Abstract
MicroRNAs are small noncoding RNAs that serve as posttranscriptional regulators of gene expression in higher eukaryotes. Their widespread and important role in animals is highlighted by recent estimates that 20%-30% of all genes are microRNA targets. Here, we report that a large set of genes involved in basic cellular processes avoid microRNA regulation due to short 3'UTRs that are specifically depleted of microRNA binding sites. For individual microRNAs, we find that coexpressed genes avoid microRNA sites, whereas target genes and microRNAs are preferentially expressed in neighboring tissues. This mutually exclusive expression argues that microRNAs confer accuracy to developmental gene-expression programs, thus ensuring tissue identity and supporting cell-lineage decisions.
MeSH terms
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3' Untranslated Regions / genetics*
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Animals
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Base Sequence
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Basic Helix-Loop-Helix Transcription Factors / genetics
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Cell Line
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Drosophila / embryology
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Drosophila / genetics*
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Drosophila Proteins / genetics
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Embryo, Nonmammalian / metabolism
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Evolution, Molecular*
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Gene Expression Regulation, Developmental / genetics*
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Homeodomain Proteins / genetics
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In Situ Hybridization
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Membrane Proteins / genetics
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MicroRNAs / genetics
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MicroRNAs / physiology*
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Molecular Sequence Data
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Muscles / embryology
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Muscles / metabolism
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Nerve Tissue Proteins / genetics
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Nervous System / embryology
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Nervous System / metabolism
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Nuclear Proteins / genetics
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RNA, Messenger / genetics
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Sequence Homology, Nucleic Acid
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Tropomyosin / genetics
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Vacuolar Proton-Translocating ATPases / genetics
Substances
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3' Untranslated Regions
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Basic Helix-Loop-Helix Transcription Factors
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Drosophila Proteins
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Homeodomain Proteins
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Membrane Proteins
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MicroRNAs
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Nerve Tissue Proteins
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Nuclear Proteins
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RNA, Messenger
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Tm1 protein, Drosophila
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Tropomyosin
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cpo protein, Drosophila
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gliotactin
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l(1)sc protein, Drosophila
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repo protein, Drosophila
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Vacuolar Proton-Translocating ATPases