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On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/0006-3002(56)90286-4openalex-snapshot

Enzymic synthesis of polynucleotides I. polynucleotide phosphorylase of Azotobacter vinelandii

inferredcites →https://doi.org/10.1016/0092-8674(89)90917-3openalex-snapshot

Replication of RNA by the DNA-dependent RNA polymerase of phage T7

inferredcites →https://doi.org/10.1016/j.cell.2009.07.040openalex-snapshot

RNA-Guided RNA Cleavage by a CRISPR RNA-Cas Protein Complex

inferredcites →https://doi.org/10.1016/j.cell.2015.04.027openalex-snapshot

Co-transcriptional DNA and RNA Cleavage during Type III CRISPR-Cas Immunity

inferredcites →https://doi.org/10.1016/j.cell.2015.12.053openalex-snapshot

Degradation of Phage Transcripts by CRISPR-Associated RNases Enables Type III CRISPR-Cas Immunity

inferredcites →https://doi.org/10.1016/j.chom.2013.05.008openalex-snapshot

Convergent Antibody Signatures in Human Dengue

inferredcites →https://doi.org/10.1016/j.mimet.2009.11.012openalex-snapshot

An efficient DNA isolation protocol for filamentous cyanobacteria of the genus Arthrospira

inferredcites →https://doi.org/10.1016/j.molcel.2011.10.023openalex-snapshot

Essential Features and Rational Design of CRISPR RNAs that Function with the Cas RAMP Module Complex to Cleave RNAs

inferredcites →https://doi.org/10.1016/j.molcel.2014.09.027openalex-snapshot

Programmable RNA Shredding by the Type III-A CRISPR-Cas System of Streptococcus thermophilus

inferredcites →https://doi.org/10.1016/j.molcel.2015.10.008openalex-snapshot

Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems

inferredcites →https://doi.org/10.1038/ismej.2015.162openalex-snapshot

Metagenomic reconstructions of bacterial CRISPR loci constrain population histories

inferredcites →https://doi.org/10.1038/nature08703openalex-snapshot

Self versus non-self discrimination during CRISPR RNA-directed immunity

inferredcites →https://doi.org/10.1038/nature13637openalex-snapshot

Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting

inferredcites →https://doi.org/10.1038/nature19094openalex-snapshot

Uncovering Earth’s virome

inferredcites →https://doi.org/10.1038/nature19366openalex-snapshot

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

inferredcites →https://doi.org/10.1038/nrmicro.2015.14openalex-snapshot

CRISPR–Cas adaptation: insights into the mechanism of action

inferredcites →https://doi.org/10.1038/nrmicro.2016.184openalex-snapshot

Diversity and evolution of class 2 CRISPR–Cas systems

inferredcites →https://doi.org/10.1038/nrmicro3569openalex-snapshot

An updated evolutionary classification of CRISPR–Cas systems

inferredcites →https://doi.org/10.1089/cmb.2012.0021openalex-snapshot

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

inferredcites →https://doi.org/10.1093/bioinformatics/btn322openalex-snapshot

Database indexing for production MegaBLAST searches

inferredcites →https://doi.org/10.1093/femsre/fuv019openalex-snapshot

DNA and RNA interference mechanisms by CRISPR-Cas surveillance complexes

inferredcites →https://doi.org/10.1093/molbev/msn081openalex-snapshot

Systematic Survey for Novel Types of Prokaryotic Retroelements Based on Gene Neighborhood and Protein Architecture

inferredcites →https://doi.org/10.1093/nar/29.12.2607openalex-snapshot

GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions

inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot

MUSCLE: multiple sequence alignment with high accuracy and high throughput

inferredcites →https://doi.org/10.1093/nar/gkm360openalex-snapshot

CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats

inferredcites →https://doi.org/10.1093/nar/gkn867openalex-snapshot

A diversity of uncharacterized reverse transcriptases in bacteria

inferredcites →https://doi.org/10.1093/nar/gks1243openalex-snapshot

CDD: conserved domains and protein three-dimensional structure

inferredcites →https://doi.org/10.1093/nar/gku1302openalex-snapshot

An archaeal CRISPR type III-B system exhibiting distinctive RNA targeting features and mediating dual RNA and DNA interference

inferredcites →https://doi.org/10.1093/nar/gkw1030openalex-snapshot

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

inferredcites →https://doi.org/10.1093/nar/gkw387openalex-snapshot

PHASTER: a better, faster version of the PHAST phage search tool

inferredcites →https://doi.org/10.1093/nar/gkw929openalex-snapshot

IMG/M: integrated genome and metagenome comparative data analysis system

inferredcites →https://doi.org/10.1101/gr.074492.107openalex-snapshot

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

inferredcites →https://doi.org/10.1111/1462-2920.12146openalex-snapshot

Reassortment of CRISPR repeat‐spacer loci in S ulfolobus islandicus

inferredcites →https://doi.org/10.1111/mmi.12152openalex-snapshot

A novel interference mechanism by a type IIIB CRISPR ‐ Cmr module in S ulfolobus

inferredcites →https://doi.org/10.1126/science.1138140openalex-snapshot

CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes

inferredcites →https://doi.org/10.1126/science.1157358openalex-snapshot

Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities

inferredcites →https://doi.org/10.1126/science.1159689openalex-snapshot

Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes

inferredcites →https://doi.org/10.1126/science.aad4234openalex-snapshot

Direct CRISPR spacer acquisition from RNA by a natural reverse transcriptase–Cas1 fusion protein

inferredcites →https://doi.org/10.1126/science.aal5056openalex-snapshot

CRISPR-Cas: Adapting to change

inferredcites →https://doi.org/10.1128/jb.00897-15openalex-snapshot

Impact of Different Target Sequences on Type III CRISPR-Cas Immunity

inferredcites →https://doi.org/10.1128/jb.01412-07openalex-snapshot

Phage Response to CRISPR-Encoded Resistance in Streptococcus thermophilus

inferredcites →https://doi.org/10.1128/jb.05535-11openalex-snapshot

Defense Islands in Bacterial and Archaeal Genomes and Prediction of Novel Defense Systems

inferredcites →https://doi.org/10.1128/mbio.00648-15openalex-snapshot

Covalent Modification of Bacteriophage T4 DNA Inhibits CRISPR-Cas9

inferredcites →https://doi.org/10.1128/mbio.01397-17openalex-snapshot

The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes

inferredcites →https://doi.org/10.1146/annurev.genet.38.072902.091600openalex-snapshot

Mobile Group II Introns

inferredcites →https://doi.org/10.1186/1471-2105-8-172openalex-snapshot

The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats

inferredcites →https://doi.org/10.1186/1471-2105-8-18openalex-snapshot

PILER-CR: Fast and accurate identification of CRISPR repeats

inferredcites →https://doi.org/10.1186/1745-6150-1-7openalex-snapshot

A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action

inferredcites →https://doi.org/10.1371/journal.pbio.1002409openalex-snapshot

Hyperexpansion of RNA Bacteriophage Diversity

inferredcites →https://doi.org/10.1371/journal.pcbi.1002195openalex-snapshot

Accelerated Profile HMM Searches

inferredcites →https://doi.org/10.1371/journal.pcbi.1002475openalex-snapshot

Persisting Viral Sequences Shape Microbial CRISPR-based Immunity

inferredcites →https://doi.org/10.1371/journal.pone.0009490openalex-snapshot

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

inferredcites →https://doi.org/10.1371/journal.pone.0114083openalex-snapshot

Comprehensive Phylogenetic Analysis of Bacterial Reverse Transcriptases

inferredcites →https://doi.org/10.1371/journal.pone.0160574openalex-snapshot

Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers

inferredcites →https://doi.org/10.3390/v8030066openalex-snapshot

Linking Virus Genomes with Host Taxonomy

inferredcites →https://doi.org/10.4049/jimmunol.1301384openalex-snapshot

Effects of Aging, Cytomegalovirus Infection, and EBV Infection on Human B Cell Repertoires

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.2139/ssrn.4047248openalex-extracted

A Five-Fold Expansion of the Global RNA Virome Reveals Multiple New Clades of RNA Bacteriophages

inferred← citeshttps://doi.org/10.1002/1873-3468.70086openalex-snapshot

Evolutionary interplay between viruses and R‐loops

inferred← citeshttps://doi.org/10.1002/9781119309697.refopenalex-snapshot

References

inferred← citeshttps://doi.org/10.1002/9781683673798.ch5openalex-snapshot

Mechanism of Type III CRISPR ‐ Cas Immunity

inferred← citeshttps://doi.org/10.1002/9781683673798.ch9openalex-snapshot

Evasion Tactics Manifested by Bacteriophages against Bacterial Immunity

inferred← citeshttps://doi.org/10.1002/bit.28858openalex-snapshot

Acetaminophen production in the edible, filamentous cyanobacterium Arthrospira platensis

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CRISPR–Cas Systems ~ Diversity and Evolution ~

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Acquired and Innate Immunity in Prokaryotes Define Their Evolutionary Story

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CRISPR rewired: from adaptive immunity to a global virulence control network in Salmonella

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Recent progress and challenges in CRISPR-Cas9 engineered algae and cyanobacteria

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CRISPR-Cas systems of lactic acid bacteria and applications in food science

inferred← citeshttps://doi.org/10.1016/j.cell.2022.08.023openalex-snapshot

Expansion of the global RNA virome reveals diverse clades of bacteriophages

inferred← citeshttps://doi.org/10.1016/j.chom.2025.07.021openalex-snapshot

Type I CRISPR-Cas immunity primes type III spacer acquisition

inferred← citeshttps://doi.org/10.1016/j.jbc.2024.107295openalex-snapshot

Unity among the diverse RNA-guided CRISPR-Cas interference mechanisms

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Cold adaptation in bacteria with special focus on cellulase production and its potential application

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Characterization of Limnospira platensis PCC 9108 R-M and CRISPR-Cas systems

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A Reverse Transcriptase-Cas1 Fusion Protein Contains a Cas6 Domain Required for Both CRISPR RNA Biogenesis and RNA Spacer Acquisition

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Beneath the surface: Unsolved questions in soil virus ecology

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Structural coordination between active sites of a CRISPR reverse transcriptase-integrase complex

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Molecular mechanisms of CRISPR–Cas spacer acquisition

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Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

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Structural biology of CRISPR–Cas immunity and genome editing enzymes

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Transcriptional recording by CRISPR spacer acquisition from RNA

inferred← citeshttps://doi.org/10.1038/s41594-020-0415-7openalex-snapshot

Real-time observation of CRISPR spacer acquisition by Cas1–Cas2 integrase

inferred← citeshttps://doi.org/10.1073/pnas.1803440115openalex-snapshot

Systematic prediction of genes functionally linked to CRISPR-Cas systems by gene neighborhood analysis

inferred← citeshttps://doi.org/10.1080/15476286.2018.1493330openalex-snapshot

CRISPR-Cas systems in multicellular cyanobacteria

inferred← citeshttps://doi.org/10.1080/15476286.2019.1639310openalex-snapshot

Multiple origins of reverse transcriptases linked to CRISPR-Cas systems

inferred← citeshttps://doi.org/10.1089/crispr.2018.0033openalex-snapshot

Classification and Nomenclature of CRISPR-Cas Systems: Where from Here?

inferred← citeshttps://doi.org/10.1093/femsre/fuab025openalex-snapshot

Prokaryotic reverse transcriptases: from retroelements to specialized defense systems

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Mobile Genetic Elements and Evolution of CRISPR-Cas Systems: All the Way There and Back

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RNAVirHost: a machine learning–based method for predicting hosts of RNA viruses through viral genomes

inferred← citeshttps://doi.org/10.1093/nar/gkaa685openalex-snapshot

Spacer acquisition by Type III CRISPR–Cas system during bacteriophage infection of Thermus thermophilus

inferred← citeshttps://doi.org/10.1093/nar/gkab1207openalex-snapshot

Identification and classification of reverse transcriptases in bacterial genomes and metagenomes

inferred← citeshttps://doi.org/10.1093/nar/gkab1299openalex-snapshot

Different modes of spacer acquisition by the Staphylococcus epidermidis type III-A CRISPR-Cas system

inferred← citeshttps://doi.org/10.1093/nar/gkad478openalex-snapshot

Reverse transcriptases prime DNA synthesis

inferred← citeshttps://doi.org/10.1093/nar/gkae1154openalex-snapshot

Adaptive immunity of type VI CRISPR-Cas systems associated with reverse transcriptase–Cas1 fusion proteins

inferred← citeshttps://doi.org/10.1093/nar/gky1127openalex-snapshot

IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes

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Origins and evolution of CRISPR-Cas systems

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Spacer acquisition in type VI CRISPR-Cas systems associated with reverse transcriptase-Cas1 fusion proteins

inferred← citeshttps://doi.org/10.1101/2025.06.12.659409openalex-snapshot

Planetary-scale metagenomic search reveals new patterns of CRISPR targeting

inferred← citeshttps://doi.org/10.1101/252296openalex-snapshot

An atypical CRISPR-Cas locus in Symbiobacterium thermophilum flanked by a transposase, a reverse transcriptase, the endonuclease MutS2 and a putative Cas9-like protein

inferred← citeshttps://doi.org/10.1101/263558openalex-snapshot

Reverse transcriptase fused CRISPR-Cas1 locus with RNA-seq expression necessitates revisiting hypothesis on acquisition of antibiotic resistance genes in multidrug-resistant Enterococcus faecalis V583

inferred← citeshttps://doi.org/10.1111/mmi.14383openalex-snapshot

Targeted transposition with Tn7 elements: safe sites, mobile plasmids, CRISPR/Cas and beyond

inferred← citeshttps://doi.org/10.1126/sciadv.aay5981openalex-snapshot

Expansion of known ssRNA phage genomes: From tens to over a thousand

inferred← citeshttps://doi.org/10.1126/sciadv.adk8791openalex-snapshot

Mechanisms used for cDNA synthesis and site-specific integration of RNA into DNA genomes by a reverse transcriptase–Cas1 fusion protein

inferred← citeshttps://doi.org/10.1134/s0006297921100114openalex-snapshot

Type III CRISPR-Cas Systems: Deciphering the Most Complex Prokaryotic Immune System

inferred← citeshttps://doi.org/10.1159/000516643openalex-snapshot

CRISPR-Cas System: The Powerful Modulator of Accessory Genomes in Prokaryotes

inferred← citeshttps://doi.org/10.1186/s12862-017-1081-1openalex-snapshot

Phylogenomics of Cas4 family nucleases

inferred← citeshttps://doi.org/10.1186/s12864-019-5439-1openalex-snapshot

CRISPR-Cas systems are present predominantly on mobile genetic elements in Vibrio species

inferred← citeshttps://doi.org/10.1371/journal.pbio.3001481openalex-snapshot

Evolutionary plasticity and functional versatility of CRISPR systems

inferred← citeshttps://doi.org/10.1615/interjalgae.v27.i1.30openalex-snapshot

The Implication and Advancement of CRISPR Genome Editing in Microalgae and Cyanobacteria

inferred← citeshttps://doi.org/10.21769/bioprotoc.2727openalex-snapshot

A Small RNA Isolation and Sequencing Protocol and Its Application to Assay CRISPR RNA Biogenesis in Bacteria

inferred← citeshttps://doi.org/10.31857/s0320972521100134openalex-snapshot

Биологическая роль и эволюционная история систем CRISPR-Cas типа III

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On the Origin and Evolutionary Relationships of the Reverse Transcriptases Associated With Type III CRISPR-Cas Systems

inferred← citeshttps://doi.org/10.3389/fmicb.2019.03078openalex-snapshot

CRISPR-Cas Systems and the Paradox of Self-Targeting Spacers

inferred← citeshttps://doi.org/10.3389/fmicb.2021.736565openalex-snapshot

Characterization of 67 Confirmed Clustered Regularly Interspaced Short Palindromic Repeats Loci in 52 Strains of Staphylococci

inferred← citeshttps://doi.org/10.3389/fmicb.2022.1069452openalex-snapshot

Global phylogenomic novelty of the Cas1 gene from hot spring microbial communities

inferred← citeshttps://doi.org/10.3389/fmicb.2022.876174openalex-snapshot

Adaptation by Type III CRISPR-Cas Systems: Breakthrough Findings and Open Questions

inferred← citeshttps://doi.org/10.3389/fmolb.2022.821197openalex-snapshot

Recruitment of Mobile Genetic Elements for Diverse Cellular Functions in Prokaryotes

inferred← citeshttps://doi.org/10.3410/f.735008588.793559530openalex-snapshot

Faculty Opinions recommendation of CRISPR-Cas systems are present predominantly on mobile genetic elements in Vibrio species.

inferred← citeshttps://doi.org/10.5483/bmbrep.2023-0050openalex-snapshot

Harnessing CRISPR-Cas adaptation for RNA recording and beyond

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