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 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

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

• 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

Genome-wide Profiling Reveals Extensive

Transcription of UCRs in Normal Human Tissues

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

Hierarchical clustering of t-UCR expression

UCRs represent noncoding transcript with tissue-specific level of expression

Distinct UCR signatures in human leukemias and carcinomas

Specific groups of UCRs are differentially expressed in tumor types

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

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

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

Negative regulation of T-UCR by direct interaction with

microRNA

Assays for miRNA:UCR interaction

Negative correlation between 87 miRNAs and T-UCRs expression levels

T-UCRs as oncogenes

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

• 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)