ArticleProceedings of the National Academy of Sciences of the United States of America2006
Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
58 citing papers in PubMed, 1 synthesis or guideline pooled it, 132 citations in OpenAlex.
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- Regulation of Immune Cells by microRNAs and microRNA-Based Cancer Immunotherapy.Advances in experimental medicine and biology · 2022Article
- Therapeutic potential of FLANC, a novel primate-specific long non-coding RNA in colorectal cancer.Gut · 2020Article
- On the expanding roles of tRNA fragments in modulating cell behavior.Nucleic acids research · 2020Review
- Ribosomal RNA fragmentation into short RNAs (rRFs) is modulated in a sex- and population of origin-specific manner.BMC biology · 2020Article
- Pyknon-Containing Transcripts Are Downregulated in Colorectal Cancer Tumors, and Loss ofFrontiers in genetics · 2020Article
- The non-coding RNome after splenectomy.Journal of cellular and molecular medicine · 2019Article
- Decrypting noncoding RNA interactions, structures, and functional networks.Genome research · 2019Review
- tRNA Fragments Show Intertwining with mRNAs of Specific Repeat Content and Have Links to Disparities.Cancer research · 2019Article
- Long Noncoding RNA N-BLR Upregulates the Migration and Invasion of Gastric Adenocarcinoma.Gut and liver · 2019Article
- Cell communication and signaling: how to turn bad language into positive one.Journal of experimental & clinical cancer research : CR · 2019Article
- Shortcuts to a functional adipose tissue: The role of small non-coding RNAs.Redox biology · 2017Review
- Long non-coding RNAs in cutaneous melanoma: clinical perspectives.Oncotarget · 2017Review
- N-BLR, a primate-specific non-coding transcript leads to colorectal cancer invasion and migration.Genome biology · 2017Article
- Consequential considerations when mapping tRNA fragments.BMC bioinformatics · 2016Article
- Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies.Oncotarget · 2015Article
- Hepatitis B virus and microRNAs: Complex interactions affecting hepatitis B virus replication and hepatitis B virus-associated diseases.World journal of gastroenterology · 2015Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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