Two novel PIWI families: roles in inter-genomic conflicts in bacteria and Mediator-dependent modulation of transcription in eukaryotes

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

R Loops: From Transcription Byproducts to Threats to Genome Stability

(2012) Andrés Aguilera et al.   MOLECULAR CELL

Argonaute proteins couple chromatin silencing to alternative splicing

(2012) Maya Ameyar-Zazoua et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The N domain of Argonaute drives duplex unwinding during RISC assembly

(2012) Pieter Bas Kwak et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Gene flow and biological conflict systems in the origin and evolution of eukaryotes

(2012) L. Aravind et al.   Frontiers in Cellular and Infection Microbiology

DNA Elimination in Ciliates: Transposon Domestication and Genome Surveillance

(2011) Douglas L. Chalker et al.   Annual Review of Genetics

Staphylococcus aureusDinG, a helicase that has evolved into a nuclease

(2011) Anne-Marie McRobbie et al.   BIOCHEMICAL JOURNAL

Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems

(2011) Kira S Makarova et al.   Biology Direct

Divergent transcription: A new feature of active promoters

(2011) Amy C. Seila et al.   CELL CYCLE

Evolution, biogenesis and function of promoter-associated RNAs

(2011) Ryan J. Taft et al.   CELL CYCLE

Function and regulation of the Mediator complex

(2011) Ronald C Conaway et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Mechanistic insights into type III restriction enzymes

(2011) Nidhanapati et al.   Frontiers in Bioscience-Landmark

Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila

(2011) Filippo M. Cernilogar et al.   NATURE

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes

(2011) Eivind Valen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Crystal structure of the MID-PIWI lobe of a eukaryotic Argonaute protein

(2011) A. Boland et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deep-sequencing of human Argonaute-associated small RNAs provides insight into miRNA sorting and reveals Argonaute association with RNA fragments of diverse origin

(2011) Alexander Maxwell Burroughs et al.   RNA Biology

A Parsimonious Model for Gene Regulation by miRNAs

(2011) S. Djuranovic et al.   SCIENCE

Hidden Markov model speed heuristic and iterative HMM search procedure

(2010) L Steven Johnson et al.   BMC BIOINFORMATICS

Dicer-Independent Primal RNAs Trigger RNAi and Heterochromatin Formation

(2010) Mario Halic et al.   CELL

Dicer-independent, Ago2-mediated microRNA biogenesis in vertebrates

(2010) Jr-Shiuan Yang et al.   CELL CYCLE

SF1 and SF2 helicases: family matters

(2010) Margaret E Fairman-Williams et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Crystal structure and ligand binding of the MID domain of a eukaryotic Argonaute protein

(2010) Andreas Boland et al.   EMBO REPORTS

RNA-directed epigenetic regulation of DNA rearrangements

(2010) Kazufumi Mochizuki   Essays in Biochemistry

A Genome-Wide RNA Interference Screen Identifies a Differential Role of the Mediator CDK8 Module Subunits for GATA/ RUNX-Activated Transcription in Drosophila

(2010) Vanessa Gobert et al.   MOLECULAR AND CELLULAR BIOLOGY

Structural basis for 5′-nucleotide base-specific recognition of guide RNA by human AGO2

(2010) Filipp Frank et al.   NATURE

Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans

(2010) Ryan J Taft et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Dali server: conservation mapping in 3D

(2010) Liisa Holm et al.   NUCLEIC ACIDS RESEARCH

Initiation of bacteriophage T4 DNA replication and replication fork dynamics: a review in the Virology Journal series on bacteriophage T4 and its relatives

(2010) Kenneth N Kreuzer et al.   Virology Journal

Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements

(2009) Kira S Makarova et al.   Biology Direct

The MED12-MED13 module of Mediator regulates the timing of embryo patterning in Arabidopsis

(2009) C. S. Gillmor et al.   DEVELOPMENT

The helicases DinG, Rep and UvrD cooperate to promote replication across transcription units in vivo

(2009) Hasna Boubakri et al.   EMBO JOURNAL

The human CDK8 subcomplex is a molecular switch that controls Mediator coactivator function

(2009) M. T. Knuesel et al.   GENES & DEVELOPMENT

Enhancement of the Seed-Target Recognition Step in RNA Silencing by a PIWI/MID Domain Protein

(2009) James S. Parker et al.   MOLECULAR CELL

Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes

(2009) Yanli Wang et al.   NATURE

Tiny RNAs associated with transcription start sites in animals

(2009) Ryan J Taft et al.   NATURE GENETICS

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

MicroRNA targeting in mammalian genomes: genes and mechanisms

(2009) S. A. Muljo et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

RNA-based viral immunity initiated by the Dicer family of host immune receptors

(2008) Roghiyh Aliyari et al.   IMMUNOLOGICAL REVIEWS

Redox Control of the DNA Damage-inducible Protein DinG Helicase Activity via Its Iron-Sulfur Cluster

(2008) Binbin Ren et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mediator Links Epigenetic Silencing of Neuronal Gene Expression with X-Linked Mental Retardation

(2008) Ning Ding et al.   MOLECULAR CELL

Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex

(2008) Yanli Wang et al.   NATURE

Structure of the guide-strand-containing argonaute silencing complex

(2008) Yanli Wang et al.   NATURE

WRN Exonuclease activity is blocked by specific oxidatively induced base lesions positioned in either DNA strand

(2008) Z. Bukowy et al.   NUCLEIC ACIDS RESEARCH

The Jpred 3 secondary structure prediction server

(2008) C. Cole et al.   NUCLEIC ACIDS RESEARCH

Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex

(2008) Henri-Marc Bourbon   NUCLEIC ACIDS RESEARCH

Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features

(2008) Timo Lassmann et al.   NUCLEIC ACIDS RESEARCH

Pygopus activates Wingless target gene transcription through the mediator complex subunits Med12 and Med13

(2008) I. Carrera et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA