Multiple transcription factors directly regulate Hox gene lin-39 expression in ventral hypodermal cells of the C. elegans embryo and larva, including the hypodermal fate regulators LIN-26 and ELT-6

Liu, Wan-Ju; Reece‐Hoyes, John S.; Walhout, Albertha J.M.; Eisenmann, David M.

doi:10.1186/1471-213x-14-17

Cited by 6 publications

(3 citation statements)

References 75 publications

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“…It is in fact not yet known how many TFs can converge in the control of a single gene in maize. If we look in C. elegans, which probably has one of the most comprehensive GRGs resulting from the combination of ChIP-seq and Y1H, 228 gene regulatory regions are targeted by 60 TFs or more, and one gene is bound by 105 TFs (Deplancke et al, 2006a;Niu et al, 2011;Reece-Hoyes et al, 2011;Liu et al, 2014). We expect that in a larger genome with significantly more regulatory factors, the number of TFs that participate in the regulation of a given gene is even larger.…”

Section: Connectivity Properties Of the Nascent Maize Grgmentioning

confidence: 99%

A Maize Gene Regulatory Network for Phenolic Metabolism

Fan

Jiang

et al. 2017

Molecular Plant

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The translation of the genotype into phenotype, represented for example by the expression of genes encoding enzymes required for the biosynthesis of phytochemicals that are important for interaction of plants with the environment, is largely carried out by transcription factors (TFs) that recognize specific cis-regulatory elements in the genes that they control. TFs and their target genes are organized in gene regulatory networks (GRNs), and thus uncovering GRN architecture presents an important biological challenge necessary to explain gene regulation. Linking TFs to the genes they control, central to understanding GRNs, can be carried out using gene- or TF-centered approaches. In this study, we employed a gene-centered approach utilizing the yeast one-hybrid assay to generate a network of protein-DNA interactions that participate in the transcriptional control of genes involved in the biosynthesis of maize phenolic compounds including general phenylpropanoids, lignins, and flavonoids. We identified 1100 protein-DNA interactions involving 54 phenolic gene promoters and 568 TFs. A set of 11 TFs recognized 10 or more promoters, suggesting a role in coordinating pathway gene expression. The integration of the gene-centered network with information derived from TF-centered approaches provides a foundation for a phenolics GRN characterized by interlaced feed-forward loops that link developmental regulators with biosynthetic genes.

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Section: Connectivity Properties Of the Nascent Maize Grgmentioning

confidence: 99%

A Maize Gene Regulatory Network for Phenolic Metabolism

Fan

Jiang

et al. 2017

Molecular Plant

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“…Sequence-verified RNAi clones used in this work were obtained from the Ahringer library ( Kamath and Ahringer 2003 ) and the Vidal library (Rual et al 2004a) (gifts from Dr. Iqbal Hamza of UMCP and Dr. Mark Wilson of JHU). RNAi on L1 and P0 animals was performed as described ( Kamat et al 2001 ; Liu et al 2014 ). Worms of the appropriate age were analyzed on a Zeiss Axioplan 2 equipped with Nikon DXM1200 digital camera for imaging.…”

Section: Methodsmentioning

confidence: 99%

Identification of Wnt Pathway Target Genes Regulating the Division and Differentiation of Larval Seam Cells and Vulval Precursor Cells inCaenorhabditis elegans

Gorrepati

Krause

Chen

et al. 2015

G3 Genes|Genomes|Genetics

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The evolutionarily conserved Wnt/β-catenin signaling pathway plays a fundamental role during metazoan development, regulating numerous processes including cell fate specification, cell migration, and stem cell renewal. Wnt ligand binding leads to stabilization of the transcriptional effector β-catenin and upregulation of target gene expression to mediate a cellular response. During larval development of the nematode Caenorhabditis elegans, Wnt/β-catenin pathways act in fate specification of two hypodermal cell types, the ventral vulval precursor cells (VPCs) and the lateral seam cells. Because little is known about targets of the Wnt signaling pathways acting during larval VPC and seam cell differentiation, we sought to identify genes regulated by Wnt signaling in these two hypodermal cell types. We conditionally activated Wnt signaling in larval animals and performed cell type–specific "mRNA tagging" to enrich for VPC and seam cell–specific mRNAs, and then used microarray analysis to examine gene expression compared to control animals. Two hundred thirty-nine genes activated in response to Wnt signaling were identified, and we characterized 50 genes further. The majority of these genes are expressed in seam and/or vulval lineages during normal development, and reduction of function for nine genes caused defects in the proper division, fate specification, fate execution, or differentiation of seam cells and vulval cells. Therefore, the combination of these techniques was successful at identifying potential cell type–specific Wnt pathway target genes from a small number of cells and at increasing our knowledge of the specification and behavior of these C. elegans larval hypodermal cells.

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“…43,44 Later in larval life Wnt signaling is required for these cells to maintain expression of lin-39 and their VPC fate, 24 however Wnt signaling is not required in the earlier lin-39-dependent fate specification process, and some factors required for initial embryonic expression of lin-39 in the precursors to these cells do not have a role in later larval expression. 45 The question that arises is why do seam cells re-use these GATA factors in larval life?…”

Section: The Reutilization Of Embryonic Specification Factors In Postmentioning

confidence: 99%

TheC. elegansembryonic fate specification factor EGL-18 (GATA) is reutilized downstream of Wnt signaling to maintain a population of larval progenitor cells

Gorrepati

Eisenmann

2015

Worm

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In metazoans, stem cells in developing and adult tissues can divide asymmetrically to give rise to a daughter that differentiates and a daughter that retains the progenitor fate. Although the short-lived nematode C. elegans does not possess adult somatic stem cells, the lateral hypodermal seam cells behave in a similar manner: they divide once per larval stage to generate an anterior daughter that adopts a non-dividing differentiated fate and a posterior daughter that retains the seam fate and the ability to divide further. Wnt signaling pathway is known to regulate the asymmetry of these divisions and maintain the progenitor cell fate in one daughter, but how activation of the Wnt pathway accomplished this was unknown. We describe here our recent work that identified the GATA transcription factor EGL-18 as a downstream target of Wnt signaling necessary for maintenance of a progenitor population of larval seam cells. EGL-18 was previously shown to act in the initial specification of the seam cells in the embryo. Thus the acquisition of a Wnt-responsive cis-regulatory module allows an embryonic fate specification factor to be reutilized later in life downstream of a different regulator (Wnt signaling) to maintain a progenitor cell population. These results support the use of seam cell development in C. elegans as a simple model system for studying stem and progenitor cell biology.

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Multiple transcription factors directly regulate Hox gene lin-39 expression in ventral hypodermal cells of the C. elegans embryo and larva, including the hypodermal fate regulators LIN-26 and ELT-6

Cited by 6 publications

References 75 publications

A Maize Gene Regulatory Network for Phenolic Metabolism

A Maize Gene Regulatory Network for Phenolic Metabolism

Identification of Wnt Pathway Target Genes Regulating the Division and Differentiation of Larval Seam Cells and Vulval Precursor Cells inCaenorhabditis elegans

TheC. elegansembryonic fate specification factor EGL-18 (GATA) is reutilized downstream of Wnt signaling to maintain a population of larval progenitor cells

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