Parent of origin DNA methylation as a potential mechanism for genomic imprinting in bees.

Genomic imprinting is defined as parent-of-origin allele-specific expression. In order for genes to be expressed in this manner an `imprinting' mark must be present to distinguish the parental alleles within the genome. In mammals imprinted genes are primarily associated with DNA methylation. Genes exhibiting parent-of-origin expression have recently been identified in two species of Hymenoptera with functional DNA methylation systems; Apis mellifera and Bombus terrestris. We carried out whole genome bisulfite sequencing of parents and offspring from reciprocal crosses of two B. terrestris subspecies in order to identify parent-of-origin DNA methylation. We were unable to survey a large enough proportion of the genome to draw a conclusion on the presence of parent-of-origin DNA methylation however we were able to characterise the sex- and caste-specific methylomes of B. terrestris for the first time. We find males differ significantly to the two female castes, with differentially methylated genes involved in many histone modification related processes. We also analysed previously generated honeybee whole genome bisulfite data to see if genes previously identified as showing parent-of-origin DNA methylation in the honeybee show consistent allele-specific methylation in independent data sets. We have identified a core set of 12 genes in female castes which may be used for future experimental manipulation to explore the functional role of parent-of-origin DNA methylation in the honeybee. Finally, we have also identified allele-specific DNA methylation in honeybee male thorax tissue which suggests a role for DNA methylation in ploidy compensation in this species.

Medium levels of transcription and replication related chromosomal instability are associated with poor clinical outcome

Genomic instability (GI) influences treatment efficacy and resistance, and an accurate measure of it is lacking. Current measures of GI are based on counts of specific structural variation (SV) and mutational signatures. Here, we present a holistic approach to measuring GI based on the quantification of the steady-state equilibrium between DNA damage and repair as assessed by the residual breakpoints (BP) remaining after repair, irrespective of SV type. We use the notion of Hscore, a BP “hotspotness” magnitude scale, to measure the propensity of genomic structural or functional DNA elements to break more than expected by chance. We then derived new measures of transcription- and replication-associated GI that we call iTRAC (transcription-associated chromosomal instability index) and iRACIN (replication-associated chromosomal instability index). We show that iTRAC and iRACIN are predictive of metastatic relapse in Leiomyosarcoma (LMS) and that they may be combined to form a new classifier called MAGIC (mixed transcription- and replication-associated genomic instability classifier). MAGIC outperforms the gold standards FNCLCC and CINSARC in stratifying metastatic risk in LMS. Furthermore, iTRAC stratifies chemotherapeutic response in LMS. We finally show that this approach is applicable to other cancers.

Probing the adsorption behavior and free energy landscape of single–stranded DNA oligonucleotides on single–layer MoS2 with molecular dynamics

Interfacing single–stranded DNA (ssDNA) with 2D transition metal dichalcogenides are important for numerous technological advancements. However, the molecular mechanism of this process, including the nature of intermolecular association and conformational details of the self–assembled hybrids is still not well understood. Here, atomistic Molecular Dynamics (MD) simulation is employed to study the distinct adsorption behavior of ssDNA on a single–layer MoS2 in aqueous environment. The ssDNA sequences [T10, G10, A10, C10, U10, (GT)5, and (AC)5] are chosen on the basis that short ssDNA segments can undergo a spontaneous conformational change upon adsorption and allow efficient sampling of the conformational landscape. Differences in hybridization is attributed to the inherent molecular recognition ability of the bases. While the binding appears to be primarily driven by energetically favorable van der Waals π–stacking interactions, equilibrium structures are modulated by the ssDNA conformational changes. The poly–purines demonstrate two concurrently competing π–stacking interactions: nucleobase–nucleobase (intramolecular) and nucleobase–MoS2 (intermolecular). The poly–pyrimidines, on the other hand, reveal enhanced π–stacking interactions, thereby maximizing the number of contacts. The results provide new molecular–level understanding of ssDNA adsorption on the MoS2 surface and facilitate future studies in design of functional DNA/MoS2 structure–based platforms for DNA sequencing, biosensing (optical, electrochemical, and electronic), and drug delivery.

Functional DNA annotation from a preliminary de novo genome assembly of Brycon orbignyanus, an endangered Neotropical migratory fish

The predicted sequence for thousands of genes revealed by a preliminary low-coverage genome assembly is presented for Brycon orbignyanus, an endangered migratory fish. Neotropical migratory fish stocks have been drastically reduced due to accumulated environmental pressure. Brycon orbignyanus, once one of the main fisheries species in the Platine Basin, is now very rare in nature and relies on spawning programs and a few well preserved or still untouched sites. The use of high-throughput DNA sequencing is still untapped regarding the functional genome information from B. orbignyanus. In order to help bridging this gap, we present a dataset resulting from the first functional annotation from a de novo genome assembly for B. orbignyanus, from short reads (90 bp), obtained by the HiSeq 2000 platform (Illumina). The annotation was performed for scaffolds over 10 kb using the Maker pipeline, with reference sequences taken from the NCBI for the Characiformes order. This annotation resulted in the prediction of 12,734 genes, classified with the aid of PANTHER. The data presented here can facilitate the development of basic research in this threatened species, along with practical biotechnological tools for different areas, such as commercial and environmental fish spawning operations (e.g. hormonal induction, growth) and human health.

The biological applications of DNA nanomaterials: current challenges and future directions

DNA, a genetic material, has been employed in different scientific directions for various biological applications as driven by DNA nanotechnology in the past decades, including tissue regeneration, disease prevention, inflammation inhibition, bioimaging, biosensing, diagnosis, antitumor drug delivery, and therapeutics. With the rapid progress in DNA nanotechnology, multitudinous DNA nanomaterials have been designed with different shape and size based on the classic Watson–Crick base-pairing for molecular self-assembly. Some DNA materials could functionally change cell biological behaviors, such as cell migration, cell proliferation, cell differentiation, autophagy, and anti-inflammatory effects. Some single-stranded DNAs (ssDNAs) or RNAs with secondary structures via self-pairing, named aptamer, possess the ability of targeting, which are selected by systematic evolution of ligands by exponential enrichment (SELEX) and applied for tumor targeted diagnosis and treatment. Some DNA nanomaterials with three-dimensional (3D) nanostructures and stable structures are investigated as drug carrier systems to delivery multiple antitumor medicine or gene therapeutic agents. While the functional DNA nanostructures have promoted the development of the DNA nanotechnology with innovative designs and preparation strategies, and also proved with great potential in the biological and medical use, there is still a long way to go for the eventual application of DNA materials in real life. Here in this review, we conducted a comprehensive survey of the structural development history of various DNA nanomaterials, introduced the principles of different DNA nanomaterials, summarized their biological applications in different fields, and discussed the current challenges and further directions that could help to achieve their applications in the future.