Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes. Export

@article{Rigoutsos2006, abstract = {Using an unsupervised pattern-discovery method, we processed the human intergenic and intronic regions and catalogued all variable-length patterns with identically conserved copies and multiplicities above what is expected by chance. Among the millions of discovered patterns, we found a subset of 127,998 patterns, termed pyknons, which have additional nonoverlapping instances in the untranslated and protein-coding regions of 30,675 transcripts from 20,059 human genes. The pyknons arrange combinatorially in the untranslated and coding regions of numerous human genes where they form mosaics. Consecutive instances of pyknons in these regions show a strong bias in their relative placement, favoring distances of approximately 22 nucleotides. We also found pyknons to be enriched in a statistically significant manner in genes involved in specific processes, e.g., cell communication, transcription, regulation of transcription, signaling, transport, etc. For approximately 1/3 of the pyknons, the intergenic/intronic instances of their reverse complement lie within 380,084 nonoverlapping regions, typically 60-80 nucleotides long, which are predicted to form double-stranded, energetically stable, hairpin-shaped RNA secondary structures; additionally, the pyknons subsume approximately 40\\% of the known microRNA sequences, thus suggesting a possible link with posttranscriptional gene silencing and RNA interference. Cross-genome comparisons reveal that many of the pyknons have instances in the 3' UTRs of genes from other vertebrates and invertebrates where they are overrepresented in similar biological processes, as in the human genome. These unexpected findings suggest potential unique functional connections between the coding and noncoding parts of the human genome.}, author = {Rigoutsos, Isidore and Huynh, Tien and Miranda, Kevin and Tsirigos, Aristotelis and Mchardy, Alice and Platt, Daniel}, citeulike-article-id = {2318695}, citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0601688103}, doi = {10.1073/pnas.0601688103}, journal = {Proc Natl Acad Sci U S A}, keywords = {3, 5, animals, base, comparative, conserved, data, dna, frames, from\_jabref, genome, human, humans, interference, introns, molecular, open, reading, regions, rna, sequence, study, untranslated}, month = {Apr}, number = {17}, pages = {6605--6610}, posted-at = {2008-02-01 09:55:11}, priority = {2}, title = {Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes.}, url = {10.1073/pnas.0601688103}, volume = {103}, year = {2006} }

TY - JOUR ID - Rigoutsos2006 L3 - citeulike-article-id:2318695 N2 - Using an unsupervised pattern-discovery method, we processed the human intergenic and intronic regions and catalogued all variable-length patterns with identically conserved copies and multiplicities above what is expected by chance. Among the millions of discovered patterns, we found a subset of 127,998 patterns, termed pyknons, which have additional nonoverlapping instances in the untranslated and protein-coding regions of 30,675 transcripts from 20,059 human genes. The pyknons arrange combinatorially in the untranslated and coding regions of numerous human genes where they form mosaics. Consecutive instances of pyknons in these regions show a strong bias in their relative placement, favoring distances of approximately 22 nucleotides. We also found pyknons to be enriched in a statistically significant manner in genes involved in specific processes, e.g., cell communication, transcription, regulation of transcription, signaling, transport, etc. For approximately 1/3 of the pyknons, the intergenic/intronic instances of their reverse complement lie within 380,084 nonoverlapping regions, typically 60-80 nucleotides long, which are predicted to form double-stranded, energetically stable, hairpin-shaped RNA secondary structures; additionally, the pyknons subsume approximately 40\\% of the known microRNA sequences, thus suggesting a possible link with posttranscriptional gene silencing and RNA interference. Cross-genome comparisons reveal that many of the pyknons have instances in the 3' UTRs of genes from other vertebrates and invertebrates where they are overrepresented in similar biological processes, as in the human genome. These unexpected findings suggest potential unique functional connections between the coding and noncoding parts of the human genome. IS - 17 JF - Proc Natl Acad Sci U S A EP - 6610 TI - Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes. VL - 103 SP - 6605 KW - 3 KW - 5 KW - animals KW - base KW - comparative KW - conserved KW - data KW - dna KW - frames KW - from_jabref KW - genome KW - human KW - humans KW - interference KW - introns KW - molecular KW - open KW - reading KW - regions KW - rna KW - sequence KW - study KW - untranslated AU - Rigoutsos, Isidore AU - Huynh, Tien AU - Miranda, Kevin AU - Tsirigos, Aristotelis AU - Mchardy, Alice AU - Platt, Daniel PY - 2006/Apr// UR - http://dx.doi.org/10.1073/pnas.0601688103 ER -