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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

Estimation of the number of transcripts with coding potential.Datasets are illustrated in different colors. “TOTAL” means the total transcript dataset whose transcript number was to be estimated. Different datasets were represented by different numbers. I represents transcripts in KNOWN and ALTSCAN datasets but not been validated by RNA-seq data used in this study; II represents transcripts in KNOWN and ALTSCAN datasets and validated by RNA-seq data used in this study; III represents VHC or VHC+VMC transcripts; IV represents novel but real transcripts in ALTSCAN datasets that have not been validated by RNA-seq data used in this study.
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f8: Estimation of the number of transcripts with coding potential.Datasets are illustrated in different colors. “TOTAL” means the total transcript dataset whose transcript number was to be estimated. Different datasets were represented by different numbers. I represents transcripts in KNOWN and ALTSCAN datasets but not been validated by RNA-seq data used in this study; II represents transcripts in KNOWN and ALTSCAN datasets and validated by RNA-seq data used in this study; III represents VHC or VHC+VMC transcripts; IV represents novel but real transcripts in ALTSCAN datasets that have not been validated by RNA-seq data used in this study.

Mentions: In spite of the advancement of RNA-seq technology, estimating the total number of human protein-coding transcripts is still an open problem. Many transcripts are expressed at low levels or in a temporally and spatially specific way. As a consequence, they are difficult to discover making it difficult to estimate the total number of human proteins. ALTSCAN can be used as an ab initio predictor and its sensitivity is no influenced by expression levels. Therefore, we may assume that ALTSCAN’s calculated sensitivity based on known transcripts is equal to the value calculated by considering the undiscovered transcripts (see Fig. 8 and Methods for details). Based on this assumption, we estimated the number of human transcripts with coding potential to be at least 204,950.


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)

Estimation of the number of transcripts with coding potential.Datasets are illustrated in different colors. “TOTAL” means the total transcript dataset whose transcript number was to be estimated. Different datasets were represented by different numbers. I represents transcripts in KNOWN and ALTSCAN datasets but not been validated by RNA-seq data used in this study; II represents transcripts in KNOWN and ALTSCAN datasets and validated by RNA-seq data used in this study; III represents VHC or VHC+VMC transcripts; IV represents novel but real transcripts in ALTSCAN datasets that have not been validated by RNA-seq data used in this study.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f8: Estimation of the number of transcripts with coding potential.Datasets are illustrated in different colors. “TOTAL” means the total transcript dataset whose transcript number was to be estimated. Different datasets were represented by different numbers. I represents transcripts in KNOWN and ALTSCAN datasets but not been validated by RNA-seq data used in this study; II represents transcripts in KNOWN and ALTSCAN datasets and validated by RNA-seq data used in this study; III represents VHC or VHC+VMC transcripts; IV represents novel but real transcripts in ALTSCAN datasets that have not been validated by RNA-seq data used in this study.
Mentions: In spite of the advancement of RNA-seq technology, estimating the total number of human protein-coding transcripts is still an open problem. Many transcripts are expressed at low levels or in a temporally and spatially specific way. As a consequence, they are difficult to discover making it difficult to estimate the total number of human proteins. ALTSCAN can be used as an ab initio predictor and its sensitivity is no influenced by expression levels. Therefore, we may assume that ALTSCAN’s calculated sensitivity based on known transcripts is equal to the value calculated by considering the undiscovered transcripts (see Fig. 8 and Methods for details). Based on this assumption, we estimated the number of human transcripts with coding potential to be at least 204,950.

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