Disease‐causing point mutations are assumed to act predominantly through subsequent individual changes in the amino acid sequence that impair normal function of proteins. However, can have a more dramatic effect by altering splicing pattern gene. Here, we describe an approach estimate overall importance mutations. This takes into account complete set genes known be involved disease and suggest that, contrary current assumptions, many causing may actually affecting genes.

Neutral nucleotide substitutions occur at varying rates along genomes, and it remains a major issue to unravel the mechanisms that cause these variations analyze their evolutionary consequences. Here, we study role of replication in neutral substitution pattern. We obtained high-resolution timing profile whole human genome by massively parallel sequencing nascent BrdU-labeled replicating DNA. These data were compared genome, aligning chimpanzee genomes using macaque orangutan as outgroups....

In this work, we investigated a large-scale organization of the human genes with respect to putative replication origins. We developed an appropriate multiscale method analyze nucleotide compositional skew along genome and found that in more than one-quarter genome, profile presents characteristic patterns consisting successions N-shaped structures, designated here N-domains, bordered by Our analysis recent experimental timing data confirmed that, number cases, domain borders coincide...

The duplication of mammalian genomes is under the control a spatiotemporal program that orchestrates positioning and timing firing replication origins. molecular mechanisms coordinating activation about predicted origins remain poorly understood, partly due to intrinsic rarity bubbles, making it difficult purify short nascent strands (SNS). precise identification based on high-throughput sequencing SNS constitutes new methodological challenge. We propose statistical method with controlled...

Genome-wide replication timing studies have suggested that mammalian chromosomes consist of megabase-scale domains coordinated origin firing separated by large originless transition regions. Here, we report a quantitative genome-wide analysis DNA kinetics in several human cell types contradicts this view. combing HeLa cells sorted into four temporal compartments S phase shows origins are spaced at 40 kb intervals and fire as small clusters whose synchrony increases during fork velocity (mean...

Abstract Public sequence databases contain information on the sequence, structure and function of proteins. Genome sequencing projects have led to a rapid increase in protein information, but reliable, experimentally verified, lags long way behind. To address this deficit, functional annotation is often inferred by similarity homologous, annotated proteins, with attendant possibility error. Now, these homologous proteins may itself been acquired through yet other it generally not possible...

In the course of evolution, mutations do not affect both strands genomic DNA equally. This imbalance mainly results from asymmetric mutation and repair processes associated with replication transcription. prokaryotes, prevalence G over C T A is frequently observed in leading strand. The sign resulting TA GC skews changes abruptly when crossing replication-origin termination sites, producing characteristic step-like transitions. mammals, transcription-coupled have been detected, but so far,...

We use the "wavelet transform microscope" to carry out a comparative statistical analysis of DNA bending profiles and corresponding texts. In three kingdoms, one reveals on both signals characteristic scale 100-200 bp that separates two different regimes power-law correlations (PLC). small-scale regime, PLC are observed in eukaryotic, double-strand viral, archaeal genomes, which contrasts with their total absence genomes eubacteria viruses. This strongly suggests related mechanisms...

Although chromatin folding is known to be of functional importance control the gene expression program, less regarding its interplay with DNA replication. Here, using Circular Chromatin Conformation Capture combined high-throughput sequencing, we identified megabase-sized self-interacting domains in nucleus a human lymphoblastoid cell line, as well cycling and resting peripheral blood mononuclear cells (PBMC). Strikingly, boundaries those coincide early-initiation zones every types....

Breast cancer is the most common type of among women and despite recent advances in medical field, there are still some inherent limitations currently used screening techniques. The radiological interpretation X-ray mammograms often leads to over-diagnosis and, as a consequence, unnecessary traumatic painful biopsies. Here we propose computer-aided multifractal analysis dynamic infrared (IR) imaging an efficient method for identifying with risk breast cancer. Using wavelet-based multi-scale...

Abstract Genome replication mapping methods profile cell populations, masking cell-to-cell heterogeneity. Here, we describe FORK-seq, a nanopore sequencing method to map of single DNA molecules at 200-nucleotide resolution. By quantifying BrdU incorporation along pulse-chased intermediates from Saccharomyces cerevisiae , orient 58,651 tracks reproducing population-based directionality profiles and 4964 4485 individual initiation termination events, respectively. Although most events cluster...

Abstract Little is known about replication fork velocity variations along eukaryotic genomes, since reference techniques to determine speed either provide no sequence information or suffer from low throughput. Here we present NanoForkSpeed, a nanopore sequencing-based method map and extract the of individual forks detected as tracks thymidine analogue bromodeoxyuridine incorporated during brief pulse-labelling asynchronously growing cells. NanoForkSpeed retrieves previous Saccharomyces...

Various wavelet-based estimators of self-similarity or long-range dependence scaling exponent are studied extensively. These mainly include the (bi)orthogonal wavelet and transform modulus maxima (WTMM) estimator. This study focuses both on short long time-series. In framework fractional autoregressive integrated moving average (FARIMA) processes, we advocate use approximately adapted estimators. For these "ideal" behavior actually extends down to smallest scale, i.e., sampling period time...

In higher eukaryotes, replication program specification in different cell types remains to be fully understood. We show for seven human lines that about half of the genome is divided domains display a characteristic U-shaped timing profile with early initiation zones at borders and late centers. Significant overlap observed between U-domains also germline exhibiting N-shaped nucleotide compositional skew. From demonstration average fork polarity directly reflected by both skew derivative...

During evolution, mutations occur at rates that can differ between the two DNA strands. In human genome, nucleotide substitutions different on transcribed and non-transcribed strands may result from transcription-coupled repair. These mutational asymmetries generate transcription-associated compositional skews. To date, existence of such associated with replication has not yet been established. Here, we compute substitution matrices around initiation zones identified as sharp peaks in timing...

Advances in genomic studies have led to significant progress understanding the epigenetically controlled interplay between chromatin structure and nuclear functions. Epigenetic modifications were shown play a key role transcription regulation genome activity during development differentiation or response environment. Paradoxically, molecular mechanisms that regulate initiation maintenance of spatio-temporal replication program higher eukaryotes, particular their links epigenetic...

Eukaryotic DNA replication initiates during S phase from origins that have been licensed in the preceding G1 phase. Here, we compare ChIP-seq profiles of licensing factors Orc2, Orc3, Mcm3, and Mcm7 with gene expression, timing, fork directionality obtained by RNA-seq, Repli-seq, OK-seq. Both, origin recognition complex (ORC) minichromosome maintenance (MCM) are significantly homogeneously depleted transcribed genes, enriched at promoters, more abundant early- than late-replicating domains....

Abstract Current temporal studies of DNA replication are either low-resolution or require complex cell synchronisation and/or sorting procedures. Here we introduce Nanotiming, a single-molecule, nanopore sequencing-based method producing high-resolution, telomere-to-telomere timing (RT) profiles eukaryotic genomes by interrogating changes in intracellular dTTP concentration during S phase through competition with its analogue bromodeoxyuridine triphosphate (BrdUTP) for incorporation into...

Nucleosomes are fundamental units of chromatin in which a length genomic DNA is wrapped around histone octamer spool left-handed superhelix. Large-scale nucleosome maps show wide distribution wrapping lengths, some cases tens base pairs (bp) shorter than the 147 bp canonical observed crystal structures. Here, we develop thermodynamic model that assumes constant free energy cost unwrapping nucleosomal bp. Our also incorporates linker DNA—short segments between neighboring nucleosomes imposed...