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One-shot analysis of translated mammalian lncRNAs with AHARIBO

  1. Luca Minati
  2. Claudia Firrito
  3. Alessia Del Piano
  4. Alberto Peretti
  5. Simone Sidoli
  6. Daniele Peroni
  7. Romina Belli
  8. Francesco Gandolfi
  9. Alessandro Romanel
  10. Paola Bernabo
  11. Jacopo Zasso
  12. Alessandro Quattrone
  13. Graziano Guella
  14. Fabio Lauria
  15. Gabriella Viero
  16. Massimiliano Clamer  Is a corresponding author
  1. IMMAGINA BioTechnology, Italy
  2. Department of Biochemistry, Albert Einstein College of Medicine, United States
  3. Mass Spectrometry Facility, Computational and Integrative Biology (CIBIO), University of Trento, Italy
  4. Laboratory of Bioinformatics and Computational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Italy
  5. Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Italy
  6. Department of Physics, University of Trento, Italy
  7. Institute of Biophysics, CNR Unit at Trento, Italy
Tools and Resources
Cite this article as: eLife 2021;10:e59303 doi: 10.7554/eLife.59303
8 figures, 4 tables, 5 data sets and 1 additional file

Figures

Figure 1 with 3 supplements
L-Azidohomoalanine (AHA) labeling of nascent peptide chains and ribosome separation.

(A) Schematic representation of AHA-mediated RIBOsome isolation (AHARIBO) workflow. After methionine depletion, AHA incubation, and sBlock treatment, cell lysates can be processed for (1) AHARIBO-rC: isolation of translational complexes (ribosomes, ribosome-associated proteins, nascent peptides, and RNAs); (2) AHARIBO-nP: isolation of de novo synthesized proteome; and (3) AHARIBO RIBO-seq: for ribosome profiling. (B) Polysomal profiles in HeLa cells. On the right of each profile, example of SDS-PAGE of protein extracts from each fraction of the profile. Staining of the membrane was performed by biotin cycloaddition followed by streptavidin-Horseradish peroxidase (HRP). RPL26 protein was used as a marker of the large ribosome subunit. (C) Box plot showing the AHA signal enrichment in the polysomal fractions of the profiles in cells untreated (NT) and treated with either cycloheximide (CHX) or sBlock. Results are shown as the median (±SE) of three independent experiments. NS: not significant. *p-value=0.05 was obtained through an unpaired t-test. (D) Volcano plots of AHARIBO-rC-isolated proteins. Data are compared with input (AHA-containing lysate, left) or with streptavidin-coated beads without biotin-DBCO (right). DBCO: dibenzocyclooctyne. Red line: t-test p-value<0.05.

Figure 1—source data 1

A table with the relative abundance of AHARIBO-rC-isolated proteins.

Relative abundance of AHARIBO-rC-isolated proteins. AHARIBO: AHA-mediated RIBOsome isolation.

https://cdn.elifesciences.org/articles/59303/elife-59303-fig1-data1-v2.xlsx
Figure 1—source data 2

Gene Ontology analysis data.

https://cdn.elifesciences.org/articles/59303/elife-59303-fig1-data2-v2.xlsx
Figure 1—figure supplement 1
L-Azidohomoalanine (AHA) incorporation, validation of AHA, and RNA capture.

(A) Labeling of nascent peptides in cells treated with AHA (250 µM) at different incubation times (10, 30, 60, and 120 min). After SDS-PAGE of cell extracts, AHA residues were biotinylated by on-membrane cycloaddition based ‘click chemistry’ and detected by streptavidin-HRP. (B) Ponceaus S staining of the membrane reported in (A). (C) RNA enrichment in AHARIBO-rC pulldown at different AHA incubation times (10, 30, and 60 min) compared to control (AHA-) and reported as % of input (1/10 of total RNA). (D) RNA enrichment in AHARIBO-rC pulldown before or after sucrose cushioning compared to control (AHA-).

Figure 1—figure supplement 2
Liquid chromatography-mass spectrometry (LC-MS) analysis of AHARIBO-rC proteins and validation by western blot.

Volcano plots showing the -Log (p-value) versus the relative abundance of AHARIBO-rC-isolated proteins. Data are compared with the non-specific signal derived from streptavidin-coated beads incubated with lysates from control (AHA-, without L-azidohomoalanine) (A) and puromycin-treated cells (without sBlock). Red broken line indicates threshold p-value<0.05. (B) Western blots of RPL26, RPS6, and actin with related quantifications of band intensities are reported on the right of each dot blot. AHARIBO: AHA-mediated RIBOsome isolation.

Figure 1—figure supplement 3
AHARIBO-rC efficiency test and validations.

(A, B) Agarose gel electrophoresis of total RNA extracted from input lysates (1/10 of the total lysate volume) and lysates subjected to AHA-mediated RIBOsome isolation (AHARIBO) pulldown, obtained from cells either treated or not treated with L-azidohomoalanine (AHA), with or without puromycin (50 µM) and with different stress. NT: non-treated cells; Ar: arsenite-treated cells; Puro: puromycin treatment (50 µM). Red broken line indicates no enrichment. (C) Total RNA enrichment after AHARIBO-rC pulldown of lysates obtained from unstimulated cells over cells treated with arsenite and heat shock. For each condition, cells were either treated or not treated with AHA. Signal ratios (AHA+/AHA-) for each pulldown sample were normalized to the respective inputs. NT: non-treated; HS: heat shock-treated (42°C for 10 min); Puro: puromycin treatment (50 µM). Square box indicates mean; stars indicate 1–99% percentile. (D) 18S rRNA qRT-PCR analysis of RNA extracted from lysates subjected to AHARIBO-rC pulldown and input lysates obtained from unstimulated cells or cells subjected to arsenite treatment. For each condition, cells were either treated or not treated with AHA. For each sample, 18S AHA+/AHA- signal ratios were normalized to the input and to the housekeeping gene HPRT1. NT: non-treated; Ar: arsenite. (E) Detection of TUG1-BOAT. Scheme of the experimental setup (left) and RT-pPCR enrichment for FUG1-BOAT transcript (right) among the three different constructs normalized to the input and for two different times of transfection (24 and 48 hr) (*p-value<0.05 compared with ΔMet).

Figure 2 with 1 supplement
AHARIBO-nP and pSILAC.

(A) Workflow for parallel AHARIBo-nP and pSILAC. mESCs: mouse embryonic stem cells; EN: mouse embryonic stem cells differentiated in early neurons. (B) Venn diagram representing the number of differentially expressed proteins (EN/mESCs) identified by AHARIBO-nP and pSILAC (p-value<0.05). (C) Volcano plot for each differentially expressed protein (EN/mESC) of AHARIBO-nP proteome versus -log2(p-value). Red broken line indicates p-value<0.05. Orange and purple dots represent upregulated proteins involved in cytoskeleton organization (GO:0007010) and neurogenesis (GO:0022008), respectively. Blue, green, and magenta dots represent downregulated proteins related to RNA processing (GO:0006396), protein synthesis (GO:0006412), and mouse pluripotency (WP1763). Gray dots represent all other proteins. (D) Schematic representation of combined cell treatments for pSILAC and AHARIBO-nP. (E) Volcano plots displaying for each protein the -log2 t-test p-value against the fold changes of protein turnover (heavy/light) in pSILAC proteome (left) and AHARIBO-nP (right) for double-treated mESCs. GO: gene ontology; AHARIBO: AHA-mediated RIBOsome isolation; pSILAC: pulsed SILAC. 

Figure 2—source data 1

A table with the pulsed SILAC (pSILAC) proteomic data.

https://cdn.elifesciences.org/articles/59303/elife-59303-fig2-data1-v2.xlsx
Figure 2—source data 2

A table with AHA-mediated RIBOsome isolation (AHARIBO) differentially expressed proteins.

Proteins are considered differentially expressed when adjusted p-values are smaller than 0.05 AHARIBO-nP differentially expressed proteins.

https://cdn.elifesciences.org/articles/59303/elife-59303-fig2-data2-v2.xlsx
Figure 2—figure supplement 1
Cell differentiation and additional proteomic analysis.

(A) Immunofluorescence for mouse embryonic stem cells (mESCs) (Oct4) and neuronal (β3-tubulin) marker expression on self-renewing mESCs and 15DIV mESC-derived neurons. Scale bar 200 μm. (B) Rank plot of fold change of full proteome (black dots) and ribosomal proteins (green dots) comparing AHA-mediated RIBOsome isolation (AHARIBO) pulldown versus input samples, mild washing (left), and urea washing (right). Since AHARIBO-rC liquid chromatography-mass spectrometry (LC-MS) analysis might cause an underestimation of the de novo synthesized proteome due to the enrichment of abundant ribosomal proteins, newly synthesized proteins bound to dibenzocyclooctyne (DBCO)-conjugate magnetic beads were separated from ribosome subunits by harsh washing conditions (8 M urea) before tryptic digestion and LC-MS analysis. The effectiveness of the washing procedure was confirmed since no evident enrichment of ribosomal proteins in the pulldown was observed. (C) The scatter plots represent protein abundance versus protein turnover in mESCs (left) and early neurons (ENs) (right). (D) Normalized protein abundance (left) and turnover distribution (right) as determined by pulsed SILAC (pSILAC) and AHARIBO. ***p-value<0.001.

Figure 3 with 1 supplement
AHARIBO-rC RNA versus de novo proteome analysis.

(A) Enrichment of a given transcript obtained with AHA-mediated RIBOsome isolation (AHARIBO) versus global translatome (x-axis) as a function of the theoretical protein length (y-axis) for mouse embryonic stem cells (mESCs) (left) and early neurons (ENs) (right). Each bar represents the number of enriched transcripts with the defined theoretical protein length. (B) Fraction of coding genes expressed above a minimum threshold in EN. The AHARIBO-rC and global translatome group are represented in yellow and cyan, respectively. For each group, the mean (solid line) and SD (shades) of the fractions for a given count per million (CPM) threshold are calculated over all samples (n = 6) in that group. (C) Scatter plot of RNA fold change (global translatome on the left, AHARIBO-rC on the right) compared to protein fold change (AHARIBO-nP) obtained by comparing EN with mESC. N: number of differentially expressed genes (DEGs) with p-value<0.05.

Figure 3—source data 1

A table with differentially expressed genes (DEGs) from RNA-seq data comprising logFC, LogCPM, LogFWER, and LogPval.

Genes are considered differentially expressed when both log fold changes are higher/smaller than 1.5/−1.5 and False Discovery Rate (FDR)-adjusted p-values are smaller than 0.01. DEGs from RNA-seq data.

https://cdn.elifesciences.org/articles/59303/elife-59303-fig3-data1-v2.txt
Figure 3—source data 2

A table with RNA and protein differentially expressed genes (DEGs) from AHARIBO-nP, pSILAC, AHARIBO-rC, and global translatome.

Genes are considered differentially expressed when both log fold changes are higher/smaller than 1.5/−1.5 and FDR-adjusted p-values are smaller than 0.01. Proteins are considered differentially expressed when adjusted p-values are smaller than 0.05. RNA and protein DEGs. AHARIBO: AHA-mediated RIBOsome isolation; pSILAC: pulsed SILAC. 

https://cdn.elifesciences.org/articles/59303/elife-59303-fig3-data2-v2.xlsx
Figure 3—figure supplement 1
RNA-seq and protein coding RNA analysis.

(A) Linear plot illustrating the fraction of coding genes (y-axis) expressed above a minimum threshold (x-axis) in mouse embryonic stem cells (mESCs). The AHARIBO-rC and the global translatome group are respectively represented in yellow and cyan as indicated. For each group, the mean (solid line) and the SD (shades) of the fractions for a given count per million (CPM) threshold are calculated over all samples (n = 6) in that group. (B) Histogram showing Pearson’s correlation analysis of AHARIBO-nP protein fold change (EN/mESC) determined by mass spectrometry versus global translatome and AHARIBO-rC RNA fold change (EN/mESC) determined by RNA-seq. N: number of differentially expressed genes (DEGs). p-value<0.05. (C) Histogram of the number of DEGs (EN/mESCs) up- and downregulated in AHARIBO-rC RNA or global translatome relative to the AHARIBO-nP proteome. (D) Scatter plot of RNA fold change (global translatome) compared to protein turnover (pSILAC). AHARIBO: AHA-mediated RIBOsome isolation; EN: early neurons; pSILAC: pulsed SILAC.

Figure 4 with 3 supplements
The AHA-mediated RIBOsome isolation (AHARIBO) platform can be used to detect ribosome-interacting long non-coding RNAs (lncRNAs).

(A) Linear plot illustrating the fraction of non-coding genes expressed above a minimum threshold in early neurons (EN). The AHARIBO-rC and the global translatome group are represented in yellow and cyan, respectively. For each group, the mean (solid line) and the SD (shades) of the fractions for a given count per million (CPM) threshold are calculated over all samples (n = 3) in that group. Expression values are indicated as normalized CPM. AHARIBO-rC was performed on the ribosome pellet after sucrose cushioning. (B) Venn diagram of the number of lncRNAs genes with at least 1 CPM identified by RNA-seq, AHARIBO-rC, RIBO-seq, and AHARIBO RIBO-seq. (C) Classification of lncRNAs interacting with ribosomes and relative detection through the multiple AHARIBO and standard approaches. ND: no detection of protein synthesis. (D) (Left) Schematic representation of the number of mouse embryonic stem cell (mESC) lncRNAs in common between AHARIBO RIBO-seq, AHARIBO-rC RNA, and standard RIBO-seq. These lnRNAs were validated by liquid chromatography-mass spectrometry (LC-MS). (Right) Example of an AHARIBO RIBO-seq ribosome occupancy profile of lncRNA 1810058I24Rik displaying the reads distribution along the entire transcript and the accumulation of reads at the known short open reading frame (shadow area and blue arrow on top).

Figure 4—source data 1

A table with the list of long non-coding RNAs (lncRNAs) identified by RNA-seq by RNA-seq in mouse embryonic stem cells (mESCs).

https://cdn.elifesciences.org/articles/59303/elife-59303-fig4-data1-v2.txt
Figure 4—source data 2

A table with the list of long non-coding RNAs (lncRNAs) identified by RIBO-seq in mouse embryonic stem cells (mESCs).

https://cdn.elifesciences.org/articles/59303/elife-59303-fig4-data2-v2.txt
Figure 4—source data 3

A table with the list of matching peptides from AHA-mediated RIBOsome isolation's (AHARIBO) identified long non-coding RNAs (lncRNAs).

https://cdn.elifesciences.org/articles/59303/elife-59303-fig4-data3-v2.xlsx
Figure 4—figure supplement 1
Isolation of long non-coding RNAs (lncRNAs) with AHA-mediated RIBOsome isolation (AHARIBO).

(A) Number of up- and downregulated differentially expressed non-coding RNAs in the global translatome and AHARIBO-rC RNA. DE: differentially expressed; ncRNA: non-coding RNA. (B) Venn diagram representing the number of differentially expressed lncRNAs identified by AHARIBO-rC (orange) and number of lncRNAs with at least 1 count per million (CPM) in Ingolia et al., 2011 (blue). (C) Linear plot illustrating the fraction of non-coding genes (y-axis) expressed above a minimum threshold (x-axis) in mouse embryonic stem cells (mESCs) (left) and early neurons (ENs) (right). The AHARIBO-rC and the global translatome group are respectively represented in yellow and cyan as indicated. For each group, the mean (solid line) and the SD (shades) of the fractions for a given CPM threshold are calculated over all samples (n = 6) in that group.

Figure 4—figure supplement 2
AHA-mediated RIBOsome isolation (AHARIBO) RIBO-seq data.

(A) Percentage of ribosome P-sites mapping to the 5′ UTR, coding sequence (CDS), and 3′ UTR of mRNA from AHARIBO RIBO-seq and standard RIBO-seq data. The percentage length of each mRNA region is indicated on the right-hand y-axis. (B) Data correlation of AHARIBO RIBO-seq and standard RIBO-seq (performed on the input) obtained in mouse embryonic stem cells (mESCs). Results are representative of two independent replicates for each method. (C) Percentage of P-sites according to the three reading frames for the 5′ UTR, 3′ UTR, and CDS for AHARIBO RIBO-seq data, reflecting the codon periodicity along the CDS.

Figure 4—figure supplement 3
Translated long non-coding RNAs (lncRNAs).

Representative data of three different lncRNAs (from left to right) displaying massive hallmarks of translation along the entire transcript. In silico translation in three different frames (from top to bottom) was performed to predict potential peptide. Shadow area: predicted in silico micropeptides. The lncRNA reported are representative of a list of translated lncRNA identified by the combination of AHA-mediated RIBOsome isolation (AHARIBO) approaches (between brackets the unique peptide or the number of putative peptides predicted): ENSMUST00000051089 (NSFVNDIFER), ENSMUST00000181328 (KIDNQINLPK), ENSMUST00000181149 (KINQLQNMVKDNK), ENSMUST00000099446 (NLMNVINVVKLLHFS), ENSMUST00000180524 (MSPSQLLELKRNQ), ENSMUST00000182499 (VCVALIINICHIMI), ENSMUST00000134140 (NGGGLLMSYVIK), ENSMUST00000180432 (ELAEQPSSALKTSNREQ), ENSMUST00000181251 (QLTDNQRVNQKA), ENSMUST00000179344 (KELQLK), ENSMUST00000181443 (KGPNDISLAQSYLPI), ENSMUST00000071101 (KNNPPPQNAKPK), ENSMUST00000180407 (IELRENLQTY), ENSMUST00000180489 (EISASANLELNGAPSQQ), ENSMUST00000188038 (LALEELR), ENSMUST00000149246 (LLLPGVIK), ENSMUST00000180396 (23), ENSMUST00000181751 (61), ENSMUST00000182010 (43), ENSMUST00000192833 (94), ENSMUST00000200021 (27), ENSMUST00000223012 (86).

Author response image 1
Total protein staining.

Left, total proteins from mESC and early neurons (EN) cell lysates (20 µg total protein for each sample measured by Bradford assay) loaded on a SDS-PAGE and the membrane stained by biotin-cycloaddition followed by streptavidin-HRP. Central and right panel, agarose gel electrophoresis of total RNA extracted from input lysates (1/10 of the total lysate volume) and lysates subjected to AHARIBO pulldown from mESC (left) or EN cells (right) either treated (+) or not (-) treated with AHA.

Author response image 2
a) HSPA4 fold change (ΔΔct) measured by qPCR in mouse embryonic stem cells and HeLa with or without heat shock (10 min at 42°C).

For each sample, HSPA5 AHA+/AHA- signal ratios were normalized to the control and to the housekeeping gene. b) Left, quantification of AHA content before (control) and after heat shock. On the right, representative image of a SDS-PAGE reporting the total protein content for heat shock (with and without AHA) and not treated sample (with and without AHA). In each lane a total of 1 ug of protein as measured by Bradford assay was loaded. Staining of the membrane was performed by biotin cycloaddition followed by streptavidin-HRP. Experiments were performed in triplicates.

Author response image 3
Protein fold change (log2) of differentially expressed proteins during cellular differentiation of mESCs to early neurons.

Comparison between pSILAC(black) and AHARIBO proteome (red).

Author response image 4
Left, P-site density initiation/CDS ratio for total RIBO-seq (input) and AHARIBO Ribo-seq.

Right, metagene profiles showing the ratio between the AHARIBO density and input read density within the first 450 codons from the start codon. Violet arrow, first 25 codons from the start codon. Blue arrow, first 50 codons from the start codon.

Tables

Key resources table
Reagent type (species)
or resource
DesignationSource or referenceIdentifiersAdditional information
Cell line (Homo sapiens)Papillomavirus-related endocervical adenocarcinomaATCCRRID:CVCL_0030
Cell line (Mus musculus)46C embryonic stem cellsATCCRRID:CVCL_Y482Quattrone A. Lab. (CIBIO)
AntibodyAnti-β3-tubulin (mouse monoclonal)PromegaCat. #G712A
RRID:AB_430874
(1:2000)
AntibodyAnti-Oct4 (mouse monoclonal)Santa Cruz BiotechnologiesCat. #SC 5279
RRID:AB_628051
(1:2000)
AntibodyAnti-human RPL26 (rabbit polyclonal)AbcamCat. #ab59567
RRID:AB_945306
(1:2000)
AntibodyAnti-human RPS6 (rabbit polyclonal)AbcamCat. #ab40820
RRID:AB_945319
(1:2000)
AntibodyAnti-human beta actin (rabbit polyclonal)AbcamCat. #ab8227 RRID:AB_2305186(1:2000)
Recombinant DNA reagentWT TUG1-BOAT (plasmid)PMID:32894169
Recombinant DNA reagentΔ TUG1-BOAT (plasmid)This paperSee 'Materials and methods section: 'TUG1-BOAT ectopic expression and qPCR’
Recombinant DNA reagent+1Met TUG1-BOAT (plasmid)This paperSee 'Materials and methods' section: 'TUG1-BOAT ectopic expression and qPCR’
Peptide, recombinant proteinPrecision Protein StrepTactin-HRP ConjugateBioRadCat. #1610380(1:5000)
Chemical compound, drugL-Arginine-13C6,15N4 hydrochlorideSigma-AldrichCat. #608033
Chemical compound, drugL-Lysine-13C6,15N2 hydrochlorideSigma-AldrichCat. #608041
Chemical compound, drugL-Azidohomoalanine (Click-IT AHA)InvitrogenCat. #C10102
Chemical compound, drugDibenzocyclooctyne-PEG4-biotin conjugateSigma-AldrichCat. #760749SML1656
Chemical compound, drugsBlockIMMAGINA BioTechnologyCat. #SM8
Chemical compound, drugPuromycinSigma-AldrichCat. #P8833
Chemical compound, drugCycloheximideSigma-Aldrich#C4859
Chemical compound, drugLipofectamine 3000 Transfection ReagentThermo Fisher Scientific.Cat. #L3000001
Chemical compound, drugMag-DBCO beadsIMMAGINA BioTechnologyCat. #MDBCO
Chemical compound, drugeMagSi-cN beadsIMMAGINA BioTechnology#018-eMS-001
commercial assay or kitSMART-Seq Stranded KitTakaraCat. #634443
Commercial assay or kitSuperScript III Reverse TranscriptaseThermo FisherCat. #18080044
Commercial assay or kitKapa Probe Fast Universal qPCR KitKapa Biosystems#KK4702
Software, algorithmImage analysisImageJRRID:SCR_003070
Software, algorithmStatistical packageedgeRRRID:SCR_012802
Author response table 1
AHARIBO-rC.

UTR regulatory elements enrichment

Regulatory factor/elementRegulated query genesEnrichment p-valueBH-corrected p-value
Tardbp119 ( 11.90 % )< 1.0E-07< 1.0E-07
Nova2175 ( 17.50 % )< 1.0E-07< 1.0E-07
Srsf3201 ( 20.10 % )< 1.0E-07< 1.0E-07
Ezh2159 ( 15.90 % )1.1E-070.00000034
Ptbp222 ( 2.20 % )1.9E-070.00000057
Apobec121 ( 2.10 % )6.3E-070.0000019
Mbnl224 ( 2.40 % )1.26E-050.00003775
Ago21 ( 2.10 % )7.72E-050.00023166
Srsf268 ( 6.80 % )0.0013780.00275579
Elavl42 ( 0.20 % )0.0016550.00331066
Elavl22 ( 0.20 % )0.0032590.00651716
Elavl13 ( 0.30 % )0.0048740.00974701
Rbms31 ( 0.10 % )0.0236890.02368882
Rbm315 ( 1.50 % )0.0364230.03642291
Rbm8a1 ( 0.10 % )0.0468170.04681703
Author response table 2
Global translatome.

UTR regulatory elements enrichment

Regulatory factor/elementRegulated query genesEnrichment p-valueBH-corrected p-value
Tardbp96 ( 9.60 % )< 1.0E-07< 1.0E-07
Nova2139 ( 13.90 % )< 1.0E-07< 1.0E-07
Srsf3168 ( 16.80 % )< 1.0E-07< 1.0E-07
Srsf256 ( 5.60 % )2.95E-061.77E-05
Apobec119 ( 1.90 % )9.13E-063.65E-05
Ptbp219 ( 1.90 % )1.08E-054.33E-05
Srsf159 ( 5.90 % )7.26E-050.0002177
Elavl22 ( 0.20 % )0.003258580.00651716
Elavl13 ( 0.30 % )0.00487350.00974701
Ago15 ( 1.50 % )0.019498880.03899777
Rbms31 ( 0.10 % )0.023688820.02368882
Rbm8a1 ( 0.10 % )0.046817030.04681703
Author response table 3
lncRNA differentially expressed in mESC after heat shock and captured by AHARIBO-rC.
geneSymbollogFClogCPMPValue
Gm285924.045326-0.185441.01E-07
Gm266352.2374280.0550597.37E-08
1110019D14Rik-2.130093.2246594.19E-07
4930467D21Rik-2.461512.5672172.90E-07
Gm26776-2.61450.7522261.83E-07
Malat1-2.6527311.844341.38E-08
AC162181.1-2.815431.3013711.40E-10
Gm30551-3.160130.5891254.86E-09
Gm5432-3.70264-0.112551.06E-07
mt-Rnr2-4.5688415.378532.27E-10
4930440I19Rik-4.611880.0149353.90E-07

Data availability

All data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided. All sequencing data are deposited in public archives and made available upon publication.

The following data sets were generated
    1. Minati L
    2. Romanel A
    3. Peretti A
    4. Gandolfi F
    5. Clamer M
    (2021) ProteomeXchangeConsortium
    ID PXD022679. One-shot analysis of translated mammalian lncRNAs with AHARIBO - Mass-spectrometry proteomics data.
    1. Minati L
    2. Romanel A
    3. Peretti A
    4. Gandolfi F
    5. Clamer M
    6. Firrito C
    (2021) GEO repository
    ID GSE167865. One-shot analysis of translated mammalian lncRNAs with AHARIBO - Ribo-seq processed data.
    1. Minati L
    2. Romanel A
    3. Peretti A
    4. Gandolfi F
    5. Clamer M
    6. Firrito C
    (2021) NCBI BioProject
    ID PRJNA692822. One-shot analysis of translated mammalian lncRNAs with AHARIBO - NGS processed BAM files.
The following previously published data sets were used
    1. Ingolia NT
    2. Lareau LF
    3. Weissman JS
    (2011) GEO
    ID GSE30839. Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes.

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