Dataset Information

Direct genome-wide identification of G-quadruplex structures by whole-genome resequencing.

ABSTRACT: We present a user-friendly and transferable genome-wide DNA G-quadruplex (G4) profiling method that identifies G4 structures from ordinary whole-genome resequencing data by seizing the slight fluctuation of sequencing quality. In the human genome, 736,689 G4 structures were identified, of which 45.9% of all predicted canonical G4-forming sequences were characterized. Over 89% of the detected canonical G4s were also identified by combining polymerase stop assays with next-generation sequencing. Testing using public datasets of 6 species demonstrated that the present method is widely applicable. The detection rates of predicted canonical quadruplexes ranged from 32% to 58%. Because single nucleotide variations (SNVs) influence the formation of G4 structures and have individual differences, the given method is available to identify and characterize G4s genome-wide for specific individuals.

SUBMITTER: Tu J

PROVIDER: S-EPMC8516911 | biostudies-literature | 2021 Oct

REPOSITORIES: biostudies-literature

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Direct genome-wide identification of G-quadruplex structures by whole-genome resequencing.

Tu Jing J Duan Mengqin M Liu Wenli W Lu Na N Zhou Yue Y Sun Xiao X Lu Zuhong Z

Nature communications 20211014 1

We present a user-friendly and transferable genome-wide DNA G-quadruplex (G4) profiling method that identifies G4 structures from ordinary whole-genome resequencing data by seizing the slight fluctuation of sequencing quality. In the human genome, 736,689 G4 structures were identified, of which 45.9% of all predicted canonical G4-forming sequences were characterized. Over 89% of the detected canonical G4s were also identified by combining polymerase stop assays with next-generation sequencing. T ...[more]

PMID: 34650044

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Project description:BackgroundTransposable elements (TEs) are DNA sequences that are able to move from their location in the genome by cutting or copying themselves to another locus. As such, they are increasingly recognized as impacting all aspects of genome function. With the dramatic reduction in cost of DNA sequencing, it is now possible to resequence whole genomes in order to systematically characterize novel TE mobilization in a particular individual. However, this task is made difficult by the inherently repetitive nature of TE sequences, which in some eukaryotes compose over half of the genome sequence. Currently, only a few software tools dedicated to the detection of TE mobilization using next-generation-sequencing are described in the literature. They often target specific TEs for which annotation is available, and are only able to identify families of closely related TEs, rather than individual elements.ResultsWe present TE-Tracker, a general and accurate computational method for the de-novo detection of germ line TE mobilization from re-sequenced genomes, as well as the identification of both their source and destination sequences. We compare our method with the two classes of existing software: specialized TE-detection tools and generic structural variant (SV) detection tools. We show that TE-Tracker, while working independently of any prior annotation, bridges the gap between these two approaches in terms of detection power. Indeed, its positive predictive value (PPV) is comparable to that of dedicated TE software while its sensitivity is typical of a generic SV detection tool. TE-Tracker demonstrates the benefit of adopting an annotation-independent, de novo approach for the detection of TE mobilization events. We use TE-Tracker to provide a comprehensive view of transposition events induced by loss of DNA methylation in Arabidopsis. TE-Tracker is freely available at http://www.genoscope.cns.fr/TE-Tracker .ConclusionsWe show that TE-Tracker accurately detects both the source and destination of novel transposition events in re-sequenced genomes. Moreover, TE-Tracker is able to detect all potential donor sequences for a given insertion, and can identify the correct one among them. Furthermore, TE-Tracker produces significantly fewer false positives than common SV detection programs, thus greatly facilitating the detection and analysis of TE mobilization events.

Project description:Copy number variation (CNV), an important source of genomic structural variation, can disturb genetic structure, dosage, regulation and expression, and is associated with phenotypic diversity and adaptation to local environments in mammals. In the present study, 24 resequencing datasets were used to characterize CNVs in three ecotypic populations of Tibetan sheep and assess CNVs related to domestication and adaptation in Qinghai-Tibetan Plateau. A total of 87,832 CNV events accounting for 0.3% of the sheep genome were detected. After merging the overlapping CNVs, 2777 CNV regions (CNVRs) were obtained, among which 1098 CNVRs were shared by the three populations. The average length of these CNVRs was more than 3 kb, and duplication events were more frequent than deletions. Functional analysis showed that the shared CNVRs were significantly enriched in 56 GO terms and 18 KEGG pathways that were mainly concerned with ABC transporters, olfactory transduction and oxygen transport. Moreover, 188 CNVRs overlapped with 97 quantitative trait loci (QTLs), such as growth and carcass QTLs, immunoglobulin QTLs, milk yield QTLs and fecal egg counts QTLs. PCDH15, APP and GRID2 overlapped with body weight QTLs. Furthermore, Vst analysis showed that RUNX1, LOC101104348, LOC105604082 and PAG11 were highly divergent between Highland-type Tibetan Sheep (HTS) and Valley-type Tibetan sheep (VTS), and RUNX1 and LOC101111988 were significantly differentiated between VTS and Oura-type Tibetan sheep (OTS). The duplication of RUNX1 may facilitate the hypoxia adaptation of OTS and HTS in Qinghai-Tibetan Plateau, which deserves further research in detail. In conclusion, for the first time, we represented the genome-wide distribution characteristics of CNVs in Tibetan sheep by resequencing, and provided a valuable genetic variation resource, which will facilitate the elucidation of the genetic basis underlying the distinct phenotypic traits and local adaptation of Tibetan sheep.

Dataset Information

Direct genome-wide identification of G-quadruplex structures by whole-genome resequencing.

Publications

Direct genome-wide identification of G-quadruplex structures by whole-genome resequencing.

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