Protocol

Genomic Structural Variants

Volume 838 of the series Methods in Molecular Biology pp 173-186

Date:

Structural Variation and Its Effect on Expression

  • Louise HarewoodAffiliated withThe Center for Integrative Genomics, University of Lausanne
  • , Evelyne ChaignatAffiliated withThe Center for Integrative Genomics, University of Lausanne
  • , Alexandre ReymondAffiliated withThe Center for Integrative Genomics, University of Lausanne Email author 

* Final gross prices may vary according to local VAT.

Get Access

Abstract

Structural variation, whether it is caused by copy number variants or present in a balanced form, such as reciprocal translocations and inversions, can have a profound and dramatic effect on the expression of genes mapping within and close to the rearrangement, as well as affecting others genome wide. These effects can be caused by altering the copy number of one or more genes or regulatory elements (dosage effect) or from physical disruption of links between regulatory elements and their associated gene or genes, resulting in perturbation of expression. Similarly, large-scale structural variants can result in genome-wide expression changes by altering the positions that chromosomes occupy within the nucleus, potentially disrupting not only local cis interactions, but also trans interactions that occur throughout the genome. Structural variation is, therefore, a significant factor in the study of gene expression and is discussed here in more detail.

Key words

Structural variation CNV Translocation Inversion Gene expression Position effect