Short non-coding RNA fragments accumulating in chloroplasts: footprints of RNA binding proteins?
Short non-coding RNA fragments accumulating in chloroplasts: footprints of RNA binding proteins?
复制标题
DOI：
10.1093/nar/gkr1138
复制
发表时间：
2012-04
影响因子：
14.9
通讯作者：
Schmitz-Linneweber C
中科院分区：
文献类型：
--
作者：
Ruwe H;Schmitz-Linneweber C
叶绿体RNA代谢是由数百种核编码的、定位于叶绿体的RNA结合蛋白控制和执行的。与核胞质或细菌相反，几乎没有证据表明非编码RNA起到了叶绿体核调节的作用。我们挖掘了深度测序数据集来识别叶绿体基因组中的短(16-28 NT)RNA，并发现了50个丰富的小RNA(SRNA)，在某些情况下，由多个，在某些情况下，数千个测序读出，而读出一般不存在于周围的序列空间。除了代表最丰富的mRNAs、tRNAs和rRNAs的sRNAs外，大多数sRNAs位于非编码区，而且许多sRNAs位于起始密码子上游很短的距离。通过转录末端作图，我们发现叶绿体RNAs的5‘和3’末端与sRNAs的末端重合。在拟南芥中发现的sRNA序列在不同被子植物之间是保守的，在一些情况下，我们在水稻深度测序数据集中发现了推测的同源基因。最近，有人提出，叶绿体小片段的产生可能是由于五肽重复序列(PPR)蛋白对核酸外切酶的保护作用，即RNA结合蛋白的足迹。我们的数据在转录组范围的水平上支持这一假设，并表明大量的sRNA实际上是PPR蛋白靶标的残基。
Chloroplast RNA metabolism is controlled and excecuted by hundreds of nuclear-encoded, chloroplast-localized RNA binding proteins. Contrary to the nucleo-cytosolic compartment or bacteria, there is little evidence for non-coding RNAs that play a role as riboregulators of chloroplasts. We mined deep-sequencing datasets to identify short (16–28 nt) RNAs in the chloroplast genome and found 50 abundant small RNAs (sRNAs) represented by multiple, in some cases, thousands of sequencing reads, whereas reads are in general absent from the surrounding sequence space. Other than sRNAs representing the most highly abundant mRNAs, tRNAs and rRNAs, most sRNAs are located in non-coding regions and many are found a short distance upstream of start codons. By transcript end mapping we show that the 5′ and 3′ termini of chloroplast RNAs coincide with the ends of sRNAs. Sequences of sRNAs identified in Arabidopsis are conserved between different angiosperm species and in several cases, we identified putative orthologs in rice deep sequencing datasets. Recently, it was suggested that small chloroplast RNA fragments could result from the protective action of pentatricopeptide repeat (PPR) proteins against exonucleases, i.e. footprints of RNA binding proteins. Our data support this scenario on a transcriptome-wide level and suggest that a large number of sRNAs are in fact remnants of PPR protein targets.
登录
查看更多内容
影响因子：
14.9
作者：
Lung B;Zemann A;Madej MJ;Schuelke M;Techritz S;Ruf S;Bock R;Hüttenhofer A
通讯作者：
Hüttenhofer A
影响因子：
5.8
作者：
Waterhouse, Andrew M.;Procter, James B.;Barton, Geoffrey J.
通讯作者：
Barton, Geoffrey J.
影响因子：
7.2
作者：
Hashimoto, M;Endo, T;Shikanai, T
通讯作者：
Shikanai, T
DOI：
10.1073/pnas.0808529106
发表时间：
2009-04-07
影响因子：
11.1
作者：
Tillich, Michael;Hardel, Simone L.;Schmitz-Linneweber, Christian
通讯作者：
Schmitz-Linneweber, Christian
CSRDB：用于谷物的小型RNA集成数据库和浏览器资源。
影响因子：
14.9
作者：
Johnson, Cameron;Bowman, Lewis;Adai, Alex T;Vance, Vicki;Sundaresan, Venkatesan
通讯作者：
Sundaresan, Venkatesan