Siddiq, Mohammad et al. (2013) International Worm Meeting "Inferring the order of mutational changes responsible for mechanistic divergence of a functionally constrained promoter."

Barriere, Antoine, Siddiq, Mohammad, Ruvinsky, Ilya

[International Worm Meeting, 2013]

Genetic systems diverge during evolution. A well-known consequence of this is inviability and infertility of hybrids from closely related and phenotypically similar species. Among possible causes of this phenomenon is the divergence of gene regulatory mechanisms that is compensated within each lineage, but because this happens in lineage-specific ways, incompatibility is revealed in hybrids. Previously we showed that while the endogenous expression patterns of unc-47 are conserved between Caenorhabditis elegans and C. briggsae, the mechanisms controlling this expression have diverged. As a result, a transgene containing C. briggsae promoter is expressed incorrectly when in C. elegans. We are seeking to understand how this incompatibility arose, even though evidence suggests that the pattern of unc-47 expression remained constant during Caenorhabditis evolution. We inferred the order of substitutions in the promoter of unc-47 by analyzing promoter sequences from the monophyletic group of species containing C. elegans and C. briggsae. By systematically characterizing their expression patterns in C. elegans, we precisely mapped the origin of the functional divergence on the Caenorhabditis phylogeny. We are currently interrogating the individual and collective effects of single nucleotide substitutions, insertions, and deletions in different trans-regulatory backgrounds. This work provides a detailed mechanistic explanation of how a trait can diverge while being maintained by stabilizing selection.

Luv Kashyap et al. (2006) European Worm Meeting "Hundreds of Alternatively Spliced New Transcripts from C. elegans Genome"

Luv Kashyap, Mohammad Tabish

[European Worm Meeting, 2006]

Luv Kashyap and Mohammad Tabish. With the completion of genome sequence of several organisms including free living soil nematode Caenorhabditis elegans, deciphering the biological information hidden in the sequence is of great importance and challenging to the biologists. The information we get from C. elegans genomic sequence is directly applicable to more complex organisms including humans because 35-40% of C. elegans genes share a direct homology with human genes. It has also been shown that human genes replace their C. elegans homologs when introduced into transgenic C. elegans. Thus studies on C. elegans genes can directly be used for better understanding of human genes. Alternative splicing of pre mRNAs is a powerful and versatile regulatory mechanism that can affect quantitative control of gene expression and functional diversification of proteins. It contributes to major developmental decisions and also to fine-tuning of gene function. Alternative splicing is found extensively in all higher eukaryotes including human.. We have undertaken a detailed analysis of the genomic sequence of one of the six chromosomes of C. elegans. In this study several bioinformatics tools including gene predictions programmes, exon predictions programmes and ORF finders etc were used to analyze the genes encoded by first chromosome of C. elegans with special reference to alternatively spliced isoforms. Using these tools we have identified more than 150 new alternatively spliced transcripts from the genes encoded by chromosome 1. These new coding sequences were identified from unusually large untranslated regions and large introns present at the 3'' and 5'' end of the genes. Our findings indicate that there could be more than one thousand alternatively spliced transcripts expressed from all six chromosomes of C. elegans which have not been annotated or identified earlier. Further studies on these alternatively spliced transcripts will enhance our understanding of the genome structure, expression and elucidate their role during the development of C. elegans. The poster will be presented to explain these findings.