NF90/ILF3 is a transcription factor that promotes proliferation over differentiation by hierarchical regulation in K562 erythroleukemia cells

PLoS One. 2018 Mar 28;13(3):e0193126. doi: 10.1371/journal.pone.0193126. eCollection 2018.

Abstract

NF90 and splice variant NF110 are DNA- and RNA-binding proteins encoded by the Interleukin enhancer-binding factor 3 (ILF3) gene that have been established to regulate RNA splicing, stabilization and export. The roles of NF90 and NF110 in regulating transcription as chromatin-interacting proteins have not been comprehensively characterized. Here, chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) identified 9,081 genomic sites specifically occupied by NF90/NF110 in K562 cells. One third of NF90/NF110 peaks occurred at promoters of annotated genes. NF90/NF110 occupancy colocalized with chromatin marks associated with active promoters and strong enhancers. Comparison with 150 ENCODE ChIP-seq experiments revealed that NF90/NF110 clustered with transcription factors exhibiting preference for promoters over enhancers (POLR2A, MYC, YY1). Differential gene expression analysis following shRNA knockdown of NF90/NF110 in K562 cells revealed that NF90/NF110 activates transcription factors that drive growth and proliferation (EGR1, MYC), while attenuating differentiation along the erythroid lineage (KLF1). NF90/NF110 associates with chromatin to hierarchically regulate transcription factors that promote proliferation and suppress differentiation.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Base Sequence
  • Cell Differentiation / genetics*
  • Cell Proliferation / genetics*
  • Chromatin / genetics
  • Chromatin / metabolism
  • Enhancer Elements, Genetic / genetics
  • Gene Expression Profiling / methods
  • Gene Expression Regulation, Leukemic*
  • Humans
  • K562 Cells
  • Leukemia, Erythroblastic, Acute / genetics
  • Leukemia, Erythroblastic, Acute / metabolism
  • Leukemia, Erythroblastic, Acute / pathology
  • Nuclear Factor 90 Proteins / genetics*
  • Nuclear Factor 90 Proteins / metabolism
  • Promoter Regions, Genetic / genetics
  • Protein Binding
  • RNA Interference

Substances

  • Chromatin
  • Nuclear Factor 90 Proteins