Limits...
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.


Comparing the periodicity in ribosome footprint counts for footprints of different lengths.Proportion of footprint counts aggregated across 1000 highly expressed annotated coding transcripts, centered at their translation initiation sites. Each subplot illustrates the proportions for footprints of a given length, with the periodicity in the proportions showing distinct features between footprints of different lengths.DOI:http://dx.doi.org/10.7554/eLife.13328.008
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4940163&req=5

fig1s6: Comparing the periodicity in ribosome footprint counts for footprints of different lengths.Proportion of footprint counts aggregated across 1000 highly expressed annotated coding transcripts, centered at their translation initiation sites. Each subplot illustrates the proportions for footprints of a given length, with the periodicity in the proportions showing distinct features between footprints of different lengths.DOI:http://dx.doi.org/10.7554/eLife.13328.008

Mentions: We observed that ribosome footprints with different lengths, arising due to incomplete nuclease digestion, show slightly different patterns of abundance when aggregated across transcripts (see Figure 1—figure supplement 6). To model these differences, we partitioned the footprints into multiple groups based on length, and modeled the data in each group with a separate set of parameters in the emission probability (all groups share the same state sequence along a transcript). Specifically, for groups of footprints, the data at the triplet in reading frame can be partitioned into components, , where denotes the triplet of RPF counts from group. Assuming that the RPF counts from different groups at a given triplet are independent, conditional on the state of the triplet, the emission probability can be written as and(13)Xg,fmn/Yg,fmn,Zf,mn=z ∼ multinomial(Yg,fmn,πg,z),(14)Yg,fmn/Zf,mn=z ∼ Poisson(μg,zfmnEn),(15)μg,zfmn ∼ gamma(αg,z,βg,z),


Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling
Comparing the periodicity in ribosome footprint counts for footprints of different lengths.Proportion of footprint counts aggregated across 1000 highly expressed annotated coding transcripts, centered at their translation initiation sites. Each subplot illustrates the proportions for footprints of a given length, with the periodicity in the proportions showing distinct features between footprints of different lengths.DOI:http://dx.doi.org/10.7554/eLife.13328.008
© Copyright Policy
Related In: Results  -  Collection

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

fig1s6: Comparing the periodicity in ribosome footprint counts for footprints of different lengths.Proportion of footprint counts aggregated across 1000 highly expressed annotated coding transcripts, centered at their translation initiation sites. Each subplot illustrates the proportions for footprints of a given length, with the periodicity in the proportions showing distinct features between footprints of different lengths.DOI:http://dx.doi.org/10.7554/eLife.13328.008
Mentions: We observed that ribosome footprints with different lengths, arising due to incomplete nuclease digestion, show slightly different patterns of abundance when aggregated across transcripts (see Figure 1—figure supplement 6). To model these differences, we partitioned the footprints into multiple groups based on length, and modeled the data in each group with a separate set of parameters in the emission probability (all groups share the same state sequence along a transcript). Specifically, for groups of footprints, the data at the triplet in reading frame can be partitioned into components, , where denotes the triplet of RPF counts from group. Assuming that the RPF counts from different groups at a given triplet are independent, conditional on the state of the triplet, the emission probability can be written as and(13)Xg,fmn/Yg,fmn,Zf,mn=z ∼ multinomial(Yg,fmn,πg,z),(14)Yg,fmn/Zf,mn=z ∼ Poisson(μg,zfmnEn),(15)μg,zfmn ∼ gamma(αg,z,βg,z),

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.