-
[
Crit Rev Biochem Mol Biol,
2012]
The CCAAT box promoter element and NF-Y, the transcription factor (TF) that binds to it, were among the first cis-elements and trans-acting factors identified; their interplay is required for transcriptional activation of a sizeable number of eukaryotic genes. NF-Y consists of three evolutionarily conserved subunits: a dimer of NF-YB and NF-YC which closely resembles a histone, and the "innovative" NF-YA. In this review, we will provide an update on the functional and biological features that make NF-Y a fundamental link between chromatin and transcription. The last 25 years have witnessed a spectacular increase in our knowledge of how genes are regulated: from the identification of cis-acting sequences in promoters and enhancers, and the biochemical characterization of the corresponding TFs, to the merging of chromatin studies with the investigation of enzymatic machines that regulate epigenetic states. Originally identified and studied in yeast and mammals, NF-Y - also termed CBF and CP1 - is composed of three subunits, NF-YA, NF-YB and NF-YC. The complex recognizes the CCAAT pentanucleotide and specific flanking nucleotides with high specificity (Dorn et al., 1997; Hatamochi et al., 1988; Hooft van Huijsduijnen et al, 1987; Kim & Sheffery, 1990). A compelling set of bioinformatics studies clarified that the NF-Y preferred binding site is one of the most frequent promoter elements (Suzuki et al., 2001, 2004; Elkon et al., 2003; Marino-Ramirez et al., 2004; FitzGerald et al., 2004; Linhart et al., 2005; Zhu et al., 2005; Lee et al., 2007; Abnizova et al., 2007; Grskovic et al., 2007; Halperin et al., 2009; Hakkinen et al., 2011). The same consensus, as determined by mutagenesis and SELEX studies (Bi et al., 1997), was also retrieved in ChIP-on-chip analysis (Testa et al., 2005; Ceribelli et al., 2006; Ceribelli et al., 2008; Reed et al., 2008). Additional structural features of the CCAAT box - position, orientation, presence of multiple Transcriptional Start Sites - were previously reviewed (Dolfini et al., 2009) and will not be considered in detail here.
-
[
Nature,
1990]
What molecular signalling machines tell a precursor cell to develop into a specialized structure? In one case, described in three papers, including that by Aroian et al. on page 693 of this issue, these machines turn out to be a receptor tyrosine kinase and a ras protein.
-
[
Cell,
2003]
Most programmed cell deaths in the nematode C. elegans require
ced-3 caspase activity. In a recent paper, Bloss et al. (2003) reveal a new C. elegans death inhibitor,
icd-1, whose loss can promote apoptosis independently of
ced-3.
-
[
1983]
In 1974, Sydney Brenner published an elegant paper that described the genetic system of Caenorhabditis elegans and led to its use in research on a wide variety of topics, including aging (Brenner, 1974). Its small size (1mm as an adult) and determinate cell lineage has allowed a description of the entire somatic cell lineage from the one-cell stage to the adult (Sulston and Horvitz, 1977; Deppe et al., 1978; Kimble and Hirsh, 1979; Suslton et al., personal communication). Its ease of culture makes it an organism of choice for studies of various aspects of anatomy and physiology, including muscle formation and function (Zengel and Epstein, 1980; Mackenzie and Epstein, 1980), cuticle formation (Cox et al, 1981), neuroanatomy (Ward et al, 1975; Ware et al, 1975; Sulston et al, 1975), and behavior (Dusenbery, 1980). Several genes have been cloned by recombinant DNA techniques ablation (Kimble, 1981; Laufer and von Ehrenstin, 1981) procedures, as well as most of the modern molecular techniques, are in use.
-
[
Cell,
1997]
The demonstrations in two papers in this issue of Cell (Rocheleau et al., 1997; Thorpe et al., 1997) of the involvement of a Wnt pathway in very early embryogenesis in Caenorhabditis elegans provides another significant step toward the ambitious but realistic goal of understanding all the basic strategies used to control embryogenesis in this model organism. At the same time, they challenge some of the prevailing models of Wnt signaling, suggesting that interactions among Wnt pathway components may vary in different developmental processes. With these papers, as well as the earlier reports on Wnt pathway genes
lin-44,
lin-17, and
pop-1 (Herman et al., 1995; Lin et al., 1995; Harris et al., 1996; Sawa et al., 1996) and new studies on Wnt pahtway genes reported in recent meetings, worm breeders have become a significant force in the army of Wnt researchers. They have also illustrated how different systems can provide important new complementary insights.
-
[
Dev Cell,
2002]
In migrating cells, Rho family GTPases and their effectors play a central role in polarizing and in organizing the actin and microtubule cytoskeletons. A study by Fukata et al. in the June 28th issue of Cell now shows that the Rac1/Cdc42 effector IQGAP1 captures microtubules by binding to CLIP170.
-
[
Bioessays,
2000]
With the extensive amount of information generated by genome-wide sequencing, the entire set of gene products in an organism can now be predicted. The challenge of understanding the function of each gene in the genome has led to the development of many large-scale and high-throughput experimental techniques. Recently, two papers, Walhout et al.(1) and Uetz et al.,(2) have described studies that add a new functional dimension to research conducted on a genome-wide scale. These two groups have utilized the yeast two-hybrid system to identify interactions among the entire complement of proteins encoded by the Caenorhabditis elegans and the Saccharomyces cerevisiae genomes, respectively. Using a set of 29 genes that have been previously characterized, Walhout et al. demonstrated the feasibility and efficiency of this technique by building an interaction matrix among a large number of proteins. On an even larger scale, Uetz et al. conducted two-hybrid analyses using proteins that represent over 87% of the total gene products in yeast and identified interactions for about 15% of the total yeast proteins. BioEssays 22:503-506, 2000.
-
[
Methods Cell Biol,
2012]
This chapter is dedicated to the study of aging in Caenorhabditis elegans (C. elegans). The assays are divided into two sections. In the first section, we describe detailed protocols for performing life span analysis in solid and liquid medium. In the second section, we describe various assays for measuring age-related changes. Our laboratory has been involved in several fruitful collaborations with non-C. elegans researchers keen on testing a role for their favorite gene in modulating aging (Carrano et al., 2009; Dong et al., 2007; Raices et al., 2008; Wolff et al., 2006). But even with the guidance of trained worm biologists, this undertaking can be daunting. We hope that this chapter will serve as a worthy compendium for those researchers who may or may not have immediate access to laboratories studying C. elegans.
-
[
Cell Metab,
2005]
In C. elegans, dauer pheromone is an indicator of population density and influences pathways that regulate metabolism, development, and aging. In a recent publication in Nature, Paik and coworkers (Jeong et al., 2005) show the purified substance to be a pyran ring conjugated to heptanoic acid, setting the stage for dissecting downstream signaling pathways.
-
[
Cell,
2005]
Biological rhythms with periods of less than a day are physiologically important but poorly understood. In this issue of Cell, Norman, Maricq, and colleagues (Norman et al., 2005) show that VAV-1, a guanine nucleotide exchange factor for Rho-family GTPases, is necessary for three rhythmic behaviors in the nematode Caenorhabditis elegans: feeding, defecation, and ovulation.