Integrative analysis using proteome and transcriptome data from yeast to unravel regulatory patterns at post-transcriptional level

Biotechnology and Bioengineering
Roberto Olivares-HernándezJens Nielsen

Abstract

Exist several studies on the correlation between proteome and transcriptome and these studies have shown that generally there is only a weak positive correlation between these two omes, which means that post-transcriptional events play an important role in determining the protein levels in the cell. In this study we combined proteome and transcriptome data from six different published dataset to identify patterns that can provide new insight into the reasons for these deviations. By using a categorization method and integrating genome-scale information we found that the relation between protein and mRNA is related to the gene function. We could further identify that for genes belonging to amino acid biosynthetic pathways there is no translational regulation, meaning that there is generally a good correlation between mRNA and protein levels. We also found that there is generally translational control for large proteins and there also evidence for a role of conserved motifs in the 3' untranslated regions in the mRNA-protein correlation, probably by controlling the level of mRNA.

References

Feb 18, 1999·Molecular and Cellular Biology·S P GygiR Aebersold
Oct 19, 1999·Molecular and Cellular Biology·B FutcherJ I Garrels
Apr 25, 2002·Proceedings of the National Academy of Sciences of the United States of America·Yulei WangPatrick O Brown
Jul 4, 2002·Molecular & Cellular Proteomics : MCP·Timothy J GriffinRuedi Aebersold
Jul 19, 2002·Proteomics·Denis F HochstrasserRon D Appel
Mar 1, 2003·Nature Biotechnology·Matthias Mann, Ole N Jensen
Mar 11, 2003·Proceedings of the National Academy of Sciences of the United States of America·Michael P WashburnJohn R Yates
Mar 14, 2003·Nature·Ruedi Aebersold, Matthias Mann
Mar 28, 2003·Proceedings of the National Academy of Sciences of the United States of America·Yoav AravaDaniel Herschlag
Apr 26, 2003·Trends in Biochemical Sciences·Gavin S WilkieNicola K Gray
Aug 22, 2003·Genetics·Hiroshi Akashi
Sep 4, 2003·Genome Biology·Dov GreenbaumMark Gerstein
Jan 8, 2004·Genome Biology·Evan H Hurowitz, Patrick O Brown
Aug 25, 2004·Molecular & Cellular Proteomics : MCP·Andreas BeyerThomas Wilhelm
Sep 28, 2004·Nucleic Acids Research·Mario dos ReisLorenz Wernisch
Feb 16, 2005·Proceedings of the National Academy of Sciences of the United States of America·Kiran Raosaheb Patil, Jens Nielsen
Oct 7, 2005·Genome Biology·Reut ShalgiYitzhak Pilpel
Apr 15, 2006·Science·Bruno Domon, Ruedi Aebersold
Aug 3, 2006·Genes & Development·J Michael ThomsonScott M Hammond
Aug 19, 2006·Proceedings of the National Academy of Sciences of the United States of America·Archana BelleErin K O'Shea
Aug 31, 2007·FEMS Yeast Research·Jens Nielsen, Michael C Jewett
Dec 28, 2007·PLoS Computational Biology·Tamir TullerEytan Ruppin
May 8, 2009·PLoS Biology·Regula E Halbeisen, André P Gerber
Sep 24, 2009·Nucleic Acids Research·Hamed Shateri NajafabadiReza Salavati

❮ Previous
Next ❯

Citations

Dec 23, 2011·FEMS Yeast Research·Il-Kwon KimJens Nielsen
Feb 27, 2017·Molecular & Cellular Proteomics : MCP·Marijke Koppenol-RaabAleksandra Nita-Lazar
Sep 18, 2014·Journal of Proteome Research·Asfa Alli ShaikJayantha Gunaratne

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.