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Planterose Jimenez, B.

Publications and source records attributed to Planterose Jimenez, B..

2 recordsLinked to original sources

Quantitative modelling of fate specification in the C. elegans postembryonicM lineage reveals a missing spatiotemporal signal

The invariant lineages of C. elegans provide tractable cell fate models to study how developing organisms robustly integrate spatial signals at the single-cell level via gene regulatory networks. For instance, during postembryonic development, a mesoderm lineage arises through a sequence of oriented cell divisions from a single progenitor. This mesoblast initially gives rise to 18 cells with three distinct fates - 14 body wall muscles (BWMs), 2 coelomocytes (CCs; dorsal), and 2 sex myoblasts (SMs; ventral). The latter cells migrate and then proliferate to contribute 16 smooth muscles to the nematodes reproductive organs. Prior work identified key symmetry breaking cues: i) ventrally restricted activation of the LIN-12 Notch pathway promoting SM over CC fate and ii) asymmetric re-distribution of SYS-1 {beta}-catenin and POP-1 TCF among daughter cells along the anteroposterior (A-P) axis, i.e. the Wnt/{beta}-catenin asymmetry pathway. However, it remains unclear whether these pathways are sufficient to specify all cell fates accordingly or whether additional symmetry breaking cues are necessary. In this study, we use quantitative modelling to better understand fate specification in the postembryonic M lineage. Specifically, we focus on the anteroposterior symmetry break by creating increasingly complex models towards robustly reproducing fate specification in wild type larvae and mutants. This iterative process resulted in two alternative models that explain the experimental observations by either introducing an additional spatial (spatial symmetry break) or temporal cue (temporal symmetry break). Finally, we evaluate their plausibility and propose a series of experiments to provide support for alternative models. Overall, our study highlights how a quantitative examination of mechanistic ideas can identify knowledge gaps and guide experimental follow-up.

systems biology↗

Simultaneous mapping of epigenetic inter-haplotype, inter-cell and inter-individual variation via the discovery of jointly regulated CpGs in pooled sequencing data

In the post-GWAS era, great interest has arisen in the mapping of epigenetic inter-individual variation towards investigating the emergence of phenotype in health and disease. Relevant DNA methylation methodologies - epigenome-wide association studies (EWAS), methylation quantitative trait loci (mQTL) mapping and allele-specific methylation (ASM) analysis - can each map certain sources of epigenetic variation and all depend on matching phenotypic/genotypic data. Here, to avoid these requirements, we developed Binokulars, a novel randomization test that identifies signatures of joint CpG regulation from reads spanning multiple CpGs. We tested and benchmarked our novel approach against EWAS and ASM on pooled whole-genome bisulfite sequencing (WGBS) data from whole blood, sperm and combined. As a result, Binokulars simultaneously discovered regions associated with imprinting, cell type- and tissue-specific regulation, mQTL, ageing and other (still unknown) epigenetic processes. To verify examples of mQTL and polymorphic imprinting, we developed JRC_sorter, another novel tool that classifies regions based on epigenotype models, which we deployed on non-pooled WGBS data from cord blood. In the future, this approach can be applied on larger pools to simultaneously map and characterise inter-haplotype, inter-cell and inter-individual variation in DNA methylation in a cost-effective fashion, a relevant pursuit towards phenome-mapping in the post-GWAS era.

genomics↗