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Specific multivalent molecules boost CRISPR-mediated transcriptional activation via optimal cis-trans interaction and functional chromatin looping [RNA-seq]

ABSTRACT: Specific multivalent molecules boost CRISPR-mediated transcriptional activation via optimal cis-trans interaction and functional chromatin looping [RNA-seq]

PROVIDER: PRJNA1044421 | ENA |

REPOSITORIES: ENA

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Specific multivalent molecules boost CRISPR-mediated transcriptional activation via optimal cis-trans interaction and functional chromatin looping [RNA-seq]

Project description:Synthetic transcriptional activators based on CRISPR/Cas technology can be enhanced by intrinsically disordered regions (IDRs). However, the potential of all IDRs in this regard remains uncertain, and the mechanisms underlying their influence are a subject of debate. Here, we examined 12 well-known IDRs by fusing them to the dCas9-VP64 activator. Our findings reveal that seven IDRs could augment activation, albeit independently of their phase separation properties. Moreover, modular domains (MDs), which facilitate multivalent interactions but are ineffective in enhancing dCas9-VP64 activity on their own, showed substantial enhancement in transcriptional activation when combined with dCas9-VP64-IDR. By varying the number of gRNA binding sites and combining dCas9-VP64 with the IDRs and MDs of different multivalent capabilities, we uncovered that optimal, rather than maximal, cis-trans cooperativity enables the most robust activation. Finally, targeting promoter-enhancer pairs with our IDR-enhanced activation system yielded synergistic effects, potentially further amplifiable by induced functional chromatin looping.

2024-06-01 | GSE248523 | GEO

Specific multivalent molecules boost CRISPR-mediated transcriptional activation via optimal cis-trans interaction and functional chromatin looping [ChIA-PET]

2024-06-01 | GSE248522 | GEO

Specific multivalent molecules boost CRISPR-mediated transcriptional activation via optimal cis-trans interaction and functional chromatin looping.

Project description:Specific multivalent molecules boost CRISPR-mediated transcriptional activation via optimal cis-trans interaction and functional chromatin looping.

| PRJNA1048838 | ENA

Specific multivalent molecules boost CRISPR-mediated transcriptional activation via optimal cis-trans interaction and functional chromatin looping [ChIA-PET]

Project description:Specific multivalent molecules boost CRISPR-mediated transcriptional activation via optimal cis-trans interaction and functional chromatin looping [ChIA-PET]

| PRJNA1044424 | ENA

Specific multivalent molecules boost CRISPR-mediated transcriptional activation via optimal cis-trans interaction and functional chromatin looping.

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-06-01 | GSE249351 | GEO

NK cell immune responses differ after prime and boost vaccination

Project description:A better understanding of innate responses induced by vaccination is critical for designing optimal vaccines. Here, we studied the diversity and dynamics of the NK cell compartment after prime-boost immunization with the modified vaccinia virus Ankara using cynomolgus macaques as a model. Mass cytometry was used to deeply characterize blood NK cells. The NK cell subphenotype composition was modified by the prime. Certain phenotypic changes induced by the prime were maintained over time and, as a result, the NK cell composition prior to boost differed from that before prime. The key phenotypic signature that distinguished NK cells responding to the boost from those responding to the prime included stronger expression of several cytotoxic, homing, and adhesion molecules, suggesting that NK cells at recall were functionally distinct. Our data reveal potential priming or imprinting of NK cells after the first vaccine injection. This study provides novel insights into prime-boost vaccination protocols that could be used to optimize future vaccines.

2019-02-19 | E-MTAB-7697 | biostudies-arrayexpress

Hormone-induced enhancer assembly requires an optimal level of hormone receptor multivalent interactions

Project description:Hormone-induced enhancer assembly requires an optimal level of hormone receptor multivalent interactions

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Hormone-induced enhancer assembly requires an optimal level of hormone receptor multivalent interactions

Project description:Hormone-induced enhancer assembly requires an optimal level of hormone receptor multivalent interactions

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Specific multivalent molecules boost CRISPR-mediated transcriptional activation.

Project description:CRISPR/Cas-based transcriptional activators can be enhanced by intrinsically disordered regions (IDRs). However, the underlying mechanisms are still debatable. Here, we examine 12 well-known IDRs by fusing them to the dCas9-VP64 activator, of which only seven can augment activation, albeit independently of their phase separation capabilities. Moreover, modular domains (MDs), another class of multivalent molecules, though ineffective in enhancing dCas9-VP64 activity on their own, show substantial enhancement in transcriptional activation when combined with dCas9-VP64-IDR. By varying the number of gRNA binding sites and fusing dCas9-VP64 with different IDRs/MDs, we uncover that optimal, rather than maximal, cis-trans cooperativity enables the most robust activation. Finally, targeting promoter-enhancer pairs yields synergistic effects, which can be further amplified via enhancing chromatin interactions. Overall, our study develops a versatile platform for efficient gene activation and sheds important insights into CRIPSR-based transcriptional activators enhanced with multivalent molecules.

| S-EPMC11341856 | biostudies-literature

mRNA expression profiles of antigen-specific CD8+ T cells induced by DNA prime-DNA boost and DNA prime-VACV boost immunization regimen

Project description:Similar with others, our data proved that antigen-specific CD8+ T cells from mice primed with DNA and boosted by VACV were much more sensitive to antigen stimulation than those from DNA-boost. Since the mechanisms of in vivo tuning of antigen sensitivity (also termed functional avidity) is still not defined, we compared this two vaccination regimen at gene expression level. Results provide important information of which genes were selectively activated by VACV boost vaccination. For example, data shows that the expression levels of genes involved in Cancer and Wnt signaling pathways is more higher in DNA prime-VACV boost regimen that DNA prime-DNA boost vaccination. To obtain sufficient of antigen-specific cells for microarray analysis, the OVA-specific CD8+ T cells from OT-1 mice were adoptively transferred into wild type mice and then immunized by DNA and VACV vaccine encoding OVA. Four week later, mice were scarificed and antigen-specific CD8+ T cells were emriched by CD45.1-PE antibody and anti-PE MicroBeads from splenocytes.Total RNA was extracted by the RNeasy Mini Kit (QIAGEN, Germany). Followed by amplification and biotin labeling, the samples were hybridized using Illumina Total Prep RNA Amplification Kit (Ambion, USA). Mouse WG-6v2 Expression BeadChips were used for analysis of transcriptome.

2013-10-30 | E-GEOD-51849 | biostudies-arrayexpress

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