3D genome organisation in Drosophila

Moretti, C.; Stévant, Isabelle; Ghavi-Helm, Yad

doi:10.1093/bfgp/elz029

Cited by 17 publications

(20 citation statements)

References 103 publications

(198 reference statements)

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“…S4). This suggests that, similarly to mammalian domain architecture, additional factors such as insulator proteins modulate domain organisation in Drosophila (Mateo et al, 2019;Moretti et al, 2020).…”

Section: Discussionmentioning

confidence: 94%

Independence of 3D chromatin conformation and gene regulation during Drosophila dorsoventral patterning

Ing-Simmons

Vaid

Mannervik

et al. 2020

Preprint

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ABSTRACTThe relationship between the 3D organisation of chromatin inside the nucleus and the regulation of gene expression remains unclear. While disruption of domains and domain boundaries can lead to mis-expression of developmental genes, acute depletion of key regulators of genome organisation, such as CTCF and cohesin, and major reorganisation of genomic regions have relatively small effects on gene expression. Therefore, it is unclear whether changes in gene expression and chromatin state drive chromatin reorganisation, or whether changes in chromatin organisation facilitate cell type-specific activation of genes and their regulatory elements. Here, using the Drosophila melanogaster dorsoventral patterning system as a model, we demonstrate the independence of 3D chromatin organisation and developmental gene regulation. We define tissue-specific enhancers and link them to expression patterns at the single-cell level using single cell RNA-seq. Surprisingly, despite tissue-specific differences in chromatin state and gene expression, 3D chromatin organisation is maintained across tissues. Our results provide strong evidence that tissue-specific chromatin conformation is not required for tissue-specific gene expression, but rather acts as an architectural framework to facilitate proper gene regulation during development.

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Section: Discussionmentioning

confidence: 94%

Independence of 3D chromatin conformation and gene regulation during Drosophila dorsoventral patterning

Ing-Simmons

Vaid

Mannervik

et al. 2020

Preprint

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“…In Anopheles spp., the nuclear envelope attachment has been proposed to reduce topological entanglement of chromosomes (George et al, 2020;Lukyanchikova et al, 2020), and Hi-C data supports a Rabl-like configuration, as in Drosophila (Moretti et al, 2020). This is characterized by the clustering of centromeres and telomeres to the nuclear envelope at opposite poles of the nucleus, and the more elongated shape of the chromosome territories (Wilkie et al, 1999;Lukyanchikova et al, 2020; Figure 1B).…”

Section: D Genome Organizationmentioning

confidence: 53%

“…The Hi-C FIGURE 1 | The regulatory genome of mosquitoes. (A) In Anopheles mosquitoes, as previously described for Drosophila (Moretti et al, 2020), the attachment of the chromatin fiber to the nuclear envelope and lamina contributes to the organization and functional 3D structure of the genome, and it determines the contact frequencies between and within chromosomes (George et al, 2020;Lukyanchikova et al, 2020). (B) The Rabl-like configuration described in Anopheles spp.…”

Section: D Genome Organizationmentioning

confidence: 98%

Chromatin Structure and Function in Mosquitoes

et al. 2020

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The principles and function of chromatin and nuclear architecture have been extensively studied in model organisms, such as Drosophila melanogaster. However, little is known about the role of these epigenetic processes in transcriptional regulation in other insects including mosquitoes, which are major disease vectors and a worldwide threat for human health. Some of these life-threatening diseases are malaria, which is caused by protozoan parasites of the genus Plasmodium and transmitted by Anopheles mosquitoes; dengue fever, which is caused by an arbovirus mainly transmitted by Aedes aegypti; and West Nile fever, which is caused by an arbovirus transmitted by Culex spp. In this contribution, we review what is known about chromatin-associated mechanisms and the 3D genome structure in various mosquito vectors, including Anopheles, Aedes, and Culex spp. We also discuss the similarities between epigenetic mechanisms in mosquitoes and the model organism Drosophila melanogaster, and advocate that the field could benefit from the cross-application of state-of-the-art functional genomic technologies that are well-developed in the fruit fly. Uncovering the mosquito regulatory genome can lead to the discovery of unique regulatory networks associated with the parasitic life-style of these insects. It is also critical to understand the molecular interactions between the vectors and the pathogens that they transmit, which could hold the key to major breakthroughs on the fight against mosquito-borne diseases. Finally, it is clear that epigenetic mechanisms controlling mosquito environmental plasticity and evolvability are also of utmost importance, particularly in the current context of globalization and climate change.

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“…Several proteins previously known for other functions in the genome have been implicated in insulator function in recent years, such as Clamp [ 13 ], Nup98 [ 14 ] and Insv [ 15 ]. Some proteins without DNA binding activity, such as fly Chriz and enhancer of yellow 2, are also involved in insulator functioning [ 16 ], and appear to act by engaging in interactions with DNA-binding proteins.…”

Section: The Discovery Of Insulators and Their Key Characteristicsmentioning

confidence: 99%

Insulators in Plants: Progress and Open Questions

Kurbidaeva

Purugganan

2021

Genes

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The genomes of higher eukaryotes are partitioned into topologically associated domains or TADs, and insulators (also known as boundary elements) are the key elements responsible for their formation and maintenance. Insulators were first identified and extensively studied in Drosophila as well as mammalian genomes, and have also been described in yeast and plants. In addition, many insulator proteins are known in Drosophila, and some have been investigated in mammals. However, much less is known about this important class of non-coding DNA elements in plant genomes. In this review, we take a detailed look at known plant insulators across different species and provide an overview of potential determinants of plant insulator functions, including cis-elements and boundary proteins. We also discuss methods previously used in attempts to identify plant insulators, provide a perspective on their importance for research and biotechnology, and discuss areas of potential future research.

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3D genome organisation in Drosophila

Cited by 17 publications

References 103 publications

Independence of 3D chromatin conformation and gene regulation during Drosophila dorsoventral patterning

Independence of 3D chromatin conformation and gene regulation during Drosophila dorsoventral patterning

Chromatin Structure and Function in Mosquitoes

Insulators in Plants: Progress and Open Questions

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