The origin of RNA interference: Adaptive or neutral evolution?

Non-adaptive complexity and biochemical function

(2022) Luca Schulz et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Constructive Neutral Evolution 20 Years Later

(2021) Sergio A. Muñoz-Gómez et al.   JOURNAL OF MOLECULAR EVOLUTION

A programmable pAgo nuclease with universal guide and target specificity from the mesophilic bacterium Kurthia massiliensis

(2021) Ekaterina Kropocheva et al.   NUCLEIC ACIDS RESEARCH

Two isoforms of the essential C. elegans Argonaute CSR-1 differentially regulate sperm and oocyte fertility

(2021) Amanda G Charlesworth et al.   NUCLEIC ACIDS RESEARCH

Emergent RNA–RNA interactions can promote stability in a facultative phototrophic endosymbiosis

(2021) Benjamin H. Jenkins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The role of purifying selection in the origin and maintenance of complex function

(2021) Tyler D.P. Brunet et al.   STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE

Transfer RNA and Origins of RNA Interference

(2021) Andrey Grigoriev   Frontiers in Molecular Biosciences

Origins and evolving functionalities of tRNA-derived small RNAs

(2021) Qi Chen et al.   TRENDS IN BIOCHEMICAL SCIENCES

Conserved chromosomal functions of RNA interference

(2020) Michael J. Gutbrod et al.   NATURE REVIEWS GENETICS

Genome-wide DNA sampling by Ago nuclease from the cyanobacterium Synechococcus elongatus

(2020) Anna Olina et al.   RNA Biology

The Signal and the Noise: Characteristics of Antisense RNA in Complex Microbial Communities

(2020) Thomas Yssing Michaelsen et al.   mSystems

Advances in bacterial transcriptome understanding: From overlapping transcription to the excludon concept

(2020) Alejandro Toledo‐Arana et al.   MOLECULAR MICROBIOLOGY

Taming the Turmoil Within: New Insights on the Containment of Transposable Elements

(2020) Erin S. Kelleher et al.   TRENDS IN GENETICS

Diverse transposable element landscapes in pathogenic and nonpathogenic yeast models: the value of a comparative perspective

(2020) Patrick H. Maxwell   Mobile DNA

Abundant expression of maternal siRNAs is a conserved feature of seed development

(2020) Jeffrey W. Grover et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The origin and rise of complex life: progress requires interdisciplinary integration and hypothesis testing

(2020) Rachel Wood et al.   Interface Focus

A hydrophobic ratchet entrenches molecular complexes

(2020) Georg K. A. Hochberg et al.   NATURE

A programmable omnipotent Argonaute nuclease from mesophilic bacteria Kurthia massiliensis

(2020) Yang Liu et al.   NUCLEIC ACIDS RESEARCH

The genomic basis of Red Queen dynamics during rapid reciprocal host–pathogen coevolution

(2019) Andrei Papkou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Concepts of the last eukaryotic common ancestor

(2019) Maureen A. O’Malley et al.   Nature Ecology & Evolution

Physiological roles of antisense RNAs in prokaryotes

(2019) Maxence Lejars et al.   BIOCHIMIE

Exogenous RNAi mechanisms contribute to transcriptome adaptation by phased siRNA clusters in Paramecium

(2019) Sivarajan Karunanithi et al.   NUCLEIC ACIDS RESEARCH

Modularity, criticality, and evolvability of a developmental gene regulatory network

(2019) Berta Verd et al.   eLife

Host–transposon interactions: conflict, cooperation, and cooption

(2019) Rachel L Cosby et al.   GENES & DEVELOPMENT

Beyond networks: mechanism and process in evo-devo

(2019) James DiFrisco et al.   BIOLOGY & PHILOSOPHY

RNAi is a critical determinant of centromere evolution in closely related fungi

(2018) Vikas Yadav et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The CSR-1 endogenous RNAi pathway ensures accurate transcriptional reprogramming during the oocyte-to-embryo transition in Caenorhabditis elegans

(2018) Christina Fassnacht et al.   PLoS Genetics

The Non-Coding Regulatory RNA Revolution in Archaea

(2018) Diego Gelsinger et al.   Genes

Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes

(2018) Fergal M. Waldron et al.   PLoS Genetics

Diverse RNA interference strategies in early-branching metazoans

(2018) Andrew D. Calcino et al.   BMC EVOLUTIONARY BIOLOGY

Fidelity in RNA-based recognition of transposable elements

(2018) Ilaria Ugolini et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Expanded Universe of Prokaryotic Argonaute Proteins

(2018) Sergei Ryazansky et al.   mBio

QTL mapping of natural variation reveals that the developmental regulator bruno reduces tolerance to P-element transposition in the Drosophila female germline

(2018) Erin S. Kelleher et al.   PLOS BIOLOGY

Structural Foundations of RNA Silencing by Argonaute

(2017) Jessica Sheu-Gruttadauria et al.   JOURNAL OF MOLECULAR BIOLOGY

Small RNA-mediated regulation of DNA dosage in the ciliate Oxytricha

(2017) Jaspreet S. Khurana et al.   RNA

Necessity Is the Mother of Invention: Ciliates, Transposons, and Transgenerational Inheritance

(2017) Sarah E. Allen et al.   TRENDS IN GENETICS

Does Sequence Conservation Provide Evidence for Biological Function?

(2017) Seila Omer et al.   TRENDS IN MICROBIOLOGY

Argonaute Utilization for miRNA Silencing Is Determined by Phosphorylation-Dependent Recruitment of LIM-Domain-Containing Proteins

(2017) Katherine S. Bridge et al.   Cell Reports

Protists and the Wild, Wild West of Gene Expression: New Frontiers, Lawlessness, and Misfits

(2016) David Roy Smith et al.   Annual Review of Microbiology

Inevitability of Genetic Parasites

(2016) Jaime Iranzo et al.   Genome Biology and Evolution

A simple physical mechanism enables homeostasis in primitive cells

(2016) Aaron E. Engelhart et al.   Nature Chemistry

Genetic drift, selection and the evolution of the mutation rate

(2016) Michael Lynch et al.   NATURE REVIEWS GENETICS

The nuclear and organellar tRNA-derived RNA fragment population in Arabidopsis thaliana is highly dynamic

(2016) Valérie Cognat et al.   NUCLEIC ACIDS RESEARCH

A bacterial Argonaute with noncanonical guide RNA specificity

(2016) Emine Kaya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bugs Are Not to Be Silenced: Small RNA Pathways and Antiviral Responses in Insects

(2016) Vanesa Mongelli et al.   Annual Review of Virology

Epigenetic regulation of serotype expression antagonizes transcriptome dynamics inParamecium tetraurelia

(2015) Miriam Cheaib et al.   DNA RESEARCH

Everything flows: A process perspective on life

(2015) J. Jaeger et al.   EMBO REPORTS

Towards a molecular understanding of microRNA-mediated gene silencing

(2015) Stefanie Jonas et al.   NATURE REVIEWS GENETICS

What's in a genome? The C-value enigma and the evolution of eukaryotic genome content

(2015) Tyler A. Elliott et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

An ancestral bacterial division system is widespread in eukaryotic mitochondria

(2015) Michelle M. Leger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanistic links between cellular trade-offs, gene expression, and growth

(2015) Andrea Y. Weiße et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNAi and Heterochromatin Assembly

(2015) Robert Martienssen et al.   Cold Spring Harbor Perspectives in Biology

Endogenous siRNAs: regulators of internal affairs

(2014) Monica J. Piatek et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Prolegomenon to patterns in evolution

(2014) Stuart A. Kauffman   BIOSYSTEMS

Renaissance of mammalian endogenous RNAi

(2014) Petr Svoboda   FEBS LETTERS

Bioattractors: dynamical systems theory and the evolution of regulatory processes

(2014) Johannes Jaeger et al.   JOURNAL OF PHYSIOLOGY-LONDON

R-loops induce repressive chromatin marks over mammalian gene terminators

(2014) Konstantina Skourti-Stathaki et al.   NATURE

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity

(2014) Marjori A. Matzke et al.   NATURE REVIEWS GENETICS

The evolutionary journey of Argonaute proteins

(2014) Daan C Swarts et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Search for MicroRNAs Expressed by Intracellular Bacterial Pathogens in Infected Mammalian Cells

(2014) Yuki Furuse et al.   PLoS One

Genomic Characterization of Variable Surface Antigens Reveals a Telomere Position Effect as a Prerequisite for RNA Interference-Mediated Silencing in Paramecium tetraurelia

(2014) Damir Baranasic et al.   mBio

Genome reduction as the dominant mode of evolution

(2013) Yuri I. Wolf et al.   BIOESSAYS

Untangling the web: The diverse functions of the PIWI/piRNA pathway

(2013) Sneha Ramesh Mani et al.   MOLECULAR REPRODUCTION AND DEVELOPMENT

Animals in a bacterial world, a new imperative for the life sciences

(2013) Margaret McFall-Ngai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanisms of Mitochondrial Fission and Fusion

(2013) A. M. van der Bliek et al.   Cold Spring Harbor Perspectives in Biology

Transposon Domestication versus Mutualism in Ciliate Genome Rearrangements

(2013) Alexander Vogt et al.   PLoS Genetics

Constructive neutral evolution: exploring evolutionary theory’s curious disconnect

(2012) Arlin Stoltzfus   Biology Direct

Piwi-Interacting RNAs Protect DNA against Loss during Oxytricha Genome Rearrangement

(2012) Wenwen Fang et al.   CELL

The Inheritance of Process: A Dynamical Systems Approach

(2012) Johannes Jaeger et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

RNAi triggered by specialized machinery silences developmental genes and retrotransposons

(2012) Soichiro Yamanaka et al.   NATURE

Transposable elements domesticated and neofunctionalized by eukaryotic genomes

(2012) Ahmed M. Alzohairy et al.   PLASMID

Transposable Elements, Epigenetics, and Genome Evolution

(2012) N. V. Fedoroff   SCIENCE

The Repatterning of Eukaryotic Genomes by Random Genetic Drift

(2011) Michael Lynch et al.   Annual Review of Genomics and Human Genetics

From snoRNA to miRNA: Dual function regulatory non-coding RNAs

(2011) Michelle S. Scott et al.   BIOCHIMIE

How a neutral evolutionary ratchet can build cellular complexity

(2011) Julius Lukeš et al.   IUBMB LIFE

Genome-wide antisense transcription drives mRNA processing in bacteria

(2011) I. Lasa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative Functional Genomics of the Fission Yeasts

(2011) N. Rhind et al.   SCIENCE

Origin of the cell nucleus, mitosis and sex: roles of intracellular coevolution

(2010) Thomas Cavalier-Smith   Biology Direct

RNAi-dependent formation of heterochromatin and its diverse functions

(2010) Shiv IS Grewal   CURRENT OPINION IN GENETICS & DEVELOPMENT

Diverse Pathways Generate MicroRNA-like RNAs and Dicer-Independent Small Interfering RNAs in Fungi

(2010) Heng-Chi Lee et al.   MOLECULAR CELL

Messy biology and the origins of evolutionary innovations

(2010) Dan S Tawfik   Nature Chemical Biology

RNAi and heterochromatin repress centromeric meiotic recombination

(2010) C. Ellermeier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Irremediable Complexity?

(2010) M. W. Gray et al.   SCIENCE

The Argonaute CSR-1 and Its 22G-RNA Cofactors Are Required for Holocentric Chromosome Segregation

(2009) Julie M. Claycomb et al.   CELL

Major Evolutionary Transitions in Centromere Complexity

(2009) Harmit S. Malik et al.   CELL

Deletional Bias across the Three Domains of Life

(2009) Chih-Horng Kuo et al.   Genome Biology and Evolution

Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila

(2009) J. Lu et al.   GENOME RESEARCH

Distinct Argonaute-Mediated 22G-RNA Pathways Direct Genome Surveillance in the C. elegans Germline

(2009) Weifeng Gu et al.   MOLECULAR CELL

Small silencing RNAs: an expanding universe

(2009) Megha Ghildiyal et al.   NATURE REVIEWS GENETICS

Small RNAs derived from snoRNAs

(2009) R. J. Taft et al.   RNA

RNAi in Budding Yeast

(2009) I. A. Drinnenberg et al.   SCIENCE

Antigenic variation in Giardia lamblia is regulated by RNA interference

(2008) César G. Prucca et al.   NATURE

The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs

(2008) Katsutomo Okamura et al.   NATURE

Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes

(2008) Toshiaki Watanabe et al.   NATURE

Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes

(2008) Oliver H. Tam et al.   NATURE

An endogenous small interfering RNA pathway in Drosophila

(2008) Benjamin Czech et al.   NATURE

The intelligent clock and the Rube Goldberg clock

(2008) Aziz Sancar   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Endogenous siRNAs Derived from Transposons and mRNAs in Drosophila Somatic Cells

(2008) M. Ghildiyal et al.   SCIENCE

Origins and evolution of eukaryotic RNA interference

(2008) S SHABALINA et al.   TRENDS IN ECOLOGY & EVOLUTION