Genomic landscape, polymorphism and possible LINE-associated delivery of G-quadruplex motifs in the bovine genes

Telomere length determines the mitochondrial copy number in blastocyst-stage embryos

Telomere length (TL) and mitochondrial DNA copy number (mt-cn) are associated with embryonic development. Here, we investigated the correlation between TL and mt-cn in bovine embryos to determine whether TL regulates mt-cn. TL and mt-cn were closely correlated in embryos derived from six bulls. Treatment of embryos with a telomerase inhibitor (TMPyP) and siTERT shortened the TL and reduced mt-cn in blastocysts. RNA-sequencing of blastocysts developed with TMPyP revealed differentially expressed genes associated with transforming growth factor-β1 signaling and inflammation. In conclusion, TL regulates mt-cn in embryos.

Genetic variations in G-quadruplex forming sequences affect the transcription of human disease-related genes

Guanine-rich DNA strands can fold into non-canonical four-stranded secondary structures named G-quadruplexes (G4s). G4s folded in proximal promoter regions (PPR) are associated either with positive or negative transcriptional regulation. Given that single nucleotide variants (SNVs) affecting G4 folding (G4-Vars) may alter gene transcription, and that SNVs are associated with the human diseases' onset, we undertook a novel comprehensive study of the G4-Vars genome-wide (G4-variome) to find disease-associated G4-Vars located into PPRs. We developed a bioinformatics strategy to find disease-related SNVs located into PPRs simultaneously overlapping with putative G4-forming sequences (PQSs). We studied five G4-Vars disturbing in vitro the folding and stability of the G4s located into PPRs, which had been formerly associated with sporadic Alzheimer's disease (GRIN2B), a severe familiar coagulopathy (F7), atopic dermatitis (CSF2), myocardial infarction (SIRT1) and deafness (LHFPL5). Results obtained in cultured cells for these five G4-Vars suggest that the changes in the G4s affect the transcription, potentially contributing to the development of the mentioned diseases. Collectively, data reinforce the general idea that G4-Vars may impact on the different susceptibilities to human genetic diseases' onset, and could be novel targets for diagnosis and drug design in precision medicine.

G-quadruplex resolution: From molecular mechanisms to physiological relevance

Guanine-rich DNA sequences can fold into stable four-stranded structures called G-quadruplexes or G4s. Research in the past decade demonstrated that G4 structures are widespread in the genome and prevalent in regulatory regions of actively transcribed genes. The formation of G4s has been tightly linked to important biological processes including regulation of gene expression and genome maintenance. However, they can also pose a serious threat to genome integrity especially by impeding DNA replication, and G4-associated somatic mutations have been found accumulated in the cancer genomes. Specialised DNA helicases and single stranded DNA binding proteins that can resolve G4 structures play a crucial role in preventing genome instability. The large variety of G4 unfolding proteins suggest the presence of multiple G4 resolution mechanisms in cells. Recently, there has been considerable progress in our detailed understanding of how G4s are resolved, especially during DNA replication. In this review, we first discuss the current knowledge of the genomic G4 landscapes and the impact of G4 structures on DNA replication and genome integrity. We then describe the recent progress on the mechanisms that resolve G4 structures and their physiological relevance. Finally, we discuss therapeutic opportunities to target G4 structures.

Genomic distribution and polymorphism of G-quadruplex motifs occupying ovine promoters and enhancers

G-quadruplexes are non-canonical DNA structures that are formed in regions with short runs of guanines. During the last decade they have gained considerable attention due to their involvement in basic cellular processes, linking them to several physiological processes and pathological conditions. Regulation of gene transcription is among the crucial roles that G-quadruplexes play in the cells. Several ways in which these structures affect transcription have been described, both negatively and positively. Recently, G-quadruplexes have been shown to be implicated in the three-dimensional rearrangement of the chromosomes that enables the interaction of enhancers and gene promoters during regulation of transcription. Sheep is a species for which almost no G-quadruplex-related studies have been conducted and thus research on this species is kept out from the progress that has been made in the G-quadruplex field. In this context, we investigated the DNA sequences with potential to form G-quadruplexes (G4-motifs) in the ovine enhancers and promoters. We describe the distribution of G4-motifs within the regulatory regions which is shown to be enriched in G4-motifs in a way similar to other mammals. Furthermore, our data suggest that G4-motifs promote promoter-enhancer interactions in sheep. The single nucleotide polymorphisms colocalizing with promoter- and enhancer-associated ovine G4-motifs constitute a considerable pool of polymorphism and given the crucial role of these specific G4-motifs on regulation of transcription, we suggest this polymorphism as an interesting target for ovine genetic studies.

Genome-wide analysis of G-quadruplex in Spodoptera frugiperda

Spodoptera frugiperda (Lepidoptera: Noctuidae) is a globally distributed lepidopteran crop pest that has developed resistance to most insecticides. The G-quadruplex (G4) is a secondary structure in the genome enriched in the promoters for regulating gene expression. However, little is known about G4 in S. frugiperda, especially whether G4 is involved in insecticide resistance and pest control. In this study, 387,875 G4 motifs in the whole genome of S. frugiperda were identified by bioinformatics prediction. We found that 66.90 % of theseG4 structures were located in genic regions and highly enriched in the upstream regions of start codons. Functional and pathway analyses showed that the genes with G4 enriched in promoter regions participate in several metabolic processes. Further analyses showed that G4 structures occurred more frequently in the promoters of P450 and CarE gene families. It was also investigated that G4 ligand N-methyl mesoporphyrin IX (NMM) decreased P450 protein activity in larval midgut tissue. Cytotoxicity and bioassay results revealed that NMM and pesticides had synergistic effects on toxicity. In conclusion, our findings suggest that G4 motif could be a new potential target for pest control.