Transcriptomics and Proteomics: Integration?

Abstract

The genes are transcribed to pre‐messenger RNA, further processed to messenger RNA (transcripts), and finally translated into protein. The transcriptome constitutes the complete set of different transcripts that is synthesized in the lifetime of a cell or a tissue. The proteome refers to the complete set of proteins that is expressed, and modified following expression in the lifetime of a cell or a given tissue. Transcriptomics refers to the study of the transcriptome, while proteomics refers to the study of the proteome using large‐scale technologies for transcript or protein analyses. The two disciplines each provide unique information and supplement each other.

Keywords: transcriptome; transcriptomics; proteome; proteomics

Figure 1.

Flow of information from DNA via mRNA to protein. A gene (DNA) is transcribed (step 1) to the various forms of RNA, first to pre‐mRNA that may be edited (step 2) and then processed (step 3) to one or by alternative splicing to several forms of mRNAs. The mRNAs are then transported (step 4) out of the nucleus to the cytosol. In the cytosol, the mRNA may be degraded (step 5) or translated (step 6) into protein. The activities of the proteins are controlled (step 7). They may be synthesized as inactive proteins that later are reversibly or irreversibly activated, or alternatively synthesized as active proteins that later are inactivated. Proteins are the ultimate effecting molecules producing the physiologic effect (step 8) in virtually every mechanism in the cell.

close

References

Adams MD, Kelley JM, Gocayne JD, et al. (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252: 1651–1656.

Anderson L and Seilhamer J (1997) A comparison of selected mRNA and protein abundances in human liver. Electrophoresis 18: 533–537.

Day DA and Tuite MF (1998) Post‐transcriptional gene regulatory mechanisms in eukaryotes: an overview. Journal of Endocrinology 157: 361–371.

Emili AQ and Cagney G (2000) Large‐scale functional analysis using peptide or protein arrays. Nature Biotechnology 18: 393–397.

Futcher B, Latter GI, Monardo P, McLaughlin CS and Garrels JI (1999) A sampling of the yeast proteome. Molecular and Cellular Biology 19: 7357–7368.

Ginzinger DG (2002) Gene quantification using real‐time quantitative PCR: an emerging technology hits the mainstream. Experimental Hematology 30: 503–512.

Görg A, Obermaier C, Boguth G, et al. (2000) The current state of two‐dimensional electrophoresis with immobilized pH gradients. Electrophoresis 21: 1037–1053.

Gygi SP, Rochon Y, Franza BR and Aebersold R (1999) Correlation between protein and mRNA abundance in yeast. Molecular and Cellular Biology 19: 1720–1730.

Honoré B (2001) Genome‐ and proteome‐based technologies: status and applications in the postgenomic era. Expert Review of Molecular Diagnostics 1: 265–274.

Kornberg RD (1999) Eukaryotic transcriptional control. Trends in Cell Biology 9: M46–M49.

Lander ES, Linton LM, Birren B, et al. (2001) Initial sequencing and analysis of the human genome. International Human Genome Sequencing Consortium. Nature 409: 860–921.

MacBeath G and Schreiber SL (2000) Printing proteins as microarrays for high‐throughput function determination. Science 289: 1760–1763.

Mann M, Hendrickson RC and Pandey A (2001) Analysis of proteins and proteomes by mass spectrometry. Annual Review of Biochemistry 70: 437–473.

Pandey A and Mann M (2000) Proteomics to study genes and genomes. Nature 405: 837–846.

Pradet‐Balade B, Bolumé F, Beug H, Müllner EW and Garcia‐Sanz JA (2001) Translation control: bridging the gap between genomics and proteomics? Trends in Biochemical Sciences 26: 225–229.

Schena M, Shalon D, Davis RW and Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467–470.

Velculescu VE, Zhang L, Vogelstein B and Kinzler KW (1995) Serial analysis of gene expression. Science 270: 484–487.

Venter JC, Adams MD, Myers EW, et al. (2001) The sequence of the human genome. Science 291: 1304–1351.

Further Reading

Alberts B, Bray D, Johnson A, et al. (1998) Essential Cell Biology. An Introduction to the Molecular Biology of the Cell. New York, NY: Garland.

Alberts B, Johnson A, Lewis J, et al. (2002) Molecular Biology of the Cell. New York, NY: Garland.

Cooper GK (2000) The Cell. A Molecular Approach. Washington, DC: ASM Press.

Lodish H, Berk A, Zipursky SL, et al. (2000) Molecular Cell Biology. New York, NY: WH Freeman & Co.

Web Links

DDBJ. The DNA Data Bank of Japan is officially certified to collect DNA sequences from researchers and to issue the internationally recognized accession number to data submitters. They collect data mainly from Japanese researchers, but accept data from researchers in any other country http://www.ddbj.nig.ac.jp/

EMBL. The EMBL (European Molecular Biology Laboratory) Nucleotide Sequence Database constitutes Europe's primary nucleotide sequence resource. Main sources for DNA and RNA sequences are direct submissions from individual researchers, genome sequencing projects and patent applications http://www.ebi.ac.uk/embl/

GenBANK. GenBANK is the NIH (National Institute of Health) genetic sequence database, an annotated collection of all publicly available DNA sequences. GenBANK is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI. These three organizations exchange data on a daily basis http://www.ncbi.nih.gov/Genbank/

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Honoré, Bent, and Østergaard, Morten(Jan 2006) Transcriptomics and Proteomics: Integration?. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0006188]