ClusterScan: simple and generalistic identification of genomic clusters

Volpe, Massimiliano; Miralto, Marco; Gustincich, Stefano; Sanges, Remo

doi:10.1093/bioinformatics/bty486

Cited by 12 publications

(9 citation statements)

References 26 publications

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“…We used the clusterdist function in ClusterScan v.0.2.2 [127] to calculate the number of genes that form clusters in the genome for the conserved group with the option dist = 500. We counted the number of conserved CN genes that were defined inside the clusters and used to calculate their proportion in the conserved CN group.…”

Section: Clustering Analysis and The Bootstrap Methodsmentioning

confidence: 99%

Genome plasticity in Paramecium bursaria revealed by population genomics

Cheng

Liu

et al. 2020

BMC Biol

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Background Ciliates are an ancient and diverse eukaryotic group found in various environments. A unique feature of ciliates is their nuclear dimorphism, by which two types of nuclei, the diploid germline micronucleus (MIC) and polyploidy somatic macronucleus (MAC), are present in the same cytoplasm and serve different functions. During each sexual cycle, ciliates develop a new macronucleus in which newly fused genomes are extensively rearranged to generate functional minichromosomes. Interestingly, each ciliate species seems to have its way of processing genomes, providing a diversity of resources for studying genome plasticity and its regulation. Here, we sequenced and analyzed the macronuclear genome of different strains of Paramecium bursaria, a highly divergent species of the genus Paramecium which can stably establish endosymbioses with green algae. Results We assembled a high-quality macronuclear genome of P. bursaria and further refined genome annotation by comparing population genomic data. We identified several species-specific expansions in protein families and gene lineages that are potentially associated with endosymbiosis. Moreover, we observed an intensive chromosome breakage pattern that occurred during or shortly after sexual reproduction and contributed to highly variable gene dosage throughout the genome. However, patterns of copy number variation were highly correlated among genetically divergent strains, suggesting that copy number is adjusted by some regulatory mechanisms or natural selection. Further analysis showed that genes with low copy number variation among populations tended to function in basic cellular pathways, whereas highly variable genes were enriched in environmental response pathways. Conclusions We report programmed DNA rearrangements in the P. bursaria macronuclear genome that allow cells to adjust gene copy number globally according to individual gene functions. Our results suggest that large-scale gene copy number variation may represent an ancient mechanism for cells to adapt to different environments.

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Section: Clustering Analysis and The Bootstrap Methodsmentioning

confidence: 99%

Genome plasticity in Paramecium bursaria revealed by population genomics

Cheng

Liu

et al. 2020

BMC Biol

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“…Middle lane: genes. Lower three lanes: Origin clusters determined using the clusterdist function of clusterscan (34), set at 30 kb (see Materials & Methods). H. Number of clusters found in each ini-seq 2 origin efficiency class.…”

Section: Resultsmentioning

confidence: 99%

“…Ini-domains were generated using the merge function at a maximum distance of 100kb, only domains containing at least 6 origins were kept. Cluster analysis of high, medium and low efficiency origins was performed using the option of (34) with a distance for determining a cluster of 30 kb. Feature coverage around origins was plotted using (35).…”

Section: Methodsmentioning

confidence: 99%

Determination of human DNA replication origin position and efficiency reveals principles of initiation zone organisation

Guilbaud

Murat

Wilkes

et al. 2021

Preprint

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Replication of the human genome initiates within broad zones of ~ 150 kb. The extent to which firing of individual DNA replication origins within initiation zones is spatially stochastic or localised at defined sites remains a matter of debate. A thorough characterisation of the dynamic activation of origins within initiation zones is hampered by the lack of a high-resolution map of both their position and efficiency. To address this shortcoming, we describe a modification of initiation site sequencing (ini-seq) based on density substitution. Newly-replicated DNA is rendered ‘heavy-light’ (HL) by incorporation of BrdUTP, unreplicated DNA remaining ‘light-light’ (LL). Replicated HL-DNA is separated from unreplicated LL-DNA by equilibrium density gradient centrifugation, then both fractions are subjected to massive parallel sequencing. This allows precise mapping of 23,905 replication origins simultaneously with an assignment of a replication initiation efficiency score to each. We show that origin firing within initiation zones is not randomly distributed. Rather, origins are arranged hierarchically with a set of very highly efficient origins marking zone boundaries. We propose that these origins explain much of the early firing activity arising within initiation zones, helping to unify the concept of replication initiation zones with the identification of discrete replication origin sites.

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“…Having defined the final set of promoters (i.e., consensus clusters), the promoter density has been calculated as follows. First, by using the clusterdist algorithm of the ClusterScan tool (-d 10,000 parameter) (Volpe et al , 2018), the zebrafish genome has been scanned grouping together all the consecutive promoters closer than 10 kb. Then, for each group of promoters (clusters), the promoter density has been calculated by dividing the number of promoters by the cluster length in kilobases.…”

Section: Methodsmentioning

confidence: 99%

The miR-430 locus with extreme promoter density is a transcription body organizer, which facilitates long range regulation in zygotic genome activation

Hadzhiev

Wheatley

Cooper

et al. 2021

Preprint

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In anamniote embryos the major wave of zygotic genome activation (ZGA) starts during the mid-blastula transition. This major wave of ZGA is facilitated by several mechanisms, including dilution of repressive maternal factors and accumulation of activating transcription factors during the fast cell division cycles preceding the mid-blastula transition. However, a set of genes escape global genome repression and are activated substantially earlier, during what is called, the minor wave of genome activation. While the mechanisms underlying the major wave of genome activation have been studied extensively, the minor wave of genome activation is little understood. In zebrafish the earliest expressed RNA polymerase II (Pol II) transcribed genes are activated in a pair of large transcription bodies depleted of chromatin, abundant in elongating Pol II and nascent RNAs (Hadzhiev et al., 2019; Hilbert et al., 2021). This transcription body includes the miR-430 gene cluster required for maternal mRNA clearance. Here we explored the genomic, chromatin organisation and cis-regulatory mechanisms of the minor wave of genome activation occurring in the transcription body. By long read genome sequencing we identified a remarkable cluster of miR-430 genes with over 300 promoters and spanning 0.6 Mb, which represent the highest promoter density of the genome. We demonstrate that the miR-430 gene cluster is required for the formation of the transcription body and acts as a transcription organiser for minor wave activation of a set of zinc finger genes scattered on the same chromosome arm, which share promoter features with the miR-430 cluster. These promoter features are shared among minor wave genes overall and include the TATA-box and sharp transcription start site profile. Single copy miR-430 promoter transgene reporter experiments indicate the importance of promoter-autonomous mechanisms regulating escape from global repression of the early embryo. These results together suggest that formation of the transcription body in the early embryo is the result of high promoter density coupled to a minor wave-specific core promoter code for transcribing key minor wave ZGA genes, which are required for the overhaul of the transcriptome during early embryonic development.

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ClusterScan: simple and generalistic identification of genomic clusters

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 12 publications

References 26 publications

Genome plasticity in Paramecium bursaria revealed by population genomics

Genome plasticity in Paramecium bursaria revealed by population genomics

Determination of human DNA replication origin position and efficiency reveals principles of initiation zone organisation

The miR-430 locus with extreme promoter density is a transcription body organizer, which facilitates long range regulation in zygotic genome activation

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