Coding region | EPFL Graph Search

The coding region of a gene, also known as the coding sequence (CDS), is the portion of a gene's DNA or RNA that codes for protein. Studying the length, composition, regulation, splicing, structures, and functions of coding regions compared to non-coding regions over different species and time periods can provide a significant amount of important information regarding gene organization and evolution of prokaryotes and eukaryotes. This can further assist in mapping the human genome and developing gene therapy. Definition Although this term is also sometimes used interchangeably with exon, it is not the exact same thing: the exon is composed of the coding region as well as the 3' and 5' untranslated regions of the RNA, and so therefore, an exon would be partially made up of coding regions. The 3' and 5' untranslated regions of the RNA, which do not code for protein, are termed non-coding regions and are not discussed on this page. There is often confusion between coding re

Characterizing the localization and role of lin-5 and era-1 mRNAs in early C. elegans embryos

Zoltán Péter Spiró

Asymmetric cell division is essential for the generation of diversity during development and the function of stem cell lineages. The Caenorhabditis elegans zygote is an attractive model to investigate the mechanisms of spindle positioning during asymmetric cell division. In this polarized cell, the asymmetric distribution of cortical force generators along the antero-posterior axis and pulling on astral microtubules leads to the unequal cleavage of the one-cell embryo. The mechanisms underlying such cortical force generation are thought to act strictly at the protein level. In this thesis work we report that the mRNA encoding the cortical force generator component LIN-5 is enriched around centrosomes in early embryos, in a manner that depends on microtubules and dynein. We established that the lin-5 coding sequence is necessary and sufficient for mRNA enrichment around centrosomes in C. elegans. In addition, we found that lin-5 mRNA is mislocalized in lin-5(ev571) mutant embryos, which harbor a 9 nucleotide insertion in the coding sequence. Moreover, an intragenic revertant of lin-5(ev571), lin-5(ev571he63), also exhibits mislocalized lin-5 mRNA distribution. We demonstrated that this is accompanied by diminished pulling forces on the posterior spindle pole, suggesting that centrosomal localization of lin-5 mRNA is important for robust pulling forces. We found also that lin-5 mRNA centrosomal enrichment is slightly asymmetric during anaphase, with more transcripts present on the anterior side. We developed a novel FRAP-based assay, which revealed that lin-5 is translated/folded preferentially in the cytoplasm compared to centrosomes. Furthermore, we found that morpholino-mediated inhibition of lin-5 translation diminishes pulling forces on the posterior side during anaphase. Together, these findings lead us to propose that preferential translation/folding of lin-5 in the posterior cytoplasm following release of the mRNA from the posterior centrosome contributes to asymmetric cortical distribution of force generators, and thus to proper spindle positioning. Moreover, we found that the mRNA of an uncharacterized gene, era-1 is enriched on the anterior side of the zygote and is inherited by the anterior blastomeres. Similar to era-1 mRNA, a YFP fusion of ERA-1 protein is also asymmetrically distributed. Moreover, asymmetric distribution of both era-1 mRNA and YFP-ERA-1 protein requires the era-1 3'UTR. Furthermore, the RNA-binding protein MEX-5 is needed for both asymmetric era-1 mRNA localization and for its translational activation. Furthermore, we report that the clathrin heavy chain CHC-1 negatively regulates pulling forces acting on centrosomes during interphase and on spindle poles during mitosis in one-cell C. elegans embryos. We establish a similar role for the cytokinesis/apoptosis/RNA-binding protein CAR-1 and uncover that CAR-1 is needed to maintain normal levels of CHC-1. We demonstrate that CHC-1 is necessary for proper organization of the cortical acto-myosin network and for full cortical tension. Furthermore, we establish that the centrosome positioning phenotype of embryos depleted of CHC-1 is alleviated by stabilizing the acto-myosin network. Conversely, we demonstrate that slight perturbations of the acto-myosin network results in excess centrosome movements. Overall, our findings lead us to propose that clathrin plays a critical role in centrosome positioning by promoting acto-myosin cortical tension.

EPFL2014

Where are the missing gene defects in inherited retinal disorders? Intronic and synonymous variants contribute at least to 4% of CACNA1F-mediated inherited retinal disorders

Vincent Meyer

Inherited retinal disorders (IRD) represent clinically and genetically heterogeneous diseases. To date, pathogenic variants have been identified in similar to 260 genes. Albeit that many genes are implicated in IRD, for 30-50% of the cases, the gene defect is unknown. These cases may be explained by novel gene defects, by overlooked structural variants, by variants in intronic, promoter or more distant regulatory regions, and represent synonymous variants of known genes contributing to the dysfunction of the respective proteins. Patients with one subgroup of IRD, namely incomplete congenital stationary night blindness (icCSNB), show a very specific phenotype. The major cause of this condition is the presence of a hemizygous pathogenic variant in CACNA1F. A comprehensive study applying direct Sanger sequencing of the gene-coding regions, exome and genome sequencing applied to a large cohort of patients with a clinical diagnosis of icCSNB revealed indeed that seven of the 189 CACNA1F-related cases have intronic and synonymous disease-causing variants leading to missplicing as validated by minigene approaches. These findings highlight that gene-locus sequencing may be a very efficient method in detecting disease-causing variants in clinically well-characterized patients with a diagnosis of IRD, like icCSNB.

WILEY2019

Computational analysis of ultraconserved non-coding DNA elements in vertebrate genomes

Slavica Dimitrieva Janeva

Recent advancements in DNA sequencing technologies, accompanied by parallel development of sophisticated computational methods, offer an unprecedented opportunity to explore and study the genetic material of many organisms. However, despite the tremendous progress in the field of genomics, our understanding of the genetic information encoded by the DNA is far from complete. Whole-genome comparisons of vertebrate species have uncovered the existence of non-coding DNA sequences that exhibit exceptionally high levels of similarity over hundreds of base pairs across distant species, referred to as ultraconserved non-coding elements (UCNEs). The existence of such sequences represents one of the biggest mysteries in current biology. Many UCNEs exhibit even stronger conservation than protein coding regions, but to date no molecular mechanism has been described that would require such a high degree of conservation over such long sequences. This thesis focuses on computational analysis of UCNEs across vertebrate genomes, with an ultimate goal to provide insights into the functioning of these elements and to unravel the reasons for their extreme conservation. Using computational approaches we studied the salient characteristics of UCNEs, and explored their genomic environment and their organization across genomes. Like previous studies, we observed that UCNEs are organized as large clusters around essential developmental genes, forming genomic regulatory blocks. Then we sought to understand the reasons behind this strong clustering of UCNEs. The clustering could reflect functional cooperativity between UCNEs. Alternatively, if each UCNE acts independently, their high concentration near developmental genes could merely reflect the extreme regulatory complexity of these genes. In a special setting of genomic context analysis, we analyzed the fate of UCNEs in teleost fish genomes that were subjected to an additional round of whole-genome duplication. We found that in most cases all UCNEs of a block were retained in one copy only, but together on the same chromosome. Conversely, the corresponding target genes were often retained in two copies, one completely devoid of UCNEs. Our results suggested that UCNEs of a cluster function in a highly cooperative manner. We propose that a multitude of cooperative cis-interactions between UCNEs is the reason for their extreme sequence conservation. Our work presents a novel hypothesis about the reasons for UCNE conservation and their mode of action, which is yet to be confirmed experimentally. The results from our study are made accessible through a new web resource called UCNEbase (http://ccg.vital-it.ch/UCNEbase). UCNEbase provides informa- tion about the genomic organization of UCNEs and their association with developmental regulatory genes, and enables all data to be explored in a genome browser environment. As part of a side project, we developed a new sparsified version of algorithms for computational prediction of RNA secondary structures and introduced a new program sibRNAfold. We performed a thorough analysis of the time complexity of sparsified RNA folding algorithms covering a large parameter space and empirically demonstrated that sparse RNA folding has cubic time complexity rather than quadratic, as claimed previously.

EPFL2013