Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Regulation of gene expression in SK-N-SH cell line

ABSTRACT: The closely linked human protocadherin (Pcdh) α, β, and γ gene clusters encode 53 distinct protein isoforms, which are expressed in a combinatorial manner to generate enormous diversity on the surface of individual neurons. This diversity is a consequence of stochastic promoter choice and alternative pre-mRNA processing. Here, we show that Pcdhα promoter choice is achieved by DNA looping between two downstream transcriptional enhancers and individual promoters driving the expression of alternate Pcdhα isoforms. In addition, we show that this DNA looping requires specific binding of the CTCF/cohesin complex to two symmetrically aligned binding sites in both the transcriptionally active promoters and in one of the enhancers. These findings have important implications regarding enhancer/promoter interactions in the generation of complex Pcdh cell surface codes for the establishment of neuronal identity and self-avoidance in individual neurons.

ORGANISM(S): Homo sapiens

PROVIDER: GSE76815 | GEO | 2016/01/13

SECONDARY ACCESSION(S): PRJNA308721

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Antisense lncRNA transcription mediates DNA demethylation to drive stochastic Protocadherin α promoter choice

Project description:Stochastic activation of clustered Protocadherin (Pcdh) α, β, and γ genes generates a cell-surface identity code in individual neurons that functions in neural circuit assembly. Here, we show that Pcdhα gene choice involves the activation of an antisense promoter located in the first exon of each Pcdhα alternate gene. Transcription of an antisense long noncoding RNA (lncRNA) from this antisense promoter extends through the sense promoter, leading to DNA demethylation of the CTCF binding sites proximal to each promoter. Demethylation-dependent CTCF binding to both promoters facilitates cohesin-mediated DNA looping with a distal enhancer (HS5-1), locking in the transcriptional state of the chosen Pcdhα gene. Uncoupling DNA demethylation from antisense transcription by Tet3 overexpression in mouse olfactory neurons promotes CTCF binding to all Pcdhα promoters, resulting in proximity-biased DNA looping of the HS5-1 enhancer. Thus, antisense transcription-mediated promoter demethylation functions as a mechanism for distance-independent enhancer/promoter DNA looping to ensure stochastic Pcdhα promoter choice.

2019-04-15 | GSE115862 | GEO

Three-dimensional genome architectural CCCTC-binding factor makes choice in duplicated enhancers at Pcdhα locus. [ChIP-seq II]

Project description:By CRISPR/Cas9 DNA-fragment editing, in conjunction with chromosome conformation capture, ChIP-seq and RNA-seq technology, we studied CRISPR single cell clones of duplicated CBS-containing enhancers or promoters in the Pcdhα gene cluster. We found that CTCF plays an essential role in determining promoter choice and enhancer selection. In addition, the choices mediated by CTCF is based on the chromatin loops formed between forward-reverse convergent CBS pairs with the proximal one dominant.

2023-03-01 | GSE147279 | GEO

Three-dimensional genome architectural CCCTC-binding factor makes choice in duplicated enhancers at Pcdhα locus. [RNA-seq]

2023-03-01 | GSE147278 | GEO

Three-dimensional genome architectural CCCTC-binding factor makes choice in duplicated enhancers at Pcdhα locus. [4C-seq]

2023-03-01 | GSE147274 | GEO

Three-dimensional genome architectural CCCTC-binding factor makes choice in duplicated enhancers at Pcdhα locus. [ChIP-seq I]

2023-03-01 | GSE147193 | GEO

Systematic Functional Characterization of Antisense eRNA of Protocadherin alpha HS5-1 Enhancer

Project description:Enhancers generate bidirectional noncoding enhancer RNAs (eRNA) that may regulate gene expression. At present, the eRNA function remains enigmatic. Here, we report a 5’ capped antisense eRNA PEARL (Pcdh eRNA associated with R-loop formation) that is transcribed from the protocadherin (Pcdh) alpha HS5-1 enhancer region. Through loss- and gain-of-function experiments with CRISPR/Cas9 DNA-fragment editing, CRISPRi, and CRISPRa as well as locked nucleic acid strategies, in conjunction with ChIRP, MeDIP, DRIP, QHR-4C, and HiChIP experiments, we find that PEARL regulates Pcdh alpha gene expression by forming local RNA-DNA duplexes (R-loops) in situ within the HS5-1 enhancer region to promote long-distance chromatin interactions between distal enhancer and target promoter. In particular, increased levels of eRNA PEARL via perturbing transcription elongation factor SPT6 leads to strengthened local three-dimensional chromatin organization within the Pcdh superTAD. These findings have important implications regarding molecular mechanisms by which the HS5-1 enhancer regulates stochastic Pcdh alpha promoter choice in single cells in the brain.

2021-10-02 | GSE148958 | GEO

WAPL functions as a rheostat of Protocadherin isoform diversity that controls neural wiring

Project description:Neural-type specific expression of clustered Protocadherin (Pcdh) proteins is essential for the establishment of connectivity patterns during brain development. In mammals, deterministic expression of the same Pcdh isoform promotes minimal overlap of tiled projections of serotonergic neuron axons throughout the brain, while stochastic expression of Pcdh genes allows for convergence of tightly packed overlapping olfactory sensory neuron axons into targeted structures. How can the same gene locus generate opposite transcriptional programs that orchestrate distinct spatial arrangements of axonal patterns? Here, we reveal that cell-type specific Pcdh expression and axonal behavior rest on the activity of cohesin and its unloader WAPL. While cohesin erases genomic-distance biases in Pcdh choice, WAPL functions as a rheostat of cohesin processivity that determines Pcdh isoform diversity.

2023-06-22 | GSE191195 | GEO

Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [VIII]

Project description:By CRISPR DNA-fragment editing, in conjunction with chromosome conformation capture, we find that CBSs, if located between enhancers and promoters in the clustered Pcdh and b-globin clusters, function as an enhancer-blocking insulator by forming distinct directional chromatin loops, regardless whether enhancers contain CBS or not. Moreover, computational simulation in silico and genetic deletions in vivo revealed balanced promoter usage in cell populations and stochastic monoallelic expression in single cells by large arrays of tandem variable CBSs. Finally, gene expression levels are negatively correlated with CBS insulators located between enhancers and promoters on a genome-wide scale. Thus, single CBS insulators ensure proper enhancer insulation and promoter activation while tandem-arrayed CBS insulators determine balanced promoter choice. This finding has interesting implications on the role of topological insulators in 3D genome folding and developmental gene regulation.

2020-03-01 | GSE140869 | GEO

Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [VII]

2020-03-01 | GSE140868 | GEO

Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [IV]

2020-03-06 | GSE138919 | GEO