Modelling the evolution of transcription factor binding preferences in complex eukaryotes

Rosanova, Antonio; Colliva, Alberto; Osella, Matteo; Caselle, Michele

doi:10.1038/s41598-017-07761-0

Cited by 25 publications

(20 citation statements)

References 50 publications

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“…Regardless of organism complexity, they are present in all domains of life. Duplication and deletion can influence transcriptional regulatory networks by increasing or reducing the number of TFs with specific binding preferences (23,24). Following the duplication of a TF gene, the two resulting gene copies are likely the same.…”

Section: Transcription Factor Evolution Amongst Life Domainsmentioning

confidence: 99%

Transcription factors and evolution: An integral part of gene expression (Review)

et al. 2020

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Gene expression is a complex process that is essential to living organisms. Gene expression plays the important role of converting information that is encoded in a gene into a functional product. The primary regulators of gene expression are transcription factors (TFs). TFs are proteins that can bind specific DNA sequences and regulate gene expression. Their evolution is influenced by a large number of factors, including epigenetic mechanisms, gene regulatory elements and molecular cofactors. These molecular mediators, along with transcription factors, form a network that governs gene expression. Elucidating the mechanisms through which TFs have evolved and how they influence the evolution of other regulatory molecules can provide information on organism evolution and on the development of phenotypic variations. The aim of this review article was to provide a summary of the current literature on transcription factor evolution, function and how such evolution has played an important role in the emergence of complex organisms. Contents

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Section: Transcription Factor Evolution Amongst Life Domainsmentioning

confidence: 99%

Transcription factors and evolution: An integral part of gene expression (Review)

et al. 2020

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“…NCG has also been used to investigate the effect of long noncoding RNAs on cancer genes [27] and to find non-duplicated cancer-related transcription factors [28].…”

Section: Introductionmentioning

confidence: 99%

The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens

Venkata

Repana

Nulsen

et al. 2018

Preprint

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The Network of Cancer Genes (NCG) is a manually curated repository of 2,372 genes whose somatic modifications have a known or predicted cancer driver role.These genes were collected from 275 publications, including two sources of known cancer genes and 273 cancer sequencing screens of 119 cancer types in 31 primary sites from 34,905 cancer donors. This represents a more than 1.5-fold increase in content as compared to the previous version. NCG also annotates properties of cancer genes, such as duplicability, evolutionary origin, RNA and protein expression, miRNA and protein interactions, protein function and essentiality. NCG is accessible at http://ncg.kcl.ac.uk/.

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“…Chemical recognition between proteins, nucleic acids, carbohydrates, lipids and other molecules, drives not only metabolic pathways, but also the assembly of protein [ 39 ], ribosomal [ 40 , 41 ] and transcriptional complexes [ 42 ], etc. Molecular recognition and binding has been molded by evolution, resulting in specialization in particular taxa [ 43 ].…”

Section: Introductionmentioning

confidence: 99%

On an algorithmic definition for the components of the minimal cell

Martínez

Reyes-Valdés

2018

PLoS ONE

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Living cells are highly complex systems comprising a multitude of elements that are engaged in the many convoluted processes observed during the cell cycle. However, not all elements and processes are essential for cell survival and reproduction under steady-state environmental conditions. To distinguish between essential from expendable cell components and thus define the ‘minimal cell’ and the corresponding ‘minimal genome’, we postulate that the synthesis of all cell elements can be represented as a finite set of binary operators, and within this framework we show that cell elements that depend on their previous existence to be synthesized are those that are essential for cell survival. An algorithm to distinguish essential cell elements is presented and demonstrated within an interactome. Data and functions implementing the algorithm are given as supporting information. We expect that this algorithmic approach will lead to the determination of the complete interactome of the minimal cell, which could then be experimentally validated. The assumptions behind this hypothesis as well as its consequences for experimental and theoretical biology are discussed.

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Modelling the evolution of transcription factor binding preferences in complex eukaryotes

Cited by 25 publications

References 50 publications

Transcription factors and evolution: An integral part of gene expression (Review)

Transcription factors and evolution: An integral part of gene expression (Review)

The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens

On an algorithmic definition for the components of the minimal cell

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