Toolkit Items

New methodologies such as circular RNA (circRNAs) ...

Ligand-activated and ligand-deactivated sgRNAs are engineered single-guide RNAs that place CRISPR-Cas9-based gene repression under small-molecule control. In the reported 2019 Nature Communications study, sgRNA function was activated or deactivated in a dose-dependent manner by two different ligands, with regulation acting directly at the level of each target-specific sgRNA.

New methods, including self-amplifying mRNA (saRNA), CRISPR-Cas9 gene editing, and tissue-specific delivery systems, enhance the therapeutic potential.

Synthetic riboswitches have undergone great development in the past decade, evolving into valuable regulatory tools.

MALAT1 is a long noncoding RNA reported in trophoblasts to promote cell migration and invasion by reducing CRY2 protein abundance. In the cited study, MALAT1 recruits the E3 ubiquitin ligase FBXW7, impairing CRY2 protein stability and inducing ubiquitin-mediated CRY2 degradation.

Smart RNA guides (SmartGuides) are engineered CRISPR-Cas9 guide RNAs that become active only in the presence of a specific RNA opener. They provide conditional RNA-responsive control of guide function and were reported in miRNA-responsive formats and Boolean logic circuit compositions.

Small interfering RNA (siRNA) is a short RNA modality used to transiently downregulate expression of a target gene by exploiting the RNA interference pathway. In the supplied evidence, siRNA is described as a gene-therapy approach for altering gene expression rather than a genome-editing reagent.

Light-controlled crRNA is a chemically modified CRISPR guide RNA in which vitamin E is attached to the 5' terminus through a photolabile linker, creating a caged crRNA that inactivates CRISPR/Cas9 until light exposure. Upon irradiation, this design restores CRISPR/Cas9 activity and supports genome editing of VEGFA and knockdown of EGFP expression in human cells.

Phytochrome mRNA is a native light-responsive RNA output measured in etiolated Avena seedlings. Its translatable abundance decreases after red-light exposure and this effect is reversed by an immediately subsequent far-red pulse, indicating phytochrome-mediated autoregulation of translatable phytochrome mRNA levels.

Upstream open reading frames (uORFs) are endogenous 5′-leader RNA elements that can take precedence over translation of the main ORF and reduce protein output. In Arabidopsis, blue light can increase use of downstream transcription start sites that bypass uORFs, enabling higher expression of light-responsive genes.

We report the identification and utilization of ... the novel gga-miRNA-1811 ... The combination of these miRNAs with key pluripotency genes significantly improved the reprogramming efficiency of CEFs into iPSCs.

We report the identification and utilization of gga-miRNA-302s ... The combination of these miRNAs with key pluripotency genes significantly improved the reprogramming efficiency of CEFs into iPSCs.

Mechanistically, EVs from ischemia-evoked neuronal activity induce neuronal apoptosis and innate immune responses by transferring higher miR-100-5p to adjacent neuron and microglia. MiR-100-5p can bind to and activate TLR7 through U18U19G20-motif, thereby activating NF-κB pathway.

Its abstract indicates a mammalian-cell RNA condensate engineering platform built from nanostar-derived RNA scaffolds.

Here, we describe the development of a sequence-activated fluorescent RNA (SaFR) technique.

Here, we develop an ultra-efficient prime editing (UtPE) system for dicots by integrating evolved PE6 variants (PE6c and PE6ec), an altered pegRNA (aepegRNA), an RNA chaperone, and a geminiviral replicon.

ASOs are under development to reduce expression of pathogenic proteins such as tau, α-synuclein, and mutant huntingtin.

Emerging therapeutic strategies aim to counteract these processes through antisense oligonucleotide-mediated splicing correction

Antisense RNA is an RNA-based regulatory tool reported in tobacco to restore fertility in genetically engineered male sterile plants. The available evidence indicates a functional phenotype in this plant system, but does not specify the target gene, antisense construct design, or molecular implementation.

Aptazyme-embedded guide RNAs are engineered CRISPR guide RNA constructs that confer ligand-responsive control over CRISPR outputs. Reported functions include ligand-responsive genome editing and ligand-responsive transcriptional activation.

This review provides a broad overview of ... newly developed calcium, and voltage indicators

its cognate stem-loop RNA (Cas6 binding site, termed CBS)

The CIb1 promoter is a Bombyx mori gene promoter characterized by firefly luciferase reporter assays in the ovary-derived BmN cell line. Deletion analysis identified promoter fragments with transcriptional activity, including an 82 bp region from -72 to +10 nt that retains basic promoter function, and an upstream segment with strong negative regulatory effects.

circular RNA (circRNA) represents an emergent platform that may offer potential for mucosal HIV vaccine development

CircZNF367 is a circular RNA reported to promote osteoclast differentiation and osteoporosis. The available evidence indicates that it acts through interaction with the RNA-binding protein FUS to maintain CRY2 mRNA stability.

CRY2 mRNA is described in the cited study as a post-transcriptionally regulated RNA whose stability is maintained through a CircZNF367–FUS interaction. In that reported context, this regulatory relationship is linked to osteoclast differentiation and osteoporosis.

Fusion guide RNAs are engineered RNA elements reported for orthogonal gene manipulation with the CRISPR effectors Cas9 and Cpf1. The available evidence indicates that they are designed to interface with both systems within a single guide-RNA framework for gene control.

A nested group II intron has been described as an RNA regulatory element for controlling homing endonuclease expression. In Escherichia coli, altering the splicing efficiency of a homing endonuclease ORF-embedded group II intron was reported to modulate homing endonuclease expression in vivo.

Guide RNA is the programmable RNA component of the CRISPR/Cas9 system that directs Cas9 to sequence-defined genomic sites. Altering the guide RNA sequence retargets Cas9 to new DNA loci for sequence-specific genome editing.

The hypoxanthine switch is a small molecule-responsive RNA element described as a hypoxanthine-sensitive switch. Available evidence indicates that its intracellular switch activity correlates with aptamer binding properties measured biochemically.

A genetically encoded glutamate sensor (iGluSnFR3.v857) was expressed in the caudate-putamen region

An ingenious logic DNAzyme system consists of Chain 1 (C1)/Chain 2 (C2) and endogenous lncRNA is designed.

The main ORF (mORF) is the protein-coding open reading frame in a transcript whose translation can be repressed by upstream ORFs (uORFs). In Arabidopsis, transcripts initiated from downstream alternative transcription start sites can bypass uORFs and thereby support expression of the mORF, including in blue-light-responsive genes.

Methylated guide RNA for CRISPR-Cas12a is a chemically modified crRNA bearing m6A or m1A marks that suppresses Cas12a activity. The methylated guide inhibits both cis- and trans-DNA cleavage, and activity can be reactivated through guide RNA demethylation.

The methylation-deactivated and demethylase-activated CRISPR-Cas12a guide RNA strategy is an RNA-level control system in which m6A or m1A modification of the Cas12a guide RNA suppresses CRISPR-Cas12a activity, while demethylation restores function. It was reported as a way to regulate Cas12a for controllable gene editing, gene expression regulation, and demethylase imaging in living cells.

miR-181d is a microRNA reported in colorectal cancer that is induced by c-Myc signaling and promotes glycolytic metabolism. The available evidence describes it as a post-transcriptional regulator involved in metabolic reprogramming in CRC cells.

miR-27a-3p is a microRNA reported to promote osteogenic differentiation through activation of the CRY2/ERK1/2 signaling axis. The available evidence supports a functional role in regulating an osteogenesis-associated pathway.

miR-7-5p is a microRNA reported to directly target CRY2 and thereby modulate osteoblast differentiation. In the cited 2019 study, miR-7-5p overexpression promoted osteogenic marker expression and osteoblast differentiation, consistent with repression of CRY2 and activation of CLOCK/BMAL1/P300 signaling.

SaFR undergoes conformational reorganization and transforms into the fluorogenic conformation of Pepper, enabling the activation of fluorophores to produce fluorescent signals.

The PORC promoter is an Arabidopsis promoter element that functions as an in vivo binding target of the scarecrow-like transcription factor SCL27. Available evidence indicates that SCL27 binds GT cis-elements within this promoter and regulates PORC promoter activity, with DELLA proteins reducing SCL27 promoter binding.

We engineered BLU-VIPR around... ribozyme-flanked gRNA. The BLU-VIPR design is genetically encoded and ensures precise excision of multiple gRNAs from a single messenger RNA transcript.

The review paper of Berens et al. [6] deals with RNA aptamers as a versatile tool to control gene expression.

This RNA platform is described as a general class of synthetic biology tools for modular, dynamic, and multi-output control over mammalian cells. The cited 2015 study also states that synthetic RNA devices were used to control the mammalian cell cycle.

SIBR is an inducible RNA-based regulatory element proposed to provide universal control of gene expression and gene regulation in bacteria. In the reported SIBR-Cas configuration, it regulates CRISPR-Cas counterselection with a temporal delay that improves genome editing in non-model bacterial hosts.

Small molecule regulated sgRNAs are engineered single-guide RNAs that confer small-molecule control over Cas9-mediated genome editing in Escherichia coli. The available evidence supports their function as RNA-level regulators of CRISPR-Cas9 editing activity in a bacterial system.

Sonic Hedgehog (SHH) is described here as a signaling element used to locally activate SHH pathway activity in a human neurodevelopment organoid model. In the cited study context, local SHH activation was sufficient to generate stereotypically patterned organoids in three dimensions.

As an individual expressing element or a co-expressing 3' UTR tag within specific mRNA, SRTS achieved quantitative regulation of the gene with 3' UTR cognate OPRTS.

we reconstructed artificial TA pairs termed SRTS-OPRTS. A platform for generating orthogonal SRTS-OPRTS pairs with cross-species application ... was developed

Synthetic small molecule-responsive RNA devices are engineered RNA elements reported to regulate the mammalian cell cycle. In the cited 2015 study, they are presented as a modular platform for dynamic and multi-output control in mammalian cells.

Toehold-gated guide RNA (thgRNA) is a synthetic riboregulatory guide RNA class that controls CRISPR/Cas9 activity in response to RNA inputs. Available evidence indicates that endogenous RNA transcripts can trigger thgRNA to activate Cas9 functions, supporting autonomous RNA-responsive control of genome-targeting activity.