CoChat
Sign Up
PreprintCited by 392RNA and protein synthesis mechanismsRNA Research and SplicingRNA modifications and cancer

The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.

Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation

Open access
Weinberg, David E., Shah, Premal, Eichhorn, Stephen W., Hussmann, Jeffrey A., Plotkin, Joshua B., Bartel, David P.·2015·Cell Reports
DOI 10.1101/021501PMC PMC4767672

Preprint — published as 10.1016/j.celrep.2016.01.043 · Paper page

Open this paper in CoChat — free accountOpen PDF

Abstract

Ribosome-footprint profiling provides genome-wide snapshots of translation, but technical challenges can confound its analysis. Here, we use improved methods to obtain ribosome-footprint profiles and mRNA abundances that more faithfully reflect gene expression in Saccharomyces cerevisiae . Our results support proposals that both the beginning of coding regions and codons matching rare tRNAs are more slowly translated. They also indicate that emergent polypeptides with as few as three basic residues within a 10-residue window tend to slow translation. With the improved mRNA measurements, the variation attributable to translational control in exponentially growing yeast was less than previously reported, and most of this variation could be predicted with a simple model that considered mRNA abundance, upstream open reading frames, cap-proximal structure and nucleotide composition, and lengths of the coding and 5’-untranslated regions. Collectively, our results reveal key features of translational control in yeast and provide a framework for executing and interpreting ribosome-profiling studies.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1101/021501

Cites

2 of 2 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 107

  1. 10.1038/nature06974 · DOI · Paper page
  2. 1990, Codon preferences in free-living microorganisms, Microbiological reviews, 54, 198, 10.1128/mr.54.2.198-210.1990 · DOI
  3. 10.1073/pnas.0635171100 · DOI · Paper page
  4. 10.1101/gr.150342.112 · DOI
  5. 10.1101/gr.175893.114 · DOI
  6. 10.1101/gr.165522.113 · DOI · Paper page
  7. 10.1091/mbc.11.3.833 · DOI
  8. 10.1093/nar/30.1.276 · DOI
  9. 1982, Codon selection in yeast, The Journal of biological chemistry, 257, 3026, 10.1016/S0021-9258(19)81068-2 · DOI
  10. 2013, Translation initiation factors eIF3 and HCR1 control translation termination and stop codon read-through in yeast cells, PLoS genetics, 9, e1003962, 10.1371/journal.pgen.1003962 · DOI
  11. 10.1016/j.cell.2012.10.044 · DOI
  12. 10.1126/science.1215110 · DOI · Paper page
  13. 1991, The selection-mutation-drift theory of synonymous codon usage, Genetics, 129, 897, 10.1093/genetics/129.3.897 · DOI
  14. 10.1371/journal.pbio.1001508 · DOI
  15. 10.1002/aja.1001780102 · DOI
  16. 10.1371/journal.pone.0009114 · DOI
  17. 10.1016/S0092-8674(00)81360-4 · DOI
  18. 10.1016/0022-2836(92)90486-4 · DOI
  19. 10.1371/journal.pgen.1005206 · DOI · Paper page
  20. 10.1038/nature07341 · DOI · Paper page
  21. 10.1016/0092-8674(92)90193-G · DOI · Paper page
  22. 10.7554/eLife.01179 · DOI
  23. 10.1016/j.molcel.2014.08.028 · DOI · Paper page
  24. Gardin, J. , Yeasmin, R. , Yurovsky, A. , Cai, Y. , Skiena, S. , and Futcher, B. (2014). Measurement of average decoding rates of the 61 sense codons in vivo. eLife 3. · DOI
  25. Gerashchenko, M.V. , and Gladyshev, V.N. (2014). Translation inhibitors cause abnormalities in ribosome profiling experiments. Nucleic acids research. · DOI · Paper page
  26. 10.1073/pnas.1120799109 · DOI · Paper page
  27. 1985, Cap accessibility correlates with the initiation efficiency of alfalfa mosaic virus RNAs, European journal of biochemistry / FEBS, 147, 549
  28. 10.1146/annurev.bi.57.070188.001215 · DOI
  29. 10.1093/nar/10.22.7055 · DOI
  30. 10.1038/nature09267 · DOI · Paper page
  31. 10.1016/j.cell.2014.02.006 · DOI
  32. 10.1016/0092-8674(85)90022-4 · DOI
  33. 10.1074/jbc.C300300200 · DOI
  34. 10.1038/nature10912 · DOI · Paper page
  35. 10.1038/nature08265 · DOI
  36. 10.1038/220481a0 · DOI
  37. 10.1016/0022-2836(81)90003-6 · DOI
  38. 1985, Codon usage and tRNA content in unicellular and multicellular organisms, Molecular biology and evolution, 2, 13
  39. 10.1038/nrg3645 · DOI
  40. 2012, The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments, Nature protocols, 7, 1534, 10.1038/nprot.2012.086 · DOI
  41. 10.1126/science.1168978 · DOI · Paper page
  42. 10.1016/j.cell.2011.10.002 · DOI · Paper page
  43. 10.1093/nar/gkr693 · DOI
  44. 10.1093/bioinformatics/btu031 · DOI
  45. 10.1091/mbc.8.10.1845 · DOI
  46. 10.1038/nature09322 · DOI
  47. 10.1126/science.1135308 · DOI · Paper page
  48. 10.1093/nar/12.9.3873 · DOI
  49. 10.1073/pnas.83.9.2850 · DOI · Paper page
  50. 10.1016/0092-8674(86)90762-2 · DOI · Paper page
  51. 10.1126/science.1170160 · DOI · Paper page
  52. 10.7554/eLife.01257 · DOI
  53. 10.1261/rna.2411710 · DOI
  54. 10.1016/j.cell.2014.02.033 · DOI
  55. 10.1038/nature10965 · DOI
  56. 10.1016/j.jmb.2008.08.089 · DOI
  57. 10.1101/gr.164996.113 · DOI · Paper page
  58. 10.1016/0092-8674(86)90384-3 · DOI
  59. 10.1126/science.1158441 · DOI · Paper page
  60. 10.1101/gr.138545.112 · DOI
  61. 10.1186/1471-2164-12-68 · DOI
  62. 2013, Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding, Nature structural & molecular biology, 20, 237, 10.1038/nsmb.2466 · DOI
  63. 10.1038/nrg2899 · DOI
  64. 2012, Balanced codon usage optimizes eukaryotic translational efficiency, PLoS genetics, 8, e1002603, 10.1371/journal.pgen.1002603 · DOI
  65. 10.1093/bioinformatics/btq509 · DOI · Paper page
  66. 10.1261/rna.035865.112 · DOI
  67. 10.1038/nature12894 · DOI
  68. 10.1016/S0092-8674(01)00505-0 · DOI
  69. 10.1038/nchembio.304 · DOI
  70. 10.1016/j.cell.2013.05.049 · DOI · Paper page
  71. 10.1073/pnas.1016719108 · DOI
  72. 10.1093/nar/15.3.1281 · DOI · Paper page
  73. 10.1126/science.1118977 · DOI
  74. 10.1186/1758-907X-3-4 · DOI
  75. 10.1016/0022-2836(91)90211-N · DOI
  76. 10.1038/nature13007 · DOI · Paper page
  77. 10.1101/gad.480508 · DOI
  78. 1996, Association of the yeast poly(A) tail binding protein with translation initiation factor eIF-4G, The EMBO journal, 15, 7168, 10.1002/j.1460-2075.1996.tb01108.x · DOI
  79. 1996, Ribosome-mediated translational pause and protein domain organization, Protein science : a publication of the Protein Society, 5, 1594, 10.1002/pro.5560050814 · DOI
  80. 10.1038/nature11083 · DOI · Paper page
  81. 10.1016/j.cell.2010.03.031 · DOI · Paper page
  82. 10.1016/0022-2836(84)90027-5 · DOI
  83. 10.1016/S1097-2765(00)80122-7 · DOI
  84. 10.1093/nar/gkn762 · DOI
  85. 10.1074/jbc.M111.325001 · DOI
  86. 1999, Papillomavirus capsid protein expression level depends on the match between codon usage and tRNA availability, Journal of virology, 73, 4972, 10.1128/JVI.73.6.4972-4982.1999 · DOI
  87. 2013, Loss of a conserved tRNA anticodon modification perturbs cellular signaling, PLoS genetics, 9, e1003675, 10.1371/journal.pgen.1003675 · DOI
  88. 10.1101/gr.150342.112 · DOI
  89. 10.1101/gr.165522.113 · DOI · Paper page
  90. 10.1126/science.1215110 · DOI · Paper page
  91. 10.1073/pnas.1106999108 · DOI
  92. 10.1016/0022-2836(89)90170-8 · DOI
  93. 10.1093/nar/gku671 · DOI · Paper page
  94. 10.1073/pnas.1120799109 · DOI · Paper page
  95. 10.1021/j100540a008 · DOI
  96. 10.1016/j.cell.2014.02.006 · DOI
  97. 1994, Fast folding and comparison of RNA secondary structures, Monatshefte für Chemie, 125, 167, 10.1007/BF00818163 · DOI
  98. 10.1126/science.1168978 · DOI · Paper page
  99. 10.1093/bioinformatics/btu031 · DOI
  100. 10.1126/science.1135308 · DOI · Paper page
  101. 10.1017/S135583820100214X · DOI
  102. 10.1101/gr.164996.113 · DOI · Paper page
  103. 10.1038/nsmb.2466 · DOI
  104. 10.1038/nchembio.304 · DOI
  105. 10.1016/j.cell.2013.05.049 · DOI · Paper page
  106. 10.1093/nar/gkn762 · DOI
  107. 10.1371/journal.pgen.1003675 · DOI

Metadata

Authors
Weinberg, D. E., Shah, P., Eichhorn, S. W., Hussmann, J. A., Plotkin, J. B., & Bartel, D. P.
Affiliations
  • University of California, San Francisco (US)
  • University of Pennsylvania (US)
  • Howard Hughes Medical Institute (US)
  • The University of Texas at Austin (US)
Corresponding author
Weinberg, David E.
ORCID
Venue
Cell Reports
Publisher
openRxiv
Published
2015-06-26
Volume
14
Issue
7
Pages
1787-1799
ISSN
2211-1247 (ISSN-L)
DOI
10.1101/021501
PMC
PMC4767672
OpenAlex
W2793056129
Cited by
392
References
2
Citations by year
2026: 11 · 2025: 32 · 2024: 41 · 2023: 38 · 2022: 25 · 2021: 51 · 2020: 45 · 2019: 42 · 2018: 38 · 2017: 41 · 2016: 26 · 2015: 2
FWCI
25.47
Type
journal article
Language
en
Open access
Licence
Locations
  • Cell Reports (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • David and Lucile Packard Foundation
  • Howard Hughes Medical Institute
  • U.S. Department of the Interior (D12AP00025)
  • Burroughs Wellcome Fund
  • Sandler Foundation
  • National Institutes of Health (DP5OD017895, GM061835)
  • University of California, San Francisco
  • National Institute of General Medical Sciences (GM061835, R01GM061835, R37GM061835)
  • Army Research Office (W911NF-12-1-0552)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
Keywords
ribosome profiling, mRNA levels, Saccharomyces cerevisiae, translational regulation, codon usage, basic residues, upstream open reading frames, mRNA cap, gene expression quantification
MeSH terms
Codon, Ribosomes, RNA, Transfer, Saccharomyces cerevisiae, Protein Biosynthesis, Models, Statistical, Gene Expression Regulation, Fungal, Open Reading Frames, Genome, Fungal, 5' Untranslated Regions, Saccharomyces cerevisiae Proteins

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review