Non-coding-regulatory regions of human brain genes delineated by bacterial artificial chromosome knock-in mice

BMC Biol. 2013 Oct 14;11:106. doi: 10.1186/1741-7007-11-106.


Background: The next big challenge in human genetics is understanding the 98% of the genome that comprises non-coding DNA. Hidden in this DNA are sequences critical for gene regulation, and new experimental strategies are needed to understand the functional role of gene-regulation sequences in health and disease. In this study, we build upon our HuGX ('high-throughput human genes on the X chromosome') strategy to expand our understanding of human gene regulation in vivo.

Results: In all, ten human genes known to express in therapeutically important brain regions were chosen for study. For eight of these genes, human bacterial artificial chromosome clones were identified, retrofitted with a reporter, knocked single-copy into the Hprt locus in mouse embryonic stem cells, and mouse strains derived. Five of these human genes expressed in mouse, and all expressed in the adult brain region for which they were chosen. This defined the boundaries of the genomic DNA sufficient for brain expression, and refined our knowledge regarding the complexity of gene regulation. We also characterized for the first time the expression of human MAOA and NR2F2, two genes for which the mouse homologs have been extensively studied in the central nervous system (CNS), and AMOTL1 and NOV, for which roles in CNS have been unclear.

Conclusions: We have demonstrated the use of the HuGX strategy to functionally delineate non-coding-regulatory regions of therapeutically important human brain genes. Our results also show that a careful investigation, using publicly available resources and bioinformatics, can lead to accurate predictions of gene expression.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amacrine Cells / cytology
  • Amacrine Cells / metabolism
  • Animals
  • Brain / metabolism*
  • COUP Transcription Factor II / genetics
  • Central Nervous System / metabolism
  • Chromosomes, Artificial, Bacterial / genetics*
  • Chromosomes, Human, X / genetics*
  • Computational Biology
  • Embryonic Stem Cells / cytology
  • Embryonic Stem Cells / metabolism
  • Gene Deletion
  • Gene Expression Regulation
  • Gene Knock-In Techniques
  • Genetic Loci
  • Genome, Human
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Membrane Proteins / genetics
  • Mice
  • Monoamine Oxidase / genetics
  • Nephroblastoma Overexpressed Protein / genetics
  • Regulatory Sequences, Nucleic Acid*
  • Retinal Ganglion Cells / cytology
  • Retinal Ganglion Cells / metabolism


  • AMOTL1 protein, human
  • CCN3 protein, human
  • COUP Transcription Factor II
  • Membrane Proteins
  • NR2F2 protein, human
  • Nephroblastoma Overexpressed Protein
  • Monoamine Oxidase
  • monoamine oxidase A, human