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Advances in the identification and analysis of allele-specific expression

Advances in the identification and analysis of allele-specific expression
Advances in the identification and analysis of allele-specific expression
Allele-specific expression (ASE) is essential for normal development and many cellular processes but, if impaired, can result in disease. ASE is a feature of organisms with genomes consisting of more than one set of homologous chromosomes. The higher the number of chromosome sets (ploidy) per cell, the higher the potential complexity of ASE. Humans, for instance, are diploid (except germ cells, which are haploid), resulting in multiple possible expression states in time and space for each set of alleles. ASE is invoked and modulated by both genetic and epigenetic changes, affecting the underlying DNA sequence or chromatin of each allele, respectively. Although numerous methods have been developed to assay ASE, they usually require RNA to be available and are dependent upon genetic polymorphisms (such as single nucleotide polymorphisms (SNPs)) to differentiate between allelic transcripts. The rapid convergence to second-generation sequencing as the method of choice to examine genomic, epigenomic and transcriptomic data enables an integrated and more general approach to define and predict ASE, independent of SNPs. This 'Omni-Seq' approach has the potential to advance our understanding of the biology and pathophysiology of ASE-mediated processes by elucidating subtle combinatorial effects, leading to the accurate delineation of sub-phenotypes with consequential benefit for improved insight into disease etiology.
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Bell, Christopher G.
44982df7-0746-4cdb-bed1-0bdfe68f1a64
Beck, Stephan
50f0c07a-19a8-4bca-adbc-af41a3800412
Bell, Christopher G.
44982df7-0746-4cdb-bed1-0bdfe68f1a64
Beck, Stephan
50f0c07a-19a8-4bca-adbc-af41a3800412

Bell, Christopher G. and Beck, Stephan (2009) Advances in the identification and analysis of allele-specific expression. Genome Medicine, 1 (5), 56. (doi:10.1186/gm56). (PMID:19490587)

Record type: Article

Abstract

Allele-specific expression (ASE) is essential for normal development and many cellular processes but, if impaired, can result in disease. ASE is a feature of organisms with genomes consisting of more than one set of homologous chromosomes. The higher the number of chromosome sets (ploidy) per cell, the higher the potential complexity of ASE. Humans, for instance, are diploid (except germ cells, which are haploid), resulting in multiple possible expression states in time and space for each set of alleles. ASE is invoked and modulated by both genetic and epigenetic changes, affecting the underlying DNA sequence or chromatin of each allele, respectively. Although numerous methods have been developed to assay ASE, they usually require RNA to be available and are dependent upon genetic polymorphisms (such as single nucleotide polymorphisms (SNPs)) to differentiate between allelic transcripts. The rapid convergence to second-generation sequencing as the method of choice to examine genomic, epigenomic and transcriptomic data enables an integrated and more general approach to define and predict ASE, independent of SNPs. This 'Omni-Seq' approach has the potential to advance our understanding of the biology and pathophysiology of ASE-mediated processes by elucidating subtle combinatorial effects, leading to the accurate delineation of sub-phenotypes with consequential benefit for improved insight into disease etiology.

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Published date: 29 May 2009
Organisations: Human Development & Health, Centre for Biological Sciences, MRC Life-Course Epidemiology Unit

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Local EPrints ID: 400992
URI: https://eprints.soton.ac.uk/id/eprint/400992
PURE UUID: 8dfde3c6-1229-4d26-b848-1b0164639728
ORCID for Christopher G. Bell: ORCID iD orcid.org/0000-0003-4601-1242

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Date deposited: 03 Oct 2016 10:24
Last modified: 05 Nov 2019 01:34

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