Genome-wide screen identifies signaling pathways that regulate autophagy during Caenorhabditis elegans development.

The mechanisms that coordinate the regulation of autophagy with developmental signaling during multicellular organism development remain largely unknown. Here, we show that impaired function of ribosomal protein RPL-43 causes an accumulation of SQST-1 aggregates in the larval intestine, which are removed upon autophagy induction. Using this model to screen for autophagy regulators, we identify 139 genes that promote autophagy activity upon inactivation.

A genome-wide RNAi screen identifies genes regulating the formation of P bodies in C. elegans and their functions in NMD and RNAi.

Cytoplasmic processing bodies, termed P bodies, are involved in diverse post-transcriptional processes including mRNA decay, nonsense-mediated RNA decay (NMD), RNAi, miRNA-mediated translational repression and storage of translationally silenced mRNAs. Regulation of the formation of P bodies in the context of multicellular organisms is poorly understood. Here we describe a systematic RNAi screen in C.

A piggyBac transposon-based mutagenesis system for the fission yeast Schizosaccharomyces pombe.

The TTAA-specific transposon piggyBac (PB), originally isolated from the cabbage looper moth, Trichoplusia ni, has been utilized as an insertional mutagenesis tool in various eukaryotic organisms. Here, we show that PB transposes in the fission yeast Schizosaccharomyces pombe and leaves almost no footprints. We developed a PB-based mutagenesis system for S.

Transcription factor NFY globally represses the expression of the C. elegans Hox gene Abdominal-B homolog egl-5.

The C. elegans Hox gene egl-5 (ortholog of Drosophila Abdominal-B) is expressed in multiple tissues in the tail region and is involved in tail patterning. In this study, we identify and clone the corresponding C.

Strand compositional asymmetries in vertebrate large genes.

Both transcription-associated and replication-associated strand compositional asymmetries have recently been shown in vertebrate genomes. In this paper, we illustrate that transcription-associated strand compositional asymmetries and replication-associated ones coexist in most vertebrate large genes, although in most case the former conceals the latter. Furthermore, we found that the transcription-associated strand compositional asymmetries of housekeeping genes are stronger than those of somatic cell expressed genes.

Replication-associated strand asymmetries in vertebrate genomes and implications for replicon size, DNA replication origin, and termination.

Strand compositional asymmetry has been observed in prokaryotes and used in predicting prokaryotic DNA replication origins and termini. However, it was not found in eukaryotic genomes by the same methods. We propose that transcription-associated strand asymmetries mask the replication-associated ones.

mRNA-mediated intron losses: evidence from extraordinarily large exons.

Multicellular eukaryotes that have high intron density have their introns almost evenly distributed within genes, but unicellular eukaryotes that are generally intron poor have their introns asymmetrically distributed toward the 5' ends of genes. This was explained by homologous recombination of genomic DNA with the cDNA reverse transcribed from the 3' polyadenylated tail of spliced mRNA. This paper is to study whether mRNA-mediated intron losses have ever occurred in multicellular eukaryotes.