ArticleAmerican journal of human genetics2008
Mapping of small RNAs in the human ENCODE regions.
Article in American journal of human genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- The role of long non-coding RNAs in lung cancer metastasis: Molecular mechanisms, pathogenesis and clinical implications.Clinical and translational medicine · 2025Review
- Reply to Verwilt et al.: Experimental evidence against DNA contamination in SILVER-seq.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Integrative Analysis of NSCLC Identifies LINC01234 as an Oncogenic lncRNA that Interacts with HNRNPA2B1 and Regulates miR-106b Biogenesis.Molecular therapy : the journal of the American Society of Gene Therapy · 2020Article
- Up-regulated LINC01234 promotes non-small-cell lung cancer cell metastasis by activating VAV3 and repressing BTG2 expression.Journal of hematology & oncology · 2020Article
- Evidence for Regulation of ECM3 Expression by Methylation of Histone H3 Lysine 4 and Intergenic Transcription in Saccharomyces cerevisiae.G3 (Bethesda, Md.) · 2016Article
- The association between H3K4me3 and antisense transcription.Genomics, proteomics & bioinformatics · 2012Article
- Deeply dissecting stemness: making sense to non-coding RNAs in stem cells.Stem cell reviews and reports · 2012Review
- Human genetics and genomics a decade after the release of the draft sequence of the human genome.Human genomics · 2011Review
- The long arm of long noncoding RNAs: roles as sensors regulating gene transcriptional programs.Cold Spring Harbor perspectives in biology · 2011Review
- Relating underrepresented genomic DNA patterns and tiRNAs: the rule behind the observation and beyond.Biology direct · 2010Article
- Regulatory roles of natural antisense transcripts.Nature reviews. Molecular cell biology · 2009Review
- Transcriptional and post-transcriptional profile of human chromosome 21.Genome research · 2009Article
- miRNA regulation of cytokine genes.Cytokine · 2009Review
- Identifying protein-coding genes in genomic sequences.Genome biology · 2009Review
- Noncoding RNA in development.Mammalian genome : official journal of the International Mammalian Genome Society · 2008Review
- Evidence for common short natural trans sense-antisense pairing between transcripts from protein coding genes.Genome biology · 2008Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The elucidation of the largely unknown transcriptome of small RNAs is crucial for the understanding of genome and cellular function. We report here the results of the analysis of small RNAs (< 50 nt) in the ENCODE regions of the human genome. Size-fractionated RNAs from four different cell lines (HepG2, HelaS3, GM06990, SK-N-SH) were mapped with the forward and reverse ENCODE high-density resolution tiling arrays. The top 1% of hybridization signals are termed SmRfrags (Small RNA fragments). Eight percent of SmRfrags overlap the GENCODE genes (CDS), given that the majority map to intergenic regions (34%), intronic regions (53%), and untranslated regions (UTRs) (5%). In addition, 9.6% and 16.8% of SmRfrags in the 5' UTR regions overlap significantly with His/Pol II/TAF250 binding sites and DNase I Hypersensitive sites, respectively (compared to the 5.3% and 9% expected). Interestingly, 17%-24% (depending on the cell line) of SmRfrags are sense-antisense strand pairs that show evidence of overlapping transcription. Only 3.4% and 7.2% of SmRfrags in intergenic regions overlap transcribed fragments (Txfrags) in HeLa and GM06990 cell lines, respectively. We hypothesized that a fraction of the identified SmRfrags corresponded to microRNAs. We tested by Northern blot a set of 15 high-likelihood predictions of microRNA candidates that overlap with smRfrags and validated three potential microRNAs ( approximately 20 nt length). Notably, most of the remaining candidates showed a larger hybridizing band ( approximately 100 nt) that could be a microRNA precursor. The small RNA transcriptome is emerging as an important and abundant component of the genome function.
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