CIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data

International audienceBackgroundDetection 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 developed to analyze NGS data but the resulting files are difficult to interpret without an additional visualization step. Circos (Genome Res, 19:1639–1645, 2009), a Perl script, is a powerful visualization software that requires setting up numerous configuration files with a large number of parameters to handle. R packages like RCircos (BMC Bioinformatics, 14:244, 2013) or ggbio (Genome Biol, 13:R77, 2012) provide functions to display genomic data as circular Circos-like plots. However, these tools are very general and lack the functions needed to filter, format and adjust specific input genomic data.ResultsWe implemented an R package called CIRCUS to analyze genomic structural variations. It generates both data and configuration files necessary for Circos, to produce graphs. Only few R pre-requisites are necessary. Options are available to deal with heterogeneous data, various chromosome numbers and multi-scale analysis.ConclusionCIRCUS allows fast and versatile analysis of genomic structural variants with Circos plots for users with limited coding skills

OKseqHMM: a genome-wide replication fork directionality analysis toolkit

International audienceDuring each cell division, tens of thousands of DNA replication origins are co-ordinately activated to ensure the complete duplication of the human genome. However, replication fork progression can be challenged by many factors, including co-directional and head-on transcription-replication conflicts (TRC). Head-on TRCs are more dangerous for genome integrity. To study the direction of replication fork movement and TRCs, we developed a bioinformatics toolkit called OKseqHMM (https://github.com/CL-CHEN-Lab/OK-Seq, https://doi.org/10.5281/zenodo.7428883). Then, we used OKseqHMM to analyse a large number of datasets obtained by Okazaki fragment sequencing to directly measure the genome-wide replication fork directionality (RFD) and to accurately predict replication initiation and termination at a fine resolution in organisms including yeast, mouse and human. We also successfully applied our analysis to other genome-wide sequencing techniques that also contain RFD information (e.g. eSPAN, TrAEL-seq). Our toolkit can be used to predict replication initiation and fork progression direction genome-wide in a wide range of cell models and growth conditions. Comparing the replication and transcription directions allows identifying loci at risk of TRCs, particularly head-on TRCs, and investigating their role in genome instability by checking DNA damage data, which is of prime importance for human health

OKseqHMM: a genome-wide replication fork directionality analysis toolkit

Motivation: During each cell division, tens of thousands of DNA replication origins are coordinately activated to ensure the complete duplication of the entire human genome. However, the progression of replication forks can be challenged by numerous factors. One such factor is transcription-replication conflicts (TRC), which can either be co-directional or headon with the latter being revealed as more dangerous for genome integrity. Results: In order to study the direction of replication fork movement and TRC, we developed a bioinformatics tool, called OKseqHMM, to directly measure the genome-wide replication fork directionality (RFD) as well as replication initiation and termination from data obtained by Okazaki fragment sequencing (OK-Seq) and related techniques

Genome-wide measurement of DNA replication fork directionality and quantification of DNA replication initiation and termination with Okazaki fragment sequencing

International audienc

Correlation between the in vivo metabolism of hexobarbital and antipyrine in rats

Two model substrates for oxidative hepatic enzyme activity, viz. hexobarbital (HB) and antipyrine (AP), were given simultaneously to rats by the oral route of administration. Blood concentrations of HB and AP were measured simultaneously by a gas chromatographic method and the urinary excretion of six metabolites arising from AP and HB also was determined; norantipyrine, 4-hydroxyantipyrine and 3-hydroxymethylantipyrine (HMA) by high-performance liquid chromatography; 3'-hydroxyhexobarbital, 3'-ketohexobarbital and 1,5-dimethylbarbituric acid by gas-liquid chromatography. The apparent intrinsic clearances of HB (CL*int,HB) and AP (CL*int,AP) and the clearance for production of the various metabolites were correlated in an attempt to establish whether HB and AP have metabolic pathways mediated by the same or very similar forms of cytochrome P-450. In order to create broadly ranging and evenly distributed clearance values, 3-methylcholanthrene (3-MC)- and phenobarbital (PB) pretreated rats were employed in conjunction with a control group of untreated animals. CL*int,HB and CL*int,AP were both increased by PB pretreatment, but 3-MC-pretreatment increased CL*int,AP, whereas CL*int,HB was decreased. CL*int,HB and CL*int,AP were found to correlate poorly, when all groups were taken into consideration (r = -0.08). The formation of AP-metabolites was inducible by both PB and 3-MC, and good correlations between rates of formation of AP-metabolites and CL*int,HB and CL3'-hydroxy-HB + 3'-keto-HB were obtained.(ABSTRACT TRUNCATED AT 250 WORDS

Additional file 7: Figure S7. of Systematic comparison of small RNA library preparation protocols for next-generation sequencing

Annotation data for the short side products (10–18 nt inserts) with human and Arabidopsis libraries. After adapter trimming the human sequences were mapped to the database of small human non-coding RNAs (DASHR), mirBase (for partial miRNA sequences), and the regulatory RNA database for piRNA sequences. The Arabidopsis sequences were mapped to databases for various non-coding RNAs (Ensemblgenomes), tRNAs (Genomic tRNA database) and miRNAs. See Methods for details. (PDF 1.01 mb

Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses

Long non-protein coding RNAs (npcRNA) represent an emerging class of riboregulators, which either act directly in this long form or are processed to shorter miRNA and siRNA. Genome-wide bioinformatic analysis of full-length cDNA databases identified 76 Arabidopsis npcRNAs. Fourteen npcRNAs were antisense to protein-coding mRNAs, suggesting cis-regulatory roles. Numerous 24-nt siRNA matched to five different npcRNAs, suggesting that these npcRNAs are precursors of this type of siRNA. Expression analyses of the 76 npcRNAs identified a novel npcRNA that accumulates in a dcl1 mutant but does not appear to produce trans-acting siRNA or miRNA. Additionally, another npcRNA was the precursor of miR869 and shown to be up-regulated in dcl4 but not in dcl1 mutants, indicative of a young miRNA gene. Abiotic stress altered the accumulation of 22 npcRNAs among the 76, a fraction significantly higher than that observed for the RNA binding protein-coding fraction of the transcriptome. Overexpression analyses in Arabidopsis identified two npcRNAs as regulators of root growth during salt stress and leaf morphology, respectively. Hence, together with small RNAs, long npcRNAs encompass a sensitive component of the transcriptome that have diverse roles during growth and differentiation