Hypothesis: Artifacts, Including Spurious Chimeric RNAs with a Short Homologous Sequence, Caused by Consecutive Reverse Transcriptions and Endogenous Random Primers.
Hypothesis: Artifacts, Including Spurious Chimeric RNAs with a Short Homologous Sequence, Caused by Consecutive Reverse Transcriptions and Endogenous Random Primers.
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DOI：
10.7150/jca.11997
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发表时间：
2015
影响因子：
3.9
通讯作者：
Liao DJ
中科院分区：
文献类型：
--
作者：
Peng Z;Yuan C;Zellmer L;Liu S;Xu N;Liao DJ
最近的RNA测序技术和相关的生物信息学已经鉴定出数以万计的假定的人类嵌合RNA，即含有来自两个不同基因的序列的RNA，其中大多数来自同一染色体上的相邻基因。在本文中，我们将“两个相邻基因”重新定义为产生单独转录本的基因，并指出了嵌合 RNA 形成的两种已知机制，即从融合基因转录或两个 RNA 的反式剪接。根据我们的定义，大多数推定的源自规范定义的邻近基因的RNA嵌合体可能是技术产物，或者是任一伙伴的5'-或3'-延伸RNA的顺式剪接产物，在本文中将其重新定义为未注释的基因，而反式剪接事件在人类细胞中很少见。因此，大多数真实的嵌合RNA源自融合基因，迄今为止已鉴定出约1,000个融合基因。我们提出了“连续逆转录（RT）”的假设，即前一个逆转录反应之后的另一个逆转录反应，关于如何在逆转录过程中产生大多数虚假嵌合RNA，尤其是那些含有短同源序列的RNA，特别是在RNA片段化的RNA测序中。我们还指出，RNA 样本含有大量 RNA 和 DNA 碎片，可作为 RT 和随后的聚合酶链式反应 (PCR) 的内源随机引物，从而在 RT-PCR 中产生伪影。
Recent RNA-sequencing technology and associated bioinformatics have led to identification of tens of thousands of putative human chimeric RNAs, i.e. RNAs containing sequences from two different genes, most of which are derived from neighboring genes on the same chromosome. In this essay, we redefine “two neighboring genes” as those producing individual transcripts, and point out two known mechanisms for chimeric RNA formation, i.e. transcription from a fusion gene or trans-splicing of two RNAs. By our definition, most putative RNA chimeras derived from canonically-defined neighboring genes may either be technical artifacts or be cis-splicing products of 5'- or 3'-extended RNA of either partner that is redefined herein as an unannotated gene, whereas trans-splicing events are rare in human cells. Therefore, most authentic chimeric RNAs result from fusion genes, about 1,000 of which have been identified hitherto. We propose a hypothesis of “consecutive reverse transcriptions (RTs)”, i.e. another RT reaction following the previous one, for how most spurious chimeric RNAs, especially those containing a short homologous sequence, may be generated during RT, especially in RNA-sequencing wherein RNAs are fragmented. We also point out that RNA samples contain numerous RNA and DNA shreds that can serve as endogenous random primers for RT and ensuing polymerase chain reactions (PCR), creating artifacts in RT-PCR.
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影响因子：
11.2
作者：
Brenner, J. Chad;Chinnaiyan, Arul M.
通讯作者：
Chinnaiyan, Arul M.
影响因子：
3
作者：
Bruno AE;Miecznikowski JC;Qin M;Wang J;Liu S
通讯作者：
Liu S
DOI：
10.3324/haematol.2009.011536
发表时间：
2010-01-01
期刊：
HAEMATOLOGICA-THE HEMATOLOGY JOURNAL
影响因子：
--
作者：
Chase, Andrew;Ernst, Thomas;Cross, Nicholas C. P.
通讯作者：
Cross, Nicholas C. P.
影响因子：
7
作者：
Akiva, P;Toporik, A;Sorek, R
通讯作者：
Sorek, R
影响因子：
3
作者：
Alldred, Melissa J.;Che, Shaoli;Ginsberg, Stephen D.
通讯作者：
Ginsberg, Stephen D.