A tissue-specific landscape of sense/antisense transcription in the mouse intestine.
A tissue-specific landscape of sense/antisense transcription in the mouse intestine.
复制标题
DOI：
10.1186/1471-2164-12-305
复制
发表时间：
2011-06-10
期刊：
影响因子：
4.4
通讯作者：
Rosenstiel P
中科院分区：
文献类型：
--
作者：
Klostermeier UC;Barann M;Wittig M;Häsler R;Franke A;Gavrilova O;Kreck B;Sina C;Schilhabel MB;Schreiber S;Rosenstiel P
肠粘膜的特点是由复杂的代谢和免疫过程驱动的高度动态的基因表达程序。随着下一代测序的出现及其用于RNA序列空间的分析，与微阵列相比，转录组的全局结构的细节水平达到了一个新的数量级。我们报告了在小鼠肠道（小肠和结肠）的两个密切相关但不同的区域中多聚腺苷酸化转录组的超深表征。我们评估了组织特异性转录组结构和新的转录活性区（nTAR）的存在。在第一步中，可以在肠中鉴定20，541个NCBI RefSeq转录物的特征（注释基因的74.1%），其中16，742个在两种组织中是共同的。尽管大多数读段可以与注释的基因相关联，但鉴定了与RefSeq或ENSEMBL中的当前基因注释不一致的27，543个nTAR。通过使用第二个独立的链特异性RNA-Seq方案，确认了20，966个这些nTAR，其中大多数在已知基因附近。我们进一步将我们的研究结果通过它们与所描述的外显子元件的相对邻近性进行分类，并研究了小肠和结肠中新转录元件的区域差异。目前的研究证明了高分辨率的原型哺乳动物肠道mRNA转录组的复杂性，并确定了新的转录活性区链特异性，单碱基分辨率。我们的分析首次显示了两种组织中nTAR的链特异性比较图，并代表了进一步研究有助于组织身份的转录过程的资源。
The intestinal mucosa is characterized by complex metabolic and immunological processes driven highly dynamic gene expression programs. With the advent of next generation sequencing and its utilization for the analysis of the RNA sequence space, the level of detail on the global architecture of the transcriptome reached a new order of magnitude compared to microarrays. We report the ultra-deep characterization of the polyadenylated transcriptome in two closely related, yet distinct regions of the mouse intestinal tract (small intestine and colon). We assessed tissue-specific transcriptomal architecture and the presence of novel transcriptionally active regions (nTARs). In the first step, signatures of 20,541 NCBI RefSeq transcripts could be identified in the intestine (74.1% of annotated genes), thereof 16,742 are common in both tissues. Although the majority of reads could be linked to annotated genes, 27,543 nTARs not consistent with current gene annotations in RefSeq or ENSEMBL were identified. By use of a second independent strand-specific RNA-Seq protocol, 20,966 of these nTARs were confirmed, most of them in vicinity of known genes. We further categorized our findings by their relative adjacency to described exonic elements and investigated regional differences of novel transcribed elements in small intestine and colon. The current study demonstrates the complexity of an archetypal mammalian intestinal mRNA transcriptome in high resolution and identifies novel transcriptionally active regions at strand-specific, single base resolution. Our analysis for the first time shows a strand-specific comparative picture of nTARs in two tissues and represents a resource for further investigating the transcriptional processes that contribute to tissue identity.
登录
查看更多内容
影响因子：
56.9
作者：
Carninci, P;Kasukawa, T;Hayashizaki, Y
通讯作者：
Hayashizaki, Y
影响因子：
48
作者：
Cloonan, Nicole;Forrest, Alistair R. R.;Grimmond, Sean M.
通讯作者：
Grimmond, Sean M.
UCSC基因组浏览器数据库：更新2010。
影响因子：
14.9
作者：
Rhead B;Karolchik D;Kuhn RM;Hinrichs AS;Zweig AS;Fujita PA;Diekhans M;Smith KE;Rosenbloom KR;Raney BJ;Pohl A;Pheasant M;Meyer LR;Learned K;Hsu F;Hillman-Jackson J;Harte RA;Giardine B;Dreszer TR;Clawson H;Barber GP;Haussler D;Kent WJ
通讯作者：
Kent WJ
影响因子：
20.1
作者：
Matkovich, Scot J.;Zhang, Yan;Dorn, Gerald W., II
通讯作者：
Dorn, Gerald W., II
影响因子：
46.9
作者：
通讯作者：
--