pha-4, anHNF-3 homolog, specifies pharyngeal organ identity inCaenorhabditis elegans

Horner, Michael A.; Quintin, Sophie; Domeier, Mary Ellen; Kimble, Judith; Labouesse, Michel; Mango, Susan E.

doi:10.1101/gad.12.13.1947

Cited by 198 publications

(267 citation statements)

References 37 publications

Supporting

Mentioning

254

Contrasting

Order By: Relevance

“…As embryonic transcription begins med-1 and -2 are induced by maternally provided SKN-1 (Fig. 7A) (41), then pha-4 and elt-5 are expressed slightly later (42,43). end-1 regulation appears to be complex (Fig.…”

Section: Taf-1 Required Broadly In C Elegans Transcriptionmentioning

confidence: 99%

An Extensive Requirement for Transcription Factor IID-specific TAF-1 in Caenorhabditis elegans Embryonic Transcription

Walker

Shi

Blackwell

2004

Journal of Biological Chemistry

View full text Add to dashboard Cite

The general transcription factor TFIID sets the mRNA start site and consists of TATA-binding protein and associated factors (TAF II s), some of which are also present in SPT-ADA-GCN5 (SAGA)-related complexes. In yeast, results of multiple studies indicate that TFIID-specific TAF II s are not required for the transcription of most genes, implying that intact TFIID may have a surprisingly specialized role in transcription. Relatively little is known about how TAF II s contribute to metazoan transcription in vivo, especially at developmental and tissuespecific genes. Previously, we investigated functions of four shared TFIID/SAGA TAF II s in Caenorhabditis elegans. Whereas TAF-4 was required for essentially all embryonic transcription, TAF-5, TAF-9, and TAF-10 were dispensable at multiple developmental and other metazoan-specific promoters. Here we show evidence that in C. elegans embryos transcription of most genes requires TFIID-specific TAF-1. TAF-1 is not as universally required as TAF-4, but it is essential for a greater proportion of transcription than TAF-5, -9, or -10 and is important for transcription of many developmental and other metazoan-specific genes. TAF-2, which binds core promoters with TAF-1, appears to be required for a similarly substantial proportion of transcription. C. elegans TAF-1 overlaps functionally with the coactivator p300/ CBP (CBP-1), and at some genes it is required along with the TBP-like protein TLF(TRF2). We conclude that during C. elegans embryogenesis TAF-1 and TFIID have broad roles in transcription and development and that TFIID and TLF may act together at certain promoters. Our findings imply that in metazoans TFIID may be of widespread importance for transcription and for expression of tissue-specific genes.Eukaryotic mRNA transcription involves formation of a preinitiation complex (PIC) 1 at the core promoter, which directs initiation. The PIC includes a set of general transcription factors (TFIIA, B, D, E, F, and H) and a mediator complex, along with RNA polymerase II (pol II) (1, 2). In Saccharomyces cerevisiae many PIC components have surprisingly specific roles at particular gene subsets (3, 4). Much less is known about how individual PIC components contribute to transcription regulation in metazoans, which have evolved a greater complexity of stage-and tissue-specific gene control and additional genes that are not present in yeast.The general transcription factor TFIID is of particular interest because it establishes the start site and provides enzymatic activities that may regulate transcription (5, 6). TFIID is comprised of the TATA-binding protein (TBP) along with ϳ14 TBP-associated factors (TAF II s). TAF II s interact with core promoter elements and contact a diverse array of upstream transactivators (5-8). TAF-1 and TAF-2 together bind directly to the initiator (Inr) element, which encompasses the start site (9). TAF-1, the largest TAF II , is also necessary for TFIID stability and possesses histone acetyltransferase, kinase, and ubiquitin conjugating activitie...

show abstract

Section: Taf-1 Required Broadly In C Elegans Transcriptionmentioning

confidence: 99%

An Extensive Requirement for Transcription Factor IID-specific TAF-1 in Caenorhabditis elegans Embryonic Transcription

Walker

Shi

Blackwell

2004

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…Studies exploiting these attributes have already led to the discovery of programmed cell death (4,5), insights into organ formation (6)(7)(8), and elucidation of fundamental signal pathways (9), including key pathways in early embryogenesis (10,11). Microarray and serial analysis of gene expression data combined with homeotic mutants (12,13), RNA enrichment methods (14), or FACS sorting of individual cells (15) reveal active genes within particular cells or stages of development.…”

mentioning

confidence: 99%

Automated cell lineage tracing in Caenorhabditis elegans

Bao

Murray

Boyle

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

357

419

View full text Add to dashboard Cite

The invariant cell lineage and cell fate of Caenorhabditis elegans provide a unique opportunity to decode the molecular mechanisms of animal development. To exploit this opportunity, we have developed a system for automated cell lineage tracing during C. elegans embryogenesis, based on 3D, time-lapse imaging and automated image analysis. Using ubiquitously expressed histone-GFP fusion protein to label cells͞nuclei and a confocal microscope, the imaging protocol captures embryogenesis at high spatial (31 planes at 1 m apart) and temporal (every minute) resolution without apparent effects on development. A set of image analysis algorithms then automatically recognizes cells at each time point, tracks cell movements, divisions and deaths over time and assigns cell identities based on the canonical naming scheme. Starting from the four-cell stage (or earlier), our software, named STARRYNITE, can trace the lineage up to the 350-cell stage in 25 min on a desktop computer. The few errors of automated lineaging can then be corrected in a few hours with a graphic interface that allows easy navigation of the images and the reported lineage tree. The system can be used to characterize lineage phenotypes of genes and͞or extended to determine gene expression patterns in a living embryo at the single-cell level. We envision that this automation will make it practical to systematically decipher the developmental genes and pathways encoded in the genome of C. elegans.embryogenesis ͉ imaging ͉ image analysis algorithms

show abstract

“…Amplification of rpl-7a from the cDNA was performed as described in (Mitrovich and Anderson 2000), and PCR products were analyzed on a 1% agarose gel. Antibody staining: To detect possible nonsense-codon, readthrough suppression, embryos were stained as described previously with an antibody that recognizes the carboxyl terminus of PHA-4 (Horner et al 1998;Kaltenbach et al 2005). Embryos from pha-4 suppressing strains were stained with a-carboxyl PHA-4 at a 1:20 dilution and costained with a-P granule (OIC1D4) at 1:10 ½received from the Developmental Studies Hybridoma Bank, University of Iowa (Beanan and Strome 1992).…”

Section: Methodsmentioning

confidence: 99%

“…Loss of FoxA activity results in severe defects in foregut-derived organs such as liver and pancreas (Weigel et al 1989;Ang and Rossant 1994;Mango et al 1994;Weinstein et al 1994;Dufort et al 1998;reviewed in Zaret 2002;Lee et al 2005). Conversely, ubiquitous expression of pha-4/FoxA in Caenorhabditis elegans is sufficient to induce ectopic foregut cells (Horner et al 1998). These data reveal that appropriately regulated expression of pha-4/FoxA is critical for its normal functions.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Genetic Suppressors ofCaenorhabditis elegans pha-4/FoxAIdentify the Predicted AAA Helicaseruvb-1/RuvB

Updike

2007

Genetics

View full text Add to dashboard Cite

FoxA transcription factors are critical regulators of gut development and function. FoxA proteins specify gut fate during early embryogenesis, drive gut differentiation and morphogenesis at later stages, and affect gut function to mediate nutritional responses. The level of FoxA is critical for these roles, yet we know relatively little about regulators for this family of proteins. To address this issue, we conducted a genetic screen for mutants that suppress a partial loss of pha-4, the sole FoxA factor of Caenorhabditis elegans. We identified 55 mutants using either chemical or insertional mutagenesis. Forty-two of these were informational suppressors that affected nonsense-mediated decay, while the remaining 13 were pha-4 suppressors. These 13 alleles defined at least six different loci. On the basis of mutational frequencies for C. elegans and the genetic dominance of four of the suppressors, we predict that many of the suppressors are either unusual loss-of-function mutations in negative regulators or rare gain-of-function mutations in positive regulators. We characterized one dominant suppressor molecularly and discovered the mutation alters a likely cisregulatory region within pha-4 itself. A second suppressor defined a new locus, the predicted AAA1 helicase ruvb-1. These results indicate that our screen successfully found cis-or trans-acting regulators of pha-4.

show abstract

pha-4, anHNF-3 homolog, specifies pharyngeal organ identity inCaenorhabditis elegans

Cited by 198 publications

References 37 publications

An Extensive Requirement for Transcription Factor IID-specific TAF-1 in Caenorhabditis elegans Embryonic Transcription

An Extensive Requirement for Transcription Factor IID-specific TAF-1 in Caenorhabditis elegans Embryonic Transcription

Automated cell lineage tracing in Caenorhabditis elegans

Genetic Suppressors ofCaenorhabditis elegans pha-4/FoxAIdentify the Predicted AAA Helicaseruvb-1/RuvB

Contact Info

Product

Resources

About