Developmental variation of the SUUR protein binding correlates with gene regulation and specific chromatin types in D. melanogaster

Abstract:Genome architecture plays a critical role in gene regulation, but how the structures seen in mature cells emerge during embryonic development remains poorly understood. Here, we study early development in medaka (the Japanese killifish, Oryzias latipes) at 12 time points before, during, and after gastrulation which is the most dramatic event in early embryogenesis, and characterize transcription, protein binding, and genome architecture. We find that gastrulation is most associated with drastic changes in genome architecture, including the formation of the first loops between sites bound by the insulator protein CTCF and great increase in the size of contact domains. However, the position of CTCF is fixed throughout medaka embryogenesis. Interestingly, genome-wide transcription precedes the emergence of mature domains and CTCF-CTCF loops.

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Synthetic protein-binding DNA sponge as a tool to tune gene expression and mitigate protein toxicity

Nature Communications ◽

10.1038/s41467-020-19552-9 ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Xinyi Wan ◽

Filipe Pinto ◽

Luyang Yu ◽

Baojun Wang

Keyword(s):

Gene Expression ◽

Gene Regulation ◽

Protein Binding ◽

Gene Networks ◽

Dynamic Range ◽

Gene Expression Regulation ◽

Single Layer ◽

Regulation Mechanism ◽

Gene Circuits ◽

Synthetic Dna

AbstractVersatile tools for gene expression regulation are vital for engineering gene networks of increasing scales and complexity with bespoke responses. Here, we investigate and repurpose a ubiquitous, indirect gene regulation mechanism from nature, which uses decoy protein-binding DNA sites, named DNA sponge, to modulate target gene expression in Escherichia coli. We show that synthetic DNA sponges can be designed to reshape the response profiles of gene circuits, lending multifaceted tuning capacities including reducing basal leakage by >20-fold, increasing system output amplitude by >130-fold and dynamic range by >70-fold, and mitigating host growth inhibition by >20%. Further, multi-layer DNA sponges for decoying multiple regulatory proteins provide an additive tuning effect on the responses of layered circuits compared to single-layer sponges. Our work shows synthetic DNA sponges offer a simple yet generalizable route to systematically engineer the performance of synthetic gene circuits, expanding the current toolkit for gene regulation with broad potential applications.

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Gene regulation inDrosophila spermatogenesis: Analysis of protein binding at the translational control element TCE

Developmental Genetics ◽

10.1002/dvg.1020140606 ◽

1993 ◽

Vol 14 (6) ◽

pp. 449-459 ◽

Cited By ~ 23

Author(s):

Elisabeth Kempe ◽

Beate Muhs ◽

Mireille Schäfer

Keyword(s):

Gene Regulation ◽

Protein Binding ◽

Translational Control ◽

Control Element

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A perspective on the molecular simulation of DNA from structural and functional aspects

Chemical Science ◽

10.1039/d0sc05329e ◽

2021 ◽

Author(s):

Manas Mondal ◽

Lijiang Yang ◽

Zhicheng Cai ◽

Piya Patra ◽

Yi Qin Gao

Keyword(s):

Gene Regulation ◽

Environmental Factors ◽

Protein Binding ◽

Structural Organization ◽

Atomistic Simulations ◽

Dna Interactions ◽

Structure And Dynamics ◽

Functional Aspects ◽

Protein Dna Interactions ◽

Base Modifications

An overview of atomistic simulations on the effect of sequences, base modifications, environmental factors and protein binding on DNA’s hierarchical structure and dynamics in the context of protein–DNA interactions, gene regulation and structural organization of chromatin.

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