Biology subjects

Lionel Christiaen

Publications and source records attributed to Lionel Christiaen.

3 recordsLinked to original sources

bioRxiv2016

Fused regression for multi-source gene regulatory network inference

Understanding gene regulatory networks is critical to understanding cellular differentiation and response to external stimuli. Methods for global network inference have been developed and applied to a variety of species. Most approaches consider the problem of network inference independently in each species, despite evidence that gene regulation can be conserved even in distantly related species. Further, network inference is often confined to single data-types (single platforms) and single cell types. We introduce a method for multi-source network inference that allows simultaneous estimation of gene regulatory networks in multiple species or biological processes through the introduction of priors based on known gene relationships such as orthology incorporated using fused regression. This approach improves network inference performance even when orthology mapping and conservation are incomplete. We refine this method by presenting an algorithm that extracts the true conserved subnetwork from a larger set of potentially conserved interactions and demonstrate the utility of our method in cross species network inference. Last, we demonstrate our methods utility in learning from data collected on different experimental platforms.

Bioinformatics↗

bioRxiv2016

Rational design and whole-genome predictions of single guide RNAs for efficient CRISPR/Cas9-mediated genome editing in Ciona

The CRISPR/Cas9 system has emerged as an important tool for various genome engineering applications. A current obstacle to high throughput applications of CRISPR/Cas9 is the imprecise prediction of highly active single guide. RNAs (sgRNAs). We previously implemented the CRISPR/Cas9 system to induce tissue-specific mutations in the tunicate Ciona. In the present study, we designed and tested 83 single guide RNA (sgRNA) vectors targeting 23 genes expressed in the cardiopharyngeal progenitors and surrounding tissues of Ciona embryo. Using high-throughput sequencing of mutagenized alleles, we identified guide sequences that correlate with sgRNA mutagenesis activity and used this information for the rational design of all possible sgRNAs targeting the Ciona transcriptome. We also describe a one-step cloning-free protocol for the assembly of sgRNA expression cassettes. These cassettes can be directly electroporated as unpurified PCR products into Ciona embryos for sgRNA expression in vivo, resulting in high frequency of CRISPR/Cas9-mediated mutagenesis in somatic cells of electroporated embryos.\n\nWe found a strong correlation between the frequency of an Ebf loss-of-function phenotype and the mutagenesis efficacies of individual Ebf-targeting sgRNAs tested using this method. We anticipate that our approach can be scaled up to systematically design and deliver highly efficient sgRNAs for the tissue-specific investigation of gene functions in Ciona.

Developmental Biology↗

bioRxiv2016

Rewiring of an ancestral Tbx1/10-Ebf-Mrf network for pharyngeal muscle specification in distinct embryonic lineages

Skeletal muscles arise from diverse embryonic origins, yet converge on common regulatory programs involving muscle regulatory factor (MRF)-family genes. Here, we compare the molecular basis of myogenesis in two separate muscle groups in the simple chordate Ciona: the atrial and oral siphon muscles. Here, we describe the ontogeny of OSM progenitors and characterize the clonal origins of OSM founders to compare mechanisms of OSM specification to what has been established for ASM. We determined that, as is the case in the ASM, Ebf and Tbx1/10 are both expressed and function upstream of Mrf in the OSM founder cells. However, regulatory relationships between Tbx1/10, Ebf and Mrf differ between the OSM and ASM lineages: while Tbx1/10, Ebf and Mrf form a linear cascade in the ASM, Ebf and Tbx1/10 are expressed in the inverse temporal order and are required together in order to activate Mrf in the OSM founder cells.

Developmental Biology↗