scholarly journals Leafy and Weedy Seadragon Genomes Connect Genic and Repetitive DNA Features to the Extravagant Biology of Syngnathid Fishes

2021 ◽  
Author(s):  
Clayton M. Small ◽  
Hope M. Healey ◽  
Mark C. Currey ◽  
Emily A. Beck ◽  
Julian Catchen ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Regulatory Networks ◽  
Natural Populations ◽  
Marine Conservation ◽  
Coding Regions ◽  
Evolutionary Innovation ◽  
Genome Wide ◽  
The Family ◽  
Gene Regulatory ◽  
Conserved Gene

AbstractSeadragons are a remarkable lineage of teleost fishes, and they are members of the family Syngnathidae renowned for having evolved male pregnancy. Comprising three known species, seadragons are widely recognized and admired for their fantastical body forms and coloration, and their specific habitat requirements have made them flagship representatives for marine conservation and natural history interests. Until recently, a gap has been the lack of significant genomic resources for seadragons. We have produced gene-annotated, chromosome-scale genome models for the leafy and weedy seadragon to advance investigations into evolutionary innovation and elaboration of morphological traits in seadragons as well as their pipefish and seahorse relatives. We identified several interesting features specific to seadragon genomes, including divergent non-coding regions near a developmental gene important for integumentary outgrowth, a high genome-wide density of repetitive DNA, and recent expansions of transposable elements and a vesicular trafficking gene family. Surprisingly, comparative analyses leveraging the seadragon genomes and additional syngnathid and outgroup genomes revealed striking, syngnathid-specific losses in the family of fibroblast growth factors (FGFs), which likely involve re-organization of highly conserved gene regulatory networks in ways that have not previously been documented in natural populations. The resources presented here serve as important tools for future evolutionary studies of developmental processes in syngnathids and will be a key resource for conservation studies of the extravagant seadragons and their relatives.

scholarly journals Inference of gene regulatory networks from genome-wide knockout fitness data

2012 ◽  
Vol 29 (3) ◽  
pp. 338-346 ◽  
Author(s):  
L. Wang ◽  
X. Wang ◽  
A. P. Arkin ◽  
M. S. Samoilov
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Genome Wide ◽  
Gene Regulatory

scholarly journals Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks

2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Adler R. Dillman ◽  
Marissa Macchietto ◽  
Camille F. Porter ◽  
Alicia Rogers ◽  
Brian Williams ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Gene Regulatory ◽  
Conserved Gene

scholarly journals Genome-wide RNAi screen for genes regulating glycolytic response to vemurafenib in BRAFV600 melanoma cells

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Lorey K. Smith ◽  
Tiffany Parmenter ◽  
Cathryn M. Gould ◽  
Piyush B. Madhamshettiwar ◽  
Karen E. Sheppard ◽  
...  
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Metabolic Response ◽  
Braf Inhibitor ◽  
Melanoma Cells ◽  
Genome Wide ◽  
Braf Inhibition ◽  
Mediate Response ◽  
Melanoma Patients ◽  
Gene Regulatory

Abstract Identification of mechanisms underlying sensitivity and response to targeted therapies, such as the BRAF inhibitor vemurafenib, is critical in order to improve efficacy of these therapies in the clinic and delay onset of resistance. Glycolysis has emerged as a key feature of the BRAF inhibitor response in melanoma cells, and importantly, the metabolic response to vemurafenib in melanoma patients can predict patient outcome. Here, we present a multiparameter genome-wide siRNA screening dataset of genes that when depleted improve the viability and glycolytic response to vemurafenib in BRAFV600 mutated melanoma cells. These datasets are suitable for analysis of genes involved in cell viability and glycolysis in steady state conditions and following treatment with vemurafenib, as well as computational approaches to identify gene regulatory networks that mediate response to BRAF inhibition in melanoma.

Condensing Biochemistry into Gene Regulatory Networks

2014 ◽  
Vol 4 (3) ◽  
pp. 1-25
Author(s):  
Alberto de la Fuente
Keyword(s):  
Gene Regulation ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Network Models ◽  
Transcriptional Regulatory Networks ◽  
Modern Biology ◽  
Genome Wide ◽  
Transcriptional Regulatory ◽  
Biochemical Systems ◽  
Gene Regulatory

Gene Regulatory Networks are models of gene regulation. Inferring such model from genome-wide gene-expression measurements is one of the key challenges in modern biology, and a large number of algorithms have been proposed for this task. As there is still much confusion in the current literature as to what precisely Gene Regulatory Networks are, it is important to provide a definition that is as unambiguous as possible. In this paper the author provides such a definition and explain what Gene Regulatory Networks are in terms of the underlying biochemical processes. The author will use a linear approximation to the in general non-linear kinetics underlying interactions in biochemical systems and show how a biochemical system can be ‘condensed' into a more compact description, i.e. Gene Regulatory Networks. Important differences between the defined Gene Regulatory Networks and other network models for gene regulation, i.e. Transcriptional Regulatory Networks and Co-Expression Networks, are also discussed.

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