Exploration of CTCF post-translation modifications uncovers Serine-224 phosphorylation by PLK1 at pericentric regions during the G2/M transition

  1. Brian C del Rosario
  2. Andrea J Kriz
  3. Amanda M del Rosario
  4. Anthony Anselmo
  5. Christopher J Fry
  6. Forest M White
  7. Ruslan I Sadreyev
  8. Jeannie T Lee  Is a corresponding author
  1. Massachusetts General Hospital, United States
  2. Koch Institute for Integrative Cancer Research at MIT, United States
  3. Cell Signaling Technologies, United States

Abstract

The zinc finger CCCTC-binding protein (CTCF) carries out many functions in the cell. Although previous studies sought to explain CTCF multivalency based on sequence composition of binding sites, few examined how CTCF post-translational modification (PTM) could contribute to function. Here, we performed CTCF mass spectrometry, identified a novel phosphorylation site at Serine 224 (Ser224-P), and demonstrate that phosphorylation is carried out by Polo kinase 1 (PLK1). CTCF Ser224-P is chromatin-associated, mapping to at least a subset of known CTCF sites. CTCF Ser224-P accumulates during the G2/M transition of the cell cycle and is enriched at pericentric regions. The phospho-obviation mutant, S224A, appeared normal. However, the phospho-mimic mutant, S224E, is detrimental to mouse embryonic stem cell colonies. While ploidy and chromatin architecture appear unaffected, S224E mutants differentially express of hundreds of genes, including p53 and p21. We have thus identified a new CTCF PTM and provided evidence of biological function.

Data availability

High-throughput sequencing data are available in the National Center for Biotechnology Information GEO repository under accession GSE119697

The following data sets were generated

Article and author information

Author details

  1. Brian C del Rosario

    Department of Molecular Biology, Massachusetts General Hospital, Boston, United States
    Competing interests
    No competing interests declared.
  2. Andrea J Kriz

    Department of Molecular Biology, Massachusetts General Hospital, Boston, United States
    Competing interests
    No competing interests declared.
  3. Amanda M del Rosario

    Koch Institute for Integrative Cancer Research at MIT, Cambridge, United States
    Competing interests
    No competing interests declared.
  4. Anthony Anselmo

    Department of Molecular Biology, Massachusetts General Hospital, Boston, United States
    Competing interests
    No competing interests declared.
  5. Christopher J Fry

    Cell Signaling Technologies, Danvers, United States
    Competing interests
    No competing interests declared.
  6. Forest M White

    Koch Institute for Integrative Cancer Research at MIT, Cambridge, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1545-1651
  7. Ruslan I Sadreyev

    Department of Molecular Biology, Massachusetts General Hospital, Boston, United States
    Competing interests
    No competing interests declared.
  8. Jeannie T Lee

    Department of Molecular Biology, Massachusetts General Hospital, Boston, United States
    For correspondence
    lee@molbio.mgh.harvard.edu
    Competing interests
    Jeannie T Lee, Reviewing editor, eLifecofounder and member of the Scientific Advisory Boards of Translate Bio and Fulcrum Therapeutics.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7786-8850

Funding

Howard Hughes Medical Institute

  • Jeannie T Lee

National Institutes of Health (R37-GM58839)

  • Jeannie T Lee

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

Copyright

© 2019, del Rosario 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

  • 2,709
    views
  • 378
    downloads
  • 21
    citations

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

Download links

Share this article

https://doi.org/10.7554/eLife.42341

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.