RNA Dust: Where are the Genes?
Piero Carninci*
Omics Science Center, RIKEN Yokohama Institute, Kanagawa, Japan
Received 24 December 2009 ; accepted 5 February 2010.
Initial gene discovery efforts through analysis of genome sequences and identification and characterization of expressed RNAs have revealed that only a relatively small portion of the genome is transcribed into protein coding mRNAs in vertebrates. However, in contrast with this paucity of protein coding ‘genes’, there is an enormous complexity in transcription and the protein coding mRNAs contribute to a very small fraction of transcripts in comparison with the different varieties of non-coding RNAs (ncRNAs). This transcriptome complexity may be hypothesized to have a regulatory role that is required for the development and function of organisms as complex as vertebrates. At the same time, it raises the fundamental question of the unequivocal definition of a gene. It is intriguing to postulate that many ncRNAs might finely modulate gene activity by acting as regulatory elements. The emerging hypotheses suggest that the gene regulatory machinery may be deeply interconnected with the world of short RNAs. These RNAs may generally act for fine-tuning of the protein-coding transcriptome.
Key words:
transcriptome;
non-coding RNAs;
sense–antisense transcription;
cDNA annotation;
RNA processing
* To whom correspondence should be addressed. Tel. +81 45-503-9331. Fax. +81 45-503-9216. Email: carninci@riken.jp
1. Frenster JH, and Hovsepian JA,
A Brief
History of Activator RNA:
2. Koh W, Sheng CT, Tan B, Lee QY, Kuznetsov V , Kiang LS ,
and Tanavde V,
"Analysis of
deep sequencing microRNA expression profile from human embryonic stem cells
derived mesenchymal stem cells reveals possible role of let-7 microRNA
family in downstream targeting of Hepatic Nuclear Factor 4 Alpha".
3. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ,
Tsai M-C, Hung T, Argani P, Rinn JL, Wang Y, Brzoska P, Kong B, Li R, West
RB, van de Vijver MJ, Sukumar S, and Chang HY,
"Long non-coding
RNA HOTAIR reprograms chromatin state to promote cancer metastasis".
4. Inui M, Martello G, and Piccolo S,
"MicroRNA
control of signal transduction".
5. Zhang H, Li Y, and Lai M,
"The
microRNA network and tumor metastasis".
6. Deng N-J, and Cieplak P,
"Free Energy
Profile of RNA Hairpins: A Molecular Dynamics Simulation Study".
7. Frenster JH, and Hovsepian JA,
"RNA and Biological
Causality":
8. Frenster JH, and Hovsepian JA,
"Models of
successive levels of resolution during individual gene transcription".
1. Each cell retains all of its embryonic genes for a lifetime.
2. Controls for embryonic genes are often absent in adults.
3. Uncontrolled embryonic genes can replicate wildly.
4. Replicating genes participate in intra-cellular competition.
5. The basis for gene competition is selective transcription.
6. MicroRNAs can reprogram embryomic transcription.
7. Gene reprogramming can produce normal phenotypes.
8. Normal phenotypes can by-pass chromosomal lesions.
9. MicroRNA therapy may need to be permanent.
10. Transplantation of microRNAs could be preferred.
1. Pathways within cell genomes involve a flow of information.
2. Information can flow by direct contact or by third parties.
3. Direct contact within whole genomes is difficult to regulate.
4. DNA-DNA direct contects are influenced by agents.
5. Nuclear agents include hydrophilic ionic and hydrophobic conforming ligands.
6. Third parties within genomes involve RNAs and proteins.
7. RNAs and proteins are easy to regulate or reverse.
8. Information can be shared, lost, or transformed.
9. System information can be hidden during system isolation.
10. Local information can be permanently lost during system entropy.
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