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Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling

View Article: PubMed Central - PubMed

ABSTRACT

Accurate annotation of protein coding regions is essential for understanding how genetic information is translated into function. We describe riboHMM, a new method that uses ribosome footprint data to accurately infer translated sequences. Applying riboHMM to human lymphoblastoid cell lines, we identified 7273 novel coding sequences, including 2442 translated upstream open reading frames. We observed an enrichment of footprints at inferred initiation sites after drug-induced arrest of translation initiation, validating many of the novel coding sequences. The novel proteins exhibit significant selective constraint in the inferred reading frames, suggesting that many are functional. Moreover, ~40% of bicistronic transcripts showed negative correlation in the translation levels of their two coding sequences, suggesting a potential regulatory role for these novel regions. Despite known limitations of mass spectrometry to detect protein expressed at low level, we estimated a 14% validation rate. Our work significantly expands the set of known coding regions in humans.

Doi:: http://dx.doi.org/10.7554/eLife.13328.001

No MeSH data available.


Related in: MedlinePlus

Characteristics of novel uaCDS.(A) Histogram of the distance between uaCDS and their corresponding mCDS. (B) Histogram of the lengths of uaCDS (median length of 16 amino acids).DOI:http://dx.doi.org/10.7554/eLife.13328.022
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fig6s1: Characteristics of novel uaCDS.(A) Histogram of the distance between uaCDS and their corresponding mCDS. (B) Histogram of the lengths of uaCDS (median length of 16 amino acids).DOI:http://dx.doi.org/10.7554/eLife.13328.022

Mentions: To this end, we adapted our approach to identify additional coding sequences within transcripts that are translated in LCLs. Assuming that the sub-codon structure of footprint abundance is similar between the main and alternate CDS, we identified 2442 novel CDSs upstream of the mCDS inferred by our method (FDR = 5%); we call them upstream alternate coding sequences or uaCDS (see Materials and methods for details; see also Figure 6—figure supplement 1). Figure 6A illustrates the ribosome footprint density within the uaCDS of the transmembrane gene TM7SF2, and its conservation across mammals. We find strong enrichment of harringtonine-treated ribosome footprints at the initiation sites of uaCDS similar to the initiation sites of mCDS in the same transcripts (Figure 6B). Using mass-spectrometry data, we identified 46 uaCDS that have at least one peptide hit, substantially lower than the expectation of 891 hits predicted by our model. Finally, comparing the substitution rates at inferred synonymous and nonsynonymous sites, we identified 317 uaCDS with highly constrained coding function (Figure 6C). Those uaCDS with a peptide match and those having evidence of constrained coding function are not concordant (Fisher’s test; p-value = 0.56), consistent with the low sensitivity of standard mass-spectrometry protocols to identify very short proteins.10.7554/eLife.13328.021Figure 6.Short translated sequences identified upstream of thousands of translated main coding sequences.


Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling
Characteristics of novel uaCDS.(A) Histogram of the distance between uaCDS and their corresponding mCDS. (B) Histogram of the lengths of uaCDS (median length of 16 amino acids).DOI:http://dx.doi.org/10.7554/eLife.13328.022
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4940163&req=5

fig6s1: Characteristics of novel uaCDS.(A) Histogram of the distance between uaCDS and their corresponding mCDS. (B) Histogram of the lengths of uaCDS (median length of 16 amino acids).DOI:http://dx.doi.org/10.7554/eLife.13328.022
Mentions: To this end, we adapted our approach to identify additional coding sequences within transcripts that are translated in LCLs. Assuming that the sub-codon structure of footprint abundance is similar between the main and alternate CDS, we identified 2442 novel CDSs upstream of the mCDS inferred by our method (FDR = 5%); we call them upstream alternate coding sequences or uaCDS (see Materials and methods for details; see also Figure 6—figure supplement 1). Figure 6A illustrates the ribosome footprint density within the uaCDS of the transmembrane gene TM7SF2, and its conservation across mammals. We find strong enrichment of harringtonine-treated ribosome footprints at the initiation sites of uaCDS similar to the initiation sites of mCDS in the same transcripts (Figure 6B). Using mass-spectrometry data, we identified 46 uaCDS that have at least one peptide hit, substantially lower than the expectation of 891 hits predicted by our model. Finally, comparing the substitution rates at inferred synonymous and nonsynonymous sites, we identified 317 uaCDS with highly constrained coding function (Figure 6C). Those uaCDS with a peptide match and those having evidence of constrained coding function are not concordant (Fisher’s test; p-value = 0.56), consistent with the low sensitivity of standard mass-spectrometry protocols to identify very short proteins.10.7554/eLife.13328.021Figure 6.Short translated sequences identified upstream of thousands of translated main coding sequences.

View Article: PubMed Central - PubMed

ABSTRACT

Accurate annotation of protein coding regions is essential for understanding how genetic information is translated into function. We describe riboHMM, a new method that uses ribosome footprint data to accurately infer translated sequences. Applying riboHMM to human lymphoblastoid cell lines, we identified 7273 novel coding sequences, including 2442 translated upstream open reading frames. We observed an enrichment of footprints at inferred initiation sites after drug-induced arrest of translation initiation, validating many of the novel coding sequences. The novel proteins exhibit significant selective constraint in the inferred reading frames, suggesting that many are functional. Moreover, ~40% of bicistronic transcripts showed negative correlation in the translation levels of their two coding sequences, suggesting a potential regulatory role for these novel regions. Despite known limitations of mass spectrometry to detect protein expressed at low level, we estimated a 14% validation rate. Our work significantly expands the set of known coding regions in humans.

Doi:: http://dx.doi.org/10.7554/eLife.13328.001

No MeSH data available.


Related in: MedlinePlus