Research Topic

Genomics approaches to understand the evolution and the function of transcriptional regulatory elements

About this Research Topic

Evolutionary biology has entered a new era. High throughput sequencing (HTS) based technologies allow us to sequence and assemble genomes at a relatively low cost. By comparing DNA in multiple species, we can now produce maps of sequence conservation and divergence in tens to hundreds of samples and draw hypotheses on the genetic bases of phenotypic diversity. At the same time, the rapid progress in the mechanistic understanding of the processes controlling transcription opens up the possibilities to identify the most interesting candidate cis-regulatory elements that orchestrate gene expression. The combination of ATAC-, DNAseI-, and ChIP-seq approaches coupled with chromatin conformation assays can be used to functionally annotate genomes while CRISPR-Cas9 assisted genetic engineering can aid in interrogating newly discovered variants in the context of transcriptional programs. This toolbox, in principle, should also allow us to build mechanistic models of evolution by tracing the history of enhancers, promoters, silencers, and insulators.


However, despite the remarkable progress in the field, determining which sequence changes in the genome are most relevant to explain the evolution of a particular trait remains extremely challenging. Likewise, understanding the functional consequences of mutations in cis-regulatory elements remains difficult and still much lower in throughput. In part, because of their redundancy, the difficulty of linking regulatory regions to target genes, the context-dependent activity of enhancers, and the complexity of epistatic interactions that frequently functionally bind multiple elements to each other. Yet, this knowledge will be instrumental for our understanding of how genomes mold phenotypes during evolution.

The relative scarcity of models of evolutionary trajectories of cis-regulatory element sequences hampers generalization and mechanistic understanding of the diversity of life forms. High throughput approaches to interrogate regulatory element activity, when used in combination with high-resolution functional analyses at the local or global genomic level, may serve to fill this gap and provide new light on how enhancers, promoters, and insulators shape the evolution of organisms. Therefore, the goal of our special issue is to gather new insights into the question of how genomes evolve. We encourage submissions that either generate or deploy state-of-the-art genomics approaches to identify and test candidate sequences driving the evolution of trait(s). In parallel, we invite reports presenting new computational approaches and models allowing the community to streamline this process and tools that will help to guide future choices of regulatory elements and genes for further functional tests.


Scope and information for Authors

       High throughput identification and inter-species comparative analysis of regulatory elements

       Functional tests measuring the impact of the evolutionary changes in the sequence of regulatory elements on traits

       Low-resolution global assays and high-resolution single loci assessments of the impact of changes in the DNA sequence on the evolution of traits

       Evolutionary changes in regulatory element sequences and their relationship with human disease

       Experimental or computational methods to interrogate and model the impact of changes in DNA regulatory elements on the evolution of gene expression and the acquisition of new traits

       New genome assembly, refinements with a special highlight on the impact of these improvements on our understanding of evolutionary processes

       Integration of data from multiple experimental sources into coherent evolutionary models 

       Evolution of gene regulatory networks  


Keywords: evolution, genomics, DNA regulatory elements, transcription, epigenetics


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

Evolutionary biology has entered a new era. High throughput sequencing (HTS) based technologies allow us to sequence and assemble genomes at a relatively low cost. By comparing DNA in multiple species, we can now produce maps of sequence conservation and divergence in tens to hundreds of samples and draw hypotheses on the genetic bases of phenotypic diversity. At the same time, the rapid progress in the mechanistic understanding of the processes controlling transcription opens up the possibilities to identify the most interesting candidate cis-regulatory elements that orchestrate gene expression. The combination of ATAC-, DNAseI-, and ChIP-seq approaches coupled with chromatin conformation assays can be used to functionally annotate genomes while CRISPR-Cas9 assisted genetic engineering can aid in interrogating newly discovered variants in the context of transcriptional programs. This toolbox, in principle, should also allow us to build mechanistic models of evolution by tracing the history of enhancers, promoters, silencers, and insulators.


However, despite the remarkable progress in the field, determining which sequence changes in the genome are most relevant to explain the evolution of a particular trait remains extremely challenging. Likewise, understanding the functional consequences of mutations in cis-regulatory elements remains difficult and still much lower in throughput. In part, because of their redundancy, the difficulty of linking regulatory regions to target genes, the context-dependent activity of enhancers, and the complexity of epistatic interactions that frequently functionally bind multiple elements to each other. Yet, this knowledge will be instrumental for our understanding of how genomes mold phenotypes during evolution.

The relative scarcity of models of evolutionary trajectories of cis-regulatory element sequences hampers generalization and mechanistic understanding of the diversity of life forms. High throughput approaches to interrogate regulatory element activity, when used in combination with high-resolution functional analyses at the local or global genomic level, may serve to fill this gap and provide new light on how enhancers, promoters, and insulators shape the evolution of organisms. Therefore, the goal of our special issue is to gather new insights into the question of how genomes evolve. We encourage submissions that either generate or deploy state-of-the-art genomics approaches to identify and test candidate sequences driving the evolution of trait(s). In parallel, we invite reports presenting new computational approaches and models allowing the community to streamline this process and tools that will help to guide future choices of regulatory elements and genes for further functional tests.


Scope and information for Authors

       High throughput identification and inter-species comparative analysis of regulatory elements

       Functional tests measuring the impact of the evolutionary changes in the sequence of regulatory elements on traits

       Low-resolution global assays and high-resolution single loci assessments of the impact of changes in the DNA sequence on the evolution of traits

       Evolutionary changes in regulatory element sequences and their relationship with human disease

       Experimental or computational methods to interrogate and model the impact of changes in DNA regulatory elements on the evolution of gene expression and the acquisition of new traits

       New genome assembly, refinements with a special highlight on the impact of these improvements on our understanding of evolutionary processes

       Integration of data from multiple experimental sources into coherent evolutionary models 

       Evolution of gene regulatory networks  


Keywords: evolution, genomics, DNA regulatory elements, transcription, epigenetics


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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Submission Deadlines

01 June 2021 Abstract
30 September 2021 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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Topic Editors

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Submission Deadlines

01 June 2021 Abstract
30 September 2021 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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