ArticleMolecular systems biology2009
Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs.
Article in Molecular systems biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
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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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
24 citing papers in PubMed, 35 citations in OpenAlex.
- The role of structure in regulatory RNA elements.Bioscience reports · 2024Review
- RNA-binding protein SAMD4A inhibits breast tumor angiogenesis by modulating the balance of angiogenesis program.Cancer science · 2021Article
- SSMART: sequence-structure motif identification for RNA-binding proteins.Bioinformatics (Oxford, England) · 2018Article
- Regulatory principles governing the maternal-to-zygotic transition: insights from Drosophila melanogaster.Open biology · 2018Review
- Revealing protein-lncRNA interaction.Briefings in bioinformatics · 2016Review
- Affinity regression predicts the recognition code of nucleic acid-binding proteins.Nature biotechnology · 2015Article
- Different motif requirements for the localization zipcode element of β-actin mRNA binding by HuD and ZBP1.Nucleic acids research · 2015Article
- Deciphering RNA Regulatory Elements Involved in the Developmental and Environmental Gene Regulation of Trypanosoma brucei.PloS one · 2015Article
- High-throughput characterization of protein-RNA interactions.Briefings in functional genomics · 2015Review
- Metastasis-suppressor transcript destabilization through TARBP2 binding of mRNA hairpins.Nature · 2014Article
- Impact of human pathogenic micro-insertions and micro-deletions on post-transcriptional regulation.Human molecular genetics · 2014Article
- Systematic identification of regulatory elements in conserved 3' UTRs of human transcripts.Cell reports · 2014Article
- Global regulation of mRNA translation and stability in the early Drosophila embryo by the Smaug RNA-binding protein.Genome biology · 2014Article
- TARBP2 binding structured RNA elements drives metastasis.Cell cycle (Georgetown, Tex.) · 2014Article
- Global identification of conserved post-transcriptional regulatory programs in trypanosomatids.Nucleic acids research · 2013Article
- RBPmotif: a web server for the discovery of sequence and structure preferences of RNA-binding proteins.Nucleic acids research · 2013Article
- Modeling the specificity of protein-DNA interactions.Quantitative biology (Beijing, China) · 2013Article
- Toward a genome-wide landscape of translational control.Cold Spring Harbor perspectives in biology · 2013Review
- Smaug1 mRNA-silencing foci respond to NMDA and modulate synapse formation.The Journal of cell biology · 2011Article
- Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome.Nucleic acids research · 2011Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Gene expression is regulated at each step from chromatin remodeling through translation and degradation. Several known RNA-binding regulatory proteins interact with specific RNA secondary structures in addition to specific nucleotides. To provide a more comprehensive understanding of the regulation of gene expression, we developed an integrative computational approach that leverages functional genomics data and nucleotide sequences to discover RNA secondary structure-defined cis-regulatory elements (SCREs). We applied our structural cis-regulatory element detector (StructRED) to microarray and mRNA sequence data from Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens. We recovered the known specificities of Vts1p in yeast and Smaug in flies. In addition, we discovered six putative SCREs in flies and three in humans. We characterized the SCREs based on their condition-specific regulatory influences, the annotation of the transcripts that contain them, and their locations within transcripts. Overall, we show that modeling functional genomics data in terms of combined RNA structure and sequence motifs is an effective method for discovering the specificities and regulatory roles of RNA-binding proteins.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.