Identification of genome-wide non-canonical spliced regions and analysis of biological functions for spliced sequences using Read-Split-Fly
Abstract Background It is generally thought that most canonical or non-canonical splicing events involving U2- and U12 spliceosomes occur within nuclear pre-mRNAs. However, the question of whether at least some U12-type splicing occurs in the cytoplasm is still unclear. In recent years next-generati...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2017-10-01
|
| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12859-017-1801-y |
| _version_ | 1819073412094492672 |
|---|---|
| author | Yongsheng Bai Jeff Kinne Lizhong Ding Ethan C. Rath Aaron Cox Siva Dharman Naidu |
| author_facet | Yongsheng Bai Jeff Kinne Lizhong Ding Ethan C. Rath Aaron Cox Siva Dharman Naidu |
| author_sort | Yongsheng Bai |
| collection | DOAJ |
| description | Abstract Background It is generally thought that most canonical or non-canonical splicing events involving U2- and U12 spliceosomes occur within nuclear pre-mRNAs. However, the question of whether at least some U12-type splicing occurs in the cytoplasm is still unclear. In recent years next-generation sequencing technologies have revolutionized the field. The “Read-Split-Walk” (RSW) and “Read-Split-Run” (RSR) methods were developed to identify genome-wide non-canonical spliced regions including special events occurring in cytoplasm. As the significant amount of genome/transcriptome data such as, Encyclopedia of DNA Elements (ENCODE) project, have been generated, we have advanced a newer more memory-efficient version of the algorithm, “Read-Split-Fly” (RSF), which can detect non-canonical spliced regions with higher sensitivity and improved speed. The RSF algorithm also outputs the spliced sequences for further downstream biological function analysis. Results We used open access ENCODE project RNA-Seq data to search spliced intron sequences against the U12-type spliced intron sequence database to examine whether some events could occur as potential signatures of U12-type splicing. The check was performed by searching spliced sequences against 5’ss and 3’ss sequences from the well-known orthologous U12-type spliceosomal intron database U12DB. Preliminary results of searching 70 ENCODE samples indicated that the presence of 5’ss with U12-type signature is more frequent than U2-type and prevalent in non-canonical junctions reported by RSF. The selected spliced sequences have also been further studied using miRBase to elucidate their functionality. Preliminary results from 70 samples of ENCODE datasets show that several miRNAs are prevalent in studied ENCODE samples. Two of these are associated with many diseases as suggested in the literature. Specifically, hsa-miR-1273 and hsa-miR-548 are associated with many diseases and cancers. Conclusions Our RSF pipeline is able to detect many possible junctions (especially those with a high RPKM) with very high overall accuracy and relative high accuracy for novel junctions. We have incorporated useful parameter features into the pipeline such as, handling variable-length read data, and searching spliced sequences for splicing signatures and miRNA events. We suggest RSF, a tool for identifying novel splicing events, is applicable to study a range of diseases across biological systems under different experimental conditions. |
| first_indexed | 2024-12-21T17:53:12Z |
| format | Article |
| id | doaj.art-9ab440cce9b4471d9780e380c7e91ff3 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-21T17:53:12Z |
| publishDate | 2017-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-9ab440cce9b4471d9780e380c7e91ff32022-12-21T18:55:17ZengBMCBMC Bioinformatics1471-21052017-10-0118S11374810.1186/s12859-017-1801-yIdentification of genome-wide non-canonical spliced regions and analysis of biological functions for spliced sequences using Read-Split-FlyYongsheng Bai0Jeff Kinne1Lizhong Ding2Ethan C. Rath3Aaron Cox4Siva Dharman Naidu5Department of Biology, Indiana State UniversityDepartment of Mathematics and Computer Science, Indiana State UniversityDepartment of Biology, Indiana State UniversityDepartment of Biology, Indiana State UniversityDepartment of Mathematics and Computer Science, Indiana State UniversityDepartment of Mathematics and Computer Science, Indiana State UniversityAbstract Background It is generally thought that most canonical or non-canonical splicing events involving U2- and U12 spliceosomes occur within nuclear pre-mRNAs. However, the question of whether at least some U12-type splicing occurs in the cytoplasm is still unclear. In recent years next-generation sequencing technologies have revolutionized the field. The “Read-Split-Walk” (RSW) and “Read-Split-Run” (RSR) methods were developed to identify genome-wide non-canonical spliced regions including special events occurring in cytoplasm. As the significant amount of genome/transcriptome data such as, Encyclopedia of DNA Elements (ENCODE) project, have been generated, we have advanced a newer more memory-efficient version of the algorithm, “Read-Split-Fly” (RSF), which can detect non-canonical spliced regions with higher sensitivity and improved speed. The RSF algorithm also outputs the spliced sequences for further downstream biological function analysis. Results We used open access ENCODE project RNA-Seq data to search spliced intron sequences against the U12-type spliced intron sequence database to examine whether some events could occur as potential signatures of U12-type splicing. The check was performed by searching spliced sequences against 5’ss and 3’ss sequences from the well-known orthologous U12-type spliceosomal intron database U12DB. Preliminary results of searching 70 ENCODE samples indicated that the presence of 5’ss with U12-type signature is more frequent than U2-type and prevalent in non-canonical junctions reported by RSF. The selected spliced sequences have also been further studied using miRBase to elucidate their functionality. Preliminary results from 70 samples of ENCODE datasets show that several miRNAs are prevalent in studied ENCODE samples. Two of these are associated with many diseases as suggested in the literature. Specifically, hsa-miR-1273 and hsa-miR-548 are associated with many diseases and cancers. Conclusions Our RSF pipeline is able to detect many possible junctions (especially those with a high RPKM) with very high overall accuracy and relative high accuracy for novel junctions. We have incorporated useful parameter features into the pipeline such as, handling variable-length read data, and searching spliced sequences for splicing signatures and miRNA events. We suggest RSF, a tool for identifying novel splicing events, is applicable to study a range of diseases across biological systems under different experimental conditions.http://link.springer.com/article/10.1186/s12859-017-1801-yRead-Split-FlyAlternative splicingNon-canonicalRNA-SeqENCODE |
| spellingShingle | Yongsheng Bai Jeff Kinne Lizhong Ding Ethan C. Rath Aaron Cox Siva Dharman Naidu Identification of genome-wide non-canonical spliced regions and analysis of biological functions for spliced sequences using Read-Split-Fly BMC Bioinformatics Read-Split-Fly Alternative splicing Non-canonical RNA-Seq ENCODE |
| title | Identification of genome-wide non-canonical spliced regions and analysis of biological functions for spliced sequences using Read-Split-Fly |
| title_full | Identification of genome-wide non-canonical spliced regions and analysis of biological functions for spliced sequences using Read-Split-Fly |
| title_fullStr | Identification of genome-wide non-canonical spliced regions and analysis of biological functions for spliced sequences using Read-Split-Fly |
| title_full_unstemmed | Identification of genome-wide non-canonical spliced regions and analysis of biological functions for spliced sequences using Read-Split-Fly |
| title_short | Identification of genome-wide non-canonical spliced regions and analysis of biological functions for spliced sequences using Read-Split-Fly |
| title_sort | identification of genome wide non canonical spliced regions and analysis of biological functions for spliced sequences using read split fly |
| topic | Read-Split-Fly Alternative splicing Non-canonical RNA-Seq ENCODE |
| url | http://link.springer.com/article/10.1186/s12859-017-1801-y |
| work_keys_str_mv | AT yongshengbai identificationofgenomewidenoncanonicalsplicedregionsandanalysisofbiologicalfunctionsforsplicedsequencesusingreadsplitfly AT jeffkinne identificationofgenomewidenoncanonicalsplicedregionsandanalysisofbiologicalfunctionsforsplicedsequencesusingreadsplitfly AT lizhongding identificationofgenomewidenoncanonicalsplicedregionsandanalysisofbiologicalfunctionsforsplicedsequencesusingreadsplitfly AT ethancrath identificationofgenomewidenoncanonicalsplicedregionsandanalysisofbiologicalfunctionsforsplicedsequencesusingreadsplitfly AT aaroncox identificationofgenomewidenoncanonicalsplicedregionsandanalysisofbiologicalfunctionsforsplicedsequencesusingreadsplitfly AT sivadharmannaidu identificationofgenomewidenoncanonicalsplicedregionsandanalysisofbiologicalfunctionsforsplicedsequencesusingreadsplitfly |