1. Biochemistry and Chemical Biology
  2. Chromosomes and Gene Expression
Download icon

Basis of specificity for a conserved and promiscuous chromatin remodeling protein

Research Article
  • Cited 0
  • Views 5,715
  • Annotations
Cite this article as: eLife 2021;10:e64061 doi: 10.7554/eLife.64061

Abstract

Eukaryotic genomes are organized dynamically through the repositioning of nucleosomes. Isw2 is an enzyme that has been previously defined as a genome-wide, non-specific nucleosome spacing factor. Here, we show that Isw2 instead acts as an obligately targeted nucleosome remodeler in vivo through physical interactions with sequence-specific factors. We demonstrate that Isw2- recruiting factors use small and previously uncharacterized epitopes, which direct Isw2 activity through highly conserved acidic residues in the Isw2 accessory protein Itc1. This interaction orients Isw2 on target nucleosomes, allowing for precise nucleosome positioning at targeted loci. Finally, we show that these critical acidic residues have been lost in the Drosophila lineage, potentially explaining the inconsistently characterized function of Isw2-like proteins. Altogether, these data suggest an 'interacting barrier model' where Isw2 interacts with a sequence-specific factor to accurately and reproducibly position a single, targeted nucleosome to define the precise border of phased chromatin arrays.

Data availability

Sequencing data have been deposited in GEO under accession code GSE149804

The following data sets were generated

Article and author information

Author details

  1. Drake A Donovan

    Institute of Molecular Biology, University of Oregon, Eugene, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Johnathan G Crandall

    Institute of Molecular Biology, University of Oregon, Eugene, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9144-3135
  3. Vi N Truong

    Institute of Molecular Biology, University of Oregon, Eugene, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Abigail L Vaaler

    Institute of Molecular Biology, University of Oregon, Eugene, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Thomas B Bailey

    Institute of Molecular Biology, University of Oregon, Eugene, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Devin Dinwiddie

    Institute of Molecular Biology, University of Oregon, Eugene, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Orion GB Banks

    Institute of Molecular Biology, University of Oregon, Eugene, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Laura E McKnight

    Institute of Molecular Biology, University of Oregon, Eugene, United States
    For correspondence
    lthom009@gmail.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4322-3066
  9. Jeffrey N McKnight

    Institute of Molecular Biology, University of Oregon, Eugene, United States
    Competing interests
    The authors declare that no competing interests exist.

Funding

National Institutes of Health (T32 GM007759)

  • Drake A Donovan
  • Orion GB Banks

National Institutes of Health (T32 GM007413)

  • Drake A Donovan
  • Vi N Truong

National Institute of General Medical Sciences (R01 GM129242)

  • Jeffrey N McKnight

Donald and Delia Baxter Foundation

  • Jeffrey N McKnight

Medical Research Foundation of Oregon

  • Jeffrey N McKnight

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

Reviewing Editor

  1. Jerry L Workman, Stowers Institute for Medical Research, United States

Publication history

  1. Received: October 15, 2020
  2. Accepted: February 11, 2021
  3. Accepted Manuscript published: February 12, 2021 (version 1)
  4. Version of Record published: March 17, 2021 (version 2)

Copyright

© 2021, Donovan 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

  • 5,715
    Page views
  • 279
    Downloads
  • 0
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

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)

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

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

Further reading

    1. Biochemistry and Chemical Biology
    2. Cell Biology
    Haitao Zhang et al.
    Tools and Resources Updated

    The human kinome comprises 538 kinases playing essential functions by catalyzing protein phosphorylation. Annotation of subcellular distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 cellular compartments. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a similar condition. KA revealed kinase family-enriched subcellular localizations and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other structures. Furthermore, KA demonstrated the role of liquid-liquid phase separation in formation of kinase condensates. Identification of MOK as a mitochondrial kinase revealed its function in cristae dynamics, respiration, and oxidative stress response. Although limited by possible mislocalization due to overexpression or epitope tagging, this subcellular map of the kinome can be used to refine regulatory mechanisms involving protein phosphorylation.

    1. Biochemistry and Chemical Biology
    2. Cell Biology
    Fatima Alghoul et al.
    Research Article

    During embryogenesis, Hox mRNA translation is tightly regulated by a sophisticated molecular mechanism that combines two RNA regulons located in their 5’UTR. First, an internal ribosome entry site (IRES) enables cap-independent translation. The second regulon is a translation inhibitory element or TIE, which ensures concomitant cap-dependent translation inhibition. In this study, we deciphered the molecular mechanisms of mouse Hoxa3 and Hoxa11 TIEs. Both TIEs possess an upstream open reading frame (uORF) that is critical to inhibit cap-dependent translation. However, the molecular mechanisms used are different. In Hoxa3 TIE, we identify an uORF which inhibits cap-dependent translation and we show the requirement of the non-canonical initiation factor eIF2D for this process. The mode of action of Hoxa11 TIE is different, it also contains an uORF but it is a minimal uORF formed by an uAUG followed immediately by a stop codon, namely a ‘start-stop’. The ‘start-stop’ sequence is species-specific and in mice, is located upstream of a highly stable stem loop structure which stalls the 80S ribosome and thereby inhibits cap-dependent translation of Hoxa11 main ORF.