Unbiased selection of localization elements reveals cis-acting determinants of mRNA bud localization in Saccharomyces cerevisiae

Jambhekar, Ashwini; McDermott, Kimberly M.; Sorber, Katherine; Shepard, Kelly A.; Vale, Ronald D.; Takizawa, Peter A.; DeRisi, Joseph L.

doi:10.1073/pnas.0509229102

Cited by 63 publications

(88 citation statements)

References 24 publications

(34 reference statements)

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“…We detected eight specific structural motifs regulating mRNAs' distinct cellular localizations ( Figure 5B; more examples in Figure S7 in Supporting Information). For ex-ample, we found a structural motif enriched in mRNAs localized to the cell bud (AUC=0.90; P<2×10 3 ), which is consistent with previous experiments that found a core CG dinucleotide in the stem of the She2p/3p mRNA [51].…”

Section: Rbps Recognize Structural Motifs To Regulate Mrna At the Possupporting

confidence: 91%

“…Some secondary structural motifs in UTRs involved in regulating mRNA decay rates and localization in yeast have been identified recently [32,50,51]. We grouped the 5′ UTR and 3′ UTR sequences according to cellular localization and decay rates, respectively, and predicted the structural motifs in the UTRs' RBP binding regions using RNApromo [32].…”

Section: Rbps Recognize Structural Motifs To Regulate Mrna At the Posmentioning

confidence: 99%

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Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae

Yang

Umetsu

2013

Sci. China Life Sci.

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Protein binding is essential to the transport, decay and regulation of almost all RNA molecules. However, the structural preference of protein binding on RNAs and their cellular functions and dynamics upon changing environmental conditions are poorly understood. Here, we integrated various high-throughput data and introduced a computational framework to describe the global interactions between RNA binding proteins (RBPs) and structured RNAs in yeast at single-nucleotide resolution. We found that on average, in terms of percent total lengths, ~15% of mRNA untranslated regions (UTRs), ~37% of canonical non-coding RNAs (ncRNAs) and ~11% of long ncRNAs (lncRNAs) are bound by proteins. The RBP binding sites, in general, tend to occur at single-stranded loops, with evolutionarily conserved signatures, and often facilitate a specific RNA structure conformation in vivo. We found that four nucleotide modifications of tRNA are significantly associated with RBP binding. We also identified various structural motifs bound by RBPs in the UTRs of mRNAs, associated with localization, degradation and stress responses. Moreover, we identified >200 novel lncRNAs bound by RBPs, and about half of them contain conserved secondary structures. We present the first ensemble pattern of RBP binding sites in the structured non-coding regions of a eukaryotic genome, emphasizing their structural context and cellular functions. . Many mRNAs are regulated by one or more RBPs as co-regulators. In Saccharomyces cerevisiae, there are approximately 600 annotated and predicted RBPs, but relatively few of them have been systematically studied to determine their regulatory targets [5]. In addition to mRNAs, numerous non-coding RNAs (ncRNAs) are targets of RBPs [6,7]. Previous studies revealed that RNAs were regulated by many RBPs post-transcriptionally [8]. It is widely accepted that altering the expression of RBPs will change cellular physiology profoundly. Studies using animal models have revealed that RBPs are involved in many human diseases, such as neurologic disorders and cancers [9]. Although the mechanisms that confer the specificity of RBP-RNA interaction are poorly understood, it is clear that this specificity is determined by both the primary sequence and secondary structure of the target RNA [10,11]. The secondary structures recognized by some RBPs are known. For example, the SAM domain of the yeast post-transcriptional regulator Vts1p recognizes the shape of the SRE of the RNA ligand [12].Currently, the most direct and powerful approach to profiling RBP-RNA interactions is UV crosslinking and immunoprecipitation (CLIP) of RNA-protein complexes,

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Section: Rbps Recognize Structural Motifs To Regulate Mrna At the Possupporting

confidence: 91%

Section: Rbps Recognize Structural Motifs To Regulate Mrna At the Posmentioning

confidence: 99%

Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae

Yang

Umetsu

2013

Sci. China Life Sci.

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“…RNA preparation and labeling 20 pmol of forward and reverse complementary oligonucleotides encoding the E2Bmin sequence [18] and the T7 RNA polymerase promotor were incubated for one minute at 95uC in 20 ml of water and annealed by cooling down the reaction slowly to room temperature (RT). E2Bmin RNA was synthesized by transcription of annealed DNA templates with T7 RNA polymerase (Promega) for two hours at 37uC.…”

Section: Methodsmentioning

confidence: 99%

Environmental Regulation of Prions in Yeast

2014

Investigations in Yeast Functional Genomics and Molecular Biology

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Hundreds of RNA-binding proteins (RBPs) control diverse aspects of post-transcriptional gene regulation. To identify novel and unconventional RBPs, we probed high-density protein microarrays with fluorescently labeled RNA and selected 200 proteins that reproducibly interacted with different types of RNA from budding yeast Saccharomyces cerevisiae. Surprisingly, more than half of these proteins represent previously known enzymes, many of them acting in metabolism, providing opportunities to directly connect intermediary metabolism with posttranscriptional gene regulation. We mapped the RNA targets for 13 proteins identified in this screen and found that they were associated with distinct groups of mRNAs, some of them coding for functionally related proteins. We also found that overexpression of the enzyme Map1 negatively affects the expression of experimentally defined mRNA targets. Our results suggest that many proteins may associate with mRNAs and possibly control their fates, providing dense connections between different layers of cellular regulation.

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“…Two other proteins have also been shown to be important for efficient ASH1 localization in yeast: Loc1p, a nuclear protein, and Khd1, which is thought to link translational repression to the localization process (Long et al 2001;Irie et al 2002;Hasegawa et al 2008). Since Ash1 mRNA localization was first discovered, .20 other mRNAs have been shown to show similar localization in Saccharomyces (Shepard et al 2003;Jambhekar et al 2005).…”

Section: Cell Lineage and Cell Cycle Control Of Ho Gene Expressionmentioning

confidence: 99%

Mating-Type Genes andMATSwitching inSaccharomyces cerevisiae

2012

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Mating type in Saccharomyces cerevisiae is determined by two nonhomologous alleles, MATa and MATa. These sequences encode regulators of the two different haploid mating types and of the diploids formed by their conjugation. Analysis of the MATa1, MATa1, and MATa2 alleles provided one of the earliest models of cell-type specification by transcriptional activators and repressors. Remarkably, homothallic yeast cells can switch their mating type as often as every generation by a highly choreographed, site-specific homologous recombination event that replaces one MAT allele with different DNA sequences encoding the opposite MAT allele. This replacement process involves the participation of two intact but unexpressed copies of mating-type information at the heterochromatic loci, HMLa and HMRa, which are located at opposite ends of the same chromosome-encoding MAT. The study of MAT switching has yielded important insights into the control of cell lineage, the silencing of gene expression, the formation of heterochromatin, and the regulation of accessibility of the donor sequences. Real-time analysis of MAT switching has provided the most detailed description of the molecular events that occur during the homologous recombinational repair of a programmed double-strand chromosome break. TABLE OF CONTENTS Abstract 33Introduction 34

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Unbiased selection of localization elements reveals cis-acting determinants of mRNA bud localization in Saccharomyces cerevisiae

Cited by 63 publications

References 24 publications

Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae

Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae

Environmental Regulation of Prions in Yeast

Mating-Type Genes andMATSwitching inSaccharomyces cerevisiae

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