Chao-I Chen et al. (2004) West Coast Worm Meeting "A Bayesian approach toward analyzing the network of genes involved in C. elegans programmed cell death"

Chao-I Chen, Vebjorn Ljosa, S Rao Jammalamadaka, Chiou-Wei Tsai, Ambuj K Singh, Thomas A McCloskey, Xiaofang Lei, Joel H Rothman

[West Coast Worm Meeting, 2004]

From an RNAi screen for genes that repress apoptosis, we have identified a set of about 130 candidates (see abstract by McCloskey et al.). We are using computational methods in an effort to predict functional networks through which these genes may act and to identify additional candidates and their relationships within the postulated networks. We are initially working with a number of datasets as the basis for our predictions: microarray expression data, the physical orientation of genes within the worm genome, phylogenetic profile data, and PSORT predictions of protein localization. The datasets are normalized according to their overlap with the worm interactome and Wormbase subcellular localization data. They are then combined using a nave Bayesian network, to yield a set of potential functionally interacting protein pairs along with a likelihood score for each pair. Finally, we construct network maps of the protein pairs that fall above a desired likelihood ratio. Our initial efforts suggest a cluster of functional interactions that are predicted from the gene set identified by the RNAi screen; refinements of the computational methods are in progress.

Lei, Haiyan et al. (2009) International Worm Meeting "Defining the embryonic muscle gene regulatory network using chromatin immunoprecipitation and an analysis of potential cis-acting elements."

Fukushige, Tetsunari, Lei, Haiyan, Krause, Michael

[International Worm Meeting, 2009]

Previous work in C. elegans has shown that posterior embryonic body wall muscle lineages are regulated through a genetically defined transcriptional cascade that includes PAL-1/Caudal activation of muscle-specific transcription factors, including HLH-1/MRF and UNC-120/SRF, which together orchestrate specification and differentiation. Using chromatin immunoprecipitation (ChIP) in embryos, we recently demonstrated direct binding of PAL-1 in vivo to an hlh-1 enhancer element (Lei et al., 2009). Through mutational analysis of the evolutionarily conserved sequences within this enhancer, we identify two cis-acting elements and their associated trans-acting factors (PAL-1 and HLH-1) that are critical for the temporal-spatial expression of hlh-1 and proper myogenesis. Our data demonstrates that hlh-1 is indeed a direct target of PAL-1 in the posterior embryonic C. elegans muscle lineages, defining a novel in vivo binding site for this critical developmental regulator. We find that the same enhancer element is also a target of HLH-1 positive auto regulation, underlying (at least in part) the sustained high levels of CeMyoD in bodywall muscle throughout development. In order to further identify the embryonic muscle gene regulatory network, we combined HLH-1 ChIP with whole-genome tiling arrays to identify binding sites throughout the genome. We are currently validating our ChIP-chip data with transgenic reporters. These types of approaches will provide a molecular framework for the gene regulatory network activating the muscle module during embryogenesis.

Ward S et al. (1991) International C. elegans Meeting "CONTINUING MOLECULAR AND GENETIC ANALYSIS OF A SPERM-SPECIFIC GENE CLUSTER ON CHROMOSOME IV."

Tharp B, Pritchard J, Varkey JP, Muhlrad PJ, Ward S

[International C. elegans Meeting, 1991]

A cluster of sperm-specific genes to the lei t of unc-22 on chromosome IV was initially identified because it contained several major sperm protein (MSP) genes (Ward et al., 1988, J. Mol Biol. 199: 1-13). Additional genes with sperm-specific transcripts were subsequently identified within this cluster. One 30Kb stretch of DNA contained three MSP genes and two other genes encoding sperm-specific products (SSP), but no somatic or other genes detectable by differential northern analysis. These five genes are arranged as follows: [See Figure] As shown by the arrows, the pairs of gs l-es msp-81, msp-10, and ssp- 10, ssp-l, are divergently transcribed. Thus promoters and perhaps regulatory elements should be between these gene pairs, so these regions were sequenced and compared. No strriking examples of sequence elements shared by both regions welt found. The 5' untranslated sequences common to all MSP genes are not found in these other sperm specific genes. However, there is an iverted repeat nearly midway between each pair of genes which could play a role in regulation. In order to determine the functions of these genes, which share no sequence similarity to genes in the data bases, we sought mutations in them by selecting spermatogenesis defective mutants under the deficiency eDfl9 which spans this region. Direct selection identified only an unlinked gene (see Varkey et al. abstract), but, following Murphy's first law of genetics, in a screen for embryonic mutations in the nearby par-S gene, Diane Shakes also found new spe mutations. She kindly provided them to us, and five of them turned out to be under eDfl9. These mutations identify four new spe genes. Preliminary results rescuing these mutants by cosmid DNA injection suggest that at least one of these new genes is in the region shown above, so rescue by subcloned fragments should reveal if it is one of the molecularly identified genes.