Dev Biol. 2003;47(7-8):695-703. Int J Dev Biol. 2003. PMID: 14756345 Review. - Deciphering the underlying mechanism of specification and differentiation: the sea urchin gene regulatory network.
Ben-Tabou de-Leon S, Davidson EH. Ben-Tabou de-Leon S, et al. Sci STKE. 2006 Nov 14;2006(361):pe47. doi: 10.1126/stke.3612006pe47. Sci STKE. 2006. PMID: 17106076 Review.
Cited by
- Identification and prediction of developmental enhancers in sea urchin embryos.
Arenas-Mena C, Miljovska S, Rice EJ, Gurges J, Shashikant T, Wang Z, Ercan S, Danko CG. Arenas-Mena C, et al. BMC Genomics. 2021 Oct 19;22(1):751. doi: 10.1186/s12864-021-07936-0. BMC Genomics. 2021. PMID: 34666684 Free PMC article. - CRISPR-Cas9 editing of non-coding genomic loci as a means of controlling gene expression in the sea urchin.
Pieplow A, Dastaw M, Sakuma T, Sakamoto N, Yamamoto T, Yajima M, Oulhen N, Wessel GM. Pieplow A, et al. Dev Biol. 2021 Apr;472:85-97. doi: 10.1016/j.ydbio.2021.01.003. Epub 2021 Jan 19. Dev Biol. 2021. PMID: 33482173 Free PMC article. - From genome to anatomy: The architecture and evolution of the skeletogenic gene regulatory network of sea urchins and other echinoderms.
Shashikant T, Khor JM, Ettensohn CA. Shashikant T, et al. Genesis. 2018 Oct;56(10):e23253. doi: 10.1002/dvg.23253. Genesis. 2018. PMID: 30264451 Free PMC article. Review. - Genome-wide use of high- and low-affinity Tbrain transcription factor binding sites during echinoderm development.
Cary GA, Cheatle Jarvela AM, Francolini RD, Hinman VF. Cary GA, et al. Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):5854-5861. doi: 10.1073/pnas.1610611114. Proc Natl Acad Sci U S A. 2017. PMID: 28584099 Free PMC article. - Comparative Study of Regulatory Circuits in Two Sea Urchin Species Reveals Tight Control of Timing and High Conservation of Expression Dynamics.
Gildor T, Ben-Tabou de-Leon S. Gildor T, et al. PLoS Genet. 2015 Jul 31;11(7):e1005435. doi: 10.1371/journal.pgen.1005435. eCollection 2015 Jul. PLoS Genet. 2015. PMID: 26230518 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Miscellaneous