Gene expression profiling of non-polyadenylated RNA-seq across species
Transcriptomes are dynamic and unique, with each cell type/tissue, developmental stage and species expressing a different repertoire of RNA transcripts. Most mRNAs and well-characterized long noncoding RNAs are shaped with a 5′ cap and 3′ poly(A) tail, thus conventional transcriptome analyses typica...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2014-12-01
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| Series: | Genomics Data |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2213596014000634 |
| _version_ | 1818543743084527616 |
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| author | Xiao-Ou Zhang Qing-Fei Yin Ling-Ling Chen Li Yang |
| author_facet | Xiao-Ou Zhang Qing-Fei Yin Ling-Ling Chen Li Yang |
| author_sort | Xiao-Ou Zhang |
| collection | DOAJ |
| description | Transcriptomes are dynamic and unique, with each cell type/tissue, developmental stage and species expressing a different repertoire of RNA transcripts. Most mRNAs and well-characterized long noncoding RNAs are shaped with a 5′ cap and 3′ poly(A) tail, thus conventional transcriptome analyses typically start with the enrichment of poly(A)+ RNAs by oligo(dT) selection, followed by deep sequencing approaches. However, accumulated lines of evidence suggest that many RNA transcripts are processed by alternative mechanisms without 3′ poly(A) tails and, therefore, fail to be enriched by oligo(dT) purification and are absent following deep sequencing analyses. We have described an enrichment strategy to purify non-polyadenylated (poly(A)−/ribo−) RNAs from human total RNAs by removal of both poly(A)+ RNA transcripts and ribosomal RNAs, which led to the identification of many novel RNA transcripts with non-canonical 3′ ends in human. Here, we describe the application of non-polyadenylated RNA-sequencing in rhesus monkey and mouse cell lines/tissue, and further profile the transcription of non-polyadenylated RNAs across species, providing new resources for non-polyadenylated RNA identification and comparison across species. |
| first_indexed | 2024-12-11T22:39:22Z |
| format | Article |
| id | doaj.art-44d5f9dfd72c47ce9176cca932968042 |
| institution | Directory Open Access Journal |
| issn | 2213-5960 |
| language | English |
| last_indexed | 2024-12-11T22:39:22Z |
| publishDate | 2014-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Genomics Data |
| spelling | doaj.art-44d5f9dfd72c47ce9176cca9329680422022-12-22T00:47:50ZengElsevierGenomics Data2213-59602014-12-012C23724110.1016/j.gdata.2014.07.005Gene expression profiling of non-polyadenylated RNA-seq across speciesXiao-Ou Zhang0Qing-Fei Yin1Ling-Ling Chen2Li Yang3Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai 200031, ChinaState Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, ChinaState Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, ChinaKey Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai 200031, ChinaTranscriptomes are dynamic and unique, with each cell type/tissue, developmental stage and species expressing a different repertoire of RNA transcripts. Most mRNAs and well-characterized long noncoding RNAs are shaped with a 5′ cap and 3′ poly(A) tail, thus conventional transcriptome analyses typically start with the enrichment of poly(A)+ RNAs by oligo(dT) selection, followed by deep sequencing approaches. However, accumulated lines of evidence suggest that many RNA transcripts are processed by alternative mechanisms without 3′ poly(A) tails and, therefore, fail to be enriched by oligo(dT) purification and are absent following deep sequencing analyses. We have described an enrichment strategy to purify non-polyadenylated (poly(A)−/ribo−) RNAs from human total RNAs by removal of both poly(A)+ RNA transcripts and ribosomal RNAs, which led to the identification of many novel RNA transcripts with non-canonical 3′ ends in human. Here, we describe the application of non-polyadenylated RNA-sequencing in rhesus monkey and mouse cell lines/tissue, and further profile the transcription of non-polyadenylated RNAs across species, providing new resources for non-polyadenylated RNA identification and comparison across species.http://www.sciencedirect.com/science/article/pii/S2213596014000634Non-polyadenylated RNAsRNA-seqlncRNAssno-lncRNAsSpecies-specific |
| spellingShingle | Xiao-Ou Zhang Qing-Fei Yin Ling-Ling Chen Li Yang Gene expression profiling of non-polyadenylated RNA-seq across species Genomics Data Non-polyadenylated RNAs RNA-seq lncRNAs sno-lncRNAs Species-specific |
| title | Gene expression profiling of non-polyadenylated RNA-seq across species |
| title_full | Gene expression profiling of non-polyadenylated RNA-seq across species |
| title_fullStr | Gene expression profiling of non-polyadenylated RNA-seq across species |
| title_full_unstemmed | Gene expression profiling of non-polyadenylated RNA-seq across species |
| title_short | Gene expression profiling of non-polyadenylated RNA-seq across species |
| title_sort | gene expression profiling of non polyadenylated rna seq across species |
| topic | Non-polyadenylated RNAs RNA-seq lncRNAs sno-lncRNAs Species-specific |
| url | http://www.sciencedirect.com/science/article/pii/S2213596014000634 |
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