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Article
Open AccessExpression of Dystrophin Dp71 Splice Variants Is Temporally Regulated During Rodent Brain Development
Dystrophin Dp71 is the major product of the Duchenne muscular dystrophy (DMD) gene in the brain, and its loss in DMD patients and mouse models leads to cognitive impairments. Dp71 is expressed as a range of prote...
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Article
Mistimed origin licensing and activation stabilize common fragile sites under tight DNA-replication checkpoint activation
Genome integrity requires replication to be completed before chromosome segregation. The DNA-replication checkpoint (DRC) contributes to this coordination by inhibiting CDK1, which delays mitotic onset. Under-...
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Article
Genome-wide measurement of DNA replication fork directionality and quantification of DNA replication initiation and termination with Okazaki fragment sequencing
Studying the dynamics of genome replication in mammalian cells has been historically challenging. To reveal the location of replication initiation and termination in the human genome, we developed Okazaki frag...
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Article
Open AccessDNA methylation and hydroxymethylation characterize the identity of D1 and D2 striatal projection neurons
Neuronal DNA modifications differ from those in other cells, including methylation outside CpG context and abundant 5-hydroxymethylation whose relevance for neuronal identities are unclear. Striatal projection...
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Article
Open AccessTranscriptome architecture and regulation at environmental transitions in flavobacteria: the case of an important fish pathogen
The family Flavobacteriaceae (phylum Bacteroidetes) is a major component of soil, marine and freshwater ecosystems. In this understudied family, Flavobacterium psychrophilum is a freshwater pathogen that infects ...
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Protocol
A Small RNA-Seq Protocol with Less Bias and Improved Capture of 2′-O-Methyl RNAs
The study of small RNAs (sRNAs) by next-generation sequencing (NGS) is challenged by bias issues during library preparation. Several types of sRNAs such as plant microRNAs (miRNAs) carry a 2′-O-methyl (2′-OMe) mo...
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Article
Open AccessTranscription-mediated organization of the replication initiation program across large genes sets common fragile sites genome-wide
Common fragile sites (CFSs) are chromosome regions prone to breakage upon replication stress known to drive chromosome rearrangements during oncogenesis. Most CFSs nest in large expressed genes, suggesting tha...
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Article
Open AccessThe evolution of the temporal program of genome replication
Genome replication is highly regulated in time and space, but the rules governing the remodeling of these programs during evolution remain largely unknown. We generated genome-wide replication timing profiles ...
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Article
Open AccessEvidence for late Pleistocene origin of Astyanax mexicanus cavefish
Cavefish populations belonging to the Mexican tetra species Astyanax mexicanus are outstanding models to study the tempo and mode of adaptation to a radical environmental change. They are currently assigned to tw...
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Article
Open AccessSystematic comparison of small RNA library preparation protocols for next-generation sequencing
Next-generation sequencing technologies have revolutionized the study of small RNAs (sRNAs) on a genome-wide scale. However, classical sRNA library preparation methods introduce serious bias, mainly during ada...
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Article
Open AccessReplication landscape of the human genome
Despite intense investigation, human replication origins and termini remain elusive. Existing data have shown strong discrepancies. Here we sequenced highly purified Okazaki fragments from two cell types and, ...
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Article
Open AccessCIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data
Detection of large genomic rearrangements, such as large indels, duplications or translocations is now commonly achieved by next generation sequencing (NGS) approaches. Recently, several tools have been develo...
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Chapter
Megabase Replication Domains Along the Human Genome: Relation to Chromatin Structure and Genome Organisation
In higher eukaryotes, the absence of specific sequence motifs, marking the origins of replication has been a serious hindrance to the understanding of (i) the mechanisms that regulate the spatio-temporal repli...
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Article
Multiscale analysis of genome-wide replication timing profiles using a wavelet-based signal-processing algorithm
In this protocol, we describe the use of the LastWave open-source signal-processing command language (http://perso.ens-lyon.fr/benjamin.audit/LastWave/) for analyz...
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Reference Work Entry In depth
Fractals and Wavelets : What Can We Learn on Transcription and Replication from Wavelet-Based Multifractal Analysis of DNA Sequences ?
Glossary
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Reference Work Entry In depth
Fractals and Wavelets : What Can We Learn on Transcription and Replication from Wavelet-Based Multifractal Analysis of DNA Sequences ?
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Article
Analysing grou** of nucleotides in DNA sequences using lumped processes constructed from Markov chains
The most commonly used models for analysing local dependencies in DNA sequences are (high-order) Markov chains. Incorporating knowledge relative to the possible grou** of the nucleotides enables to define de...
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Article
Wavelet Analysis of DNA Bending Profiles reveals Structural Constraints on the Evolution of Genomic Sequences
Analyses of genomic DNA sequences have shown in previous works that base pairs are correlated at large distances with scale-invariant statistical properties. We show in the present study that these correlation...
