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MiR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction [III]

ABSTRACT: Identifying the interaction partners of non-coding RNAs is essential for elucidating their functions. We have developed an approach, termed microRNA-cross-linking and immunoprecipitation (miR-CLIP), using pre-miRNAs modified with psoralen and biotin to capture their targets in cells. Photo-cross-linking and Argonaute 2-immunopurification followed by streptavidin affinity-purification of probe-linked RNAs provided selectivity in the capture of targets, identified by deep-sequencing. MiR-CLIP with pre-miR-106a, a miR-17-5p family member, identified hundreds of putative targets in HeLa cells, many carrying conserved sequences complementary to the miRNA seed but also many that were not predicted computationally. MiR-106a overexpression experiments confirmed that miR-CLIP captured functional targets, including H19, a long-non-coding RNA that is expressed during skeletal muscle cell differentiation. We showed that miR-17-5p family members bind H19 in HeLa cells and myoblasts. During myoblast differentiation levels of H19, miR-17-5p family members and mRNA targets changed in a manner suggesting that H19 acts as a sponge for these miRNAs. Two replicates of three cDNA libraries were submitted to deep sequencing: a sample from RNA-7-transfected cells; a sample from pre-miR-106a transfected cells; and a control sample.

ORGANISM(S): Homo sapiens

SUBMITTER: Jochen Imig

PROVIDER: E-GEOD-62678 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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MiR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction [IV]

Project description:Identifying the interaction partners of non-coding RNAs is essential for elucidating their functions. We have developed an approach, termed microRNA-cross-linking and immunoprecipitation (miR-CLIP), using pre-miRNAs modified with psoralen and biotin to capture their targets in cells. Photo-cross-linking and Argonaute 2-immunopurification followed by streptavidin affinity-purification of probe-linked RNAs provided selectivity in the capture of targets, identified by deep-sequencing. MiR-CLIP with pre-miR-106a, a miR-17-5p family member, identified hundreds of putative targets in HeLa cells, many carrying conserved sequences complementary to the miRNA seed but also many that were not predicted computationally. MiR-106a overexpression experiments confirmed that miR-CLIP captured functional targets, including H19, a long-non-coding RNA that is expressed during skeletal muscle cell differentiation. We showed that miR-17-5p family members bind H19 in HeLa cells and myoblasts. During myoblast differentiation levels of H19, miR-17-5p family members and mRNA targets changed in a manner suggesting that H19 acts as a sponge for these miRNAs. Two replicates of two cDNA libraries were submitted to deep sequencing: a sample from siH19-transfected cells and a control sample.

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MiR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction [IV]

2014-12-22 | GSE62679 | GEO

MiR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction [III]

2014-12-22 | GSE62678 | GEO

MiR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction [II]

2014-12-22 | GSE62677 | GEO

MiR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction [I]

2014-12-22 | GSE62675 | GEO

MiR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction [II]

Project description:Identifying the interaction partners of non-coding RNAs is essential for elucidating their functions. We have developed an approach, termed microRNA-cross-linking and immunoprecipitation (miR-CLIP), using pre-miRNAs modified with psoralen and biotin to capture their targets in cells. Photo-cross-linking and Argonaute 2-immunopurification followed by streptavidin affinity-purification of probe-linked RNAs provided selectivity in the capture of targets, identified by deep-sequencing. MiR-CLIP with pre-miR-106a, a miR-17-5p family member, identified hundreds of putative targets in HeLa cells, many carrying conserved sequences complementary to the miRNA seed but also many that were not predicted computationally. MiR-106a overexpression experiments confirmed that miR-CLIP captured functional targets, including H19, a long-non-coding RNA that is expressed during skeletal muscle cell differentiation. We showed that miR-17-5p family members bind H19 in HeLa cells and myoblasts. During myoblast differentiation levels of H19, miR-17-5p family members and mRNA targets changed in a manner suggesting that H19 acts as a sponge for these miRNAs. Two replicates of four cDNA libraries were submitted to deep sequencing: an RNA M-bM-^@M-^\InputM-bM-^@M-^] sample from RNA-12-transfected cells; a sample of the Ago2-immunopurified RNA from cells treated with transfection reagent (M-bM-^@M-^\MockM-bM-^@M-^]); a sample of the Ago2-immunopurified RNA from RNA-12-treatment (M-bM-^@M-^\Ago2-IPM-bM-^@M-^]); and the sample from miR-CLIP-purified RNA (M-bM-^@M-^\miR-CLIPM-bM-^@M-^]).

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Project description:Identifying the interaction partners of non-coding RNAs is essential for elucidating their functions. We have developed an approach, termed microRNA-cross-linking and immunoprecipitation (miR-CLIP), using pre-miRNAs modified with psoralen and biotin to capture their targets in cells. Photo-cross-linking and Argonaute 2-immunopurification followed by streptavidin affinity-purification of probe-linked RNAs provided selectivity in the capture of targets, identified by deep-sequencing. MiR-CLIP with pre-miR-106a, a miR-17-5p family member, identified hundreds of putative targets in HeLa cells, many carrying conserved sequences complementary to the miRNA seed but also many that were not predicted computationally. MiR-106a overexpression experiments confirmed that miR-CLIP captured functional targets, including H19, a long-non-coding RNA that is expressed during skeletal muscle cell differentiation. We showed that miR-17-5p family members bind H19 in HeLa cells and myoblasts. During myoblast differentiation levels of H19, miR-17-5p family members and mRNA targets changed in a manner suggesting that H19 acts as a sponge for these miRNAs. Two replicates of four cDNA libraries were submitted to deep sequencing: an RNA M-bM-^@M-^\InputM-bM-^@M-^] sample from RNA-7-transfected cells; a sample of the Ago2-immunopurified RNA from cells treated with transfection reagent (M-bM-^@M-^\MockM-bM-^@M-^]); a sample of the Ago2-immunopurified RNA from RNA-7-treatment (M-bM-^@M-^\Ago2-IPM-bM-^@M-^]); and the sample from miR-CLIP-purified RNA (M-bM-^@M-^\miR-CLIPM-bM-^@M-^]).

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miR-106a-5p inhibits the proliferation and migration of astrocytoma cells and promotes apoptosis by targeting FASTK

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MicroRNAs in the miR-106b family regulate p21/CDKN1A and promote cell cycle progression.

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