Academic journal article Genetics

Genes and Small RNA Transcripts Exhibit Dosage-Dependent Expression Pattern in Maize Copy-Number Alterations

Academic journal article Genetics

Genes and Small RNA Transcripts Exhibit Dosage-Dependent Expression Pattern in Maize Copy-Number Alterations

Article excerpt

DNA copy-number alterations, whether involving chromosome segments or entire chromosomes, can have dramatic phenotypic impacts. Aneuploidy, one kind of DNA copy-number alteration (Birchler 2013), results from changes of chromosome number, i.e., gain or loss of one or more entire chromosome(s). In most animals aneuploidy is detrimental and may cause severe genetic disorders. In humans, the gain of a single extra copy of chromosome 21 (trisomy 21) causes Down syndrome; most other aneuploidies result in severe developmental disorders and do not survive to term. For instance, most spontaneous abortions and developmental abnormalities in humans are caused by aneuploidy (Hassold and Hunt 2001). In addition, many human cancer cells are highly aneuploid, although the mutual causality of aneuploidy and tumorigenesis is still unclear (Weaver and Cleveland 2007). However, aneuploidy in plants is typically far less detrimental. Trisomics for each of the chromosomes have been recovered in several plant species, and even monosomics for all of the 10 maize chromosomes have been recovered and are viable (Weber 1994).

In contrast to the severe effects of aneuploidy, other copynumber alterations such as segmental aneuploidy and copynumber variation (CNV) often have milder phenotypic effects, which may facilitate their retention and possible accumulation in a population. CNV, involving segments of 1 kb to 1 Mb in size (Birchler 2013), is widespread across many species including mammals (Iafrate et al. 2004; Sebat et al. 2004; Redon et al. 2006) and major crop plants (Springer et al. 2009; Lai et al. 2010; Swanson-Wagner et al. 2010; Saintenac et al. 2011; P. Yu et al. 2011; Zheng et al. 2011; Jiao et al. 2012; McHale et al. 2012). For example, .10% of the human genome is composed of CNVs and segmental duplications with sizes ranging from a few kb to several Mb (Iafrate et al. 2004; Sebat et al. 2004; Redon et al. 2006; Stankiewicz and Lupski 2010). In rice, tandem-arrayed genes account for up to 20% of the duplicated genes (Rizzon et al. 2006).

In addition to the effects of CNV and segmental duplications on creating genomic diversity, CNV and segmental duplications in eukaryotes can dramatically affect organismal phenotype. For example, gain or loss of one copy of human 1q21.1, a genomic region associated with developmental abnormalities (O'Donovan et al. 2008), confers a higher risk of mental disorders (Stefansson et al. 2008, 2009). In addition, microdeletion or microduplication of human 16p11.2 has an association with autism (Weiss et al. 2008). CNV can be advantageous as well. For instance, changes in copy number of an amylase gene (AMY2B) greatly facilitated the adaptation of dogs to starchrich diets associated with domestication (Axelsson et al. 2013), and increased copy number of the human AMY1 gene may aid the digestion of starchy foods (Perry et al. 2007). In plants, several important traits are directly affected by CNV (Xiao et al. 2008; Cook et al. 2012; Diaz et al. 2012; Li et al. 2012; Maron et al. 2013). For example, a recent study in rice showed that a tandem duplication that increases copy number of the GL7 locus has a significant effect on grain length (Wang et al. 2015). However, despite the fact that CNV and segmental duplications are pervasive and often have major effects, the question of precisely how copy-number alterations affect gene expression and contribute to phenotypic diversity remains largely unanswered.

Dosage compensation and dosage sensitivity are two major responses of gene expression to changes in DNA dosage (Guo et al. 1996; Gupta et al. 2006; Birchler 2010; Birchler and Veitia 2012). Several recent studies in humans and plants showed that the change in the expression of genes with altered copy number is a causative factor for the phenotypic impact of CNV (Golzio et al. 2012; Li et al. 2012). Specifically, elevated expression [messenger RNA (mRNA) and/or protein levels] of genes located within the trisomy or segmental trisomy region is largely responsible for the aneuploid syndromes (Kahlem et al. …

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