Deep sequencing the transcriptome reveals seasonal adaptive mechanisms in a hibernating mammal.
Deep sequencing the transcriptome reveals seasonal adaptive mechanisms in a hibernating mammal.
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DOI：
10.1371/journal.pone.0027021
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发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Andrews MT
中科院分区：
文献类型：
--
作者：
Hampton M;Melvin RG;Kendall AH;Kirkpatrick BR;Peterson N;Andrews MT
哺乳动物冬眠是一种复杂的表型，涉及代谢率降低、心动过缓、体温过低以及对储存脂肪的依赖，这使得动物能够在假死状态下在没有食物的情况下生存数月。为了确定十三系地松鼠 (Ictidomys tridecemlineatus) 中导致这种表型的基因，我们使用 Roche 454 平台对全年六个时间点从三个关键组织中分离出的 mRNA 进行测序：心脏、骨骼肌和白色脂肪组织 (WAT)。深度测序从 18 个样本（6 个时间点×3 个组织）中生成了大约 370 万个 cDNA 读数，平均读数长度为 335 个碱基。其中，3,125,337 个读数被组装成 140,703 个重叠群。大约 90% 的序列与人类 UniProt 数据库中的蛋白质相匹配。与地松鼠转录本匹配的不同人类蛋白质总数为：心脏 13,637 个、骨骼肌 12,496 个、WAT 14,351 个。广泛的线粒体 RNA 序列使得使用转录组构建 I. tridecemlineatus 完整线粒体基因组的新方法成为可能。满足我们严格的错误发现率截止值 (1.0×10−11) 的 mRNA 水平的季节性和活动特异性变化被用来识别涉及冬眠表型各个方面的基因表达模式。在这些模式中，编码心脏蛋白 AT1A1、NAC1 和 RYR2 的差异表达基因控制着低体温下收缩和舒张所需的离子运输。骨骼肌中编码泛素通路蛋白 ASB2、UBC 和 DDB1 的大量 RNA 在 10 月份达到峰值，表明肌肉蛋白水解增加。最后，WAT 中编码参与脂肪生成的蛋白质（ACOD、FABP4）的基因在 8 月份高表达，但在向脂肪分解的季节过渡期间表达逐渐下降。
Mammalian hibernation is a complex phenotype involving metabolic rate reduction, bradycardia, profound hypothermia, and a reliance on stored fat that allows the animal to survive for months without food in a state of suspended animation. To determine the genes responsible for this phenotype in the thirteen-lined ground squirrel (Ictidomys tridecemlineatus) we used the Roche 454 platform to sequence mRNA isolated at six points throughout the year from three key tissues: heart, skeletal muscle, and white adipose tissue (WAT). Deep sequencing generated approximately 3.7 million cDNA reads from 18 samples (6 time points ×3 tissues) with a mean read length of 335 bases. Of these, 3,125,337 reads were assembled into 140,703 contigs. Approximately 90% of all sequences were matched to proteins in the human UniProt database. The total number of distinct human proteins matched by ground squirrel transcripts was 13,637 for heart, 12,496 for skeletal muscle, and 14,351 for WAT. Extensive mitochondrial RNA sequences enabled a novel approach of using the transcriptome to construct the complete mitochondrial genome for I. tridecemlineatus. Seasonal and activity-specific changes in mRNA levels that met our stringent false discovery rate cutoff (1.0×10−11) were used to identify patterns of gene expression involving various aspects of the hibernation phenotype. Among these patterns are differentially expressed genes encoding heart proteins AT1A1, NAC1 and RYR2 controlling ion transport required for contraction and relaxation at low body temperatures. Abundant RNAs in skeletal muscle coding ubiquitin pathway proteins ASB2, UBC and DDB1 peak in October, suggesting an increase in muscle proteolysis. Finally, genes in WAT that encode proteins involved in lipogenesis (ACOD, FABP4) are highly expressed in August, but gradually decline in expression during the seasonal transition to lipolysis.
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影响因子：
10.7
作者：
Castresana, J
通讯作者：
Castresana, J
影响因子：
4.6
作者：
Brauch, KM;Dhruv, ND;Andrews, MT
通讯作者：
Andrews, MT
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
6.5
作者：
Anisimova, Maria;Gascuel, Olivier
通讯作者：
Gascuel, Olivier
DOI：
10.1152/ajpregu.2001.281.4.r1186
发表时间：
2001-10-01
影响因子：
2.8
作者：
Bauer, VW;Squire, TL;Andrews, MT
通讯作者：
Andrews, MT