scholarly journals Gene regulatory networks and network models in development and evolution

2017 ◽  
Vol 114 (23) ◽  
pp. 5782-5783 ◽  
Author(s):  
Neil Shubin
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Network Models ◽  
Gene Regulatory ◽  
Development And Evolution

What are Gene Regulatory Networks?

2010 ◽  
pp. 1-27 ◽  
Author(s):  
Alberto de la Fuente
Keyword(s):  
Gene Expression ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Network Models ◽  
Transcriptional Regulatory Networks ◽  
Biochemical Processes ◽  
Transcriptional Regulatory ◽  
Biochemical Systems ◽  
Gene Regulatory

This book deals with algorithms for inferring and analyzing Gene Regulatory Networks using mainly gene expression data. What precisely are the Gene Regulatory Networks that are inferred by such algorithms from this type of data? There is still much confusion in the current literature and it is important to start a book about computational methods for Gene Regulatory Networks with a definition that is as unambiguous as possible. In this chapter, I provide a definition and try to clearly explain what Gene Regulatory Networks are in terms of the underlying biochemical processes. To do the latter in a formal way, I 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 the more compact description of Gene Regulatory Networks. Important differences between the defined Gene Regulatory Networks and other network models for gene regulation, such as Transcriptional Regulatory Networks and Co-Expression Networks, will be highlighted.

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.

scholarly journals An atlas of transcription factors expressed in the Drosophila melanogaster pupal terminalia

2019 ◽  
Author(s):  
Ben J. Vincent ◽  
Gavin R. Rice ◽  
Gabriella M. Wong ◽  
William J. Glassford ◽  
Kayla I. Downs ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Transcription Factors ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Rna Seq ◽  
Pupal Development ◽  
Searchable Database ◽  
Gene Regulatory ◽  
Development And Evolution

AbstractDuring development, transcription factors and signaling molecules govern gene regulatory networks to direct the formation of unique morphologies. As changes in gene regulatory networks are often implicated in morphological evolution, mapping transcription factor landscapes is important, especially in tissues that undergo rapid evolutionary change. The terminalia (genital and anal structures) of Drosophila melanogaster and its close relatives exhibit dramatic changes in morphology between species. While previous studies have found network components important for patterning the larval genital disc, the networks governing adult structures during pupal development have remained uncharted. Here, we performed RNA-seq in whole Drosophila melanogaster terminalia followed by in situ hybridization for 100 highly expressed transcription factors during pupal development. We find that the terminalia is highly patterned during pupal stages and that specific transcription factors mark separate structures and substructures. Our results are housed online in a searchable database (flyterminalia.pitt.edu) where they can serve as a resource for the community. This work lays a foundation for future investigations into the gene regulatory networks governing the development and evolution of Drosophila terminalia.SummaryWe performed RNA-seq in whole Drosophila melanogaster terminalia (genitalia and analia) followed by in situ hybridization for 100 highly expressed transcription factors during pupal development. We find that the pupal terminalia is highly patterned with specific transcription factors marking separate structures and substructures. Our results are housed online in a searchable database (flyterminalia.pitt.edu) where they can serve as a resource for the community. This work lays a foundation for future investigations into the gene regulatory networks governing the development and evolution of Drosophila terminalia.

scholarly journals Evolving Views on the Pallium

2021 ◽  
pp. 1-19
Author(s):  
Loreta Medina ◽  
Antonio Abellán ◽  
Ester Desfilis
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Double Ring ◽  
Neural Populations ◽  
Research Questions ◽  
Gene Regulatory ◽  
Architecture Development ◽  
Activity Dependent ◽  
Organizing Principles ◽  
Development And Evolution

The pallium is the largest part of the telencephalon in amniotes, and comparison of its subdivisions across species has been extremely difficult and controversial due to its high divergence. Comparative embryonic genoarchitecture studies have greatly contributed to propose models of pallial fundamental divisions, which can be compared across species and be used to extract general organizing principles as well as to ask more focused and insightful research questions. The use of these models is crucial to discern between conservation, convergence or divergence in the neural populations and networks found in the pallium. Here we provide a critical review of the models proposed using this approach, including tetrapartite, hexapartite and double-ring models, and compare them to other models. While recognizing the power of these models for understanding brain architecture, development and evolution, we also highlight limitations and comment on aspects that require attention for improvement. We also discuss on the use of transcriptomic data for understanding pallial evolution and advise for better contextualization of these data by discerning between gene regulatory networks involved in the generation of specific units and cell populations versus genes expressed later, many of which are activity dependent and their expression is more likely subjected to convergent evolution.

Sign in / Sign up

Export Citation Format

Share Document