Biology subjects

Jain, P. K.

Publications and source records attributed to Jain, P. K..

10 recordsLinked to original sources

bioRxiv2026

Guide RNA binding induces reverse transcription bias during RT-qPCR analysis of RNA-targeting CRISPR/Cas systems

RNA-targeting CRISPR systems are commonly evaluated by RT-qPCR, but guide RNA binding can confound these measurements. We show that crRNA alone produces apparent knockdown without reducing target RNA abundance, whereas RNA sequencing remains unbiased and reveals guide-associated transcriptomic perturbations. A simple RNA denaturation step before reverse transcription restores accurate RT-qPCR quantification, providing practical guidance for RNA-targeting CRISPR analysis and guide design.

genomics↗

bioRxiv2026

Asymmetric DNA targeting by RNA-guided TIGR-Tas systems

Tandem interspaced guide RNA (TIGR)-TIGR-associated (Tas) are RNA-guided defense systems, which use a dual-repeat or stem-loop tigRNA to direct a Tas dimer to DNA targets through RNA-DNA heteroduplex formation between both DNA strands. While previous work has shown the basic principles of DNA targeting, how the guide architecture influences target recognition and whether recognition and cleavage are coordinated across the two RNA-DNA heteroduplexes at a target site remain poorly understood. Here, we combine cryo-electron microscopy, biochemistry, and cell-based assays to investigate two TIGR-Tas effectors: the nuclease-lacking Peromyscus leucopus TasA (PlTasA), associated with a stem-loop tigRNA, and the nuclease-active Salicola phage TasH (SpTasH). Cryo-EM structures of PlTasA binary and ternary complexes reveal a dimeric scaffold similar to SpTasH and TaTasR with a distinct stem-loop tigRNA architecture and additional peripheral structural elements. Binding assays using DNA substrates containing local bubbles across the spacer-matching region show equivalent bubbles produced position- and spacer-dependent effects, indicating that target engagement is asymmetric in both PlTasA and SpTasH. Kinetic and cryo-EM analyses of SpTasH further reveal stepwise heteroduplex formation, with a partially engaged intermediate that undergoes substantial conformational rearrangements of the second protomer, preceding a fully paired state poised for catalytic activation. Cleavage of the two DNA strands occurs through a coordinated, slow process and productive cleavage requires stringent surveillance of both heteroduplexes. Together, these findings define a conserved, ordered mechanism of bipartite target recognition and activation shared by TIGR-Tas effectors, expanding our understanding of the molecular principles underlying programmable DNA targeting by TIGR-Tas systems.

biochemistry↗

bioRxiv2026

Behavioral and Functional Profiling of Acomys cahirinus Fibroblasts Reveals Enhanced Matrix Remodeling Capacity

The African spiny mouse (Acomys cahirinus) exhibits a unique capacity among mammals for scarless tissue regeneration, making it a compelling model for investigating the cellular mechanisms underlying regenerative healing. To determine how cellular heterogeneity and specific phenotypes influence fibroblast behavior, we established an immortalized Acomys fibroblast line along with a CRISPR/Cas9-mediated Col3A1 knockout variant and a DNA damage-induced senescent population. Compared with Mus musculus, NIH 3T3 fibroblasts, Acomys cells displayed distinct morphology, similar migration speeds, reduced directional persistence, and greater biophysical heterogeneity. While previous studies have linked regenerative wound healing to the elevated expression of collagen type III (Col3A1), CRISPR-mediated knockout of Col3A1 in Acomys fibroblasts yielded comparable biophysical profiles to wild-type cells in 2D culture. To examine additional contributors to the enhanced wound-like matrix environment, we established a senescence model in which Acomys fibroblasts exhibited elevated resistance to DNA-damaging agents, complete loss of proliferation, and altered single-cell morphology. In 3D collagen gel contraction assays, Col3A1 knockout attenuated matrix remodeling capacity, whereas the introduction of a small fraction of senescent cells enhanced gel contraction and remodeling dynamics, suggesting that senescent fibroblasts can modulate collective matrix behaviors. Together, these findings demonstrate that both Col3A1 expression and senescence-associated cell states contribute to fibroblast-driven matrix remodeling, highlighting Acomys fibroblasts as a valuable model for investigating how cellular heterogeneity and senescence-associated cell phenotypes could influence regenerative wound healing.

bioengineering↗

bioRxiv2026

TAMIPAMI: Software and methods for PAM/TAM identification for CRISPR and OMEGA gene editing systems

Protospacer adjacent motifs (PAMs) and target-adjacent motifs (TAMs) are essential for target recognition by CRISPR-Cas and TnpB nucleases. Here we present TAMIPAMI, an efficient experimental and computational framework for rapid PAM/TAM identification. TAMIPAMI requires only a single control library and Cas or TnpB-treated library, simplifying experimental design, reducing cost, and providing greater accessibility for users. The platform interprets sequencing data with interactive visualizations and introduces a novel algorithm that determines the minimal exact set of degenerate IUPAC sequences describing the observed PAM/TAM patterns. Using this approach, we accurately recovered canonical motifs for several nucleases, including SpCas9, LbCas12a, AsCas12a, BrCas12b, Cas12i1, and AmaTnpB. TAMIPAMI is available as both a web application and command-line tool, ultimately providing an accessible and efficient platform for PAM/TAM discovery and characterization across CRISPR and OMEGA systems.

bioinformatics↗

bioRxiv2026

Architecture of a DNA-guided Cas12a

CRISPR/Cas systems have largely been restricted to RNA-guided nucleases. Here, we present the cryo-EM structure of Acidaminococcus sp. Cas12a (AsCas12a) bound to a pseudo-DNA ({Psi}DNA) guide and RNA target, revealing how Cas12a accomplishes DNA-guided RNA recognition. The {Psi}DNA hairpin bridges the recognition and nuclease lobes, mimicking a PAM-proximal duplex and positioning the spacer to allow formation of a canonical RNA-DNA heteroduplex along the REC lobe. This provides a structural framework for its activity and provides a blueprint for future engineering.

biochemistry↗

bioRxiv2025

Single-nucleotide Resolution Epitranscriptomic Profiling Uncovers Dynamic m6A Regulation in Bovine Preimplantation Development

RNA N6-methyladenosine (m6A) plays a crucial role in regulating gene expression during early embryonic development. However, the m6A dynamics at single-nucleotide resolution in preimplantation development remain uncharacterized, and the functional significance of site specific m6A modifications in key developmental regulators is largely unknown. Here, using SAC-seq, a single-base resolution, antibody-independent m6A profiling method, we generate the first comprehensive m6A landscape in bovine oocytes and preimplantation embryos. We identify a previously uncharacterized m6A site in RPL12 transcript that is essential for embryonic development. Loss of m6A at this site leads to reduced protein synthesis, disrupted expression of translation-related genes, and impaired zygotic genome activation and blastocyst formation. Notably, supplementation with wild-type RPL12 mRNA fails to rescue the developmental arrest, indicating that m6A regulation extends beyond transcript abundance. Our findings provide a valuable resource of m6A at single-nucleotide resolution in mammalian embryogenesis and uncover a critical mechanism by which precise, site-specific m6A regulates translation and developmental competence in early embryos.

developmental biology↗

bioRxiv2024

Efficient Genome Editing with Chimeric Oligonucleotide-Directed Editing

Prime editing has emerged as a precise and powerful genome editing tool, offering a favorable gene editing profile compared to other Cas9-based approaches. Here we report new nCas9-DNA polymerase fusion proteins to create chimeric oligonucleotide-directed editing (CODE) systems for search-and-replace genome editing. Through successive rounds of engineering, we developed CODEMax and CODEMax(exo+) editors that achieve efficient genome modifications in human cells with low unintended edits. CODEMax and CODEMax(exo+) contain an engineered Bst DNA polymerase derivative known for its robust strand displacement ability. Additionally, CODEMax(exo+) features a 5 to 3 exonuclease activity that promotes effective strand invasion and repair outcomes favoring the incorporation of the desired edit. We demonstrate CODEs can perform small insertions, deletions, and substitutions with improved efficiency compared to PEMax at many loci. Overall, CODEs complement existing prime editors to expand the toolbox for genome manipulations without double-stranded breaks.

bioengineering↗

bioRxiv2023

CRISPR-based diagnostics detects invasive insect pests

Rapid identification of organisms is essential across many biological and medical disciplines, from understanding basic ecosystem processes and how organisms respond to environmental change, to disease diagnosis and detection of invasive pests. CRISPR-based diagnostics offers a novel and rapid alternative to other identification methods and can revolutionize our ability to detect organisms with high accuracy. Here we describe a CRISPR-based diagnostic developed with the universal cytochrome-oxidase 1 gene (CO1). The CO1 gene is the most sequenced gene among Animalia, and therefore our approach can be adopted to detect nearly any animal. We tested the approach on three difficult-to-identify moth species (Keiferia lycopersicella, Phthorimaea absoluta, and Scrobipalpa atriplicella) that are major invasive pests globally. We designed an assay that combines recombinase polymerase amplification (RPA) with CRISPR for signal generation. Our approach has a much higher sensitivity than other real time-PCR assays and achieved 100% accuracy for identification of all three species, with a detection limit of up to 120 fM for P. absoluta and 400 fM for the other two species. Our approach does not require a lab setting, reduces the risk of cross-contamination, and can be completed in less than one hour. This work serves as a proof of concept that has the potential to revolutionize animal detection and monitoring.

genetics↗

bioRxiv2023

Programmable RNA detection with CRISPR-Cas12a

CRISPR is a prominent bioengineering tool and the type V CRISPR-associated protein complex, Cas12a, is widely used in diagnostic platforms due to its innate ability to cleave DNA substrates. Here we demonstrate that Cas12a can also be programmed to directly detect RNA substrates without the need for reverse transcription or strand displacement. We discovered that while the PAM-proximal "seed" region of the crRNA exclusively recognizes DNA for initiating trans-cleavage, the PAM-distal region or 3-end of the crRNA can tolerate both RNA and DNA substrates. Utilizing this property, we developed a method named Split Activators for Highly Accessible RNA Analysis or SAHARA to detect RNA sequences at the PAM-distal region of the crRNA by merely supplying a short ssDNA or a PAM containing dsDNA to the seed region. Notably, SAHARA is Mg2+ concentration- and pH-dependent, and it was observed to work robustly at room temperature with multiple orthologs of Cas12a. SAHARA also displayed a significant improvement in the specificity for target recognition as compared to the wild-type CRISPR-Cas12a, at certain positions along the crRNA. By employing SAHARA we achieved amplification-free detection of picomolar concentrations of miRNA-155 and hepatitis C virus RNA. Finally, SAHARA can use a PAM-proximal DNA as a switch to control the trans-cleavage activity of Cas12a for the detection of both DNA and RNA targets. With this, multicomplex arrays can be made to detect distinct DNA and RNA targets with pooled crRNA/Cas12a complexes. In conclusion, SAHARA is a simple, yet powerful nucleic acid detection platform based on Cas12a that can be applied in a multiplexed fashion and potentially be expanded to other CRISPR-Cas enzymes. O_FIG O_LINKSMALLFIG WIDTH=125 HEIGHT=200 SRC="FIGDIR/small/525716v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@5edb2dorg.highwire.dtl.DTLVardef@187678borg.highwire.dtl.DTLVardef@9f0184org.highwire.dtl.DTLVardef@11cb1a4_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2020

Enhancement of trans-cleavage activity of Cas12a with engineered crRNA enables amplified nucleic acid detection

The CRISPR/Cas12a RNA-guided complexes have a tremendous potential for nucleic acid detection due to its ability to indiscriminately cleave ssDNA once bound to a target DNA. However, the current CRISPR/Cas12a systems are limited to detecting DNA in a picomolar detection limit without an amplification step. Here, we developed a platform with engineered crRNAs and optimized conditions that enabled us to detect DNA, DNA/RNA heteroduplex and methylated DNA with higher sensitivity, achieving a limit of detection of in femtomolar range without any target pre-amplification step. By extending the 3- or 5-ends of the crRNA with different lengths of ssDNA, ssRNA, and phosphorothioate ssDNA, we discovered a new self-catalytic behavior and an augmented rate of LbCas12a-mediated collateral cleavage activity as high as 3.5-fold compared to the wild-type crRNA. We applied this sensitive system to detect as low as 25 fM dsDNA from the PCA3 gene, an overexpressed biomarker in prostate cancer patients, in simulated urine over 6 hours. The same platform was used to detect as low as ~700 fM cDNA from HIV, 290 fM RNA from HCV, and 370 fM cDNA from SARS-CoV-2, all within 30 minutes without a need for target amplification. With isothermal amplification of SARS-CoV-2 RNA using RT-LAMP, the modified crRNAs were incorporated in a paper-based lateral flow assay that could detect the target with up to 23-fold higher sensitivity within 40-60 minutes.

bioengineering↗