TFIIS-Dependent Non-coding Transcription Regulates Developmental Genome Rearrangements

Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development

(2014) Cheng Sun et al.   BMC GENOMICS

Functional Diversification of Dicer-like Proteins and Small RNAs Required for Genome Sculpting

(2014) Pamela Y. Sandoval et al.   DEVELOPMENTAL CELL

Elements and machinery of non-coding RNAs: toward their taxonomy

(2014) T. Hirose et al.   EMBO REPORTS

The ENCODE Project and Perspectives on Pathways

(2014) Vinicius Tragante et al.   GENETIC EPIDEMIOLOGY

Insights into Three Whole-Genome Duplications Gleaned from the Paramecium caudatum Genome Sequence

(2014) Casey L. McGrath et al.   GENETICS

Differential retention and divergent resolution of duplicate genes following whole-genome duplication

(2014) Casey L. McGrath et al.   GENOME RESEARCH

Genome-defence small RNAs exapted for epigenetic mating-type inheritance

(2014) Deepankar Pratap Singh et al.   NATURE

Genome-wide analysis of genetic and epigenetic control of programmed DNA deletion

(2014) Estienne C. Swart et al.   NUCLEIC ACIDS RESEARCH

Transcription factors IIS and IIF enhance transcription efficiency by differentially modifying RNA polymerase pausing dynamics

(2014) Toyotaka Ishibashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Local Effect of Enhancer of Zeste-Like Reveals Cooperation of Epigenetic and cis-Acting Determinants for Zygotic Genome Rearrangements

(2014) Maoussi Lhuillier-Akakpo et al.   PLoS Genetics

Ku-Mediated Coupling of DNA Cleavage and Repair during Programmed Genome Rearrangements in the Ciliate Paramecium tetraurelia

(2014) Antoine Marmignon et al.   PLoS Genetics

Is Non-Homologous End-Joining Really an Inherently Error-Prone Process?

(2014) Mireille Bétermier et al.   PLoS Genetics

Long Noncoding RNAs: Past, Present, and Future

(2013) J. T. Y. Kung et al.   GENETICS

Long non-coding RNAs: new players in cell differentiation and development

(2013) Alessandro Fatica et al.   NATURE REVIEWS GENETICS

Identification and function of long non-coding RNA

(2013) Carl Ernst et al.   Frontiers in Cellular Neuroscience

Convergent Transcription Induces Dynamic DNA Methylation at disiRNA Loci

(2013) Yunkun Dang et al.   PLoS Genetics

RNA-guided DNA rearrangements in ciliates: Is the best genome defence a good offence?

(2012) Robert S. Coyne et al.   BIOLOGY OF THE CELL

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

(2012) Wenwen Fang et al.   CELL

The role of long non-coding RNA in transcriptional gene silencing

(2012) Andrzej T Wierzbicki   CURRENT OPINION IN PLANT BIOLOGY

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

Transcription Elongation FactorTcea3Regulates the Pluripotent Differentiation Potential of Mouse Embryonic Stem Cells Via theLefty1-Nodal-Smad2 Pathway

(2012) Kyung-Soon Park et al.   STEM CELLS

The Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences

(2012) Olivier Arnaiz et al.   PLoS Genetics

Uniting Germline and Stem Cells: The Function of Piwi Proteins and the piRNA Pathway in Diverse Organisms

(2011) Celina Juliano et al.   Annual Review of Genetics

Functional Study of Genes Essential for Autogamy and Nuclear Reorganization in Paramecium

(2011) Jacek K. Nowak et al.   EUKARYOTIC CELL

Functional specialization of Piwi proteins in Paramecium tetraurelia from post-transcriptional gene silencing to genome remodelling

(2011) Khaled Bouhouche et al.   NUCLEIC ACIDS RESEARCH

Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells

(2011) Lucie Carrière et al.   NUCLEIC ACIDS RESEARCH

Highly Precise and Developmentally Programmed Genome Assembly in Paramecium Requires Ligase IV–Dependent End Joining

(2011) Aurélie Kapusta et al.   PLoS Genetics

Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia

(2010) Olivier Arnaiz et al.   BMC GENOMICS

ParameciumDB in 2011: new tools and new data for functional and comparative genomics of the model ciliate Paramecium tetraurelia

(2010) O. Arnaiz et al.   NUCLEIC ACIDS RESEARCH

Temporal and spatial regulatory functions of the V(D)J recombinase

(2010) Stephen Desiderio   SEMINARS IN IMMUNOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

PiggyMac, a domesticated piggyBac transposase involved in programmed genome rearrangements in the ciliate Paramecium tetraurelia

(2009) C. Baudry et al.   GENES & DEVELOPMENT

Microarray Analyses of Gene Expression during the Tetrahymena thermophila Life Cycle

(2009) Wei Miao et al.   PLoS One

Developmental genome rearrangements in ciliates: a natural genomic subtraction mediated by non-coding transcripts

(2009) Sandra Duharcourt et al.   TRENDS IN GENETICS

Maternal noncoding transcripts antagonize the targeting of DNA elimination by scanRNAs in Paramecium tetraurelia

(2008) G. Lepere et al.   GENES & DEVELOPMENT

Genome-wide location analysis reveals a role of TFIIS in RNA polymerase III transcription

(2008) Y. Ghavi-Helm et al.   GENES & DEVELOPMENT

Silencing-associated and meiosis-specific small RNA pathways in Paramecium tetraurelia

(2008) Gersende Lepère et al.   NUCLEIC ACIDS RESEARCH

Developmentally programmed DNA splicing in Paramecium reveals short-distance crosstalk between DNA cleavage sites

(2008) Ariane Gratias et al.   NUCLEIC ACIDS RESEARCH

Functional diversification of centrins and cell morphological complexity

(2007) D. Gogendeau et al.   JOURNAL OF CELL SCIENCE