Literature DB >> 28968519

Using synthetic biology to study gene regulatory evolution.

Justin Crocker1, Garth R Ilsley2.   

Abstract

Transcriptional enhancers specify the precise time, level, and location of gene expression. Disentangling and characterizing the components of enhancer activity in multicellular eukaryotic development has proven challenging because enhancers contain activator and repressor binding sites for multiple factors that each exert nuanced, context-dependent control of enhancer activity. Recent advances in synthetic biology provide an almost unlimited ability to create and modify regulatory elements and networks, offering unprecedented power to study gene regulation. Here we review several studies demonstrating the utility of synthetic biology for studying enhancer function during development and evolution. These studies clearly show that synthetic biology can provide a way to reverse-engineer and reengineer transcriptional regulation in animal genomes with enormous potential for understanding evolution.
Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

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Year:  2017        PMID: 28968519     DOI: 10.1016/j.gde.2017.09.001

Source DB:  PubMed          Journal:  Curr Opin Genet Dev        ISSN: 0959-437X            Impact factor:   5.578


  6 in total

1.  DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers.

Authors:  Bernardo P de Almeida; Franziska Reiter; Michaela Pagani; Alexander Stark
Journal:  Nat Genet       Date:  2022-05-12       Impact factor: 41.307

2.  Synthetic reconstruction of the hunchback promoter specifies the role of Bicoid, Zelda and Hunchback in the dynamics of its transcription.

Authors:  Gonçalo Fernandes; Huy Tran; Maxime Andrieu; Youssoupha Diaw; Carmina Perez Romero; Cécile Fradin; Mathieu Coppey; Aleksandra M Walczak; Nathalie Dostatni
Journal:  Elife       Date:  2022-04-01       Impact factor: 8.713

Review 3.  A synthetic synthesis to explore animal evolution and development.

Authors:  Mindy Liu Perkins; Lautaro Gandara; Justin Crocker
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2022-05-30       Impact factor: 6.671

4.  Dense and pleiotropic regulatory information in a developmental enhancer.

Authors:  Timothy Fuqua; Jeff Jordan; Maria Elize van Breugel; Aliaksandr Halavatyi; Christian Tischer; Peter Polidoro; Namiko Abe; Albert Tsai; Richard S Mann; David L Stern; Justin Crocker
Journal:  Nature       Date:  2020-10-14       Impact factor: 49.962

Review 5.  Enhancer grammar in development, evolution, and disease: dependencies and interplay.

Authors:  Granton A Jindal; Emma K Farley
Journal:  Dev Cell       Date:  2021-03-08       Impact factor: 12.270

6.  Base-resolution models of transcription-factor binding reveal soft motif syntax.

Authors:  Žiga Avsec; Melanie Weilert; Avanti Shrikumar; Sabrina Krueger; Amr Alexandari; Khyati Dalal; Robin Fropf; Charles McAnany; Julien Gagneur; Anshul Kundaje; Julia Zeitlinger
Journal:  Nat Genet       Date:  2021-02-18       Impact factor: 38.330

  6 in total

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