Trisomy of a Down Syndrome Critical Region Globally Amplifies Transcription via HMGN1 Overexpression

Cell Rep. 2018 Nov 13;25(7):1898-1911.e5. doi: 10.1016/j.celrep.2018.10.061.


Down syndrome (DS, trisomy 21) is associated with developmental abnormalities and increased leukemia risk. To reconcile chromatin alterations with transcriptome changes, we performed paired exogenous spike-in normalized RNA and chromatin immunoprecipitation sequencing in DS models. Absolute normalization unmasks global amplification of gene expression associated with trisomy 21. Overexpression of the nucleosome binding protein HMGN1 (encoded on chr21q22) recapitulates transcriptional changes seen with triplication of a Down syndrome critical region on distal chromosome 21, and HMGN1 is necessary for B cell phenotypes in DS models. Absolute exogenous-normalized chromatin immunoprecipitation sequencing (ChIP-Rx) also reveals a global increase in histone H3K27 acetylation caused by HMGN1. Transcriptional amplification downstream of HMGN1 is enriched for stage-specific programs of B cells and B cell acute lymphoblastic leukemia, dependent on the developmental cellular context. These data offer a mechanistic explanation for DS transcriptional patterns and suggest that further study of HMGN1 and RNA amplification in diverse DS phenotypes is warranted.

Keywords: B cells; ChIP-Rx; DSCR; Down syndrome; Down syndrome critical region; HMGN1; RNA sequencing; leukemia; spike-in normalization; transcriptional amplification; trisomy 21.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acetylation
  • Animals
  • B-Lymphocytes / metabolism
  • Cell Line
  • Down Syndrome / genetics*
  • Genome
  • HMGN1 Protein / genetics*
  • HMGN1 Protein / metabolism
  • Histones / metabolism
  • Humans
  • Lysine / metabolism
  • Mice, Inbred C57BL
  • Models, Genetic
  • Nucleosomes / metabolism
  • Phenotype
  • RNA / genetics
  • Transcription, Genetic*
  • Transcriptome / genetics
  • Trisomy / genetics*
  • Up-Regulation / genetics


  • HMGN1 Protein
  • Histones
  • Nucleosomes
  • RNA
  • Lysine

Supplementary concepts

  • Down Syndrome Critical Region