Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins
- Université de Sherbrooke, Canada
- Québec Network for Research on Protein Function, Structure and Engineering, Canada
- Université de Lille, France
- Université Laval, Canada
Figures
Figure 1 with 2 supplements
Annotation of human altORFs.
(a) AltORF nomenclature. AltORFs partially overlapping the CDS must be in a different reading frame. (b) Pipeline for the identification of altORFs. (c) Size distribution of alternative (empty bars, …
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Figure 1—source data 1
Annotation of human altORFs.
- https://doi.org/10.7554/eLife.27860.008
Figure 1—figure supplement 1
10% of altORFs are present in different classes of repeats.
While more than half of the human genome is composed of repeated sequences, only 9.83% or 18,003 altORFs are located inside these repeats (a), compared to 2,45% or 1,677 CDSs (b). AltORFs and CDSs …
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Figure 1—figure supplement 1—source data 1
10% altORFs are present in different classes of repeats.
- https://doi.org/10.7554/eLife.27860.005
Figure 1—figure supplement 2
The proportion of altORFs with a translation initiation site (TIS) with a Kozak motif in hg38 is significantly different from 100 shuffled hg38 transcriptomes.
Percentage of altORFs with a TIS within an optimal Kozak sequence in hg38 (dark blue) compared to 100 shuffled hg38 (light blue). Mean and standard deviations for sequence shuffling are displayed, …
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Figure 1—figure supplement 2—source data 1
Proportion of altORFs with a Kozak motif in hg38 and shuffled hg38.
- https://doi.org/10.7554/eLife.27860.007
Figure 2
Conservation of alternative and reference proteins across different species.
(a) Number of orthologous and paralogous alternative and reference proteins between H. sapiens and other species (pairwise study). (b) Phylogenetic tree: conservation of alternative (blue) and …
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Figure 2—source data 1
Conservation of alternative and reference proteins across different species.
- https://doi.org/10.7554/eLife.27860.011
Figure 3
AltORFs completely nested within CDSs show more extreme PhyloP values (more conserved or faster evolving) than their CDSs.
Differences between altORF and CDS PhyloP scores (altORF PhyloP – CDS PhyloP, y-axis) are plotted against PhyloPs for their respective CDSs (x-axis). We restricted the analysis to altORF-CDS pairs …
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Figure 3—source data 1
Number of orthologous and co-conserved alternative and reference proteins between H. sapiens and other species (pairwise).
- https://doi.org/10.7554/eLife.27860.013
Figure 4
First, second, and third codon nucleotide PhyloP scores for 100 vertebrate species for the CDSs of the NTNG1, RET and VTI1A genes.
Chromosomal coordinates for the different CDSs and altORFs are indicated on the right. The regions highlighted in red indicate the presence of an altORF characterized by a region with elevated …
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Figure 4—source data 1
AltORFs completely nested within CDSs show more extreme PhyloP values (more conserved or faster evolving) than their CDSs.
- https://doi.org/10.7554/eLife.27860.015
Figure 5 with 4 supplements
Expression of human altORFs.
(a) Percentage of CDSs and altORFs with detected TISs by ribosomal profiling and footprinting of human cells (Iacono et al., 2005). The total number of CDSs and altORFs with a detected TIS is …
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Figure 5—source data 1
Expression of human altORFs.
- https://doi.org/10.7554/eLife.27860.021
Figure 5—figure supplement 1
Spectra validation for altSLC35A45’.
Example of validation for altSLC35A45’ specific peptide RVEDEVNSGVGQDGSLLSSPFLK. (a) Experimental MS/MS spectra (PeptideShaker graphic interface output). (b) MS/MS spectra of the synthetic peptide. …
Figure 5—figure supplement 2
Spectra validation for altRELT5’.
Example of validation for altRELT5’-specific peptide VALELLK. (a) Experimental MS/MS spectra (PeptideShaker graphic interface output). (b) MS/MS spectra of the synthetic peptide. Matching peaks are …
Figure 5—figure supplement 3
Spectra validation for altLINC01420nc.
Example of validation for altLINC01420nc-specific peptide WDYPEGTPNGGSTTLPSAPPPASAGLK. (a) Experimental MS/MS spectra (PeptideShaker graphic interface output). (b) MS/MS spectra of the synthetic …
Figure 5—figure supplement 4
Spectra validation for altSRRM2CDS.
Example of validation for altSRRM2CDS-specific peptide EVILDPDLPSGVGPGLHR. (a) Experimental MS/MS spectra (PeptideShaker graphic interface output). (b) MS/MS spectra of the synthetic peptide. …
Figure 6 with 1 supplement
The alternative phosphoproteome in mitosis and EGF-treated cells.
Heatmap showing relative levels of spectral counts for phosphorylated peptides following the indicated treatment (Sharma et al., 2014). For each condition, heatmap colors show the percentage of …
Figure 6—figure supplement 1
Example of a phosphorylated peptide in mitosis - alternative protein AltLINC01420nc (LOC550643, IP_305449.1).
(a) AltLINC01420nc amino acid sequence with detected peptides underlined and phosphorylated peptide in bold (73,9% sequence coverage). (b) MS/MS spectrum for the phosphorylated peptide …
Figure 7
Number of alternative proteins detected by ribosome profiling and mass spectrometry.
The expression of 467 alternative proteins was detected by both ribosome profiling (translation initiation sites, TIS) and mass spectrometry (MS).
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Figure 7—source data 1
Number of alternative proteins detected by ribosome profiling and mass spectrometry.
- https://doi.org/10.7554/eLife.27860.025
Figure 8 with 1 supplement
Human alternative proteome sequence analysis and classification using InterProScan.
(a) InterPro annotation pipeline. (b) Alternative and reference proteins with InterPro signatures. (c) Number of alternative and reference proteins with transmembrane domains (TM), signal peptides …
Figure 8—figure supplement 1
Alternative proteome sequence analysis and classification in P. troglodytes, M. musculus, B. Taurus, D. melanogaster and S. cerevisiae.
For each organism, the number of InterPro signatures (top graphs) and proteins with transmembrane (TM), signal peptide (SP), or TM +SP features (bottom pie charts) is indicated for alternative and …
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Figure 8—figure supplement 1—source data 1
Alternative proteome sequence analysis and classification in P. troglodytes, M. musculus, B. Taurus, D. melanogaster and S. cerevisiae.
- https://doi.org/10.7554/eLife.27860.028
Figure 9
Gene ontology (GO) annotations for human alternative proteins.
GO terms assigned to InterPro entries are grouped into 13 categories for each of the three ontologies. (a) 34 GO terms were categorized into cellular component for 107 alternative proteins. (b) 64 …
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Figure 9—source data 1
Gene ontology(GO) annotations for human alternative proteins.
- https://doi.org/10.7554/eLife.27860.030
Figure 10
Main InterPro entries in human alternative proteins.
(a) The top 10 InterPro families in the human alternative proteome. (b) A total of 110 alternative proteins have between 1 and 23 zinc finger domains.
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Figure 10—source data 1
Main InterPro entries in human alternative proteins.
- https://doi.org/10.7554/eLife.27860.032
Figure 11 with 3 supplements
Some reference and alternative proteins have identical functional domains.
(a) Distribution of the number of identical InterPro entries co-ocurring between alternative and reference proteins coded by the same transcripts. 138 pairs of alternative and reference proteins …
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Figure 11—source data 1
Distribution of the percentage of sequence identity and overlap between alternative-reference protein pairs with (20) or without (80) identical Interpro signature.
- https://doi.org/10.7554/eLife.27860.038
Figure 11—figure supplement 1
Matrix of co-occurrence of InterPro entries between alternative/reference protein pairs coded by the same transcript.
Pixels show the number of times entries co-occur in reference and alternative proteins. Blue pixels indicate that these domains do not co-occur, white pixels indicate that they co-occur once, and …
Figure 11—figure supplement 2
Some reference and alternative proteins have identical functional domains.
The number of reference/alternative protein pairs with identical domains (n = 49) is higher than expected by chance alone (p<0.001). The distribution of expected pairs with identical domains and the …
Figure 11—figure supplement 3
Distribution of the percentage of sequence identity and overlap between alternative-reference protein pairs with (20) or without (80) identical Interpro signature.
There is no significant differences between both groups (p-value=0.6272; Kolmogorov Smirnov test). We conclude that there is no significant association between identity/overlap and functional …
Figure 12 with 6 supplements
AltMiD515’ expression induces mitochondrial fission.
(a) AltMiD515’ coding sequence is located in exon two or the MiD51/MIEF1/SMCR7L gene and in the 5’UTR of the canonical mRNA (RefSeq NM_019008).+2 and+1 indicate reading frames. AltMiD51 amino acid …
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Figure 12—source data 1
Mitochondrial morphologies in HeLa cells.
- https://doi.org/10.7554/eLife.27860.046
Figure 12—figure supplement 1
Spectra validation for altMiD51.
Example of validation for altMiD51 specific peptides YTDRDFYFASIR and GLVFLNGK. (a,c) Experimental MS/MS spectra (PeptideShaker graphic interface output). (b,d) MS/MS spectra of the synthetic …
Figure 12—figure supplement 2
MiD51 expression results in mitochondrial fission.
(a) Confocal microscopy of HeLa cells transfected with MiD51GFP immunostained with anti-TOM20 (red channel) monoclonal antibodies. In each image, boxed areas are shown at higher magnification in the …
Figure 12—figure supplement 3
AltMiD51 is localized in the mitochondrial matrix.
Trypan blue quenching experiment performed on HeLa cells stably expressing the indicated constructs: Matrix-Venus (Mx-Venus) and Intermembrane space-Venus (IMS-Venus). The fluorescence remaining …
Figure 12—figure supplement 4
Mitochondrial function parameters.
(a) Oxygen consumption rates (OCR) in HeLa cells transfected with empty vector (mock) or altMiD51Flag. Mitochondrial function parameters were assessed in basal conditions (basal), in the presence of …
Figure 12—figure supplement 5
Representative confocal images of cells co-expressing altMiD51GFP and Drp1(K38A)HA.
(a) Confocal microscopy of HeLa cells co-transfected with altMiD51GFP and Drp1(K38A)HA immunostained with anti-TOM20 (blue channel) and anti-HA (red channel) monoclonal antibodies. In each image, …
Figure 12—figure supplement 6
Protein immunoblot showing the expression of different constructs in HeLa cells.
HeLa cells were transfected with empty vector (pcDNA3.1), altMiD51(WT)Flag, altMID51(LYR→AAA)Flag, Drp1(K38A)HA, or Drp1(K38A)HA and altMiD51(WT)Flag, as indicated. Proteins were extracted and …
Figure 13
AltMiD51-induced mitochondrial fragmentation is dependent on Drp1.
(a) Bar graphs show mitochondrial morphologies in HeLa cells treated with non-target or Drp1 siRNAs. Cells were mock-transfected (pcDNA3.1) or transfected with altMiD51Flag. Means of three …
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Figure 13—source data 1
Mitochondrial morphologies in HeLa cells treated with non-target or Drp1 siRNAs.
- https://doi.org/10.7554/eLife.27860.048
Figure 14 with 2 supplements
AltDDIT35’ co-localizes and interacts with DDIT3.
(a) AltDDIT35’ coding sequence is located in exons 1 and 2 or the DDIT3/CHOP/GADD153 gene and in the 5’UTR of the canonical mRNA (RefSeq NM_004083.5).+2 and+1 indicate reading frames. AltDDIT3 amino …
Figure 14—figure supplement 1
Protein immunoblot showing the expression of different constructs in HeLa cells.
HeLa cells were co-transfected with GFP and mCherry, or altDDIT3GFP and DDIT3mCherry, as indicated. Proteins were extracted and analyzed by western blot with antibodies, as indicated. Molecular …
Figure 14—figure supplement 2
Colocalization of altDDIT3 with DDIT3.
Scatter plots of Pearson’s Correlation Coefficient and Manders’ Correlation Coefficient after Costes’ automatic threshold (p-value<0.001, based on 1000 rounds of Costes’ randomization colocalization …
Author response image 1
Author response image 2
Tables
Table 1
AltORF and alternative protein annotations in different organisms.
https://doi.org/10.7554/eLife.27860.009| Genomes | Features | |||||
|---|---|---|---|---|---|---|
| Transcripts | Current annotations | Annotations of alternative protein coding sequences | ||||
| mRNAs | Others1* | CDSs | Proteins | AltORFs | Alternative proteins | |
| H. sapiens GRCh38 RefSeq GCF_000001405.26 | 67,765 | 11,755 | 68,264 | 54,498 | 539,134 | 183,191 |
| P. troglodytes 2.1.4 RefSeq GCF_000001515.6 | 55,034 | 7527 | 55,243 | 41,774 | 416,515 | 161,663 |
| M. musculus GRCm38p2, RefSeq GCF_000001635.22 | 73,450 | 18,886 | 73,55 1 | 53,573 | 642,203 | 215,472 |
| B. Taurus UMD3.1.86 | 22,089 | 838 | 22,089 | 21,915 | 79,906 | 73,603 |
| X. tropicalis Ensembl JGI_4.2 | 28,462 | 4644 | 28,462 | 22,614 | 141,894 | 69,917 |
| D. rerio Ensembl ZV10.84 | 44,198 | 8196 | 44,198 | 41,460 | 214,628 | 150,510 |
| D. melanogaster RefSeq GCA_000705575.1 | 30,255 | 3474 | 30,715 | 20,995 | 174,771 | 71,705 |
| C. elegans WBcel235, RefSeq GCF_000002985.6 | 28,653 | 25,256 | 26,458 | 25,750 | 131,830 | 45,603 |
| S. cerevisiae YJM993_v1, RefSeq GCA_000662435.1 | 5471 | 1463 | 5463 | 5423 | 12,401 | 9492 |
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*Other transcripts include miRNAs, rRNAs, ncRNAs, snRNAs, snoRNAs, tRNAs.
†Annotated retained-intron and processed transcripts were classified as mRNAs.
Table 2
Alternative zinc finger proteins detected by mass spectrometry (MS) and ribosome profiling (RP)
https://doi.org/10.7554/eLife.27860.033| Alternative protein accession | Detection method* | Gene | Amino acid sequence | AltORF localization |
|---|---|---|---|---|
| IP_238718.1 | MS | RP11 | MLVEVACSSCRSLLHKGAGASEDGAALEPAHTGGKENGATT | nc |
| IP_278905.1 | RP | ZNF761 | MSVARPLVGSHILYAIIDFILERNLISVMSVARTLVRSHPLYATIDFILERNLTSVMSVARPLVRSQTLHAIVDFILEKNKCNECGEVFNQQAHLAGHHRIHTGEKP | CDS |
| IP_278745.1 | MS and RP | ZNF816 | MSVARPSVRNHPFNAIIYFTLERNLTNVKNVTMFTFADHTLKDIGRFILERDHTNVRFVTRFSGVIHTLQNIREFILERNHTSVINVAGVSVGSHPFNTIIHFTLERNLTHVMNVARFLVEEKTLHVIIDFMLERNLTNVKNVTKFSVADHTLKDIGEFILGKNHTNVRFVTRLSGVIHALQTIREFILERNLTSVINVRRFLIKKESLHNIREFILERNLTSVMNVARFLIKKQALQNIREFILQRNLTSVMSVAKPLLDSQHLFTIKQSMGVGKLYKCNDCHKVFSNATTIANHYRIHIEERSTSVINVANFSDVIHNL | CDS |
| IP_138289.1 | MS | ZSCAN31 | MNIGGATLERNPINVRSVGKPSVPAMASLDTEESTQGKNHMNAKCVGRLSSSAHALFSIRGYTLERSAISVVSVAKPSFRMQGFSSISESTLVRNPISAVSAVNSLVSGHFLRNIRKSTLERDHKGDEFGKAFSHHCNLIRHFRIHTVPAELD | CDS |
| IP_278564.1 | MS | ZNF808 | MIVTKSSVTLQQLQIIGESMMKRNLLSVINVACFSDIVHTLQFIGNLILERNLTNVMIEARSSVKLHPMQNRRIHTGEKPHKCDDCGKAFTSHSHLVGHQRIHTGQKSCKCHQCGKVFSPRSLLAEHEKIHF | 3’UTR |
| IP_275012.1 | MS | ZNF780A | MKPCECTECGKTFSCSSNIVQHVKIHTGEKRYNVRNMGKHLLWMISCLNIRKFRIVRNFVTIRSVDKPSLCTKNLLNTRELILMRNLVNIKECVKNFHHGLGFAQLLSIHTSEKSLSVRNVGRFIATLNTLEFGEDNSCEKVFE | 3’UTR |
| IP_270595.1† | MS | ZNF440 | MHSVERPYKCKICGRGFYSAKSFQIHEKSYTGEKPYECKQCGKAFVSFTSFRYHERTHTGENPYECKQFGKAFRSVKNLRFHKRTHTGEKPCECKKCRKAFHNFSSLQIHERMHRGEKLCECKHCGKAFISAKIL | CDS |
| IP_270643.1† | MS | ZNF763 | MKKLTLERNPINACHVVKPSIFPVPFSIMKGLTLERNPMSVSVGKPSDVPHTFEGMVGLTGEKPYECKECGKAFRSASHLQIHERTQTHIRIHSGERPYKCKTCGKGFYSPTSFQRHEKTHTAEKPYECKQCGKAFSSSSSFWYHERTHTGEKPYECKQCGKAFRSASIQMHAGTHPEEKPYECKQCGKAFRSAPHLRIHGRTHTGEKPYECKECGKAFRSAKNLRIHERTQTHVRMHSVERPYKCKICGKGFYSAKSFQIPEKSYTGEKPYECKQCGKAFISFTSFR | 3’UTR |
| IP_270597.1‡ | MS | ZNF440 | MKNLTLERNPMSVSNVGKPLFPSLPFDIMKGLTLERTPMSVSNLGKPSDLSKIFDFIKGHTLERNPVNVRNVEKHSIISLLCKYMKGCTEERSSVNVSIVGKHSYLPRSFEYMQEHTMERNPMNVKNAEKHSACLLPFIDMKRLTLEGNTMNASNVAKLSLLPVLFNIMKEHTREKPYQCKQCAKAFISSTSFQYHERTHMGEKPYECMPSGKAFISSSSLQYHERTHTGEKPYEYKQCGKAFRSASHLQMHGRTHTGEKPYECKQYGKAFRPDKIL | 3’UTR |
| IP_270609.1‡ | MS | ZNF439 | MNVSNVAKAFTSSSSFQYHERTHTGEKPYQCKQCGKAVRSASRLQMHGSTHTWQKLYECKQYGKAFRSARIL | 3’UTR |
| IP_270663.1‡ | MS | ZNF844 | MHGRTHTQEKPYECKQCGKAFIFSTSFRYHERTHTGEKPYECKQCGKAFRSATQLQMHRKIHTGEKPYECKQCGKAYRSVSQLLVHERTHTVEQPYEYKQYGKAFRFAKNLQIQTMNVNN | CDS |
| IP_270665.1‡ | MS | ZNF844 | MHRKIHTGEKPYECKQCGKAYRSVSQLLVHERTHTVEQPYEYKQYGKAFRFAKNLQIQTMNVNN | CDS |
| IP_270668.1‡ | MS | ZNF844 | MSSTAFQYHEKTHTREKHYECKQCGKAFISSGSLRYHERTHTGEKPYECKQCGKAFRSATQLQMHRKIHTGEKPYECKQCGKAYRSVSQLLVHERTHTVEQPYEYKQYGKAFRFAKNLQIQTMNVNN | 3’UTR |
| IP_138139.1 | MS | ZNF322 | MLSPSRCKRIHTGEQLFKCLQCQLCCRQYEHLIGPQKTHPGEKPQQV | 3’UTR |
| IP_204754.1 | RP | ZFP91-CNTF | MPGETEEPRPPEQQDQEGGEAAKAAPEEPQQRPPEAVAAAPAGTTSSRVLRGGRDRGRAAAAAAAAAVSRRRKAEYPRRRRSSPSARPPDVPGQQPQAAKSPSPVQGKKSPRLLCIEKVTTDKDPKEEKEEEDDSALPQEVSIAASRPSRGWRSSRTSVSRHRDTENTRSSRSKTGSLQLICKSEPNTDQLDYDVGEEHQSPGGISSEEEEEEEEEMLISEEEIPFKDDPRDETYKPHLERETPKPRRKSGKVKEEKEKKEIKVEVEVEVKEEENEIREDEEPPRKRGRRRKDDKSPRLPKRRKKPPIQYVRCEMEGCGTVLAHPRYLQHHIKYQHLLKKKYVCPHPSCGRLFRLQKQLLRHAKHHTDQRDYICEYCARAFKSSHNLAVHRMIHTGEKPLQCEICGFTCRQKASLNWHMKKHDADSFYQFSCNICGKKFEKKDSVVAHKAKSHPEVLIAEALAANAGALITSTDILGTNPESLTQPSDGQGLPLLPEPLGNSTSGECLLLEAEGMSKSYCSGTERSIHR | nc |
| IP_098649.1 | RP | INO80B-WBP1 | MSKLWRRGSTSGAMEAPEPGEALELSLAGAHGHGVHKKKHKKHKKKHKKKHHQEEDAGPTQPSPAKPQLKLKIKLGGQVLGTKSVPTFTVIPEGPRSPSPLMVVDNEEEPMEGVPLEQYRAWLDEDSNLSPSPLRDLSGGLGGQEEEEEQRWLDALEKGELDDNGDLKKEINERLLTARQRALLQKARSQPSPMLPLPVAEGCPPPALTEEMLLKREERARKRRLQAARRAEEHKNQTIERLTKTAATSGRGGRGGARGERRGGRAAAPAPMVRYCSGAQGSTLSFPPGVPAPTAVSQRPSPSGPPPRCSVPGCPHPRRYACSRTGQALCSLQCYRINLQMRLGGPEGPGSPLLATFESCAQE | nc |
| IP_115174.1 | RP | ZNF721 | MYIGEFILERNPTHVENVAKPLDSLQIFMRIRKFILERNPTRVETVAKPLDSLQIFMHIRKFILEIKPYKCKECGKAFKSYYSILKHKRTHTRGMSYEGDECRGL | CDS |
| IP_275016.1 | RP | ZNF780A | MNVRSVGKALIVVHTLFSIRKFIPMRNLLYVGNVRWPLDIIANLLNILEFILVTSHLNVKTVGRPSIVAQALFNIRVFTLVRSPMNVRSVGRLLDFTYNFPNIRKLTQVKNHLNVRNVGNSFVVVQILINIEVFILERNPLNVRNVGKPFDFICTLFDIRNCILVRNPLNVRSVGKPFDFICNLFDIRNCILVRNPLNVRNVERFLVFPPSLIAIRTFTQVRRHLECKECGKSFNRVSNHVQHQSIRAGVKPCECKGCGKGFICGSNVIQHQKIHSSEKLFVCKEWRTTFRYHYHLFNITKFTLVKNPLNVKNVERPSVF | CDS or 3’UTR |
| IP_278870.1 | RP | ZNF845 | MNVARFLIEKQNLHVIIEFILERNIRNMKNVTKFTVVNQVLKDRRIHTGEKAYKCKSL | CDS |
| IP_278888.1 | RP | ZNF765 | MSVARPSAGRHPLHTIIDFILDRNLTNVKIVMKLSVSNQTLKDIGEFILERNYTCNECGKTFNQELTLTCHRRLHSGEKPYKYEELDKAYNFKSNLEIHQKIRTEENLTSVMSVARP | CDS |
| IP_278918.1 | RP | ZNF813 | MNVARVLIGKHTLHVIIDFILERNLTSVMNVARFLIEKHTLHIIIDFILEINLTSVMNVARFLIKKHTLHVTIDFILERNLTSVMNVARFLIKKQTLHVIIDFILERNLTSLMSVAKLLIEKQSLHIIIQFILERNKCNECGKTFCHNSVLVIHKNSYWRETSVMNVAKFLINKHTFHVIIDFIVERNLRNVKHVTKFTVANRASKDRRIHTGEKAYKGEEYHRVFSHKSNLERHKINHTAEKP | CDS |
| IP_280349.1 | RP | ZNF587 | MNAVNVGNHFFPALRFMFIKEFILDKSLISAVNVENPFLNVPVSLNTGEFTLEKGLMNAPNVEKHFSEALPSFIIRVHTGERPYECSEYGKSFAEASRLVKHRRVHTGERPYECCQCGKHQNVCCPRS | CDS |
| IP_280385.1 | RP | ZNF417 | MNAMNVGNHFFPALRFMFIKEFILDKSLISAVNVENPLLNVPVSLNTGEFTLEKGLMNVPNVEKHFSEALPSFIIRVHTGERPYECSEYGKSFAETSRLIKHRRVHTGERPYECCQSGKHQNVCSPWS | CDS |
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*MS, mass spectrometry; RP, ribosome profiling.
† These two proteins were not detected with unique peptides but with shared peptides. One protein only was counted in subsequent analyses.
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These five proteins were not detected with unique peptides but with shared peptides. One protein only was counted in subsequent analyses.
Table 3
Examples of proteins encoded in the same gene and functionally interacting
https://doi.org/10.7554/eLife.27860.052| Gene | Polypeptides* | Reference | altORF localization | altORF size aa | Conservation | Summary of functional relationship with the annotated protein |
|---|---|---|---|---|---|---|
| CDKN2A, INK4 | Cyclin-dependent kinase inhibitor 2A or p16-INK4 (P42771), and p19ARF (Q8N726) | (61) | 5'UTR | 169 | Human, mouse | the unitary inheritance of p16INK4a and p19ARF may underlie their dual requirement in cell cycle control. |
| GNAS, XLalphas | Guanine nucleotide-binding protein G(s) subunit alpha isoforms XLαs (Q5JWF2) and Alex (P84996) | (62) | 5'UTR | +700 | Human, mouse, rat | Both subunits transduce receptor signals into stimulation of adenylyl cyclase. |
| ATXN1 | Ataxin-1 (P54253) and altAtaxin-1 | (63) | CDS | 185 | Human, chimpanzee, cow | Direct interaction |
| Adora2A | A2A adenosine receptor (P30543) and uORF5 | (64) | 5'UTR | 134 | Human, chimpanzee, rat, mouse | A2AR stimulation increases the level of the uORF5 protein via post-transcriptional regulation. |
| AGTR1 | Angiotensin type 1a receptor (P25095) and PEP7 | (65) | 5'UTR | 7 | Highly conserved across mammalian species | Inhibits non-G protein-coupled signalling of angiotensin II, without altering the classical G protein-coupled pathway activated by the ligand. |
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*The UniProtKB accession is indicated when available.
Additional files
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Supplementary file 1
12,616 alternative proteins and 26,531 reference proteins with translation initiation sites detected by ribosome profiling after re-analysis of large-scale studies.
Sheet 1: general information. Sheet 2: list of alternative proteins; sheet 3: pie chart of corresponding altORFs localization. Sheet 4: Sheet 2: list of reference proteins
- https://doi.org/10.7554/eLife.27860.053
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Supplementary file 2
4,872 alternative proteins detected by mass spectrometry (MS) after re-analysis of large proteomic studies.
Sheet 1: MS identification parameters; sheet 2: raw MS output; sheet 3: list of detected alternative proteins; sheet 4: pie chart of corresponding altORFs localization.
- https://doi.org/10.7554/eLife.27860.054
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Supplementary file 3
List of phosphopeptides.
- https://doi.org/10.7554/eLife.27860.055
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Supplementary file 4
Linker sequences separating adjacent zinc finger motifs.
- https://doi.org/10.7554/eLife.27860.056
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Supplementary file 5
100 alternative proteins with 25% to 100% identity and 10% to 100% overlap with their reference protein pairs.
Sheet 1: BlastP output and protein domains.
- https://doi.org/10.7554/eLife.27860.057
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Supplementary file 6
383 alternative proteins detected by mass spectrometry in the interactome of 118 zinc finger proteins.
Sheet 1: MS identification parameters; sheet 2: raw MS output; sheet 3: list of detected alternative proteins.
- https://doi.org/10.7554/eLife.27860.058
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Supplementary file 7
High-confidence list of predicted functional alternative proteins based on conservation and expression analyses.
Sheet 1: high-confidence list in mammals; sheet 2: high-confidence list in in vertebrates.
- https://doi.org/10.7554/eLife.27860.059
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Source code 1
Extraction of PhyloP scores.
- https://doi.org/10.7554/eLife.27860.060
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Transparent reporting form
- https://doi.org/10.7554/eLife.27860.061
