Anopheles mosquitoes reveal new principles of 3D genome organization in insects

Varvara Lukyanchikova, Miroslav Nuriddinov, Polina Belokopytova, Alena Taskina, Jiangtao Liang, Maarten J. M. F. Reijnders, Livio Ruzzante, Romain Feron, Robert M. Waterhouse, Yang Wu, Chunhong Mao, Zhijian Tu, Igor V. Sharakhov () and Veniamin Fishman ()
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Varvara Lukyanchikova: Virginia Polytechnic Institute and State University
Miroslav Nuriddinov: Institute of Cytology and Genetics SB RAS
Polina Belokopytova: Institute of Cytology and Genetics SB RAS
Alena Taskina: Institute of Cytology and Genetics SB RAS
Jiangtao Liang: Virginia Polytechnic Institute and State University
Maarten J. M. F. Reijnders: University of Lausanne and Swiss Institute of Bioinformatics
Livio Ruzzante: University of Lausanne and Swiss Institute of Bioinformatics
Romain Feron: University of Lausanne and Swiss Institute of Bioinformatics
Robert M. Waterhouse: University of Lausanne and Swiss Institute of Bioinformatics
Yang Wu: Virginia Polytechnic Institute and State University
Chunhong Mao: University of Virginia
Zhijian Tu: Virginia Polytechnic Institute and State University
Igor V. Sharakhov: Virginia Polytechnic Institute and State University
Veniamin Fishman: Institute of Cytology and Genetics SB RAS

Nature Communications, 2022, vol. 13, issue 1, 1-22

Abstract: Abstract Chromosomes are hierarchically folded within cell nuclei into territories, domains and subdomains, but the functional importance and evolutionary dynamics of these hierarchies are poorly defined. Here, we comprehensively profile genome organizations of five Anopheles mosquito species and show how different levels of chromatin architecture influence each other. Patterns observed on Hi-C maps are associated with known cytological structures, epigenetic profiles, and gene expression levels. Evolutionary analysis reveals conservation of chromatin architecture within synteny blocks for tens of millions of years and enrichment of synteny breakpoints in regions with increased genomic insulation. However, in-depth analysis shows a confounding effect of gene density on both insulation and distribution of synteny breakpoints, suggesting limited causal relationship between breakpoints and regions with increased genomic insulation. At the level of individual loci, we identify specific, extremely long-ranged looping interactions, conserved for ~100 million years. We demonstrate that the mechanisms underlying these looping contacts differ from previously described Polycomb-dependent interactions and clustering of active chromatin.

Date: 2022
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DOI: 10.1038/s41467-022-29599-5

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