Rapid reorganization of the transcriptional regulatory network after genome duplication in yeast

Conant, Gavin C.

doi:10.1098/rspb.2009.1592

Cited by 21 publications

(16 citation statements)

References 54 publications

(79 reference statements)

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“…It is now well accepted that this mechanism has contributed to the evolution of genomes and their regulatory networks. Several studies [56][57][58][59] have investigated the role of WGD on network evolution. Such studies have revealed that (i) genes targeted by many TFs appear to be preferentially retained in duplicate after WGD, (ii) duplicate TFs produced by WGD rapidly evolve to perform distinct functional roles in the regulatory network, (iii) newly formed transcriptional pathways remain connected (paths are not broken) and are preferentially cross-connected with ancestral ones, and (iv) duplicated TFs through WGD may have contributed to the evolution of some network motifs in yeast.…”

Section: Impact Of Gene Duplication On Trn Evolutionmentioning

confidence: 99%

Structure, evolution and dynamics of transcriptional regulatory networks

Babu

2010

Biochemical Society Transactions

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The availability of entire genome sequences and the wealth of literature on gene regulation have enabled researchers to model an organism's transcriptional regulation system in the form of a network. In such a network, TFs (transcription factors) and TGs (target genes) are represented as nodes and regulatory interactions between TFs and TGs are represented as directed links. In the present review, I address the following topics pertaining to transcriptional regulatory networks. (i) Structure and organization: first, I introduce the concept of networks and discuss our understanding of the structure and organization of transcriptional networks. (ii) Evolution: I then describe the different mechanisms and forces that influence network evolution and shape network structure. (iii) Dynamics: I discuss studies that have integrated information on dynamics such as mRNA abundance or half-life, with data on transcriptional network in order to elucidate general principles of regulatory network dynamics. In particular, I discuss how cell-to-cell variability in the expression level of TFs could permit differential utilization of the same underlying network by distinct members of a genetically identical cell population. Finally, I conclude by discussing open questions for future research and highlighting the implications for evolution, development, disease and applications such as genetic engineering.

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Section: Impact Of Gene Duplication On Trn Evolutionmentioning

confidence: 99%

Structure, evolution and dynamics of transcriptional regulatory networks

Babu

2010

Biochemical Society Transactions

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“…Given that previous work in allopolyploids (e.g. wheat (Pfeifer et al ., ) and cotton (Hu et al ., )) was mainly based on aggregated co‐expression relationships of homoeologs, one future direction is to generate networks considering homoeolog expression separately, thereby allowing the direct evaluation of topological dynamics in terms of gain and loss of intra‐ and inter‐subgenome relationships (Conant & Wolfe, , ; Conant, ). Although co‐expression relationships do not necessarily represent physical interactions between cis and trans regulatory elements, the gene‐to‐gene interconnections that are inferred based on the ‘guilt‐by‐association’ principle provide an alternative and parallel approach for understanding the impact of genomic merger and doubling, under the same analytical framework used for genes outside of a network context.…”

Section: The Extended Cis–trans Framework and Expression Patterns In mentioning

confidence: 99%

Cis–trans controls and regulatory novelty accompanying allopolyploidization

Wendel

2018

New Phytologist

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Summary Allopolyploidy is a prevalent process in plants, having important physiological, ecological and evolutionary consequences. Transcriptomic responses to genomic merger and doubling have been demonstrated in many allopolyploid systems, encompassing a diversity of phenomena including homoeolog expression bias, genome dominance, expression‐level dominance and revamping of co‐expression networks. Notwithstanding the foregoing, there remains a need to develop a conceptual framework that will stimulate a deeper understanding of these diverse phenomena and their mechanistic interrelationships. Here we introduce considerations relevant to this framework with a focus on cis–trans interactions among duplicated genes and alleles in hybrids and allopolyploids. By extending classic allele‐specific expression analysis to the allopolyploid level, we distinguish the distinct effects of progenitor regulatory interactions from the novel intergenomic interactions that arise from genome merger and allopolyploidization. This perspective informs experiments designed to reveal the molecular genetic basis of gene regulatory control, and will facilitate the disentangling of genetic from epigenetic and higher‐order effects that impact gene expression. Finally, we suggest that the extended cis–trans model may help conceptually unify several presently disparate hallmarks of allopolyploid evolution, including genome‐wide expression dominance and biased fractionation, and lead to a new level of understanding of phenotypic novelty accompanying polyploidy.

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“…Whole genome duplications and small-scale duplications have very different consequences. Selective retention of different duplicates, and enrichment of signaling proteins and transcription factors, have been observed in yeast, plants, early vertebrate and fish following whole genome duplications (Conant 2010;Gout, Duret and Kahn 2009;Huminiecki and Heldin 2010;Kassahn et al 2009;Manning and Scheeff 2010). This indicates that the individual duplication of signaling proteins and transcriptional regulators may be deleterious, since interactions between them are relatively transient and subtle, requiring a dosage balance from the whole genome duplication to survive.…”

Section: Regional Duplicationmentioning

confidence: 99%