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Mammalian Genome

, Volume 28, Issue 7–8, pp 275–282 | Cite as

CRISPR/Cas9-mediated deletion of lncRNA Gm26878 in the distant Foxf1 enhancer region

  • Przemyslaw Szafranski
  • Justyna A. Karolak
  • Denise Lanza
  • Marzena Gajęcka
  • Jason HeaneyEmail author
  • Paweł StankiewiczEmail author
Article

Abstract

Recent genome editing techniques, including CRISPR mutagenesis screens, offer unparalleled opportunities to study the regulatory non-coding genomic regions, enhancers, promoters, and functional non-coding RNAs. Heterozygous point mutations in FOXF1 and genomic deletion copy-number variants at chromosomal region 16q24.1 involving FOXF1 or its regulatory region mapping ~300 kb upstream of FOXF1 and leaving it intact have been identified in the vast majority of patients with a lethal neonatal lung disease, alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV). Homozygous Foxf1 −/− mice have been shown to die by embryonic day 8.5 because of defects in the development of extraembryonic and lateral mesoderm-derived tissues, whereas heterozygous Foxf1 +/− mice exhibit features resembling ACDMPV. We have previously defined a human lung-specific enhancer region encoding two long non-coding RNAs, LINC01081 and LINC01082, expressed in the lungs. To investigate the biological significance of lncRNAs in the Foxf1 enhancer region, we have generated a CRISPR/Cas9-mediated ~2.4 kb deletion involving the entire lncRNA-encoding gene Gm26878, located in the mouse region syntenic with the human Foxf1 upstream enhancer. Very recently, this mouse genomic region has been shown to function as a Foxf1 enhancer. Our results indicate that homozygous loss of Gm26878 is neonatal lethal with low penetrance. No changes in Foxf1 expression were observed, suggesting that the regulation of Foxf1 expression differs between mouse and human.

Keywords

Transcription Factor Binding Site Genome Editing UCSC Genome Browser Deletion Allele lncRNA Gene 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgements

This work was supported by the National Institutes of Health (Grant No. RO1HL101975) to P.S. and the National Organization for Rare Disorders (Grant No. NORD grants 2012 and 2014) to P.Sz.

Supplementary material

335_2017_9686_MOESM1_ESM.docx (448 kb)
Supplementary material 1 (DOCX 447 KB)
335_2017_9686_MOESM2_ESM.xlsx (12 kb)
Supplementary material 2 (XLSX 12 KB)

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Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  • Przemyslaw Szafranski
    • 1
  • Justyna A. Karolak
    • 1
    • 2
    • 3
  • Denise Lanza
    • 1
  • Marzena Gajęcka
    • 2
    • 3
  • Jason Heaney
    • 1
    Email author
  • Paweł Stankiewicz
    • 1
    Email author
  1. 1.Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUSA
  2. 2.Department of Genetics and Pharmaceutical MicrobiologyPoznan University of Medical SciencesPoznanPoland
  3. 3.Institute of Human GeneticsPolish Academy of SciencesPoznanPoland

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