Global Analysis of the Human RNA Degradome Reveals Widespread Decapped and Endonucleolytic Cleaved Transcripts
RNA decay is an important regulatory mechanism for gene expression at the posttranscriptional level. Although the main pathways and major enzymes that facilitate this process are well defined, global analysis of RNA turnover remains under-investigated. Recent advances in the application of next-gene...
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MDPI AG
2020-09-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/21/18/6452 |
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| author | Jung-Im Won JaeMoon Shin So Young Park JeeHee Yoon Dong-Hoon Jeong |
| author_facet | Jung-Im Won JaeMoon Shin So Young Park JeeHee Yoon Dong-Hoon Jeong |
| author_sort | Jung-Im Won |
| collection | DOAJ |
| description | RNA decay is an important regulatory mechanism for gene expression at the posttranscriptional level. Although the main pathways and major enzymes that facilitate this process are well defined, global analysis of RNA turnover remains under-investigated. Recent advances in the application of next-generation sequencing technology enable its use in order to examine various RNA decay patterns at the genome-wide scale. In this study, we investigated human RNA decay patterns using parallel analysis of RNA end-sequencing (PARE-seq) data from <i>XRN1</i>-knockdown HeLa cell lines, followed by a comparison of steady state and degraded mRNA levels from RNA-seq and PARE-seq data, respectively. The results revealed 1103 and 1347 transcripts classified as stable and unstable candidates, respectively. Of the unstable candidates, we found that a subset of the <i>replication-dependent histone</i> transcripts was polyadenylated and rapidly degraded. Additionally, we identified 380 endonucleolytically cleaved candidates by analyzing the most abundant PARE sequence on a transcript. Of these, 41.4% of genes were classified as unstable genes, which implied that their endonucleolytic cleavage might affect their mRNA stability. Furthermore, we identified 1877 decapped candidates, including <i>HSP90B1</i> and <i>SWI5,</i> having the most abundant PARE sequences at the 5′-end positions of the transcripts. These results provide a useful resource for further analysis of RNA decay patterns in human cells. |
| first_indexed | 2024-03-10T16:35:26Z |
| format | Article |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T16:35:26Z |
| publishDate | 2020-09-01 |
| publisher | MDPI AG |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-fc01453c09bf4fa8a1657264c4ee53ff2023-11-20T12:32:42ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-09-012118645210.3390/ijms21186452Global Analysis of the Human RNA Degradome Reveals Widespread Decapped and Endonucleolytic Cleaved TranscriptsJung-Im Won0JaeMoon Shin1So Young Park2JeeHee Yoon3Dong-Hoon Jeong4Smart Computing Lab., Hallym University, Chuncheon 24252, KoreaSmart Computing Lab., Hallym University, Chuncheon 24252, KoreaDepartment of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, KoreaSchool of Software, Hallym University, Chuncheon 24252, KoreaDepartment of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, KoreaRNA decay is an important regulatory mechanism for gene expression at the posttranscriptional level. Although the main pathways and major enzymes that facilitate this process are well defined, global analysis of RNA turnover remains under-investigated. Recent advances in the application of next-generation sequencing technology enable its use in order to examine various RNA decay patterns at the genome-wide scale. In this study, we investigated human RNA decay patterns using parallel analysis of RNA end-sequencing (PARE-seq) data from <i>XRN1</i>-knockdown HeLa cell lines, followed by a comparison of steady state and degraded mRNA levels from RNA-seq and PARE-seq data, respectively. The results revealed 1103 and 1347 transcripts classified as stable and unstable candidates, respectively. Of the unstable candidates, we found that a subset of the <i>replication-dependent histone</i> transcripts was polyadenylated and rapidly degraded. Additionally, we identified 380 endonucleolytically cleaved candidates by analyzing the most abundant PARE sequence on a transcript. Of these, 41.4% of genes were classified as unstable genes, which implied that their endonucleolytic cleavage might affect their mRNA stability. Furthermore, we identified 1877 decapped candidates, including <i>HSP90B1</i> and <i>SWI5,</i> having the most abundant PARE sequences at the 5′-end positions of the transcripts. These results provide a useful resource for further analysis of RNA decay patterns in human cells.https://www.mdpi.com/1422-0067/21/18/6452mRNA decayparallel analysis of RNA endsXRN1decapping |
| spellingShingle | Jung-Im Won JaeMoon Shin So Young Park JeeHee Yoon Dong-Hoon Jeong Global Analysis of the Human RNA Degradome Reveals Widespread Decapped and Endonucleolytic Cleaved Transcripts International Journal of Molecular Sciences mRNA decay parallel analysis of RNA ends XRN1 decapping |
| title | Global Analysis of the Human RNA Degradome Reveals Widespread Decapped and Endonucleolytic Cleaved Transcripts |
| title_full | Global Analysis of the Human RNA Degradome Reveals Widespread Decapped and Endonucleolytic Cleaved Transcripts |
| title_fullStr | Global Analysis of the Human RNA Degradome Reveals Widespread Decapped and Endonucleolytic Cleaved Transcripts |
| title_full_unstemmed | Global Analysis of the Human RNA Degradome Reveals Widespread Decapped and Endonucleolytic Cleaved Transcripts |
| title_short | Global Analysis of the Human RNA Degradome Reveals Widespread Decapped and Endonucleolytic Cleaved Transcripts |
| title_sort | global analysis of the human rna degradome reveals widespread decapped and endonucleolytic cleaved transcripts |
| topic | mRNA decay parallel analysis of RNA ends XRN1 decapping |
| url | https://www.mdpi.com/1422-0067/21/18/6452 |
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