Computational dissection of Arabidopsis smRNAome leads to discovery of novel microRNAs and short interfering RNAs associated with transcription start sites
The profiling of small RNAs by high-throughput sequencing (smRNA-Seq) has revealed the complexity of the RNA world. Here, we describe a computational scheme for dissecting the plant smRNAome by integrating smRNA-Seq datasets in Arabidopsis thaliana. Our analytical approach first defines ab initio th...
| Main Authors: | , , , , |
|---|---|
| Other Authors: | |
| Format: | Article |
| Language: | en_US |
| Published: |
Elsevier
2014
|
| Online Access: | http://hdl.handle.net/1721.1/92050 |
| _version_ | 1826208364154060800 |
|---|---|
| author | Wang, Xiangfeng Laurie, John D. Liu, Tao Wentz, Jacqueline Liu, X. Shirley |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Wang, Xiangfeng Laurie, John D. Liu, Tao Wentz, Jacqueline Liu, X. Shirley |
| author_sort | Wang, Xiangfeng |
| collection | MIT |
| description | The profiling of small RNAs by high-throughput sequencing (smRNA-Seq) has revealed the complexity of the RNA world. Here, we describe a computational scheme for dissecting the plant smRNAome by integrating smRNA-Seq datasets in Arabidopsis thaliana. Our analytical approach first defines ab initio the genomic loci that produce smRNAs as basic units, then utilizes principal component analysis (PCA) to predict novel miRNAs. Secondary structure prediction of candidates' putative precursors discovered a group of long hairpin double-stranded RNAs (lh-dsRNAs) formed by inverted duplications of decayed coding genes. These gene remnants produce miRNA-like small RNAs which are predominantly 21- and 22-nt long, dependent of DCL1 but independent of RDR2 and DCL2/3/4, and associated with AGO1. Additionally, we found two classes of transcription start site associated (TSSa) RNAs located at sense (+) and antisense (−) approximately 100–200 bp downstream of TSSs, but are differentially incorporated into AGO1 and AGO4, respectively. |
| first_indexed | 2024-09-23T14:04:18Z |
| format | Article |
| id | mit-1721.1/92050 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T14:04:18Z |
| publishDate | 2014 |
| publisher | Elsevier |
| record_format | dspace |
| spelling | mit-1721.1/920502022-10-01T18:59:27Z Computational dissection of Arabidopsis smRNAome leads to discovery of novel microRNAs and short interfering RNAs associated with transcription start sites Wang, Xiangfeng Laurie, John D. Liu, Tao Wentz, Jacqueline Liu, X. Shirley Massachusetts Institute of Technology. Department of Biological Engineering Wentz, Jacqueline The profiling of small RNAs by high-throughput sequencing (smRNA-Seq) has revealed the complexity of the RNA world. Here, we describe a computational scheme for dissecting the plant smRNAome by integrating smRNA-Seq datasets in Arabidopsis thaliana. Our analytical approach first defines ab initio the genomic loci that produce smRNAs as basic units, then utilizes principal component analysis (PCA) to predict novel miRNAs. Secondary structure prediction of candidates' putative precursors discovered a group of long hairpin double-stranded RNAs (lh-dsRNAs) formed by inverted duplications of decayed coding genes. These gene remnants produce miRNA-like small RNAs which are predominantly 21- and 22-nt long, dependent of DCL1 but independent of RDR2 and DCL2/3/4, and associated with AGO1. Additionally, we found two classes of transcription start site associated (TSSa) RNAs located at sense (+) and antisense (−) approximately 100–200 bp downstream of TSSs, but are differentially incorporated into AGO1 and AGO4, respectively. 2014-12-08T17:35:02Z 2014-12-08T17:35:02Z 2011-02 2010-10 Article http://purl.org/eprint/type/JournalArticle 08887543 1089-8646 http://hdl.handle.net/1721.1/92050 Wang, Xiangfeng, John D. Laurie, Tao Liu, Jacqueline Wentz, and X. Shirley Liu. “Computational Dissection of Arabidopsis smRNAome Leads to Discovery of Novel microRNAs and Short Interfering RNAs Associated with Transcription Start Sites.” Genomics 97, no. 4 (April 2011): 235–243. en_US http://dx.doi.org/10.1016/j.ygeno.2011.01.006 Genomics Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf Elsevier Elsevier |
| spellingShingle | Wang, Xiangfeng Laurie, John D. Liu, Tao Wentz, Jacqueline Liu, X. Shirley Computational dissection of Arabidopsis smRNAome leads to discovery of novel microRNAs and short interfering RNAs associated with transcription start sites |
| title | Computational dissection of Arabidopsis smRNAome leads to discovery of novel microRNAs and short interfering RNAs associated with transcription start sites |
| title_full | Computational dissection of Arabidopsis smRNAome leads to discovery of novel microRNAs and short interfering RNAs associated with transcription start sites |
| title_fullStr | Computational dissection of Arabidopsis smRNAome leads to discovery of novel microRNAs and short interfering RNAs associated with transcription start sites |
| title_full_unstemmed | Computational dissection of Arabidopsis smRNAome leads to discovery of novel microRNAs and short interfering RNAs associated with transcription start sites |
| title_short | Computational dissection of Arabidopsis smRNAome leads to discovery of novel microRNAs and short interfering RNAs associated with transcription start sites |
| title_sort | computational dissection of arabidopsis smrnaome leads to discovery of novel micrornas and short interfering rnas associated with transcription start sites |
| url | http://hdl.handle.net/1721.1/92050 |
| work_keys_str_mv | AT wangxiangfeng computationaldissectionofarabidopsissmrnaomeleadstodiscoveryofnovelmicrornasandshortinterferingrnasassociatedwithtranscriptionstartsites AT lauriejohnd computationaldissectionofarabidopsissmrnaomeleadstodiscoveryofnovelmicrornasandshortinterferingrnasassociatedwithtranscriptionstartsites AT liutao computationaldissectionofarabidopsissmrnaomeleadstodiscoveryofnovelmicrornasandshortinterferingrnasassociatedwithtranscriptionstartsites AT wentzjacqueline computationaldissectionofarabidopsissmrnaomeleadstodiscoveryofnovelmicrornasandshortinterferingrnasassociatedwithtranscriptionstartsites AT liuxshirley computationaldissectionofarabidopsissmrnaomeleadstodiscoveryofnovelmicrornasandshortinterferingrnasassociatedwithtranscriptionstartsites |