N-BLR: a pyknon-containing, primate-specific long non-coding RNA

The pyknon-containing N-BLR is a novel modulator of the epithelial-to-mesenchymal-transition process and of the apoptotic pathway in colorectal cancer

We discovered a new lncRNA, N-BLR. We showed that N-BLR plays key roles in the context of colorectal cancer (CRC), and that its abundance is associated with tumor stage, invasion potential, and overall patient survival 1. The importance of N-BLR for the clinical context was validated through independent cohorts of CRC patients making it a potential novel biomarker for this disease.
A key element to the mechanistic involvement of N-BLR in cellular processes is a 20 nt pyknon motif 3 near its 3′ end. We showed that targeted deletion of the pyknon affected colony formation, invasion, and migration. We also found several more pyknon-containing loci whose expression correlates with the overall survival of CRC patients. Parallel experiments with a custom-designed pyknon microarray that probed hundreds of pyknon-containing regions of the genome showed evidence of controlled transcription that was both tissue-specific and disease-specific. Because pyknons are primate-specific sequences 3,4,5 the findings suggest the possibility that these motifs could herald a novel class of biomarkers and therapeutic targets.

For a list of human and mouse pyknons and their genomic locations visit our pyknon page.


  1. Rigoutsos, I, Lee, SK, Nam, SY, Anfossi, S, Pasculli, B, Pichler, M et al.. N-BLR, a primate-specific non-coding transcript leads to colorectal cancer invasion and migration. Genome Biol. 2017;18 (1):98. doi: 10.1186/s13059-017-1224-0. PubMed PMID:28535802 PubMed Central PMC5442648.

  2. Primate-specific long non-codingRNAs and the cancer link, BioMed Central blog
  3. Rigoutsos, I, Huynh, T, Miranda, K, Tsirigos, A, McHardy, A, Platt, D et al.. Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes. Proc. Natl. Acad. Sci. U.S.A. 2006;103 (17):6605-10. doi: 10.1073/pnas.0601688103. PubMed PMID:16636294 PubMed Central PMC1447521.

  4. Tsirigos, A, Rigoutsos, I. Human and mouse introns are linked to the same processes and functions through each genome's most frequent non-conserved motifs. Nucleic Acids Res. 2008;36 (10):3484-93. doi: 10.1093/nar/gkn155. PubMed PMID:18450818 PubMed Central PMC2425492.

  5. Rigoutsos, I. Short RNAs: how big is this iceberg?. Curr. Biol. 2010;20 (3):R110-3. doi: 10.1016/j.cub.2009.12.036. PubMed PMID:20144771 .



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