Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2021.05.04.442622

Comprehensive PAM prediction for CRISPR-Cas systems reveals evidence for spacer sharing, preferred strand targeting and conserved links with CRISPR repeats

Vink, J. N.·Baijens, J. H.·Brouns, S. J.
View original source ↗Export metadata ↓

Abstract

The adaptive CRISPR-Cas immune system stores sequences from past invaders as spacers in CRISPR arrays and thereby provides direct evidence that links invaders to hosts. Mapping CRISPR spacers has revealed many aspects of CRISPR biology, including target requirements such as the protospacer adjacent motif (PAM). However, studies have so far been limited by a low number of mapped spacers in the database. By using vast metagenomic sequence databases, we mapped one third ([~]70,000) of more than 200,000 unique CRISPR spacers from a variety of microbes, and derived a catalog of more than one hundred unique PAM sequences associated with specific CRISPR subtypes. These PAMs were further used to correctly assign the orientation of CRISPR arrays, revealing conserved patterns between the last nucleotides of the CRISPR repeat and PAM. From the curated CRISPR arrays dataset we could also deduce CRISPR subtype specific preferences for targeting either template or coding strand of open reading frames. While some DNA-targeting systems (e.g. Type I-E and Type II systems) prefer the template strand and avoid mRNA, other DNA- and RNA-targeting systems (i.e. Type I-A, I-B and Type III systems) prefer the coding strand and mRNA. In addition, we found large scale evidence that both CRISPR adaptation machinery and CRISPR arrays are shared between different CRISPR-Cas systems. This could lead to simultaneous DNA- and RNA targeting of invaders, which may be effective at combating mobile genetic invaders.

Explore related subjects

bioinformaticsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Vink, J. N., Baijens, J. H., Brouns, S. J.. 2021-05-04. Comprehensive PAM prediction for CRISPR-Cas systems reveals evidence for spacer sharing, preferred strand targeting and conserved links with CRISPR repeats. https://doi.org/10.1101/2021.05.04.442622

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

StableProt: Structure-Aware Deep Learning for Protein Thermostability (Tm) and Environmental Adaptation (OGT) Prediction

Predicting protein melting temperature (Tm) and organismal optimal growth temperature (OGT) is essential for enzyme engineering, biocatalyst design, and metagenomic bioprospecting, yet computational prediction faces several fundamental bottlenecks: sequence-only representations miss tertiary packing; dual-task coupling induces destructive gradient conflict; natural database skew (>87% mesophiles) drives mesophilic collapse; and existing tools produce uncalibrated point predictions. To address these challenges, we present StableProt, a structure-aware framework that couples amino acid sequences with Foldseek 3Di structural tokens via a frozen SaProt backbone to capture 3D contacts. Disjoint heads condition thermodynamic stability on ecological context without gradient conflict, while targeted 14% mesophilic subsampling expands thermophile representation to eliminate mesophilic collapse. Calibrated ensemble modeling reduces calibration error to 1.92%, providing dependable 95% confidence intervals. Evaluating models across 10{degrees}C temperature intervals reveals severe baseline collapse at thermal extremes, whereas StableProt maintains robust accuracy across regimes. On ProThermDB and zero-shot FireProtDB, StableProt achieves state-of-the-art probabilistic accuracy (CRPS = 4.52{degrees}C and 8.71{degrees}C) while recovering 92.0% of hyperthermophiles ([≥]80{degrees}C), and in prospective validation, its calibrated intervals capture both enzyme stability (75.3% coverage) and host environmental growth temperatures (78.1% coverage). StableProt is freely accessible as an interactive web server at https://stableprot.dixitlab.org/.

bioinformatics↗
bioRxiv2026

RoDPAA: A Robust Dissimilarity-Based Principal Angle Analysis Framework for Multi-View Microbiome Data Integration

Multiview microbiome studies profile the same participants across body sites or molecular layers, but integration is hampered by sparse, compositional data, modest sample sizes and methods that recognize only exact sharing. We present RoDPAA (Robust Dissimilarity-based Principal Angle Analysis), a framework that represents each view through any data-appropriate dissimilarity, such as Bray--Curtis, without log-ratio transformation or likelihood assumptions. RoDPAA aligns view-specific signal subspaces through principal angles, captures complete and partial sharing, and tests by permutation how many components are shared, using only eigendecomposition and little tuning. In Gaussian simulations, RoDPAA matched JIVE and MOFA given true ranks, ran faster and alone recovered the shared dimension in every replicate. In two inflammatory bowel disease (IBD) cohorts with sparse, zero-inflated data, Bray--Curtis-based RoDPAA recovered shared structure that was stable to prevalence filtering, whereas log-ratio-based alternatives were not. Its leading microbiome--metabolome factors, learned without disease labels, were the only ones associated with IBD.

bioinformatics↗
bioRxiv2026

Deducing splicing events from transcript sets with splicelogic

Long-read RNA sequencing captures a greater proportion of full-length transcripts, enabling more accurate isoform identification, discovery of novel isoforms, and more precise differential transcript usage analysis. However, comparing transcripts, whether between conditions or between sets such as novel and annotated isoforms, yields complex isoform changes that are hard to manipulate, summarize, and visualize. This is compounded by vertical integration of some tools, where downstream analysis depends on the specific output of a particular upstream tool. To address this gap, we have developed splicelogic, an R/Bioconductor package that makes transcript-set comparisons biologically interpretable by turning them into discrete splicing events, such as exon skipping, alternative splice sites, intron retention, and alternative transcription start and end sites. We designed splicelogic to integrate easily with existing RNA-seq workflows and tools. The splicelogic functions are modular, readable, and extensible, making it easy for users to adapt core logic to their own custom scientific questions or novel splicing definitions. By obtaining interpretable splicing events from transcript changes, splicelogic enables downstream analyses, including annotation of RNA-binding protein recognition sites, alongside summary statistics and visualization. The splicelogic package is publicly available and distributed through Bioconductor.

bioinformatics↗