Drosophila SUMM4 complex couples insulator function and DNA replication control

  1. Evgeniya N Andreyeva
  2. Alexander V Emelyanov
  3. Markus Nevil
  4. Lu Sun
  5. Elena Vershilova
  6. Christina A Hill
  7. Michael-C Keogh
  8. Robert J Duronio
  9. Arthur I Skoultchi
  10. Dmitry V Fyodorov  Is a corresponding author
  1. Albert Einstein College of Medicine, United States
  2. University of North Carolina at Chapel Hill, United States
  3. EpiCypher, United States

Abstract

Asynchronous replication of chromosome domains during S phase is essential for eukaryotic genome function, but the mechanisms establishing which domains replicate early versus late in different cell types remain incompletely understood. Intercalary heterochromatin domains replicate very late in both diploid chromosomes of dividing cells and in endoreplicating polytene chromosomes where they are also underrelicated. Drosophila SNF2-related factor SUUR imparts locus-specific underreplication of polytene chromosomes. SUUR negatively regulates DNA replication fork progression; however, its mechanism of action remains obscure. Here we developed a novel method termed MS-Enabled Rapid protein Complex Identification (MERCI) to isolate a stable stoichiometric native complex SUMM4 that comprises SUUR and a chromatin boundary protein Mod(Mdg4)-67.2. Mod(Mdg4) stimulates SUUR ATPase activity and is required for a normal spatiotemporal distribution of SUUR in vivo. SUUR and Mod(Mdg4)-67.2 together mediate the activities of gypsy insulator that prevent certain enhancer-promoter interactions and establish euchromatin-heterochromatin barriers in the genome. Furthermore, SuUR or mod(mdg4) mutations reverse underreplication of intercalary heterochromatin. Thus, SUMM4 can impart late replication of intercalary heterochromatin by attenuating the progression of replication forks through euchromatin/heterochromatin boundaries. Our findings implicate a SNF2 family ATP-dependent motor protein SUUR in the insulator function, reveal that DNA replication can be delayed by a chromatin barrier and uncover a critical role for architectural proteins in replication control. They suggest a mechanism for the establishment of late replication that does not depend on an asynchronous firing of late replication origins.

Data availability

NGS data has been submitted to Gene Expression Omnibus (GEO, accession number GSE189421).

The following data sets were generated

Article and author information

Author details

  1. Evgeniya N Andreyeva

    Department of Cell Biology, Albert Einstein College of Medicine, Bronx, United States
    Competing interests
    No competing interests declared.
  2. Alexander V Emelyanov

    Department of Cell Biology, Albert Einstein College of Medicine, Bronx, United States
    Competing interests
    No competing interests declared.
  3. Markus Nevil

    University of North Carolina at Chapel Hill, Durham, United States
    Competing interests
    No competing interests declared.
  4. Lu Sun

    EpiCypher, Durham, United States
    Competing interests
    Lu Sun, Lu Sun is employed by Epicypher, Inc., a commercial developer and supplier of the EpiDyne® nucleosomes and associated remodeling assay platforms used in this study..
  5. Elena Vershilova

    Department of Cell Biology, Albert Einstein College of Medicine, Bronx, United States
    Competing interests
    No competing interests declared.
  6. Christina A Hill

    Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, United States
    Competing interests
    No competing interests declared.
  7. Michael-C Keogh

    EpiCypher, Durham, United States
    Competing interests
    Michael-C Keogh, Michael C Keogh is employed by Epicypher, Inc., a commercial developer and supplier of the EpiDyne® nucleosomes and associated remodeling assay platforms used in this study..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2219-8623
  8. Robert J Duronio

    Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, United States
    Competing interests
    No competing interests declared.
  9. Arthur I Skoultchi

    Department of Cell Biology, Albert Einstein College of Medicine, New York, United States
    Competing interests
    No competing interests declared.
  10. Dmitry V Fyodorov

    Department of Cell Biology, Albert Einstein College of Medicine, Bronx, United States
    For correspondence
    dmitry.fyodorov@einsteinmed.org
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3080-1787

Funding

National Institutes of Health (R01 GM074233)

  • Dmitry V Fyodorov

National Institutes of Health (R01 GM129244)

  • Arthur I Skoultchi

National Institutes of Health (R01 GM124201)

  • Robert J Duronio

National Institutes of Health (R44 GM123869)

  • Michael-C Keogh

National Institutes of Health (T32 CA217824)

  • Markus Nevil

National Institutes of Health (K12 GM000678)

  • Markus Nevil

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2022, Andreyeva et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 611
    views
  • 129
    downloads
  • 2
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Evgeniya N Andreyeva
  2. Alexander V Emelyanov
  3. Markus Nevil
  4. Lu Sun
  5. Elena Vershilova
  6. Christina A Hill
  7. Michael-C Keogh
  8. Robert J Duronio
  9. Arthur I Skoultchi
  10. Dmitry V Fyodorov
(2022)
Drosophila SUMM4 complex couples insulator function and DNA replication control
eLife 11:e81828.
https://doi.org/10.7554/eLife.81828

Share this article

https://doi.org/10.7554/eLife.81828

Further reading

    1. Chromosomes and Gene Expression
    Shihui Chen, Carolyn Marie Phillips
    Research Article

    RNA interference (RNAi) is a conserved pathway that utilizes Argonaute proteins and their associated small RNAs to exert gene regulatory function on complementary transcripts. While the majority of germline-expressed RNAi proteins reside in perinuclear germ granules, it is unknown whether and how RNAi pathways are spatially organized in other cell types. Here, we find that the small RNA biogenesis machinery is spatially and temporally organized during Caenorhabditis elegans embryogenesis. Specifically, the RNAi factor, SIMR-1, forms visible concentrates during mid-embryogenesis that contain an RNA-dependent RNA polymerase, a poly-UG polymerase, and the unloaded nuclear Argonaute protein, NRDE-3. Curiously, coincident with the appearance of the SIMR granules, the small RNAs bound to NRDE-3 switch from predominantly CSR-class 22G-RNAs to ERGO-dependent 22G-RNAs. NRDE-3 binds ERGO-dependent 22G-RNAs in the somatic cells of larvae and adults to silence ERGO-target genes; here we further demonstrate that NRDE-3-bound, CSR-class 22G-RNAs repress transcription in oocytes. Thus, our study defines two separable roles for NRDE-3, targeting germline-expressed genes during oogenesis to promote global transcriptional repression, and switching during embryogenesis to repress recently duplicated genes and retrotransposons in somatic cells, highlighting the plasticity of Argonaute proteins and the need for more precise temporal characterization of Argonaute-small RNA interactions.

    1. Chromosomes and Gene Expression
    2. Genetics and Genomics
    Steven Henikoff, David L Levens
    Insight

    A new method for mapping torsion provides insights into the ways that the genome responds to the torsion generated by RNA polymerase II.