Gene silencing

Inactivation of gene expression can occur at both the level of transcription and post-transcription. All silencing mechanisms are identical in that they require a small RNA species to provide the necessary gene sequence specificity and effector molecules that bind to the RNAs to process the RNA and to direct its inhibitory activity. Studies of these mechanisms in C. elegans has elucidated a number of different RNA-mediated post-transcriptional mechanisms. These mechanisms differ in the species of small RNAs involved. The different classes of small RNAs in C. elegans includes, microRNAs (miRNA), small interfering RNAs (siRNAs or rasi's), X-chromosome cluster RNAs (X-cluster), tiny noncoding RNAs (tncRNAs), and Piwi-associated RNAs (piRNAs). Gene silencing is accepted as a defense mechanism that evolved to protect the host from exogenous (foreign) sequence such as viral and transposon sequence. It has also been shown that gene silencing plays a critical role in endogenous gene expression to control the developmental timing of genes require for cell specificity, as well as playing a role in aging.

Organogenesis

The formation and development of an organ (a structural part of an organism that performs a specialized function) requires the coordination of many intrinsic and extrinsic cues that control cellular processes such as cell division and specificity, cell movement, cell-cell interaction, and cell polarity. C. elegans has proved to be a model organism for studying key organs, e.g., pharynx, intestine, and vulva, in part due to the small number of traceable cells that make up these specialized group of cells.

RNA splicing

During pre-messenger RNA (pre-mrRNA) processing, cis-splicing reactions remove non-coding introns and joins coding exons. The majority of splicing is catalyzed by spliceosomes, large RNA-protein complexes composed of small nuclear ribonucleoproteins (snRNPs) that recognize splice donor and acceptor sites within the nascent RNA strand. Alternative mRNAs for a given gene can be created during the splicing reactions through varying the degree of cutting and splicing of introns and exons guided by alternative splice sites. C. elegans also exhibits trans-splicing where sequences from different primary RNA transcripts are used to make the mRNA. In C. elegans, ~70% of transcripts are trans-spliced with either a splice leader sequence SL1 or SL2 joined to the final transcript. Splice leaders are important

Trans-splicing

Trans-splicing is an RNA processing event that fuses together sections of two different pre-mRNA sequences. In C. elegans, ~70% of mRNAs are trans-spliced to one of two 22 nucleotide spliced leaders, SL1 or SL2, with more than half of all transcripts undergoing SL1 splicing. During SL1 splicing, the 5' ends of pre-mRNAs are removed and replaced with SL1 sequence in a process very closely related to cis-splicing (intron/exon processing). SL1 sequence is ~100nt and is donated by small nuclear ribonucleoprotein particles (snRNPs). The remaining genes are trans-spliced by SL2. These genes are all downstream genes in closely spaced gene clusters similar to bacterial operons. They are transcribed from a promoter at the 5' end of the cluster of between 2 and 8 genes. This transcription makes a polycistronic pre-mRNA that is co-transcriptionally processed by cleavage and polyadenylation at the 3' end of each gene, and this event is closely coupled to the SL2 trans-splicing event that occurs only ~100 nt further downstream. Recent studies on the mechanism of SL2 trans-splicing have revealed that one of the 3' end formation proteins, CstF, interacts with the only protein known to be specific to the SL2 snRNP.