Transcriptome

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The transcriptome is the sum of all genes transcribed in a cell at a certain point in time , i.e. the genes transcribed from DNA into RNA, i.e. the totality of all RNA molecules produced in a cell .

properties

The term can be compared with the proteome , the entirety of the proteins present in a cell at a certain point in time . But since not every RNA present after transcription, such as e.g. B. rRNA or the RNA of ribonucleoproteins , is translated ( translated ) into a protein and mRNAs can still be processed , the proteome and transcriptome of a cell are not identical.

To analyze the transcriptome, methods such as RT-PCR with degenerate primers are generally used , followed by a DNA microarray or high-throughput DNA sequencing ( RNA-Seq ). RNA-protein interactions can be investigated using methods such as RIP-Chip , CLIP-Seq , PAR-CLIP or ICLIP . Another method in which the activity of unknown genes can also be observed is the so-called serial analysis of gene expression (SAGE) and SuperSAGE .

The term transcriptomics is the study of the mRNA expression of a cell. The term is an analogy to the term proteomics and synonymous with gene expression analysis .

literature

Individual evidence

  1. ↑ Khalil AM, Guttman M, Huarte M, et al. : Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression . In: Proc. Natl. Acad. Sci. USA . 106, No. 28, July 2009, pp. 11667-72. doi : 10.1073 / pnas.0904715106 . PMID 19571010 . PMC 2704857 (free full text).
  2. ↑ Darnell RB: HITS-CLIP: panoramic views of protein-RNA regulation in living cells . In: Wiley Interdiscip Rev RNA. . 1, 2010, pp. 266-86. doi : 10.1002 / wrna.31 .
  3. ↑ Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M Jr, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T .: Transcriptome- wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. . In: Cell . 141, No. 1, 2010, pp. 129-141. doi : 10.1016 / j.cell.2010.03.009 . PMID 20371350 . PMC 2861495 (free full text).
  4. ^ J. Koenig, K. Zarnack, G. Rot, T. Curk, M. Kayikci, B. Zupan, DJ Turner, NM Luscombe, J. Ule: iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. In: Nature Structural Molecular Biology (2010), Volume 17, Issue 7, pp. 909-915. doi : 10.1038 / nsmb.1838 . PMID 20601959 ; PMC 3000544 (free full text).