Comparative studies of genomic and epigenetic factors influencing transcriptional variation in two insect species.
Comparative studies of genomic and epigenetic factors influencing transcriptional variation in two insect species.
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DOI：
10.1093/g3journal/jkac230
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发表时间：
2022-11-04
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影响因子：
--
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不同的基因表现出不同程度的表达变异性。例如，高表达的基因往往表现出较少的表达变异性。启动子具有TATA盒和启动子基序的基因往往具有更高的表达变异性。另一方面，在许多物种中，转录单位的DNA甲基化或基因体DNA甲基化与基因表达变异性的降低有关。有趣的是，一些昆虫谱系，尤其是双翅目昆虫，包括典型的模式昆虫黑腹果蝇，已经失去了DNA甲基化。因此，确定基因组特征是否类似地影响有和没有DNA甲基化的谱系中的基因表达变异性是很有意义的。我们分析了最近生成的黑腹大蠊和蜜蜂（Apis mellifera）的大规模数据集来调查这些问题。我们的分析表明，在这两个物种中，基因表达水平的增加始终与表达变异性的降低相关，而TATA box的存在始终与基因表达变异性的增加相关。相比之下，启动子基序和基因长度的影响较弱，仅限于某些数据集。重要的是，我们发现指示基因体DNA甲基化的序列特征与蜜蜂的基因表达变异性呈强烈负相关，而在D. melanogaster中则没有这种关联。这些结果表明，一些昆虫谱系中DNA甲基化的进化缺失重塑了基因表达变异性调控的分子机制。
Different genes show different levels of expression variability. For example, highly expressed genes tend to exhibit less expression variability. Genes whose promoters have TATA box and initiator motifs tend to have increased expression variability. On the other hand, DNA methylation of transcriptional units, or gene body DNA methylation, is associated with reduced gene expression variability in many species. Interestingly, some insect lineages, most notably Diptera including the canonical model insect Drosophila melanogaster, have lost DNA methylation. Therefore, it is of interest to determine whether genomic features similarly influence gene expression variability in lineages with and without DNA methylation. We analyzed recently generated large-scale data sets in D. melanogaster and honey bee (Apis mellifera) to investigate these questions. Our analysis shows that increased gene expression levels are consistently associated with reduced expression variability in both species, while the presence of TATA box is consistently associated with increased gene expression variability. In contrast, initiator motifs and gene lengths have weak effects limited to some data sets. Importantly, we show that a sequence characteristics indicative of gene body DNA methylation is strongly and negatively associate with gene expression variability in honey bees, while it shows no such association in D. melanogaster. These results suggest the evolutionary loss of DNA methylation in some insect lineages has reshaped the molecular mechanisms concerning the regulation of gene expression variability.
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DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
3.9
作者：
Huh I;Zeng J;Park T;Yi SV
通讯作者：
Yi SV
DOI：
10.1093/bioinformatics/btn142
发表时间：
2008-07-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Ho JW;Stefani M;dos Remedios CG;Charleston MA
通讯作者：
Charleston MA
影响因子：
64.8
作者：
Hagai T;Chen X;Miragaia RJ;Rostom R;Gomes T;Kunowska N;Henriksson J;Park JE;Proserpio V;Donati G;Bossini-Castillo L;Vieira Braga FA;Naamati G;Fletcher J;Stephenson E;Vegh P;Trynka G;Kondova I;Dennis M;Haniffa M;Nourmohammad A;Lässig M;Teichmann SA
通讯作者：
Teichmann SA
影响因子：
10.7
作者：
Kim, SH;Yi, SV
通讯作者：
Yi, SV