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Revealing Missing Human Protein Isoforms Based on Ab Initio Prediction, RNA-seq and Proteomics.

Hu Z, Scott HS, Qin G, Zheng G, Chu X, Xie L, Adelson DL, Oftedal BE, Venugopal P, Babic M, Hahn CN, Zhang B, Wang X, Li N, Wei C - Sci Rep (2015)

Bottom Line: Based on these novel transcripts, at least 36 novel proteins were detected from shotgun proteomics data of 41 breast samples.We also showed L1 retrotransposons have a more significant impact on the origin of new transcripts/genes than previously thought.In the end, the total number of human transcripts with protein-coding potential was estimated to be at least 204,950.

View Article: PubMed Central - PubMed

Affiliation: 1] School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China [2] Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Pudong District, Shanghai 201203, China.

ABSTRACT
Biological and biomedical research relies on comprehensive understanding of protein-coding transcripts. However, the total number of human proteins is still unknown due to the prevalence of alternative splicing. In this paper, we detected 31,566 novel transcripts with coding potential by filtering our ab initio predictions with 50 RNA-seq datasets from diverse tissues/cell lines. PCR followed by MiSeq sequencing showed that at least 84.1% of these predicted novel splice sites could be validated. In contrast to known transcripts, the expression of these novel transcripts were highly tissue-specific. Based on these novel transcripts, at least 36 novel proteins were detected from shotgun proteomics data of 41 breast samples. We also showed L1 retrotransposons have a more significant impact on the origin of new transcripts/genes than previously thought. Furthermore, we found that alternative splicing is extraordinarily widespread for genes involved in specific biological functions like protein binding, nucleoside binding, neuron projection, membrane organization and cell adhesion. In the end, the total number of human transcripts with protein-coding potential was estimated to be at least 204,950.

No MeSH data available.


Related in: MedlinePlus

Distribution of alternative splicing in KNOWN and novel datasets.A. Distributions of transcript number per gene in KNOWN, KNOWN+VHC and KNOWN+VMC datasets. Genes are grouped by their transcript number. X-axis stands for the group (the number of transcripts per gene), and Y-axis stands for the numbers of genes in each group. All genes with transcript numbers greater than 20 were merged in the same group. B. The number of different AS events in KNOWN, KNOWN + VHC and KNOWN+VMC datasets. In order to be comparable, number of AS events involved in each type were measured by using the number of splice sites (see Supplementary material for details).
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f7: Distribution of alternative splicing in KNOWN and novel datasets.A. Distributions of transcript number per gene in KNOWN, KNOWN+VHC and KNOWN+VMC datasets. Genes are grouped by their transcript number. X-axis stands for the group (the number of transcripts per gene), and Y-axis stands for the numbers of genes in each group. All genes with transcript numbers greater than 20 were merged in the same group. B. The number of different AS events in KNOWN, KNOWN + VHC and KNOWN+VMC datasets. In order to be comparable, number of AS events involved in each type were measured by using the number of splice sites (see Supplementary material for details).

Mentions: Recent RNA-seq analysis indicated that 95% of human multi-exon genes are alternatively spliced11. However, until now, there were still 5,166 multi-exon genes with only one transcript in the KNOWN dataset. We introduced 31,566 VMC/11,549 VHC transcripts (pseudo-transcript removed), which increased the average transcript number per gene from 2.76 to 4.18/3.30 and decreased the proportion of multi-exon genes with single transcripts from 30.5% to 25.6%/27.2% (Fig. 7A).


Revealing Missing Human Protein Isoforms Based on Ab Initio Prediction, RNA-seq and Proteomics.

Hu Z, Scott HS, Qin G, Zheng G, Chu X, Xie L, Adelson DL, Oftedal BE, Venugopal P, Babic M, Hahn CN, Zhang B, Wang X, Li N, Wei C - Sci Rep (2015)

Distribution of alternative splicing in KNOWN and novel datasets.A. Distributions of transcript number per gene in KNOWN, KNOWN+VHC and KNOWN+VMC datasets. Genes are grouped by their transcript number. X-axis stands for the group (the number of transcripts per gene), and Y-axis stands for the numbers of genes in each group. All genes with transcript numbers greater than 20 were merged in the same group. B. The number of different AS events in KNOWN, KNOWN + VHC and KNOWN+VMC datasets. In order to be comparable, number of AS events involved in each type were measured by using the number of splice sites (see Supplementary material for details).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4496727&req=5

f7: Distribution of alternative splicing in KNOWN and novel datasets.A. Distributions of transcript number per gene in KNOWN, KNOWN+VHC and KNOWN+VMC datasets. Genes are grouped by their transcript number. X-axis stands for the group (the number of transcripts per gene), and Y-axis stands for the numbers of genes in each group. All genes with transcript numbers greater than 20 were merged in the same group. B. The number of different AS events in KNOWN, KNOWN + VHC and KNOWN+VMC datasets. In order to be comparable, number of AS events involved in each type were measured by using the number of splice sites (see Supplementary material for details).
Mentions: Recent RNA-seq analysis indicated that 95% of human multi-exon genes are alternatively spliced11. However, until now, there were still 5,166 multi-exon genes with only one transcript in the KNOWN dataset. We introduced 31,566 VMC/11,549 VHC transcripts (pseudo-transcript removed), which increased the average transcript number per gene from 2.76 to 4.18/3.30 and decreased the proportion of multi-exon genes with single transcripts from 30.5% to 25.6%/27.2% (Fig. 7A).

Bottom Line: Based on these novel transcripts, at least 36 novel proteins were detected from shotgun proteomics data of 41 breast samples.We also showed L1 retrotransposons have a more significant impact on the origin of new transcripts/genes than previously thought.In the end, the total number of human transcripts with protein-coding potential was estimated to be at least 204,950.

View Article: PubMed Central - PubMed

Affiliation: 1] School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China [2] Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Pudong District, Shanghai 201203, China.

ABSTRACT
Biological and biomedical research relies on comprehensive understanding of protein-coding transcripts. However, the total number of human proteins is still unknown due to the prevalence of alternative splicing. In this paper, we detected 31,566 novel transcripts with coding potential by filtering our ab initio predictions with 50 RNA-seq datasets from diverse tissues/cell lines. PCR followed by MiSeq sequencing showed that at least 84.1% of these predicted novel splice sites could be validated. In contrast to known transcripts, the expression of these novel transcripts were highly tissue-specific. Based on these novel transcripts, at least 36 novel proteins were detected from shotgun proteomics data of 41 breast samples. We also showed L1 retrotransposons have a more significant impact on the origin of new transcripts/genes than previously thought. Furthermore, we found that alternative splicing is extraordinarily widespread for genes involved in specific biological functions like protein binding, nucleoside binding, neuron projection, membrane organization and cell adhesion. In the end, the total number of human transcripts with protein-coding potential was estimated to be at least 204,950.

No MeSH data available.


Related in: MedlinePlus