Marco Magistri 09-11-2007, Journal Club

1. Marco Magistri 09-11-2007, Journal Club

2. “Structural genes encode proteins and regulatory genes produce non-coding RNAs” 1961, Jacob and Monod 21561 protein-coding genes VS 69185 transcribed regions A non-coding RNA (ncRNA) is any RNA molecule that is not translated into a protein Genome paradox: as an organism’s complexity increases, the protein coding contribution of its genome decreases. ncRNAs may contribute to the complex networks that regulate cell function and could be the ultimate answer to the genome paradox

3. Regulatory ncRNAsExpressed at certain stages of development, during cell differentiation, or as a response to external stimuli, wich can affect the expression of other genes at the level of transcription or translation.i.e.: small interfering RNAs (siRNA), microRNA, etc. Housekeeping ncRNAsConstitutively expressed and required for normal function and viability of the cell.i.e.: transfer RNAs (tRNA), ribosomal RNAs (rRNA), small nuclear RNA (snRNAs), small nucleolar RNAs (snoRNA), etc. ncRNA are emerging as new and exciting players in gene regulatory networks, and their deregulation may underlie or be a marker for many complex diseases Prasanth and Spector GENES & DEVELOPMENT 2007

4. Genomic Ultraconserved Region UCR • The UCRs are a subset of absolutely conserved (100%) sequences that are located in both intra- and intergenic regions • Nonexonic: no evidence of encoding protein • Exonic: overlapping mRNA of known function • Possibly exonic • The UCRs rapresent a small fraction of the human genome that are likely to be functional but not encoding proteins and have been called the ‘‘dark matter’’ of the human genome (Bejerano et al., 2004).

5. Genome-wide Profiling Reveals ExtensiveTranscription of UCRs in Normal Human Tissues

6. Transcribed UCR (T-UCR) are expressed in normal tissue both ubiquitously and in a tissue-specific manner Expressed in the minority of tissues Expressed in the majority of tissues Ubiquitously expressed Tissue specifically expressed

7. Hierarchical clustering of t-UCR expression UCRs represent noncoding transcript with tissue-specific level of expression

8. Distinct UCR signatures in human leukemias and carcinomas Specific groups of UCRs are differentially expressed in tumor types

9. Comparison of UCRs expression between normal and tumor cell of the same origin 9.1% are differentially expressed at a higly statistically significant level Both upregulated and downregulated in cancer

10. Signatures: CLL: 19 UCRs (8up- and 11 downregulated) CRC: 61 UCRs (59up- and 2 downregulated) HCC: 8 UCRs (3up- and 5 downregulated) T-UCR expression profiles can be used to differentiate human cancer

11. UCRs are frequently located at fragile sites (FRA) and cancer associated genomic regions (CAGR) T-UCRs differentially expressed in human cancers are located in CAGRs specifically associated with that type of cancer

12. Negative regulation of T-UCR by direct interaction with microRNA

13. Assays for miRNA:UCR interaction Negative correlation between 87 miRNAs and T-UCRs expression levels

14. T-UCRs as oncogenes

15. Conclusions • Some UCRs represent noncoding transcripts in human normal tissues and their expression is tissue-specific • T-UCRs expression profiles can be used to differentiate human cancers • UCRs are located in genomic regions altered during malignant process, suggesting that T-UCR could be candidate genes for cancer susceptibility • Noncoding T-UCR represent possible targets of miRNAs and these interaction may have biological and prognostic significance for cancer patients • In some cases T-UCRs behaves like oncogenes by increasing the number of malignant cells as a consequence of reduced apoptosis

16. What is the key experiment? (the one confirming the statement in the title) • What is the strongest point? • What is the weakest point? and What to do to strenghten it? • What is the take home message? (summarize it in a sentence)