Transcription regulation and animal diversity

Levine, Michael; Tjian, Robert

doi:10.1038/nature01763

Cited by 1,114 publications

(922 citation statements)

References 72 publications

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“…76 In response to the requirements of a cell, each step in the process of gene expression is regulated by complex cellular mechanisms, from the transcription of DNA into mRNA to the post-translational modification of proteins. The conversion of the information stored in DNA into proteins takes place through several phases that are highly regulated in response to the functional requirements of proteins by the cell.…”

Section: Towards a Quantitative Biology Based On Physico-chemical Primentioning

confidence: 99%

Quantitative approaches to defining normal and aberrant protein homeostasis

Vendruscolo

2009

Faraday Discuss.

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Protein homeostasis refers to the ability of cells to generate and regulate the levels of their constituent proteins in terms of conformations, interactions, concentrations and cellular localisation. We discuss here an approach in which physico-chemical properties of proteins and their environments are used to understand the underlying principles governing this process, which is crucial in all living systems. By adopting the strategy of characterising the origins of specific diseases to inform us about normal biology, we are bringing together methods and concepts from chemistry, physics, engineering, genetics and medicine. In particular, we are using a combination of in vitro, in silico and in vivo approaches to study protein homeostasis through the analysis of the effects that result from its perturbation in a select group of specific proteins, from either amino acid mutations, or changes in concentration and solubility, or interactions with other molecules. By developing a coherent and quantitative description of such phenomena, we are finding that it is possible to shed new light on how the physical and chemical properties of the cellular components can provide an understanding of the normal and aberrant behaviour of living systems. Through such an approach it is possible to provide new insights into the origin and consequences of the failure to maintain homeostasis that is associated with neurodegenerative diseases, in particular, and the phenomenon of ageing, in general, and hence provide a framework for the rational design of therapeutic approaches.

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Section: Towards a Quantitative Biology Based On Physico-chemical Primentioning

confidence: 99%

Quantitative approaches to defining normal and aberrant protein homeostasis

Vendruscolo

2009

Faraday Discuss.

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“…Within well-studied animal subgroups, such as vertebrates among the chordates, the variability in the coding contents of nuclear genetic material is minimal implicating a crucial role of regulatory elements in phenotypic evolution (Levine and Tjian, 2003;Abbasi, 2008). In fact, with an increasing body of empirical evidence emerging from the fields of evolutionary developmental biology and comparative genomics, it is now broadly accepted that increased morphological complexity and diversity in animals is associated with the evolution of cisacting DNA elements that regulate the expression of developmental regulators (Carroll, 2008).…”

Section: Mechanisms To Generate Morphologi-cal Complexitymentioning

confidence: 99%

“…transcriptional factors that bind to them (Carroll, 2001;Levine and Tjian, 2003). For instance, the unicellular yeast genome encodes a total of $300 transcription factors, while the genome sequences of Caenorhabditis elegans and Drosophila reveal at least 1,000 transcription factors each (Ruvkun and Hobert, 1998;Aoyagi and Wassarman, 2000).…”

Section: Mechanisms To Generate Morphologi-cal Complexitymentioning

confidence: 99%

Evolution of vertebrate appendicular structures: Insight from genetic and palaeontological data

Abbasi

2011

Developmental Dynamics

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The new body of evidence from fossils and comparative-developmental analysis of subset of appendicular patterning genes has revealed that limb elements seen in tetrapods are assembled in fish fin over evolutionary time. However, despite of deep homology in basic structure and underlying developmental system, there remains a large morphological gap between distal elements of tetrapod limb and distal fin skeleton of tetrapodomorph fish. Understanding the genetic basis of major transformations in distal-limb morphology is the next challenge for evolutionary developmental biologists. Here by integrating data from fossils, comparative-developmental and genetic studies, models are proposed describing the evolution of cis-regulatory elements as a basis for diversification of appendicular architecture. Instead of emphasizing the subset of developmental genes, for instance Hoxd genes, the focus here is on the significance of elucidating cis-regulatory elements for multiple other key molecular players of limb/fin development and genetic/ molecular interactions among them, for a better understanding of the developmental and genetic basis of limb evolution. Developmental Dynamics 240:1005-1016,

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“…In eukaryotes, the regulation of gene expression underlies fundamental biological processes such as cell differentiation, organism development, and biodiversity [1]. A major regulatory target during gene expression is the synthesis of messenger RNA (mRNA) by RNA polymerase II (Pol II).…”

Section: Introductionmentioning

confidence: 99%

A structural perspective on Mediator function

Larivière

Seizl

Cramer

2012

Current Opinion in Cell Biology

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Gene transcription by RNA polymerase II requires the multiprotein coactivator complex Mediator. Mediator was identified two decades ago, but its molecular mechanisms remain poorly understood, because structural studies are hampered by its large size, modularity, and flexibility. Here we collect all available structural data on Mediator and discuss their functional implications. Progress was made in understanding the interactions of Mediator with gene-specific transcriptional regulators and the general transcription machinery. However, around 80% of the Mediator structure remains unknown and details on the Mediator-Pol II interface are lacking. In the future, an integrated structural biology approach may unravel the functional architecture of Mediatorregulated promoter assemblies and holds the promise of understanding a key mechanism of gene regulation.

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Transcription regulation and animal diversity

Cited by 1,114 publications

References 72 publications

Quantitative approaches to defining normal and aberrant protein homeostasis

Quantitative approaches to defining normal and aberrant protein homeostasis

Evolution of vertebrate appendicular structures: Insight from genetic and palaeontological data

A structural perspective on Mediator function

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