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Trans-activating crRNA

Trans-activating CRISPR RNA (tracrRNA) is a small, non-coding RNA molecule essential to Type II CRISPR-Cas immune systems in bacteria, where it pairs with precursor CRISPR RNA (pre-crRNA) to enable the maturation of guide RNAs that direct the Cas9 nuclease to cleave invading viral DNA.^[1] This trans-encoded RNA, typically 50–90 nucleotides long, contains repeat-complementary regions that hybridize with the repeat sequences in pre-crRNA transcripts, facilitating their processing by the host RNase III enzyme into mature CRISPR RNAs (crRNAs).^[1] The resulting crRNA-tracrRNA duplex then binds to Cas9, forming a ribonucleoprotein complex that recognizes and cleaves target DNA sequences complementary to the crRNA spacer, thereby providing adaptive immunity against phages and plasmids.^[2] tracrRNA was first identified in 2011 through differential small RNA sequencing in the bacterium Streptococcus pyogenes, a common human pathogen, by Emmanuelle Charpentier and her team at Umeå University.^[1] This discovery revealed that tracrRNA is transcribed from a locus adjacent to the CRISPR array and cas genes, and its absence abolishes crRNA maturation and Cas9-mediated interference, confirming its indispensable role in the system.^[1] The finding built on earlier characterizations of CRISPR loci as adaptive immune elements and provided the mechanistic link for how Type II systems process and utilize guide RNAs, distinguishing them from Type I and Type III variants that rely on different processing pathways.^[3] In CRISPR-Cas9 biotechnology, tracrRNA's function has been harnessed by fusing it with synthetic crRNA into a single-guide RNA (sgRNA), simplifying the delivery and application of the system for genome editing, transcriptional regulation, and epigenetic modification in diverse organisms.^[2] This engineering breakthrough, demonstrated in 2012, enabled programmable targeting of specific genomic loci with high precision and efficiency, revolutionizing fields like gene therapy, agriculture, and basic research.^[2] Variations in tracrRNA sequences across bacterial species have also informed the development of orthogonal Cas9 variants for multiplexed editing and reduced off-target effects.^[3]

Discovery and characterization

Initial identification

tracrRNA (a trans-encoded small RNA) was initially identified in 2011 through a study led by Elitza Deltcheva and colleagues, focusing on the type II CRISPR-Cas system in the bacterium Streptococcus pyogenes. This work aimed to elucidate the molecular mechanisms underlying bacterial adaptive immunity against phages and plasmids, building on prior observations of CRISPR repeat arrays and their role in acquired resistance to viral infections.^[4] Using differential RNA sequencing in S. pyogenes, the researchers discovered tracrRNA featuring 24-nucleotide complementarity to the repeat sequences within the precursor CRISPR RNA (pre-crRNA). To confirm its expression and processing, they employed Northern blotting, which detected tracrRNA alongside crRNA species. Co-immunoprecipitation assays further demonstrated in vivo interactions between tracrRNA, pre-crRNA, the host endoribonuclease RNase III, and the CRISPR-associated protein Csn1. Genetic screening in mutant strains lacking tracrRNA, RNase III, or Csn1 linked these components to effective CRISPR interference against invading nucleic acids.^[4] A pivotal finding was that tracrRNA is essential for the maturation of pre-crRNA into functional crRNA, directing site-specific cleavage by RNase III in a process facilitated by Csn1; this maturation step proved critical for S. pyogenes immunity against prophage-derived DNA targets.^[4]

Biochemical and functional validation

Following the initial identification of a trans-encoded small RNA essential for crRNA maturation in 2011, biochemical and functional validation of tracrRNA was rigorously established in 2012 through in vitro experiments that elucidated its mechanistic roles in the type II CRISPR-Cas system of Streptococcus pyogenes.^[4]^[5] In the landmark study by Jinek et al., the term trans-activating crRNA (tracrRNA) was formally introduced to describe the ~75-nucleotide non-coding RNA that base-pairs with the repeat regions of precursor crRNA (pre-crRNA) transcripts, distinguishing it from the cis-encoded crRNA that carries the targeting spacer sequence.^[5] The research demonstrated tracrRNA's dual critical functions: it directs the processing of pre-crRNA by forming a partial duplex that recruits the host double-stranded RNA-specific endoribonuclease RNase III, with Cas9 acting as a cofactor to facilitate precise cleavage and generate mature ~36-nucleotide crRNAs; additionally, tracrRNA assembles a binary ribonucleoprotein complex with Cas9, which then binds crRNA to form the active ternary complex for DNA interference.^[5] These roles were confirmed via co-immunoprecipitation of tracrRNA and Cas9 from bacterial lysates, in vitro RNA processing assays using synthetic pre-crRNA substrates, and electrophoretic mobility shift assays showing stable complex formation dependent on tracrRNA-crRNA hybridization.^[5] In vitro reconstitution experiments provided direct evidence of the Cas9-tracrRNA-crRNA complex's programmability and endonuclease activity. Purified Cas9 protein was incubated with synthetic 42-nucleotide crRNA (containing a 20-nucleotide spacer) and 75-nucleotide tracrRNA to form the complex, which was then tested on supercoiled plasmid DNA or short double-stranded DNA substrates harboring a protospacer adjacent motif (PAM) sequence (5'-NGG-3').^[5] The complex cleaved target DNA site-specifically three nucleotides upstream of the PAM, producing blunt-ended double-strand breaks, with activity strictly requiring Mg²⁺ as the divalent cation.^[5] Assays were performed in a buffer composed of 20 mM HEPES (pH 7.5), 150 mM KCl, 10 mM MgCl₂, 0.5 mM DTT, and 0.1 mM EDTA, with 50–500 nM concentrations of each component and incubation at 37°C for 60 minutes; cleavage efficiency was assessed by agarose gel electrophoresis, revealing single-turnover rates of approximately 1.6–2.5 min⁻¹ for matched targets.^[6] Reprogramming was achieved by altering the crRNA spacer to match new protospacers, confirming specificity without off-target activity on mismatched sequences.^[5] Mutational analyses further validated tracrRNA's necessity for Cas9 function, emphasizing the repeat-antirepeat duplex as a pivotal structural element. Point mutations or deletions disrupting the 8–14 base pairs between tracrRNA's antirepeat region and crRNA's repeat abolished duplex formation, preventing pre-crRNA processing by RNase III and eliminating Cas9 endonuclease activity in DNA cleavage assays.^[5] In contrast, a truncated tracrRNA variant (nucleotides 23–48) fully supported complex assembly and targeted cleavage equivalent to the full-length molecule, as shown by denaturing polyacrylamide gel electrophoresis of radiolabeled RNA products and phosphorimaging of cleavage reactions.^[5] These findings, using variants with 5' or 3' deletions in the crRNA repeat, highlighted that while the 5'-proximal duplex region is indispensable for activation, the 3'-end is more tolerant, underscoring tracrRNA's role in bridging crRNA maturation and Cas9 targeting.^[5]

Molecular structure

Primary sequence features

Trans-activating crRNA (tracrRNA) in type II CRISPR-Cas systems typically ranges from 60 to 90 nucleotides in length, reflecting its role as a small non-coding RNA transcribed independently of the CRISPR array. In the well-studied system of Streptococcus pyogenes SF370, the primary tracrRNA transcripts are 171 nucleotides and 89 nucleotides long, with the 89-nucleotide form serving as the predominant mature species essential for crRNA processing.^[4]^[3] The primary sequence of tracrRNA features distinct motifs that enable its interaction with crRNA precursors. At the 5' end lies the antirepeat region, a conserved stretch of approximately 24 nucleotides that is partially complementary to the repeat sequences in the pre-crRNA, forming an imperfect duplex critical for maturation. Toward the 3' end, tracrRNA includes stem-loop structures that contribute to its stability, while the 3' terminus often ends in a Rho-independent terminator hairpin rich in GC content, facilitating transcription termination. These elements are encoded in the bacterial genome adjacent to the cas operon, typically upstream of the cas9 gene within or near the CRISPR locus, allowing coordinated expression with other system components.^[4]^[7] Sequence conservation across type II systems is notably high in the antirepeat region, which maintains complementarity to the crRNA repeat (e.g., forming a ~14-nucleotide duplex core in S. pyogenes), but variable in linker and stem-loop regions, reflecting adaptation to diverse host factors. For example, alignments between S. pyogenes and other streptococci like Streptococcus mutans reveal near-identity in the antirepeat (e.g., 5'-ACCAUUU-3' anti-tag pairing with crRNA 3'-UGGUAAA-5'), with divergences accumulating in non-essential linkers. This selective conservation underscores the antirepeat's functional primacy in duplex formation.^[7]^[4]

Secondary structure and motifs

The trans-activating crRNA (tracrRNA) from Streptococcus pyogenes adopts a compact secondary structure comprising three principal stem-loop domains, which collectively form a T-shaped architecture essential for its role in the CRISPR-Cas9 complex.^[8] The 5' region includes the antirepeat sequence that base-pairs with the crRNA repeat to form a partial duplex of 8-14 base pairs, while the downstream portion folds into stem-loop 1 (nexus), stem-loop 2, and stem-loop 3, with the latter two located at the 3' terminus and contributing to Cas9 recognition.^[5]^[8] Key structural motifs within this fold include the lower stem of the repeat:antirepeat duplex, which facilitates recognition by RNase III during pre-crRNA processing, and the nexus helix (stem-loop 1), which directly engages the Cas9 REC lobe to stabilize complex assembly.^[5]^[8] The antirepeat duplex exhibits a characteristic three-way junction with a G:U wobble pair, while the stems feature conserved Watson-Crick base pairs such as multiple U:A and G:C interactions that maintain rigidity.^[8] High-resolution insights into these elements derive from the 2.5 Å crystal structure of the S. pyogenes Cas9-tracrRNA-crRNA complex, which delineates the tracrRNA-Cas9 interface, including hydrogen bonding at the nexus helix and stem-loops 2 and 3 with domains like REC1 and the PAM-interacting region.^[8] Secondary structure predictions from early biochemical studies corroborated the three-hairpin model, with stem-loop 3 protruding to interact with the Cas9 NUC lobe.^[5] In certain type V CRISPR-Cas systems, tracrRNAs are notably shorter and lack one or more 3' stem-loops, relying instead on minimal duplex formation with crRNA for effector guidance.^[9]

Mechanism of action

Interaction with crRNA

The trans-activating crRNA (tracrRNA) interacts with CRISPR RNA (crRNA) through a specific base-pairing mechanism involving the antirepeat region of tracrRNA and the repeat sequence of crRNA. In Streptococcus pyogenes, this partial duplex formation occurs via approximately 24 nucleotides of complementarity, enabling the structural alignment necessary for downstream processing.^[4] The resulting RNA hybrid adopts a defined secondary structure, with the tracrRNA contributing additional stem-loop elements that stabilize the complex.^[5] This interaction is integral to the crRNA maturation pathway, where tracrRNA recruits the precursor crRNA (pre-crRNA) transcript to the host enzyme RNase III. The base-paired duplex positions the repeat-antirepeat junctions for precise cleavage by RNase III, generating the mature crRNA:tracrRNA hybrid.^[4] This processing step occurs in a coordinated manner, requiring the presence of the CRISPR-associated protein Csn1 (also known as Cas9) to facilitate efficient duplex recognition and cleavage both in vivo and in vitro.^[5] The binding between tracrRNA and crRNA follows a 1:1 stoichiometry, forming a stable heteroduplex that protects the crRNA spacer sequence from degradation and enhances its availability for target recognition.^[4] By stabilizing the 5' end of the mature crRNA, tracrRNA ensures the integrity of the spacer region, which is critical for subsequent guide-target hybridization.^[5] Experimental validation of this interaction has been achieved through in vitro duplex formation assays, which demonstrate rapid and specific hybridization between tracrRNA and pre-crRNA fragments. These assays, often monitored by gel electrophoresis or cleavage efficiency, confirm the robustness of the RNA-RNA pairing under physiological conditions.^[5]

Role in Cas9 complex formation and activation

The trans-activating crRNA (tracrRNA) plays a pivotal role in assembling the Cas9 ribonucleoprotein (RNP) complex by first binding to the Cas9 protein through its characteristic stem-loop structures, particularly stem-loop 1, which serves as a primary recognition motif. This initial binary interaction creates a scaffold that facilitates the subsequent loading of the CRISPR RNA (crRNA), forming a stable ternary Cas9-crRNA-tracrRNA complex essential for DNA targeting. Structural studies reveal that the tracrRNA's lower stem-loop regions engage specific pockets on Cas9's recognition (REC) lobe, positioning the RNA duplex for integration into the enzyme's active architecture.^[10] Upon ternary complex formation, tracrRNA induces critical conformational changes in Cas9, transitioning the enzyme from an inactive, closed state to an open bilobed structure comprising the REC and nuclease (NUC) lobes. This rearrangement accommodates the guide RNA and enables the HNH and RuvC nuclease domains to align for sequential cleavage of the non-target and target DNA strands, respectively, resulting in a double-strand break. The activation is RNA-dependent, with tracrRNA ensuring the crRNA spacer sequence is properly oriented for hybridization.^[10]^[11] In target recognition, tracrRNA stabilizes the crRNA spacer, promoting PAM-proximal base pairing with the target DNA at the canonical NGG motif, which is required for initial DNA unwinding and R-loop formation. Biochemical assays demonstrate high-affinity interactions, with dissociation constants (Kd) for the Cas9-RNA complex approaching ~0.5 nM as measured by electrophoretic mobility shift assays (EMSA), underscoring the efficiency of assembly. Kinetic studies further indicate cleavage rates of 0.3–1 min⁻¹ under saturating conditions, highlighting tracrRNA's contribution to rapid and specific activation.^[5]^[11]

Evolutionary and comparative aspects

Distribution across CRISPR-Cas types

Trans-activating crRNA (tracrRNA) is a critical component primarily in class 2 CRISPR-Cas systems, where it is essential for crRNA maturation and effector complex assembly. It is prominently featured in all type II subtypes, including type II-A as exemplified by the Cas9 system in Streptococcus pyogenes, and type II-B in organisms such as Listeria monocytogenes. Additionally, tracrRNA is required in certain type V subtypes, notably type V-B (also known as C2c1 or Cas12b) found in bacteria like Bacillus thermoamylovorans. In contrast, tracrRNA is absent in type I and type III systems, which utilize multi-subunit Cascade complexes or Csm/Cmr modules for crRNA processing without a dedicated trans-activating RNA.^[12]^[13]^[14] Type-specific adaptations of tracrRNA reflect the evolutionary divergence within these systems. In type II CRISPR-Cas, tracrRNA is typically a full-length non-coding RNA (approximately 50-100 nucleotides) characterized by a three-stem-loop secondary structure: stem-loop 1 (SL1) for antirepeat base-pairing, SL2 for stabilization, and SL3 often functioning as a terminator with non-canonical base pairs like A-G. This structure enables duplex formation with pre-crRNA repeats, recruiting host RNase III for processing into mature crRNAs, as seen in S. pyogenes type II-A and Listeria type II-B homologs. In type V-B systems, tracrRNAs are generally shorter (e.g., ~79 nucleotides in B. thermoamylovorans Cas12b) and integrate similarly, facilitating their processing by the host RNase III enzyme into mature crRNAs to guide the single-subunit effector, supporting temperature-optimized activity around 50°C. Recent classifications (as of 2025) further highlight tracrRNA's presence in type II-D systems, which employ alternative processing pathways in the absence of RNase III, such as via Cas9d or other RNases, and expanded roles in additional type V variants. These features highlight tracrRNA's role in simplifying RNA-guided interference in class 2 systems compared to multi-protein class 1 counterparts.^[12]^[13] Bioinformatic approaches have been key to identifying tracrRNA homologs across diverse taxa. Tools utilizing covariance models, built from sequence-structure alignments of validated tracrRNAs, scan genomes for candidates based on antirepeat complementarity, stem-loop motifs, and free energy parameters, achieving high sensitivity (e.g., >90% on test sets). For instance, such models clustered tracrRNAs into 15 groups, revealing homologs in Listeria (type II-B) that enable functional phage resistance and in Francisella novicida (associated with type V-U explorations but featuring type II-B-like tracrRNA for dual immunity and regulatory roles). These methods underscore tracrRNA's patchy yet conserved distribution, aiding the discovery of over 275 instances across 165 bacterial genera.^[15]^[16]^[12]

Sequence conservation and variations

The antirepeat region of tracrRNA exhibits high sequence conservation, with over 80% identity observed across streptococcal species, reflecting its critical role in base-pairing with crRNA repeats. In contrast, linker regions between structural elements display significantly lower conservation, typically ranging from 20-50% identity, allowing for greater sequence flexibility while maintaining functional duplex formation. These patterns are evident in phylogenetic analyses of type II systems, where 2018 studies revealed clustered branches such as branch 1 (encompassing streptococci, Listeria, and Lactobacilli), showing congruent evolutionary trajectories with Cas9 orthologs.^[9] Variations in tracrRNA sequences are pronounced in type V CRISPR-Cas systems, where truncations are common; for instance, certain Cas12 variants feature shortened tracrRNAs of approximately 40 nucleotides, often lacking the 5' stem-loop structure present in canonical type II forms. In non-type II and non-type V systems, tracrRNA genes are frequently absent, with some loci containing pseudogenes that have lost functionality due to mutations or incomplete annotation in genomic surveys. These divergences highlight the modular evolution of trans-activating RNAs, constrained by effector protein compatibility.^[17]^[9] Evolutionary analyses indicate strong co-evolution between tracrRNA and cas genes, as evidenced by correlated phylogenetic trees in bacterial and archaeal genomes, where sequence divergences mirror Cas9 subfamily splits. Metagenomic studies further support horizontal gene transfer events, identifying novel tracrRNA variants in uncultivated microbes that form stable hybrids with non-native repeats, suggesting acquisition across distant lineages. Computational prediction tools, such as those employing Infernal covariance models, achieve high sensitivity exceeding 80% for detecting tracrRNAs in type II genomes by scanning for conserved antirepeat motifs adjacent to cas9 loci.^[9]^[12]

Applications in biotechnology

Integration into single-guide RNAs

The integration of trans-activating CRISPR RNA (tracrRNA) with CRISPR RNA (crRNA) into a single-guide RNA (sgRNA) represents a key engineering advance that simplifies the CRISPR-Cas9 system by reducing the need for two separate RNA components. In 2012, Jinek et al. designed the first synthetic sgRNA by fusing the 3' end of the crRNA—specifically its 20-nucleotide spacer sequence—to the 5' end of the tracrRNA scaffold, connected via a GAAA tetraloop to mimic the native duplex formation between the two RNAs.^[5] This chimeric construct streamlines the dual-RNA system into one molecule, facilitating easier synthesis and application while preserving the guide's ability to direct Cas9 to target DNA sites.^[5] The canonical sgRNA architecture spans approximately 100 nucleotides, comprising the 20-nucleotide spacer for target recognition, followed by the tracrRNA-derived stem-loop structures that recruit and activate Cas9, and a 3' poly-T terminator sequence for efficient transcription termination in eukaryotic systems.^[5] In vitro cleavage assays demonstrated that this sgRNA guides Cas9-mediated DNA cleavage with efficiency comparable to the native crRNA-tracrRNA duplex, achieving robust double-strand breaks at targeted sites without significant loss in activity.^[5] Subsequent optimizations enhanced sgRNA utility for cellular applications. For instance, variants incorporating MS2 RNA hairpins into the sgRNA scaffold enable affinity purification through binding to MS2 coat protein, aiding in quality control and isolation of the guide RNA during production. In eukaryotic cells, sgRNAs are commonly expressed from RNA polymerase III promoters such as U6, which drives high-level, nuclear-localized transcription and supports stable guide accumulation for genome editing.^[18] The sgRNA format offers practical advantages, including simplified delivery via single vectors or plasmids, which reduces complexity in transfection or viral packaging compared to co-delivering separate crRNA and tracrRNA.^[18] A landmark demonstration came in 2013, when Mali et al. used U6-expressed sgRNAs to achieve targeted editing at the endogenous AAVS1 locus in human 293T cells, yielding mutation rates of 10-25%—the first reported instance of sgRNA-mediated genome modification in human cells.^[18]

Engineered modifications and variants

Engineered modifications to tracrRNA have focused on optimizing its scaffold to improve CRISPR-Cas9 performance, such as the development of a truncated 67-nucleotide (nt) version that enhances on-target activity compared to the full 89-nt natural tracrRNA from Streptococcus pyogenes.^[19] This truncation maintains the essential anti-repeat and stem-loop structures for Cas9 binding but eliminates non-essential 3' extensions, enabling more efficient ribonucleoprotein (RNP) complex formation in applications like genome editing.^[20] Dual-guide variants, or dgRNAs, incorporate two crRNA spacers into a single tracrRNA scaffold, allowing one Cas9 RNP to perform multiplexed editing at two sites simultaneously, with sequence features in the tracrRNA repeat-anti-repeat region optimizing pairing efficiency and reducing interference between guides.^[21] Repurposing efforts have reprogrammed the crRNA-tracrRNA base-pairing interface to hijack endogenous cellular RNAs as functional crRNAs, enabling Cas9 to target DNA based on the presence of specific transcripts without exogenous guide delivery. In a 2022 study, engineered tracrRNAs with altered anti-repeat sequences allowed S. pyogenes Cas9 to use mRNAs, such as those from the RFP gene, as crRNA proxies, with approximately 40% of tested variants exhibiting higher activity than wild-type guides in CRISPR interference and activation assays.^[22] This approach links RNA abundance to CRISPR output, with linear correlations (R² > 0.99) observed between mRNA levels and transcriptional activation, facilitating applications in synthetic gene circuits and biosensors.^[22] Specialized tracrRNA variants support derivative CRISPR tools, including base editing with nCas9 (a D10A Cas9 nickase mutant), where chemical modifications like 2'-O-methyl and 3'-phosphorothioate at the termini stabilize the tracrRNA-crRNA duplex, boosting editing efficiencies by 2- to 5-fold in mammalian cells without increasing off-target effects.^[23] For imaging, dCas9 paired with tracrRNA scaffolds engineered to include MS2 RNA aptamer loops in the stem regions recruits MS2 coat protein fused to fluorescent tags (e.g., GFP), enabling multicolor visualization of genomic loci with signal-to-noise ratios improved by up to 3-fold over unmodified systems.^[24] These aptamer integrations, often placed in the tetraloop or lower stem of the tracrRNA-derived scaffold, allow orthogonal labeling for tracking multiple sites in live cells.^[24] To aid design of such engineered tracrRNAs, the CRISPRtracrRNA pipeline, introduced in 2022, computationally screens genomes for candidate sequences by predicting anti-repeat complementarity and secondary structures, outperforming prior tools in sensitivity (recovering 95% of known tracrRNAs) and enabling rapid prototyping for synthetic biology applications like orthogonal Cas9 systems.^[15]

References

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