Drosophila rDNA Genes Shape the Stable Contacts with the Tlk Gene at the Expression Area of Small RNAs and Affect on Looped Domains inside the Gene

In experiments on mouse and human cells it was demonstrated that rDNA plays an important role in epigenetic regulation of many genes. To identify and study rDNA-contacting genes in Drosophila we used the 4С (circular chromosome conformation capture) approach. We detected very stable contacts of rDNA genes within a 5-kb region inside the Tlk gene residing in X chromosome. This 5-kb region corresponds to small RNAs. After heat shock treatment both the amount of contacts, and the expression level of the gene were increased. Tlk and Rala are genes that share the same short bidirectional promoter but exhibit different expression levels. Around the region of rDNA contacts inside the Tlk gene, looped domains were formed. We conclude that rDNA contact-dependent epigenetic regulation is guided by small RNAs and that the contacts are involved in rearrangements of the looped domains.

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Funding

The study was financially supported by the Russian Foundation for Basic Research (project no. 18-04-00198). Statistical analysis was supported by the Russian Science Foundation (no. 18-14-00122).

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Correspondence to N. A. Tchurikov.

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The authors declare they have no conflict of interest.

The work did not use biological materials obtained from animals or humans.

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Abbreviations: Tlk, serine-threonine kinase gene; Rala, Ras-like protein gene; Hip-r, coshaperone gene stabilizing conformation of Hsp70; RNA sec, deep RNA sequencing; TSS, start of transcription.

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Kretova, O.V., Fedoseeva, D.M., Slovohotov, I.Y. et al. Drosophila rDNA Genes Shape the Stable Contacts with the Tlk Gene at the Expression Area of Small RNAs and Affect on Looped Domains inside the Gene. Mol Biol 54, 391–395 (2020). https://doi.org/10.1134/S0026893320020089

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Keywords:

  • Tlk
  • Rala
  • HIP-R
  • 4C
  • chromosomal contacts
  • rDNA
  • epigenetics
  • deep sequencing
  • RNA-Seq
  • looped domains