ArticleBMC genomics2012
Transcripts with in silico predicted RNA structure are enriched everywhere in the mouse brain.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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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
11 citing papers in PubMed, 15 citations in OpenAlex.
- Characterizing highly conserved fragments in 3'UTRs via statistical and transfer learning approaches.NAR genomics and bioinformatics · 2026Article
- Clusters of mammalian conserved RNA structures in UTRs associate with RBP binding sites.NAR genomics and bioinformatics · 2024Article
- Expansion of the RNAStructuromeDB to include secondary structural data spanning the human protein-coding transcriptome.Scientific reports · 2022Article
- From Junk to Function: LncRNAs in CNS Health and Disease.Frontiers in molecular neuroscience · 2021Review
- A Polymer Physics Framework for the Entropy of Arbitrary Pseudoknots.Biophysical journal · 2019Article
- Associating transcription factors and conserved RNA structures with gene regulation in the human brain.Scientific reports · 2017Article
- A molecular conundrum involving hypothalamic responses to and roles of long non-coding RNAs following food deprivation.Molecular and cellular endocrinology · 2016Review
- Analysis of spatial-temporal gene expression patterns reveals dynamics and regionalization in developing mouse brain.Scientific reports · 2016Article
- Long non-coding RNAs in corticogenesis: deciphering the non-coding code of the brain.The EMBO journal · 2015Review
- A novel approach to represent and compare RNA secondary structures.Nucleic acids research · 2014Article
- Computational analysis of conserved RNA secondary structure in transcriptomes and genomes.Annual review of biophysics · 2014Review
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPost-transcriptional control of gene expression is mostly conducted by specific elements in untranslated regions (UTRs) of mRNAs, in collaboration with specific binding proteins and RNAs. In several well characterized cases, these RNA elements are known to form stable secondary structures. RNA secondary structures also may have major functional implications for long noncoding RNAs (lncRNAs). Recent transcriptional data has indicated the importance of lncRNAs in brain development and function. However, no methodical efforts to investigate this have been undertaken. Here, we aim to systematically analyze the potential for RNA structure in brain-expressed transcripts.
resultsBy comprehensive spatial expression analysis of the adult mouse in situ hybridization data of the Allen Mouse Brain Atlas, we show that transcripts (coding as well as non-coding) associated with in silico predicted structured probes are highly and significantly enriched in almost all analyzed brain regions. Functional implications of these RNA structures and their role in the brain are discussed in detail along with specific examples. We observe that mRNAs with a structure prediction in their UTRs are enriched for binding, transport and localization gene ontology categories. In addition, after manual examination we observe agreement between RNA binding protein interaction sites near the 3' UTR structures and correlated expression patterns.
conclusionsOur results show a potential use for RNA structures in expressed coding as well as noncoding transcripts in the adult mouse brain, and describe the role of structured RNAs in the context of intracellular signaling pathways and regulatory networks. Based on this data we hypothesize that RNA structure is widely involved in transcriptional and translational regulatory mechanisms in the brain and ultimately plays a role in brain function.
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