Integration of high-throughput reporter assays identify a critical enhancer of the Ikzf1 gene

PLoS One. 2020 May 26;15(5):e0233191. doi: 10.1371/journal.pone.0233191. eCollection 2020.

Abstract

The Ikzf1 locus encodes the lymphoid specific transcription factor Ikaros, which plays an essential role in both T and B cell differentiation, while deregulation or mutation of IKZF1/Ikzf1 is involved in leukemia. Tissue-specific and cell identity genes are usually associated with clusters of enhancers, also called super-enhancers, which are believed to ensure proper regulation of gene expression throughout cell development and differentiation. Several potential regulatory regions have been identified in close proximity of Ikzf1, however, the full extent of the regulatory landscape of the Ikzf1 locus is not yet established. In this study, we combined epigenomics and transcription factor binding along with high-throughput enhancer assay and 4C-seq to prioritize an enhancer element located 120 kb upstream of the Ikzf1 gene. We found that deletion of the E120 enhancer resulted in a significant reduction of Ikzf1 mRNA. However, the epigenetic landscape and 3D topology of the locus were only slightly affected, highlighting the complexity of the regulatory landscape regulating the Ikzf1 locus.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Line
  • Enhancer Elements, Genetic / physiology*
  • Epigenomics
  • Gene Expression Regulation / physiology*
  • Genes, Reporter
  • Genetic Loci / physiology*
  • Ikaros Transcription Factor / biosynthesis*
  • Ikaros Transcription Factor / genetics
  • Mice
  • RNA, Messenger / biosynthesis
  • RNA, Messenger / genetics

Substances

  • RNA, Messenger
  • Zfpn1a1 protein, mouse
  • Ikaros Transcription Factor

Grant support

We thank the Transcriptomics and Genomics Marseille-Luminy (TGML) platform for sequencing the ChIP-seq samples and the Marseille-Luminy cell biology platform for the management of cell culture. Sequencing of 4C samples was performed by the IGBMC GenomEast platform. TGML and GenomEast platforms are member of the France Genomique consortium (ANR-10-INBS-0009). Work in the laboratory of S.S. was supported by recurrent funding from INSERM and Aix-Marseille University and specific grants from the Ligue contre le Cancer (Equipe Labellisée LIGUE 2018), the Agence Nationale pour la Recherche, ANR (ANR-17-CE12-0035; ANR-18-CE12-0019), Cancéropôle PACA, Institut National contre le Cancer (PLBIO018-031 INCA_12619), the Excellence Initiative of Aix-Marseille University - A*Midex, a French “Investissements d’Avenir” programme (ANR-11-IDEX-0001-02). Work in the lab of TS is supported by funds from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Starting Grant 678624 - CHROMTOPOLOGY), the ATIP-Avenir program, and the grant ANR-10-LABX-0030-INRT, a French State fund managed by the Agence Nationale de la Recherche under the frame program Investissements d’Avenir ANR-10-IDEX-0002-02. AMM is supported by funds from IDEX (University of Strasbourg) and the Institut National du Cancer. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.