TSS-Seq analysis of low pH-induced gene expression in intercalated cells in the renal collecting duct.
TSS-Seq analysis of low pH-induced gene expression in intercalated cells in the renal collecting duct.
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DOI：
10.1371/journal.pone.0184185
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发表时间：
2017
期刊：
影响因子：
3.7
通讯作者：
Mukoyama M
中科院分区：
文献类型：
--
作者：
Izumi Y;Inoue H;Nakayama Y;Eguchi K;Yasuoka Y;Matsuo N;Nonoguchi H;Kakizoe Y;Kuwabara T;Mukoyama M
代谢性酸中毒通常由慢性肾脏疾病引起;反过来，代谢性酸中毒加速了肾损伤的进展。酸中毒如何促进肾损伤的机制尚未完全了解。为了研究低pH是否直接影响控制肾小管局部稳态的基因的表达，我们使用来自大鼠肾集合管闰细胞的细胞系IN-IC细胞进行转录起始位点测序（TSS-Seq），酸负荷24 h。峰调用确定651上调和128下调TSS在pH 7.0相比，在pH 7.4。其中424个和38个TSS的Log 2倍数变化≥ 1.0和≤ -1.0，分别注释为193个上调基因和34个下调基因。我们使用基因本体分析和人工策展来描绘上调基因。分析表明，许多上调的基因参与了肾纤维化，提示代谢性酸中毒诱导的潜在分子机制。为了验证泛素-蛋白酶体系统（UPS）（酸中毒激活的候选途径）的活性，我们检测了用蛋白酶体抑制剂MG 132处理的细胞中蛋白质的表达。泛素化蛋白的表达在pH 7.0时比在pH 7.4时更大，表明低pH激活UPS。体内研究表明，酸负荷增加了小鼠肾脏集合管细胞中泛素蛋白的表达。基序分析显示，Egr 1，其mRNA表达增加，在低pH值，作为一个候选因素，可能刺激基因表达，在响应低pH值。总之，代谢性酸中毒可以促进肾脏疾病过程中的肾损伤和纤维化，通过局部激活各种途径在肾小管。
Metabolic acidosis often results from chronic kidney disease; in turn, metabolic acidosis accelerates the progression of kidney injury. The mechanisms for how acidosis facilitates kidney injury are not fully understood. To investigate whether low pH directly affects the expression of genes controlling local homeostasis in renal tubules, we performed transcription start site sequencing (TSS-Seq) using IN-IC cells, a cell line derived from rat renal collecting duct intercalated cells, with acid loading for 24 h. Peak calling identified 651 up-regulated and 128 down-regulated TSSs at pH 7.0 compared with those at pH 7.4. Among them, 424 and 38 TSSs were ≥ 1.0 and ≤ -1.0 in Log2 fold change, which were annotated to 193 up-regulated and 34 down-regulated genes, respectively. We used gene ontology analysis and manual curation to profile the up-regulated genes. The analysis revealed that many up-regulated genes are involved in renal fibrosis, implying potential molecular mechanisms induced by metabolic acidosis. To verify the activity of the ubiquitin-proteasome system (UPS), a candidate pathway activated by acidosis, we examined the expression of proteins from cells treated with a proteasome inhibitor, MG132. The expression of ubiquitinated proteins was greater at pH 7.0 than at pH 7.4, suggesting that low pH activates the UPS. The in vivo study demonstrated that acid loading increased the expression of ubiquitin proteins in the collecting duct cells in mouse kidneys. Motif analysis revealed Egr1, the mRNA expression of which was increased at low pH, as a candidate factor that possibly stimulates gene expression in response to low pH. In conclusion, metabolic acidosis can facilitate renal injury and fibrosis during kidney disease by locally activating various pathways in the renal tubules.
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DOI：
10.1093/bioinformatics/btr064
发表时间：
2011-04-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Grant CE;Bailey TL;Noble WS
通讯作者：
Noble WS
发现具有任意插入和删除的序列基序。
影响因子：
4.3
作者：
Frith, Martin C.;Saunders, Neil F. W.;Kobe, Bostjan;Bailey, Timothy L.
通讯作者：
Bailey, Timothy L.
DOI：
10.1152/ajprenal.90482.2008
发表时间：
2008-11-01
影响因子：
4.2
作者：
Chen, Guangping;Huang, Haidong;Sands, Jeff M.
通讯作者：
Sands, Jeff M.
影响因子：
4.6
作者：
Cheval, Lydie;Morla, Luciana;Doucet, Alain
通讯作者：
Doucet, Alain
影响因子：
13.6
作者：
Izumi, Yuichiro;Hori, Kahori;Nonoguchi, Hiroshi
通讯作者：
Nonoguchi, Hiroshi