Systematic analysis of naturally occurring insertions and deletions that alter transcription factor spacing identifies tolerant and sensitive transcription factor pairs

  1. Zeyang Shen
  2. Rick Z Li
  3. Thomas A Prohaska
  4. Marten A Hoeksema
  5. Nathan J Spann
  6. Jenhan Tao
  7. Gregory J Fonseca
  8. Thomas Le
  9. Lindsey K Stolze
  10. Mashito Sakai
  11. Casey E Romanoski
  12. Christopher K Glass  Is a corresponding author
  1. University of California, San Diego, United States
  2. University of Arizona, United States
  3. Nippon Medical School, Japan
  4. University of California San Diego, United States

Abstract

Regulation of gene expression requires the combinatorial binding of sequence-specific transcription factors (TFs) at promoters and enhancers. Prior studies showed that alterations in the spacing between TF binding sites can influence promoter and enhancer activity. However, the relative importance of TF spacing alterations resulting from naturally occurring insertions and deletions (InDels) has not been systematically analyzed. To address this question, we first characterized the genome-wide spacing relationships of 73 TFs in human K562 cells as determined by ChIP-seq. We found a dominant pattern of a relaxed range of spacing between collaborative factors, including 45 TFs exclusively exhibiting relaxed spacing with their binding partners. Next, we exploited millions of InDels provided by genetically diverse mouse strains and human individuals to investigate the effects of altered spacing on TF binding and local histone acetylation. These analyses suggested that spacing alterations resulting from naturally occurring InDels are generally tolerated in comparison to genetic variants directly affecting TF binding sites. To experimentally validate this prediction, we introduced synthetic spacing alterations between PU.1 and C/EBPβ binding sites at six endogenous genomic loci in a macrophage cell line. Remarkably, collaborative binding of PU.1 and C/EBPβ at these locations tolerated changes in spacing ranging from 5-bp increase to >30-bp decrease. Collectively, these findings have implications for understanding mechanisms underlying enhancer selection and for the interpretation of non-coding genetic variation.

Data availability

All sequencing data generated during this study have been deposited in GEO under accession code GSE178080. For reviewer access, please go to https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE178080 and enter token inyjgyqcbrsnrwz into the box.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Zeyang Shen

    Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Rick Z Li

    Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Thomas A Prohaska

    Department of Medicine, University of California, San Diego, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Marten A Hoeksema

    Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Nathan J Spann

    Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Jenhan Tao

    Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Gregory J Fonseca

    Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Thomas Le

    Division of Biological Sciences, University of California, San Diego, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Lindsey K Stolze

    Department of Cellular and Molecular Medicine, University of Arizona, Tucson, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Mashito Sakai

    Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4908-2727
  11. Casey E Romanoski

    Department of Cellular and Molecular Medicine, University of Arizona, Tucson, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0149-225X
  12. Christopher K Glass

    Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, United States
    For correspondence
    ckg@ucsd.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4344-3592

Funding

National Institutes of Health (DK091183)

  • Christopher K Glass

National Institutes of Health (HL147835)

  • Christopher K Glass

Leducq Transatlantic Network (16CVD01)

  • Christopher K Glass

National Institutes of Health (T32DK007044)

  • Thomas A Prohaska

American Heart Association (postdoctoral grant)

  • Marten A Hoeksema

Netherlands Organization for Scientific Research (Rubicon grant)

  • Marten A Hoeksema

Amsterdam Cardiovascular Sciences Institute (postdoctoral grant)

  • Marten A Hoeksema

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

Ethics

Animal experimentation: Bone marrow cells were isolated from femurs and tibias of Cas9-expressing transgenic mice (Jackson Laboratory, No.028555) housed at the University of California San Diego animal facility on a 12-hour/12-hour light/dark cycle with free access to normal chow food and water. All of the mice were handled according to approved institutional animal care and use committee (IACUC) protocols (S01015) of the University of California San Diego to minimize pain and suffering.

Reviewing Editor

  1. Jessica K Tyler, Weill Cornell Medicine, United States

Version history

  1. Preprint posted: April 3, 2020 (view preprint)
  2. Received: June 1, 2021
  3. Accepted: January 12, 2022
  4. Accepted Manuscript published: January 20, 2022 (version 1)
  5. Version of Record published: February 2, 2022 (version 2)

Copyright

© 2022, Shen 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.

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  1. Zeyang Shen
  2. Rick Z Li
  3. Thomas A Prohaska
  4. Marten A Hoeksema
  5. Nathan J Spann
  6. Jenhan Tao
  7. Gregory J Fonseca
  8. Thomas Le
  9. Lindsey K Stolze
  10. Mashito Sakai
  11. Casey E Romanoski
  12. Christopher K Glass
(2022)
Systematic analysis of naturally occurring insertions and deletions that alter transcription factor spacing identifies tolerant and sensitive transcription factor pairs
eLife 11:e70878.
https://doi.org/10.7554/eLife.70878

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