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Genome-wide survey of YY1 targets in C2C12 cells by High-throughput sequencing

ABSTRACT: By applying ChIP-seq, we generated genome-wide maps of YY1 in skeletal myoblasts and myotubes. We found that YY1 binds to 1820 confident target with a large portion residing in the intergenic regions. In addition, YY1 was found to activate many loci, and there is no significant overlap between YY1 and Ezh2 targets, suggensting a Ezh2-independent manner. Further detailed study revealed that YY1 can regulate some lincRNAs which are fucntional in skeletal myogenesis. In this study, we identified a YY1-Yam-1-miR-715 (TF-lincRNA-miRNA) regulatory curcuit in myogensis.

ORGANISM(S): Mus musculus

PROVIDER: GSE45875 | GEO | 2013/08/15

SECONDARY ACCESSION(S): PRJNA196689

REPOSITORIES: GEO

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Genome-wide survey of YY1 targets in C2C12 cells by High-throughput sequencing

Project description:By applying ChIP-seq, we generated genome-wide maps of YY1 in skeletal myoblasts and myotubes. We found that YY1 binds to 1820 confident target with a large portion residing in the intergenic regions. In addition, YY1 was found to activate many loci, and there is no significant overlap between YY1 and Ezh2 targets, suggensting a Ezh2-independent manner. Further detailed study revealed that YY1 can regulate some lincRNAs which are fucntional in skeletal myogenesis. In this study, we identified a YY1-Yam-1-miR-715 (TF-lincRNA-miRNA) regulatory curcuit in myogensis. Examination of YY1 targets in myoblast versus myotubes

2013-08-15 | E-GEOD-45875 | biostudies-arrayexpress

Transcriptome Analysis Identifies Linc-Yy1, A Novel Functional LincRNA During Myogenesis

Project description:Little is known how lincRNAs are involved in skeletal myogenesis. Here we describe the discovery of a novel lincRNA, Linc-YY1 from the promoter of transcription factor (TF) Yin Yang 1 (YY1) gene. We demonstrate that Linc-YY1 is dynamically regulated during myogenesis in vitro and in vivo. Gain or loss of function of Linc-YY1 in C2C12 myoblast cells or satellite cells alters myogenic differentiation and in injured muscles impacts the course of regeneration. Further studies suggest LincYY1 may interact with YY1 through its middle domain to evict YY1

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EZH2 RIP-seq identifies pNEAT1 as regulator of myogenesis in pigs

Project description:We introduced RIP-seq and lincRNA-seq methods to identify EZH2-binding lincRNAs.

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A novel YY1-miR-1 regulatory circuit in skeletal myogenesis revealed by genome-wide prediction of YY1-miRNA network

Project description:microRNAs (miRNAs) are non-coding RNAs that regulate gene expression post-transcriptionally, and mounting evidences support the prevalence and functional significance of their interplay with transcription factors (TFs). Here we describe the identification of a regulatory circuit between muscle miRNAs (miR-1, miR-133 and miR-206) and Yin Yang 1 (YY1), an epigenetic repressor of skeletal myogenesis. Genome-wide identification of potential YY1 down-stream targets by combining computational prediction with expression profiling data reveals a large number of putative miRNA targets of YY1 during skeletal myoblasts differentiation into myotubes with muscle miRs rank on top of the list. Murine skeletal muscle cells (C2C12 cells) were differentiated for 0, 1 or 3 days. Total RNAs were isolated from the cells and used for array profiling of miRNA expression.

2011-12-31 | E-GEOD-32238 | biostudies-arrayexpress

A novel YY1-miR-1 regulatory circuit in skeletal myogenesis revealed by genome-wide prediction of YY1-miRNA network

2011-12-31 | GSE32238 | GEO

Disruption of YY1-EZH2 Interaction using Synthetic Peptides Inhibits Breast Cancer Development

Project description:Enhancer of zeste homolog 2 (EZH2) is a methyltransferase to mediate lysine 27 trimethylation in histone H3 (i.e., H3K27me3) and repress gene expression. In solid tumors, EZH2 promotes oncogenesis, and is considered a therapeutic target. As a transcription factor, Yin Yang 1 (YY1) recruits EZH2 through its oncoprotein binding (OPB) domain to establish gene repression. In this study, we mapped the YY1 protein binding (YPB) domain on EZH2 to a region of 27 amino acids. Both YPB and OPB domain synthetic peptides could disrupt YY1-EZH2 interaction, markedly reduce breast cancer cell viability, and efficiently inhibit tumor growth in a xenograft mouse model. We analyzed MDA-MB-231 cells treated with YPB, OPB and control peptides by chromatin immunoprecipitation DNA sequencing (ChIP-seq) using an antibody against H3K27me3. YPB and OPB treatments altered H3K27me3 on 465 and 1,137 genes, respectively, compared to the control. Of these genes, 145 overlapped between the two peptides. Among them, PTENP1, the PTEN pseudogene, showed reduced H3K27me3 signal when treated by either YPB or OPB peptide. Consistently, the two peptides enhanced both PTENP1 and PTEN expression with concomitantly reduced AKT activation. Further studies validated PTENP1’s contribution to the anticancer activity of YPB and OPB peptides.

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Expression Profiling of Arabidopsis Long Intergenic Nongcoding RNA in Inflorescences, Leaves, and Roots

Project description:Long intergenic noncoding RNAs (lincRNA) transcribed from intergenic regions of eukaryotic genomes play important roles in key biological processes; yet, plant lincRNAs remain poorly characterized. Here we profiled lincRNA expression in inflorescences, leaves and roots using ATH lincRNA v1 array. we found 92% lincRNAs could be detected in at least 2 ATH lincRNA v1 arrays and majority of the lincRNAs were expressed at levels higher than those of pri-miRNAs but lower than those of mRNAs.Using a cut-off of 2-fold change, we identified 149 lincRNAs preferentially expressed in inflorescences, 232 in leaves and 164 in roots.

2011-08-06 | GSE30394 | GEO

Assessing the dynamics and macromolecular interactions of the intrinsically disordered protein YY1

Project description:YY1 is a ubiquitously expressed, intrinsically disordered transcription factor involved in neural development. The oligomeric state of YY1 varies depending on the environment. These changes may alter its DNA binding ability and hence its transcriptional activity. In addition to its oligomeric state, the interaction of YY1 with proteins such as FOXP2 can impact its role in transcription. The aim of this work is to study the structure and dynamics of YY1 binding to DNA and to determine the influence of oligomerisation and associations with FOXP2 on its DNA binding mechanism. Size exclusion chromatography, fluorescence anisotropy and electrophoretic mobility shift assays were used to study YY1 oligomerisation and interaction with FOXP2. To better understand potential structural changes to YY1 upon DNA binding, hydrogen deuterium exchange mass spectrometry was used. The results indicate that YY1 consists of specific structured regions, while most of the sequence remains disordered. Furthermore, the oligomeric nature of the protein is dependent on ionic strength. DNA affects oligomerisation and the protein undergoes changes in structure and dynamics upon DNA binding. YY1 and FOXP2 were found to interact with each other both in isolation and in the presence of YY1-specific DNA. The heterogeneous, dynamic multimerisation of YY1 identified in this work is, therefore, likely to be important for its ability to make heterologous associations with other proteins such as FOXP2. The interactions that YY1 forms with itself, FOXP2 and DNA form part of an intricate mechanism of transcriptional regulation by YY1, which is vital for appropriate neural development.

2024-01-26 | PXD038431 | Pride

Expression Profiling of Arabidopsis Long Intergenic Nongcoding RNA in Inflorescences, Leaves, and Roots

2011-08-05 | E-GEOD-30394 | biostudies-arrayexpress

Genome-wide maps of c-Myc binding sites in myoblasts and myotubes

Project description:By applying ChIP-seq, we generated genome-wide maps of c-Myc in skeletal myoblasts and myotubes. We found that c-Myc binds to 19354 confident target with a large portion residing in the intergenic regions. In addition, c-Myc was found to regulate many loci. Further detailed study revealed that c-Myc can regulate some genes, miRNAs, and lincRNAs which are fucntional in skeletal myogenesis. In this study, we identified a c-Myc induced regulatory pathway in myogensis.

2018-01-17 | GSE109223 | GEO

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