![Page 1: Marco Magistri 09-11-2007, Journal Club. A non-coding RNA (ncRNA) is any RNA molecule that is not translated into a protein “Structural genes encode proteins](https://reader033.vdocuments.us/reader033/viewer/2022052702/56649ef65503460f94c0a089/html5/thumbnails/1.jpg)
Marco Magistri
09-11-2007, Journal Club
![Page 2: Marco Magistri 09-11-2007, Journal Club. A non-coding RNA (ncRNA) is any RNA molecule that is not translated into a protein “Structural genes encode proteins](https://reader033.vdocuments.us/reader033/viewer/2022052702/56649ef65503460f94c0a089/html5/thumbnails/2.jpg)
A non-coding RNA (ncRNA) is any RNA molecule that is not
translated into a protein
“Structural genes encode proteins and regulatory genes produce non-coding RNAs”
21561 protein-coding genes VS 69185 transcribed regions
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
1961, Jacob and Monod
![Page 3: Marco Magistri 09-11-2007, Journal Club. A non-coding RNA (ncRNA) is any RNA molecule that is not translated into a protein “Structural genes encode proteins](https://reader033.vdocuments.us/reader033/viewer/2022052702/56649ef65503460f94c0a089/html5/thumbnails/3.jpg)
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.
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.
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
![Page 4: Marco Magistri 09-11-2007, Journal Club. A non-coding RNA (ncRNA) is any RNA molecule that is not translated into a protein “Structural genes encode proteins](https://reader033.vdocuments.us/reader033/viewer/2022052702/56649ef65503460f94c0a089/html5/thumbnails/4.jpg)
• 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).
Genomic Ultraconserved Region UCR
![Page 5: Marco Magistri 09-11-2007, Journal Club. A non-coding RNA (ncRNA) is any RNA molecule that is not translated into a protein “Structural genes encode proteins](https://reader033.vdocuments.us/reader033/viewer/2022052702/56649ef65503460f94c0a089/html5/thumbnails/5.jpg)
Genome-wide Profiling Reveals Extensive
Transcription of UCRs in Normal Human Tissues
![Page 6: Marco Magistri 09-11-2007, Journal Club. A non-coding RNA (ncRNA) is any RNA molecule that is not translated into a protein “Structural genes encode proteins](https://reader033.vdocuments.us/reader033/viewer/2022052702/56649ef65503460f94c0a089/html5/thumbnails/6.jpg)
Transcribed UCR (T-UCR) are expressed in normal tissue both ubiquitously and in a tissue-specific manner
Ubiquitously expressed
Expressed in the
majority of tissues
Expressed in the minority
of tissues
Tissue specifically expressed
![Page 7: Marco Magistri 09-11-2007, Journal Club. A non-coding RNA (ncRNA) is any RNA molecule that is not translated into a protein “Structural genes encode proteins](https://reader033.vdocuments.us/reader033/viewer/2022052702/56649ef65503460f94c0a089/html5/thumbnails/7.jpg)
Hierarchical clustering of t-UCR expression
UCRs represent noncoding transcript with tissue-specific level of expression
![Page 8: Marco Magistri 09-11-2007, Journal Club. A non-coding RNA (ncRNA) is any RNA molecule that is not translated into a protein “Structural genes encode proteins](https://reader033.vdocuments.us/reader033/viewer/2022052702/56649ef65503460f94c0a089/html5/thumbnails/8.jpg)
Distinct UCR signatures in human leukemias and carcinomas
Specific groups of UCRs are differentially expressed in tumor types
![Page 9: Marco Magistri 09-11-2007, Journal Club. A non-coding RNA (ncRNA) is any RNA molecule that is not translated into a protein “Structural genes encode proteins](https://reader033.vdocuments.us/reader033/viewer/2022052702/56649ef65503460f94c0a089/html5/thumbnails/9.jpg)
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
![Page 10: Marco Magistri 09-11-2007, Journal Club. A non-coding RNA (ncRNA) is any RNA molecule that is not translated into a protein “Structural genes encode proteins](https://reader033.vdocuments.us/reader033/viewer/2022052702/56649ef65503460f94c0a089/html5/thumbnails/10.jpg)
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
![Page 11: Marco Magistri 09-11-2007, Journal Club. A non-coding RNA (ncRNA) is any RNA molecule that is not translated into a protein “Structural genes encode proteins](https://reader033.vdocuments.us/reader033/viewer/2022052702/56649ef65503460f94c0a089/html5/thumbnails/11.jpg)
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
![Page 12: Marco Magistri 09-11-2007, Journal Club. A non-coding RNA (ncRNA) is any RNA molecule that is not translated into a protein “Structural genes encode proteins](https://reader033.vdocuments.us/reader033/viewer/2022052702/56649ef65503460f94c0a089/html5/thumbnails/12.jpg)
Negative regulation of T-UCR by direct interaction with
microRNA
![Page 13: Marco Magistri 09-11-2007, Journal Club. A non-coding RNA (ncRNA) is any RNA molecule that is not translated into a protein “Structural genes encode proteins](https://reader033.vdocuments.us/reader033/viewer/2022052702/56649ef65503460f94c0a089/html5/thumbnails/13.jpg)
Assays for miRNA:UCR interaction
Negative correlation between 87 miRNAs and T-UCRs expression levels
![Page 14: Marco Magistri 09-11-2007, Journal Club. A non-coding RNA (ncRNA) is any RNA molecule that is not translated into a protein “Structural genes encode proteins](https://reader033.vdocuments.us/reader033/viewer/2022052702/56649ef65503460f94c0a089/html5/thumbnails/14.jpg)
T-UCRs as oncogenes
![Page 15: Marco Magistri 09-11-2007, Journal Club. A non-coding RNA (ncRNA) is any RNA molecule that is not translated into a protein “Structural genes encode proteins](https://reader033.vdocuments.us/reader033/viewer/2022052702/56649ef65503460f94c0a089/html5/thumbnails/15.jpg)
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
![Page 16: Marco Magistri 09-11-2007, Journal Club. A non-coding RNA (ncRNA) is any RNA molecule that is not translated into a protein “Structural genes encode proteins](https://reader033.vdocuments.us/reader033/viewer/2022052702/56649ef65503460f94c0a089/html5/thumbnails/16.jpg)
• 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)