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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Cis regulated role of lncRNA in transcriptional or developmental process

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Mus musculus

SUBMITTER: Yuyang Lu

PROVIDER: E-GEOD-70420 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Divergent lncRNAs Regulate Gene Expression and Lineage Differentiation in Pluripotent Cells.

Luo Sai S Lu J Yuyang JY Liu Lichao L Yin Yafei Y Chen Chunyan C Han Xue X Wu Bohou B Xu Ronggang R Liu Wei W Yan Pixi P Shao Wen W Lu Zhi Z Li Haitao H Na Jie J Tang Fuchou F Wang Jianlong J Zhang Yong E YE Shen Xiaohua X

Cell stem cell 20160317 5

Divergent lncRNAs that are transcribed in the opposite direction to nearby protein-coding genes comprise a significant proportion (∼20%) of total lncRNAs in mammalian genomes. Through genome-wide analysis, we found that the distribution of this lncRNA class strongly correlates with essential developmental regulatory genes. In pluripotent cells, divergent lncRNAs regulate the transcription of nearby genes. As an example, the divergent lncRNA Evx1as promotes transcription of its neighbor gene, EVX ...[more]

PMID: 26996597

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cis regulated role of lncRNA in transcriptional or developmental process (ChIRP-Seq)

Project description:We report that long noncoding RNAs contribute to transcription and developmental process. Thousands of lncRNAs have been identified in the whole genome, and tend to located closely to protein-coding genes. To study position relationship between lncRNA and protein-coding genes, we classified all of lncRNA to several subgroups based on the genome position with their coding neighbors. XH, the head to head subgroup is associated with transcription and development in GO analysis. Here, we knockdown serveral XH lncRNA by shRNA in embryonic stem cells and induce nondirectional differnetiation by removing LIF or neural differnetiation by RA. Knockdown of XH lncRNAs led to uniform downregulation of nearby coding genes, and form regulatory circuits with its nearby coding genes to fine-tune embryonic lineage development. In addition, we also knockout one lncRNA-Evx1as and its nearby protein-coding gene-EVX1 by CRISPR, and get similar results as knockdown.We propose that XH lncRNA may function primarily as 'cis-regulators' of the expression of nearby protein-coding genes, and tend to participate in transcriptional or development regulations as their coding neighbors. All RNA-seq(s) were designed to reveal the differentially expressed genes between wild-type and XH lncRNA knockdown/knockout ESCs during differentiation.

2016-03-24 | E-GEOD-79541 | biostudies-arrayexpress

Evx1as and EVX1 knockouts by CRISPR

2016-03-24 | E-GEOD-70419 | biostudies-arrayexpress

Opposing roles for the lncRNA Haunt and its genomic locus in regulating HOXA gene activation during embryonic stem cell differentiation

Project description:Long noncoding RNAs (lncRNAs) have been implicated in controlling various aspects of embryonic stem cell (ESC) biology, although the functions of specific lncRNAs, and the molecular mechanisms through which they act, remain unclear. Here, we demonstrate discrete and opposing roles for the lncRNA transcript Haunt and its genomic locus in regulating the HOXA gene cluster during ESC differentiation. Reducing or enhancing Haunt expression, with minimal disruption of the Haunt locus, led to up- or down-regulation of HOXA genes, respectively. In contrast, increasingly large genomic deletions within the Haunt locus attenuated HOXA activation. The Haunt DNA locus contains potential enhancers of HOXA activation, whereas Haunt RNA acts to prevent aberrant HOXA expression. This work reveals a multi-faceted model of lncRNA-mediated transcriptional regulation of the HOXA cluster, with distinct roles for a lncRNA transcript and its genomic locus, while illustrating the power of rapid CRISPR/Cas9-based genome editing for assigning lncRNA functions. All RNA-seq(s) were designed to reveal the differentially expressed genes among different stages of ESCs differentiation, or differentially expressed genes between wild-type or Haunt or HOXA mutant cells during RA-induced differentiation. All ChIRP-Seq were used to reveal the DNA or RNA targets of Haunt before or after RA treatment.

2015-04-20 | E-GEOD-58514 | biostudies-arrayexpress

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2014-11-24 | E-GEOD-48666 | biostudies-arrayexpress

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2016-03-09 | E-GEOD-77705 | biostudies-arrayexpress

A toggle-switch between miR-142 and LIF-signaling creates heterogeneity among mouse ES cells.

Project description:Time course RNA-seq of mouse embryonic stem cells with different expression levels of miR-142 differentiated to endoderm

2015-12-31 | E-MTAB-3234 | biostudies-arrayexpress

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Transcription profiling of mouse Rex-1 knockout cell lines was compared to that of J1 wild type cellsRex-1 knockout cell lines was compared to that of J1 wild type cells in the presence and absence of LIF

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