scholarly journals Identifying gene regulatory network rewiring using latent differential graphical models

2016 ◽  
Vol 44 (17) ◽  
pp. e140-e140 ◽  
Author(s):  
Dechao Tian ◽  
Quanquan Gu ◽  
Jian Ma
Keyword(s):  
Gene Regulatory Network ◽  
Graphical Models ◽  
Regulatory Network ◽  
Gene Regulatory ◽  
Network Rewiring

scholarly journals Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution

2017 ◽  
Author(s):  
David Dylus ◽  
Liisa M. Blowes ◽  
Anna Czarkwiani ◽  
Maurice R. Elphick ◽  
Paola Oliveri
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
De Novo ◽  
Sea Urchins ◽  
Brittle Star ◽  
Stages Of Development ◽  
Sequence Alignments ◽  
Amphiura Filiformis ◽  
Gene Regulatory ◽  
Network Rewiring

ABSTRACTAmongst the echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance, developmental and regenerative biology. However, compared to other echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue we have generated and assembled a large RNAseq data set of four key stages of development in the brittle star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model echinoderm - the sea urchin Strongyloncentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/. With a focus on skeleton development, we have identified highly conserved genes associated with the development of a biomineralized skeleton. We also identify important class-specific characters, including the independent duplication of the msp130 class of genes in different echinoderm classes and the unique occurrence of spicule matrix (sm) genes in echinoids. Using a new quantification pipeline for our de novo transcriptome, validated with other methodologies, we find major differences between brittle stars and sea urchins in the temporal expression of many transcription factor genes. This divergence in developmental regulatory states is more evident in early stages of development when cell specification begins, than when cells initiate differentiation. Our findings indicate that there has been a high degree of gene regulatory network rewiring in the evolution of echinoderm larval development.Data DepositionsAll sequence reads are available at Genbank SRR4436669 - SRR4436674. Any sequence alignments used are available by the corresponding author upon request.

scholarly journals Gene Regulatory Network Rewiring in the Immune Cells Associated with Cancer

Genes ◽  
2017 ◽  
Vol 8 (11) ◽  
pp. 308 ◽  
Author(s):  
Pengyong Han ◽  
Chandrasekhar Gopalakrishnan ◽  
Haiquan Yu ◽  
Edwin Wang
Keyword(s):  
Gene Regulatory Network ◽  
Immune Cells ◽  
Regulatory Network ◽  
Gene Regulatory ◽  
Network Rewiring

scholarly journals Gene regulatory network rewiring by an adaptively evolving microRNA cluster in Drosophila

2017 ◽  
Author(s):  
Yang Lyu ◽  
Zhongqi Liufu ◽  
Juan Xiao ◽  
Yuxin Chen ◽  
Chung-I Wu ◽  
...  
Keyword(s):  
Gene Regulatory Network ◽  
Biological Networks ◽  
Regulatory Network ◽  
Regulatory Networks ◽  
De Novo ◽  
Target Prediction ◽  
New Members ◽  
Microrna Cluster ◽  
Gene Regulatory ◽  
Network Rewiring

AbstractNew miRNAs are evolutionarily important but their impact on existing biological networks remains unclear. We report the evolution of a microRNA cluster, mir-972C, that arose de novo and the subsequently rewired gene regulatory networks in Drosophila. Molecular evolution analyses revealed that mir-972C originated in the common ancestor of Drosophila where it comprises five old miRNAs. It subsequently recruited five new members in the melanogaster subgroup after conservative evolution for at least 50 million years. Population genetics analyses reveal that young and old mir-972C miRNAs evolved rapidly under positive selection in both seed and non-seed regions. Combining target prediction and cell transfection experiments, we find that sequence changes in individual mir-972C members resulted in extensive gene regulatory network divergence among D. melanogaster, D. simulans, and D. virilis, whereas the target pool of the cluster as a whole remains relatively conserved. Our results suggest that clustering of young and old miRNAs at the same locus broadens target repertoires, resulting in the gain of new targets without losing many old ones. This may facilitate the establishment of new miRNAs within existing regulatory networks.

Sign in / Sign up

Export Citation Format

Share Document