Genomic imbalance refers to the more severe phenotypic consequences of changing part of a chromosome compared with the whole genome set.Previous genome imbalance studies in maize have identified prevalent inverse modu...Genomic imbalance refers to the more severe phenotypic consequences of changing part of a chromosome compared with the whole genome set.Previous genome imbalance studies in maize have identified prevalent inverse modulation of genes on the unvaried chromosomes(trans)with both the addition or subtraction of chromosome arms.Transposable elements(TEs)comprise a substantial fraction of the genome,and their reaction to genomic imbalance is therefore of interest.Here,we analyzed TE expression using RNA-seq data of aneuploidy and ploidy series and found that most aneuploidies showed an inverse modulation of TEs,but reductions in monosomy and increases in disomy and trisomy were also common.By contrast,the ploidy series showed little TE modulation.The modulation of TEs and genes in the same experimental group were compared,and TEs showed greater modulation than genes,especially in disomy.Class Ⅰ and Ⅱ TEs were differentially modulated in most aneuploidies,and some superfamilies in each TE class also showed differential modulation.Finally,the significantly upregulated TEs in three disomies(TB-7Lb,TB9Lc,and TB-10L19)did not increase the proportion of adjacent gene expression when compared with non-differentially expressed TEs,indicating that modulations of TEs do not compound the effect on genes.These results suggest that the prevalent inverse TE modulation in aneuploidy results from stoichiometric upset of the regulatory machinery used by TEs,similar to the response of core genes to genomic imbalance.展开更多
Aneuploidy has profound effects on an organism,typically more so than polyploidy,and the basis of this contrast is not fully understood.A dosage series of the maize long arm of chromosome 1(1L)was used to compa re rel...Aneuploidy has profound effects on an organism,typically more so than polyploidy,and the basis of this contrast is not fully understood.A dosage series of the maize long arm of chromosome 1(1L)was used to compa re relative global gene expression in diffe rent types and degrees of aneuploidy to gain insights into how the magnitude of genomic imbalance as well as hypoploidy affects global gene expression.While previously available methods require a selective examination of specific genes,RNA sequencing provides a whole-genome view of gene expression in aneuploids.Most studies of global aneuploidy effects have concentrated on individual types of aneuploids because multiple dose aneuploidies of the same genomic region are difficult to produce in most model genetic organisms.The genetic toolkit of maize allows the examination of multiple ploidies and 1-4 doses of chromosome arms.Thus,a detailed examination of expression changes both on the varied chromosome arms and elsewhere in the genome is possible,in both hypoploids and hyperploids,compared with euploid controls.Previous studies observed the inverse trans effect,in which genes not varied in DNA dosage were expressed in a negative relationship to the varied chromosomal region.This response was also the major type of changes found globally in this study.Many genes varied in dosage showed proportional expression changes,though some were seen to be partly or fully dosage compensated.It was also found that the effects of aneuploidy were progressive,with more severe aneuploids producing effects of greater magnitude.展开更多
基金supported by National Science Foundation USA grant IOS-1545780Computation for this work was performed on the highperformance computing infrastructure provided by Research Computing Support Services and in part by the National Science Foundation USA under grant number CNS-1429294 at the University of Missouri,Columbia,MO,https://doi.org/10.32469/10355/69802.
文摘Genomic imbalance refers to the more severe phenotypic consequences of changing part of a chromosome compared with the whole genome set.Previous genome imbalance studies in maize have identified prevalent inverse modulation of genes on the unvaried chromosomes(trans)with both the addition or subtraction of chromosome arms.Transposable elements(TEs)comprise a substantial fraction of the genome,and their reaction to genomic imbalance is therefore of interest.Here,we analyzed TE expression using RNA-seq data of aneuploidy and ploidy series and found that most aneuploidies showed an inverse modulation of TEs,but reductions in monosomy and increases in disomy and trisomy were also common.By contrast,the ploidy series showed little TE modulation.The modulation of TEs and genes in the same experimental group were compared,and TEs showed greater modulation than genes,especially in disomy.Class Ⅰ and Ⅱ TEs were differentially modulated in most aneuploidies,and some superfamilies in each TE class also showed differential modulation.Finally,the significantly upregulated TEs in three disomies(TB-7Lb,TB9Lc,and TB-10L19)did not increase the proportion of adjacent gene expression when compared with non-differentially expressed TEs,indicating that modulations of TEs do not compound the effect on genes.These results suggest that the prevalent inverse TE modulation in aneuploidy results from stoichiometric upset of the regulatory machinery used by TEs,similar to the response of core genes to genomic imbalance.
基金This work was supported by the National Science Foundation grants IOS-1545780,NSF 1615789,and NSF 1853556。
文摘Aneuploidy has profound effects on an organism,typically more so than polyploidy,and the basis of this contrast is not fully understood.A dosage series of the maize long arm of chromosome 1(1L)was used to compa re relative global gene expression in diffe rent types and degrees of aneuploidy to gain insights into how the magnitude of genomic imbalance as well as hypoploidy affects global gene expression.While previously available methods require a selective examination of specific genes,RNA sequencing provides a whole-genome view of gene expression in aneuploids.Most studies of global aneuploidy effects have concentrated on individual types of aneuploids because multiple dose aneuploidies of the same genomic region are difficult to produce in most model genetic organisms.The genetic toolkit of maize allows the examination of multiple ploidies and 1-4 doses of chromosome arms.Thus,a detailed examination of expression changes both on the varied chromosome arms and elsewhere in the genome is possible,in both hypoploids and hyperploids,compared with euploid controls.Previous studies observed the inverse trans effect,in which genes not varied in DNA dosage were expressed in a negative relationship to the varied chromosomal region.This response was also the major type of changes found globally in this study.Many genes varied in dosage showed proportional expression changes,though some were seen to be partly or fully dosage compensated.It was also found that the effects of aneuploidy were progressive,with more severe aneuploids producing effects of greater magnitude.