Integration of Transcriptomics, Proteomics, and MicroRNA Analyses Reveals Novel MicroRNA Regulation of Targets in the Mammalian Inner Ear
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{"title"=>"Integration of transcriptomics, proteomics, and microRNA analyses reveals novel microrna regulation of targets in the mammalian inner ear", "type"=>"journal", "authors"=>[{"first_name"=>"Tal", "last_name"=>"Elkan-Miller", "scopus_author_id"=>"36113127800"}, {"first_name"=>"Igor", "last_name"=>"Ulitsky", "scopus_author_id"=>"8980428200"}, {"first_name"=>"Ronna", "last_name"=>"Hertzano", "scopus_author_id"=>"6507790490"}, {"first_name"=>"Anya", "last_name"=>"Rudnicki", "scopus_author_id"=>"37119183000"}, {"first_name"=>"Amiel A.", "last_name"=>"Dror", "scopus_author_id"=>"15924836700"}, {"first_name"=>"Danielle R.", "last_name"=>"Lenz", "scopus_author_id"=>"36114134500"}, {"first_name"=>"Ran", "last_name"=>"Elkon", "scopus_author_id"=>"6507427079"}, {"first_name"=>"Martin", "last_name"=>"Irmler", "scopus_author_id"=>"6603578523"}, {"first_name"=>"Johannes", "last_name"=>"Beckers", "scopus_author_id"=>"7102969746"}, {"first_name"=>"Ron", "last_name"=>"Shamir", "scopus_author_id"=>"7005411902"}, {"first_name"=>"Karen B.", "last_name"=>"Avraham", "scopus_author_id"=>"7007074258"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"79953693020", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0018195", "pmid"=>"21483685", "pui"=>"361559492", "scopus"=>"2-s2.0-79953693020", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)"}, "id"=>"2397fcea-5b13-35f0-a8a0-5922116e7131", "abstract"=>"We have employed a novel approach for the identification of functionally important microRNA (miRNA)-target interactions, integrating miRNA, transcriptome and proteome profiles and advanced in silico analysis using the FAME algorithm. Since miRNAs play a crucial role in the inner ear, demonstrated by the discovery of mutations in a miRNA leading to human and mouse deafness, we applied this approach to microdissected auditory and vestibular sensory epithelia. We detected the expression of 157 miRNAs in the inner ear sensory epithelia, with 53 miRNAs differentially expressed between the cochlea and vestibule. Functionally important miRNAs were determined by searching for enriched or depleted targets in the transcript and protein datasets with an expression consistent with the dogma of miRNA regulation. Importantly, quite a few of the targets were detected only in the protein datasets, attributable to regulation by translational suppression. We identified and experimentally validated the regulation of PSIP1-P75, a transcriptional co-activator previously unknown in the inner ear, by miR-135b, in vestibular hair cells. Our findings suggest that miR-135b serves as a cellular effector, involved in regulating some of the differences between the cochlear and vestibular hair cells.", "link"=>"http://www.mendeley.com/research/integration-transcriptomics-proteomics-microrna-analyses-reveals-novel-microrna-regulation-targets-m", "reader_count"=>98, "reader_count_by_academic_status"=>{"Unspecified"=>6, "Professor > Associate Professor"=>6, "Researcher"=>27, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>29, "Student > Postgraduate"=>2, "Other"=>7, "Student > Master"=>12, "Student > Bachelor"=>1, "Professor"=>6}, "reader_count_by_user_role"=>{"Unspecified"=>6, "Professor > Associate Professor"=>6, "Researcher"=>27, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>29, "Student > Postgraduate"=>2, "Other"=>7, "Student > Master"=>12, "Student > Bachelor"=>1, "Professor"=>6}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>8, "Biochemistry, Genetics and Molecular Biology"=>19, "Mathematics"=>1, "Agricultural and Biological Sciences"=>54, "Medicine and Dentistry"=>6, "Neuroscience"=>5, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Computer Science"=>2, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>6}, "Neuroscience"=>{"Neuroscience"=>5}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>54}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>19}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>8}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"Sweden"=>1, "United States"=>4, "Japan"=>1, "China"=>1, "Brazil"=>1, "South Africa"=>1, "France"=>1, "Portugal"=>1}, "group_count"=>3}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/786726"], "description"=>"<p>(<b>A</b>) qRT-PCR showing the relative <i>Psip1</i> transcript expression in the cochlear and vestibular sensory epithelia (n = 3, <i>P</i> = 0.34)<b>.</b> (<b>B</b>) PSIP1-P75 protein differential expression as measured by western blotting. (<i>Top</i>) A representative blot comparing PSIP1-P75 expression in the cochlear and vestibular sensory epithelia. HSC70 loading control is shown for both samples. (<i>Bottom</i>) Relative PSIP-P75 expression as measured using the Image J software and following averaging of three independent experiments; (*) <i>P</i><0.05 versus the vestibule. (<b>C</b>) Immunolabeling of PSIP1-P75 in P2 cochlear inner hair cells (green). Phalloidin stains the stereocilia (red) and DAPI the nucleus (blue). PSIP1-P75 is localized specifically to the nucleus. Scale bar: 5 µm. A schematic representation of an inner hair cell is shown to the right. (<b>D, E</b>) An RNAi system was used to measure the ability of miR-135b to reduce PSIP1-P75 protein expression. shRNA targeting miR-135b (X-miR-135b, oligoengine) or an anti-miR negative control were transfected to Cal51 cells that naturally express miR-135b. After selection, miR-135b and <i>Psip1</i> mRNA levels were measured using qRT-PCR and the protein level of the P75 isoform was measured using semi-quantitative western blot analysis. (<b>D</b>) qRT-PCR showing the relative <i>Psip1</i> transcript expression (n = 3, <i>P</i> = 0.66). (<b>E</b>) (<i>Top</i>) A representative blot showing the relative PSIP1-P75 protein expression. HSC70 loading control is shown for both samples. (<i>Bottom</i>) Relative PSIP1-P75 protein expression as measured using the image J software and following averaging of three independent experiments. (<b>F</b>) Dual luciferase reporter assay showing the effect of miR-135b on <i>Psip1-P75</i>-3′UTR and <i>Psip1-P75</i>-3′UTR-M in MCF-7 cells. Relative luciferase expression following averaging of three independent experiments, each conducted in triplicates. (**) <i>P<<</i>0.005.</p>", "links"=>[], "tags"=>["regulates", "psip1-p75", "inhibition"], "article_id"=>457089, "categories"=>["Molecular Biology", "Biochemistry", "Genetics"], "users"=>["Tal Elkan-Miller", "Igor Ulitsky", "Ronna Hertzano", "Anya Rudnicki", "Amiel A. Dror", "Danielle R. Lenz", "Ran Elkon", "Martin Irmler", "Johannes Beckers", "Ron Shamir", "Karen B. Avraham"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0018195.g004", "stats"=>{"downloads"=>2, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_miR_135b_regulates_PSIP1_P75_expression_by_inhibition_of_translation_/457089", "title"=>"miR-135b regulates PSIP1-P75 expression by inhibition of translation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-04-05 01:58:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/786605"], "description"=>"<p>(<b>A</b>) Schematic illustrations of a P0 whole inner ear, cochlea and vestibule: utricle (ut), saccule (sa), spiral ganglia (sg), scala media (sm), scala vestibule (sv), scala tympani (st). In purple, cochlear hair cells (chc) and vestibular hair cells (vhc). (<b>B-D</b>) Specific expression patterns were demonstrated for the miRNAs by ISH in whole mount inner ears, followed by cryosectioning. For each miRNA images of the whole inner ear (top) and magnified cochlea (middle) and vestibule (utricle or saccule, bottom) are shown separately. (<b>B</b>) A probe for miR-182 was used as a positive control and confirmed probe penetration and staining throughout the inner ear. miR-182 is expressed in the inner ear hair cells and spiral ganglia at this age <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0018195#pone.0018195-Weston1\" target=\"_blank\">[31]</a>. Expression patterns for miR-135b (<b>C</b>) and miR-205 (<b>D</b>) were consistent with the miRNA array analysis. Scale bars: 100 µm.</p>", "links"=>[], "tags"=>["spatial", "patterns", "mir-135b", "mir-205", "newborn"], "article_id"=>456962, "categories"=>["Molecular Biology", "Biochemistry", "Genetics"], "users"=>["Tal Elkan-Miller", "Igor Ulitsky", "Ronna Hertzano", "Anya Rudnicki", "Amiel A. Dror", "Danielle R. Lenz", "Ran Elkon", "Martin Irmler", "Johannes Beckers", "Ron Shamir", "Karen B. Avraham"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0018195.g003", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distinct_spatial_expression_patterns_of_miR_135b_and_miR_205_in_the_newborn_mouse_inner_ear_/456962", "title"=>"Distinct spatial expression patterns of miR-135b and miR-205 in the newborn mouse inner ear.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-04-05 01:56:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/786400"], "description"=>"<p>(<b>A</b>) Heat map representation of the 52 differentially expressed miRNAs between the P2 cochlear and vestibular sensory epithelia (fold change of at least 1.25 and <i>P</i><0.05). The log<sub>2</sub> of the ratio between the expression in the vestibular epithelial and the cochlea is shown. Results were averaged for three independent experiments, designated by three columns, each with two technical replicates. miRNAs shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0018195#pone-0018195-g001\" target=\"_blank\">figure 1B</a> are labeled by a grey box. (<b>B</b>) miRNA clusters differentially expressed in the studied tissues. miRNAs up-regulated in vestibule are marked in red and those up-regulated in cochlea are marked in green. Other miRNAs in the same clusters are not shown. miR-377 is the only member of the large miRNA cluster on chromosome 12qF1 significantly up-regulated in the cochlea. (<b>C</b>) qRT-PCR analysis of selected miRNAs. miR-135b and miR-124a, the miRNAs with the highest differential expression in the array, exhibited significant differential expression between the cochlear and vestibular sensory epithelia in the validation (4-fold and 8-fold, respectively). n = 3; (*) <i>P</i><0.05, (**) <i>P</i><0.005 versus the other tissue. miR-299, miR-182, miR-23a and miR-125b are representative of varying degrees of differential expression in the array. All PCR results were consistent with the array results. n = 3. Abbreviations: co-cochlea; ves-vestibule; oc-organ of Corti; s-saccule; u-utricle; c-cristea.</p>", "links"=>[], "tags"=>["mirna", "cochlear", "vestibular", "sensory"], "article_id"=>456757, "categories"=>["Molecular Biology", "Biochemistry", "Genetics"], "users"=>["Tal Elkan-Miller", "Igor Ulitsky", "Ronna Hertzano", "Anya Rudnicki", "Amiel A. Dror", "Danielle R. Lenz", "Ran Elkon", "Martin Irmler", "Johannes Beckers", "Ron Shamir", "Karen B. Avraham"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0018195.g001", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differential_miRNA_expression_profile_in_the_cochlear_and_vestibular_sensory_epithelia_/456757", "title"=>"Differential miRNA expression profile in the cochlear and vestibular sensory epithelia.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-04-05 01:52:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/393748", "https://ndownloader.figshare.com/files/393773", "https://ndownloader.figshare.com/files/393785", "https://ndownloader.figshare.com/files/393794", "https://ndownloader.figshare.com/files/393803", "https://ndownloader.figshare.com/files/393813", "https://ndownloader.figshare.com/files/393831"], "description"=>"<div><p>We have employed a novel approach for the identification of functionally important microRNA (miRNA)-target interactions, integrating miRNA, transcriptome and proteome profiles and advanced <em>in silico</em> analysis using the FAME algorithm. Since miRNAs play a crucial role in the inner ear, demonstrated by the discovery of mutations in a miRNA leading to human and mouse deafness, we applied this approach to microdissected auditory and vestibular sensory epithelia. We detected the expression of 157 miRNAs in the inner ear sensory epithelia, with 53 miRNAs differentially expressed between the cochlea and vestibule. Functionally important miRNAs were determined by searching for enriched or depleted targets in the transcript and protein datasets with an expression consistent with the dogma of miRNA regulation. Importantly, quite a few of the targets were detected only in the protein datasets, attributable to regulation by translational suppression. We identified and experimentally validated the regulation of PSIP1-P75, a transcriptional co-activator previously unknown in the inner ear, by miR-135b, in vestibular hair cells. Our findings suggest that miR-135b serves as a cellular effector, involved in regulating some of the differences between the cochlear and vestibular hair cells.</p> </div>", "links"=>[], "tags"=>["microrna", "analyses", "reveals", "targets", "mammalian"], "article_id"=>137753, "categories"=>["Molecular Biology", "Biochemistry", "Genetics"], "users"=>["Tal Elkan-Miller", "Igor Ulitsky", "Ronna Hertzano", "Anya Rudnicki", "Amiel A. Dror", "Danielle R. Lenz", "Ran Elkon", "Martin Irmler", "Johannes Beckers", "Ron Shamir", "Karen B. Avraham"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0018195.s001", "https://dx.doi.org/10.1371/journal.pone.0018195.s002", "https://dx.doi.org/10.1371/journal.pone.0018195.s003", "https://dx.doi.org/10.1371/journal.pone.0018195.s004", "https://dx.doi.org/10.1371/journal.pone.0018195.s005", "https://dx.doi.org/10.1371/journal.pone.0018195.s006", "https://dx.doi.org/10.1371/journal.pone.0018195.s007"], "stats"=>{"downloads"=>49, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Integration_of_Transcriptomics_Proteomics_and_MicroRNA_Analyses_Reveals_Novel_MicroRNA_Regulation_of_Targets_in_the_Mammalian_Inner_Ear/137753", "title"=>"Integration of Transcriptomics, Proteomics, and MicroRNA Analyses Reveals Novel MicroRNA Regulation of Targets in the Mammalian Inner Ear", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-04-05 02:09:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/786849"], "description"=>"<p>miR-135b (blue) is expressed in the vestibular hair cells, whereas no expression is detected in the cochlear hair cells. miR-135b down-regulates PSIP1-P75 (red) expression in the vestibular hair cells while its expression remains relatively high in the cochlear hair cells. Due to this differential expression, PSIP1-P75 regulates (red arrows) different process in the cochlear hair cells and only to a lesser extent in the vestibular hair cells. These processes include development, differentiation, cell fate determination, cell survival and protection against stress.</p>", "links"=>[], "tags"=>["mir-135b"], "article_id"=>457210, "categories"=>["Molecular Biology", "Biochemistry", "Genetics"], "users"=>["Tal Elkan-Miller", "Igor Ulitsky", "Ronna Hertzano", "Anya Rudnicki", "Amiel A. Dror", "Danielle R. Lenz", "Ran Elkon", "Martin Irmler", "Johannes Beckers", "Ron Shamir", "Karen B. Avraham"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0018195.g005", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_representation_of_a_possible_role_of_miR_135b_in_the_inner_ear_/457210", "title"=>"Schematic representation of a possible role of miR-135b in the inner ear.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-04-05 02:00:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/786494"], "description"=>"<p>(<b>A</b>) Enrichment and depletion of miRNA targets in co-expressed clusters of mRNAs, proteins, both or proteins only down-regulated in either the cochlea or vestibule. Green squares indicate over-representation of miRNA targets in a cluster and purple squares indicate under-representation. Only miRNA-target cluster pairs with <i>P</i><0.05 are shown. miRNAs shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0018195#pone-0018195-g002\" target=\"_blank\">figure 2B</a> are labeled by a grey box. (<b>B</b>) Differentially expressed miRNAs with significant target enrichments and depletions. (<i>Left</i>) Enrichment and depletion of miRNA targets in the co-expressed clusters for miRNAs that showed differential expression based on the miRNA array. (<i>Right</i>) The relative expression of the miRNAs on the left represented by the log of the ratio between the expressions in the cochlea as compared to the vestibule. (<b>C</b>) An outline of our miRNA target identification approach. Circles represent miRNAs and cochlea/vestibule cartoons represent mRNA/proteins sets that are differentially expressed between the two tissues. Arrows connect miRNA with mRNA/protein sets that are significantly enriched with its predicted targets based on TargetScan predictions. Only miRNAs that have enriched predicted targets in the differentially expressed gene sets are presented. Cases where a miRNA is differentially expressed between the two tissues (shown in B) are marked by a grey circle, while other cases are marked by a brown circle. Abbreviations: co-cochlea; ves-vestibule.</p>", "links"=>[], "tags"=>["mrna"], "article_id"=>456859, "categories"=>["Molecular Biology", "Biochemistry", "Genetics"], "users"=>["Tal Elkan-Miller", "Igor Ulitsky", "Ronna Hertzano", "Anya Rudnicki", "Amiel A. Dror", "Danielle R. Lenz", "Ran Elkon", "Martin Irmler", "Johannes Beckers", "Ron Shamir", "Karen B. Avraham"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0018195.g002", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_miRNA_target_identification_by_integration_of_mRNA_and_protein_expression_with_in_silico_target_prediction_/456859", "title"=>"miRNA target identification by integration of mRNA and protein expression with <i>in silico</i> target prediction.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-04-05 01:54:19"}

PMC Usage Stats | Further Information

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