Kobi Perl1,2, Kathy Ushakov1, Yair Pozniak1, Ofer Yizhar-Barnea1, Yoni Bhonker1, Shaked Shivatzki1, Tamar Geiger1, Karen B Avraham3, Ron Shamir4. 1. Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel. 2. Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, 6997801, Israel. 3. Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel. karena@post.tau.ac.il. 4. Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, 6997801, Israel. rshamir@tau.ac.il.
Abstract
BACKGROUND: The quantitative relations between RNA and protein are fundamental to biology and are still not fully understood. Across taxa, it was demonstrated that the protein-to-mRNA ratio in steady state varies in a direction that lessens the change in protein levels as a result of changes in the transcript abundance. Evidence for this behavior in tissues is sparse. We tested this phenomenon in new data that we produced for the mouse auditory system, and in previously published tissue datasets. A joint analysis of the transcriptome and proteome was performed across four datasets: inner-ear mouse tissues, mouse organ tissues, lymphoblastoid primate samples and human cancer cell lines. RESULTS: We show that the protein levels are more conserved than the mRNA levels in all datasets, and that changes in transcription are associated with translational changes that exert opposite effects on the final protein level, in all tissues except cancer. Finally, we observe that some functions are enriched in the inner ear on the mRNA level but not in protein. CONCLUSIONS: We suggest that partial buffering between transcription and translation ensures that proteins can be made rapidly in response to a stimulus. Accounting for the buffering can improve the prediction of protein levels from mRNA levels.
BACKGROUND: The quantitative relations between RNA and protein are fundamental to biology and are still not fully understood. Across taxa, it was demonstrated that the protein-to-mRNA ratio in steady state varies in a direction that lessens the change in protein levels as a result of changes in the transcript abundance. Evidence for this behavior in tissues is sparse. We tested this phenomenon in new data that we produced for the mouse auditory system, and in previously published tissue datasets. A joint analysis of the transcriptome and proteome was performed across four datasets: inner-ear mouse tissues, mouse organ tissues, lymphoblastoid primate samples and humancancer cell lines. RESULTS: We show that the protein levels are more conserved than the mRNA levels in all datasets, and that changes in transcription are associated with translational changes that exert opposite effects on the final protein level, in all tissues except cancer. Finally, we observe that some functions are enriched in the inner ear on the mRNA level but not in protein. CONCLUSIONS: We suggest that partial buffering between transcription and translation ensures that proteins can be made rapidly in response to a stimulus. Accounting for the buffering can improve the prediction of protein levels from mRNA levels.
Entities:
Keywords:
Cochlea; Inner ear; Mass spectrometry; RNA-seq; Translation
Authors: Y Ma; P R Hof; S C Grant; S J Blackband; R Bennett; L Slatest; M D McGuigan; H Benveniste Journal: Neuroscience Date: 2005-09-13 Impact factor: 3.590
Authors: Thomas D Pfister; William C Reinhold; Keli Agama; Shalu Gupta; Sonny A Khin; Robert J Kinders; Ralph E Parchment; Joseph E Tomaszewski; James H Doroshow; Yves Pommier Journal: Mol Cancer Ther Date: 2009-07-07 Impact factor: 6.261
Authors: Simon Rogers; Mark Girolami; Walter Kolch; Katrina M Waters; Tao Liu; Brian Thrall; H Steven Wiley Journal: Bioinformatics Date: 2008-10-30 Impact factor: 6.937
Authors: Christian Oertlin; Julie Lorent; Carl Murie; Luc Furic; Ivan Topisirovic; Ola Larsson Journal: Nucleic Acids Res Date: 2019-07-09 Impact factor: 16.971
Authors: Cindy T J van Velthoven; Antoine de Morree; Ingrid M Egner; Jamie O Brett; Thomas A Rando Journal: Cell Rep Date: 2017-11-14 Impact factor: 9.423
Authors: Yu Han; Sara A Wennersten; Julianna M Wright; R W Ludwig; Edward Lau; Maggie P Y Lam Journal: Am J Physiol Heart Circ Physiol Date: 2022-08-05 Impact factor: 5.125
Authors: P K Smitha; Christopher Bathula; Anil M Kumar; K N Chandrashekara; Sujan K Dhar; Manjula Das Journal: 3 Biotech Date: 2021-05-22 Impact factor: 2.893
Authors: Matthew B Greenblatt; Noriaki Ono; Ugur M Ayturk; Shawon Debnath; Sarfaraz Lalani Journal: J Bone Miner Res Date: 2019-07 Impact factor: 6.741