Using next-generation RNA sequencing to identify imprinted genes View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2014-03-12

AUTHORS

X Wang, A G Clark

ABSTRACT

Genomic imprinting is manifested as differential allelic expression (DAE) depending on the parent-of-origin. The most direct way to identify imprinted genes is to directly score the DAE in a context where one can identify which parent transmitted each allele. Because many genes display DAE, simply scoring DAE in an individual is not sufficient to identify imprinted genes. In this paper, we outline many technical aspects of a scheme for identification of imprinted genes that makes use of RNA sequencing (RNA-seq) from tissues isolated from F1 offspring derived from the pair of reciprocal crosses. Ideally, the parental lines are from two inbred strains that are not closely related to each other. Aspects of tissue purity, RNA extraction, library preparation and bioinformatic inference of imprinting are all covered. These methods have already been applied in a number of organisms, and one of the most striking results is the evolutionary fluidity with which novel imprinted genes are gained and lost within genomes. The general methodology is also applicable to a wide range of other biological problems that require quantification of allele-specific expression using RNA-seq, such as cis-regulation of gene expression, X chromosome inactivation and random monoallelic expression. More... »

PAGES

156-166

References to SciGraph publications

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  • 2002. Quantitative RT-PCR-Based Analysis of Allele-Specific Gene Expression in GENOMIC IMPRINTING
  • 2002-05-28. Aberrant patterns of X chromosome inactivation in bovine clones in NATURE GENETICS
  • 2004-12. Conservation of genomic imprinting at the XIST, IGF2, and GTL2 loci in the bovine in MAMMALIAN GENOME
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  • 2012-07-21. A survey of tissue-specific genomic imprinting in mammals in MOLECULAR GENETICS AND GENOMICS
  • 2007-10-23. A genome-wide approach to identifying novel-imprinted genes in HUMAN GENETICS
  • 1976-08. Non-random inactivation of X chromosome in the rat yolk sac in NATURE
  • 2009-12-09. Mechanisms and evolution of genomic imprinting in plants in HEREDITY
  • 2001-01-01. Genomic imprinting: parental influence on the genome in NATURE REVIEWS GENETICS
  • 2011-03-21. Genome-wide assessment of imprinted expression in human cells in GENOME BIOLOGY
  • 2002-09-13. A novel approach for identifying candidate imprinted genes through sequence analysis of imprinted and control genes in HUMAN GENETICS
  • 2012-05-15. Mechanisms and consequences of widespread random monoallelic expression in NATURE REVIEWS GENETICS
  • 2001-10. Microarray expression profiling of tissues from mice with uniparental duplications of Chromosomes 7 and 11 to identify imprinted genes in MAMMALIAN GENOME
  • 2010-03-10. Transcriptome genetics using second generation sequencing in a Caucasian population in NATURE
  • 2012-07-17. Insights on Imprinting from Beyond Mice and Men in GENOMIC IMPRINTING
  • 2012-07-17. Nonmammalian Parent-of-Origin Effects in GENOMIC IMPRINTING
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/hdy.2014.18

    DOI

    http://dx.doi.org/10.1038/hdy.2014.18

    DIMENSIONS

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/24619182


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