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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

Comparing the amino acid content between annotated and novel CDS.The overall amino acid content is largely similar between annotated CDSs and novel CDSs (mCDS, pseudogenes and uaCDS), with a substantially higher proportion of lysine and isoleucine residues in CDSs within pseudogenes, and a higher proportion of alanine, arginine, glycine, and proline residues within mCDS and uaCDS.DOI:http://dx.doi.org/10.7554/eLife.13328.014
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fig3s2: Comparing the amino acid content between annotated and novel CDS.The overall amino acid content is largely similar between annotated CDSs and novel CDSs (mCDS, pseudogenes and uaCDS), with a substantially higher proportion of lysine and isoleucine residues in CDSs within pseudogenes, and a higher proportion of alanine, arginine, glycine, and proline residues within mCDS and uaCDS.DOI:http://dx.doi.org/10.7554/eLife.13328.014

Mentions: Unlike current CDS annotations, which almost exclusively start at the methionine codon AUG, these novel mCDS taken together have a substantially higher usage of non-canonical codons, particularly CUG (Figure 3B), consistent with recent observations in mouse embryonic stem cells (Ingolia et al., 2011) and human embryonic kidney cells (Lee et al., 2012). This is despite the fact that we inferred the initiation site by assuming shared properties between novel and annotated CDS. Although riboHMM has a high error rate when identifying translation initiation sites, our use of a hierarchical model for the initiation sites suggests that the errors in our inferred start codons are likely to be unbiased. These novel mCDS are also significantly shorter than annotated CDSs (median lengths 23 vs. 339 amino acids, Mann-Whitney test p-value < 2.2 × 10−16; Figure 3C). The overall amino acid content within novel mCDS is comparable to that within annotated CDS, with a slight enrichment for arginine, alanine, cysteine, glycine, proline, and tryptophan residues (binomial test, p-value < 1.1 × 10−16; Figure 3—figure supplement 2).


Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling
Comparing the amino acid content between annotated and novel CDS.The overall amino acid content is largely similar between annotated CDSs and novel CDSs (mCDS, pseudogenes and uaCDS), with a substantially higher proportion of lysine and isoleucine residues in CDSs within pseudogenes, and a higher proportion of alanine, arginine, glycine, and proline residues within mCDS and uaCDS.DOI:http://dx.doi.org/10.7554/eLife.13328.014
© Copyright Policy
Related In: Results  -  Collection

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

fig3s2: Comparing the amino acid content between annotated and novel CDS.The overall amino acid content is largely similar between annotated CDSs and novel CDSs (mCDS, pseudogenes and uaCDS), with a substantially higher proportion of lysine and isoleucine residues in CDSs within pseudogenes, and a higher proportion of alanine, arginine, glycine, and proline residues within mCDS and uaCDS.DOI:http://dx.doi.org/10.7554/eLife.13328.014
Mentions: Unlike current CDS annotations, which almost exclusively start at the methionine codon AUG, these novel mCDS taken together have a substantially higher usage of non-canonical codons, particularly CUG (Figure 3B), consistent with recent observations in mouse embryonic stem cells (Ingolia et al., 2011) and human embryonic kidney cells (Lee et al., 2012). This is despite the fact that we inferred the initiation site by assuming shared properties between novel and annotated CDS. Although riboHMM has a high error rate when identifying translation initiation sites, our use of a hierarchical model for the initiation sites suggests that the errors in our inferred start codons are likely to be unbiased. These novel mCDS are also significantly shorter than annotated CDSs (median lengths 23 vs. 339 amino acids, Mann-Whitney test p-value < 2.2 × 10−16; Figure 3C). The overall amino acid content within novel mCDS is comparable to that within annotated CDS, with a slight enrichment for arginine, alanine, cysteine, glycine, proline, and tryptophan residues (binomial test, p-value < 1.1 × 10−16; Figure 3—figure supplement 2).

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