Replication origin location might contribute to genetic variability in Trypanosoma cruzi

Conservation and Variation in Strategies for DNA Replication of Kinetoplastid Nuclear Genomes

(2018) Catarina A. Marques et al.   CURRENT GENOMICS

I-motif DNA structures are formed in the nuclei of human cells

(2018) Mahdi Zeraati et al.   Nature Chemistry

Chromatin conformation regulates the coordination between DNA replication and transcription

(2018) Ricardo Almeida et al.   Nature Communications

The Dynamics of Replication in Trypanosoma cruzi Parasites by Single-Molecule Analysis

(2018) Christiane B. de Araujo et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Intragenic origins due to short G1 phases underlie oncogene-induced DNA replication stress

(2018) Morgane Macheret et al.   NATURE

The gastrula transition reorganizes replication-origin selection in Caenorhabditis elegans

(2017) Marta Rodríguez-Martínez et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Dormant origins and fork protection mechanisms rescue sister forks arrested by transcription

(2017) Alessandra Brambati et al.   NUCLEIC ACIDS RESEARCH

Nuclear DNA Replication in Trypanosomatids: There Are No Easy Methods for Solving Difficult Problems

(2017) Marcelo S. da Silva et al.   TRENDS IN PARASITOLOGY

The gastrula transition reorganizes replication-origin selection in Caenorhabditis elegans

(2017) Marta Rodríguez-Martínez et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Recombination-driven generation of the largest pathogen repository of antigen variants in the protozoan Trypanosoma cruzi

(2016) D. Brent Weatherly et al.   BMC GENOMICS

Conflict Resolution in the Genome: How Transcription and Replication Make It Work

(2016) Stephan Hamperl et al.   CELL

Kinetoplastid Phylogenomics Reveals the Evolutionary Innovations Associated with the Origins of Parasitism

(2016) Andrew P. Jackson et al.   CURRENT BIOLOGY

DNA replication origins—where do we begin?

(2016) Marie-Noëlle Prioleau et al.   GENES & DEVELOPMENT

Diverged composition and regulation of theTrypanosoma bruceiorigin recognition complex that mediates DNA replication initiation

(2016) Catarina A. Marques et al.   NUCLEIC ACIDS RESEARCH

Single-molecule analysis of DNA replication reveals novel features in the divergent eukaryotes Leishmania and Trypanosoma brucei versus mammalian cells

(2016) Slavica Stanojcic et al.   Scientific Reports

Transcriptionally Driven DNA Replication Program of the Human Parasite Leishmania major

(2016) Rodrigo Lombraña et al.   Cell Reports

Subtelomeric I-SceI-Mediated Double-Strand Breaks Are Repaired by Homologous Recombination in Trypanosoma cruzi

(2016) Miguel A. Chiurillo et al.   Frontiers in Microbiology

Chromosomal copy number variation reveals differential levels of genomic plasticity in distinct Trypanosoma cruzi strains

(2015) João Luís Reis-Cunha et al.   BMC GENOMICS

Error-Prone Repair of DNA Double-Strand Breaks

(2015) Kasey Rodgers et al.   JOURNAL OF CELLULAR PHYSIOLOGY

DNA replication origin activation in space and time

(2015) Michalis Fragkos et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Single molecule analysis of Trypanosoma brucei DNA replication dynamics

(2015) Simone Guedes Calderano et al.   NUCLEIC ACIDS RESEARCH

Replication and transcription on a collision course: eukaryotic regulation mechanisms and implications for DNA stability

(2015) Alessandra Brambati et al.   Frontiers in Genetics

Polymerase Stalling during Replication, Transcription and Translation

(2014) Ellen R. Edenberg et al.   CURRENT BIOLOGY

High-resolution analysis of DNA synthesis start sites and nucleosome architecture at efficient mammalian replication origins

(2013) Rodrigo Lombraña et al.   EMBO JOURNAL

Causes and consequences of replication stress

(2013) Michelle K. Zeman et al.   NATURE CELL BIOLOGY

Rescuing Stalled or Damaged Replication Forks

(2013) J. T. P. Yeeles et al.   Cold Spring Harbor Perspectives in Biology

Regulating DNA Replication in Eukarya

(2013) K. Siddiqui et al.   Cold Spring Harbor Perspectives in Biology

Anatomy and evolution of telomeric and subtelomeric regions in the human protozoan parasite Trypanosoma cruzi

(2012) Roberto R Moraes Barros et al.   BMC GENOMICS

New insights into replication origin characteristics in metazoans

(2012) Christelle Cayrou et al.   CELL CYCLE

Conservation of replication timing reveals global and local regulation of replication origin activity

(2012) C. A. Muller et al.   GENOME RESEARCH

Multigene Families in Trypanosoma cruzi and Their Role in Infectivity

(2012) Luis Miguel De Pablos et al.   INFECTION AND IMMUNITY

Preventing Replication Stress to Maintain Genome Stability: Resolving Conflicts between Replication and Transcription

(2012) Rodrigo Bermejo et al.   MOLECULAR CELL

Trypanosoma bruceiOrc1 is essential for nuclear DNA replication and affects bothVSGsilencing andVSGswitching

(2012) Imaan Benmerzouga et al.   MOLECULAR MICROBIOLOGY

The conflict between DNA replication and transcription

(2012) Peter McGlynn et al.   MOLECULAR MICROBIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Unraveling cell type–specific and reprogrammable human replication origin signatures associated with G-quadruplex consensus motifs

(2012) Emilie Besnard et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genome-wide Analysis Reveals Extensive Functional Interaction between DNA Replication Initiation and Transcription in the Genome of Trypanosoma brucei

(2012) Calvin Tiengwe et al.   Cell Reports

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Conserved nucleosome positioning defines replication origins

(2010) M. L. Eaton et al.   GENES & DEVELOPMENT

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Cell Biology of the Trypanosome Genome

(2010) J.-P. Daniels et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Posttranscriptional control and the role of RNA-binding proteins in gene regulation in trypanosomatid protozoan parasites

(2010) Sandra M. Fernández-Moya et al.   Wiley Interdisciplinary Reviews-RNA

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Localization and Developmental Regulation of a Dispersed Gene Family 1 Protein in Trypanosoma cruzi

(2009) N. Lander et al.   INFECTION AND IMMUNITY

Homology, paralogy and function of DGF-1, a highly dispersed Trypanosoma cruzi specific gene family and its implications for information entropy of its encoded proteins

(2009) Silvia Y. Kawashita et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY