Coding Region Research Articles

Characterization of cancer-driving nucleotides (CDNs) across genes, cancer types, and patients

A central goal of cancer genomics is to identify, in each patient, all the cancer-driving mutations. Among them, point mutations are referred to as cancer-driving nucleotides (CDNs), which recur in cancers. The companion study shows that the probability of i recurrent hits in n patients would decrease exponentially with i; hence, any mutation with i ≥ 3 hits in The Cancer Genome Atlas (TCGA) database is a high-probability CDN. This study characterizes the 50–150 CDNs identifiable for each cancer type of TCGA (while anticipating 10 times more undiscovered ones) as follows: (i) CDNs tend to code for amino acids of divergent chemical properties. (ii) At the genic level, far more CDNs (more than fivefold) fall on noncanonical than canonical cancer-driving genes (CDGs). Most undiscovered CDNs are expected to be on unknown CDGs. (iii) CDNs tend to be more widely shared among cancer types than canonical CDGs, mainly because of the higher resolution at the nucleotide than the whole-gene level. (iv) Most important, among the 50–100 coding region mutations carried by a cancer patient, 5–8 CDNs are expected but only 0–2 CDNs have been identified at present. This low level of identification has hampered functional test and gene-targeted therapy. We show that, by expanding the sample size to 105, most CDNs can be identified. Full CDN identification will then facilitate the design of patient-specific targeting against multiple CDN-harboring genes.

Characterization of cancer-driving nucleotides (CDNs) across genes, cancer types, and patients.

A central goal of cancer genomics is to identify, in each patient, all the cancer-driving mutations. Among them, point mutations are referred to as cancer-driving nucleotides (CDNs), which recur in cancers. The companion study shows that the probability of i recurrent hits in n patients would decrease exponentially with i; hence, any mutation with i ≥ 3 hits in The Cancer Genome Atlas (TCGA) database is a high-probability CDN. This study characterizes the 50-150 CDNs identifiable for each cancer type of TCGA (while anticipating 10 times more undiscovered ones) as follows: (i) CDNs tend to code for amino acids of divergent chemical properties. (ii) At the genic level, far more CDNs (more than fivefold) fall on noncanonical than canonical cancer-driving genes (CDGs). Most undiscovered CDNs are expected to be on unknown CDGs. (iii) CDNs tend to be more widely shared among cancer types than canonical CDGs, mainly because of the higher resolution at the nucleotide than the whole-gene level. (iv) Most important, among the 50-100 coding region mutations carried by a cancer patient, 5-8 CDNs are expected but only 0-2 CDNs have been identified at present. This low level of identification has hampered functional test and gene-targeted therapy. We show that, by expanding the sample size to 105, most CDNs can be identified. Full CDN identification will then facilitate the design of patient-specific targeting against multiple CDN-harboring genes.

Novel variants impairing Sp1 transcription factor binding in the COL7A1 promoter cause mild cases of recessive dystrophic epidermolysis bullosa.

Recessive dystrophic epidermolysis bullosa (RDEB) is a rare and most often severe genodermatosis characterized by recurrent blistering and erosions of the skin and mucous membranes after minor trauma, leading to major local and systemic complications. RDEB is caused by loss-of-function mutations in COL7A1 encoding type VII collagen (C7), the main component of anchoring fibrils which form attachment structures stabilizing the cutaneous basement membrane zone. Most of the previously reported COL7A1 mutations are located in the coding or intronic regions. We describe 6 patients with localized or intermediate RDEB for whom one recessive pathogenic variant in the coding region and a second variant in the COL7A1 promoter were identified. These substitutions, three of which are novel, are localized in two Sp1 binding sites of the promoter region. DNA pull-down assay showed a drastic reduction of Sp1 binding consistent with a dramatic decrease in COL7A1 transcript and almost undetectable C7 protein levels. Our results reveal that mutations in the COL7A1 promoter on the background of a null allele can underlie localized or intermediate RDEB. They further emphasize the functional importance of Sp1 motifs in the proximal COL7A1 promoter which should be carefully investigated for regulatory mutations in the case of RDEB with only one pathogenic variant identified in the coding or intronic regions.

Osmotic disruption of chromatin induces Topoisomerase 2 activity at sites of transcriptional stress

Transcription generates superhelical stress in DNA that poses problems for genome stability, but determining when and where such stress arises within chromosomes is challenging. Here, using G1-arrested S. cerevisiae cells, and employing rapid fixation and ultra-sensitive enrichment, we utilise the physiological activity of endogenous topoisomerase 2 (Top2) as a probe of transcription-induced superhelicity. We demonstrate that Top2 activity is surprisingly uncorrelated with transcriptional activity, suggesting that superhelical stress is obscured from Top2 within chromatin in vivo. We test this idea using osmotic perturbation—a treatment that transiently destabilises chromatin in vivo—revealing that Top2 activity redistributes within sub-minute timescales into broad zones patterned by long genes, convergent gene arrays, and transposon elements—and also by acute transcriptional induction. We propose that latent superhelical stress is normally absorbed by the intrinsic topological buffering capacity of chromatin, helping to avoid spurious topoisomerase activity arising within the essential coding regions of the genome.

Repeat-induced point mutations driving Parastagonospora nodorum genomic diversity are balanced by selection against non-synonymous mutations

Parastagonospora nodorum is necrotrophic fungal pathogen of wheat with significant genomic resources. Population-level pangenome data for 173 isolates, of which 156 were from Western Australia (WA) and 17 were international, were examined for overall genomic diversity and effector gene content. A heterothallic core population occurred across all regions of WA, with asexually-reproducing clonal clusters in dryer northern regions. High potential for SNP diversity in the form of repeat-induced point mutation (RIP)-like transitions, was observed across the genome, suggesting widespread ‘RIP-leakage’ from transposon-rich repetitive sequences into non-repetitive regions. The strong potential for RIP-like mutations was balanced by negative selection against non-synonymous SNPs, that was observed within protein-coding regions. Protein isoform profiles of known effector loci (SnToxA, SnTox1, SnTox3, SnTox267, and SnTox5) indicated low-levels of non-synonymous and high-levels of silent RIP-like mutations. Effector predictions identified 186 candidate secreted predicted effector proteins (CSEPs), 69 of which had functional annotations and included confirmed effectors. Pangenome-based effector isoform profiles across WA were distinct from global isolates and were conserved relative to population structure, and may enable new approaches for monitoring crop disease pathotypes.

Immunohistochemical Localization and Expression of Aquaporin 3-2 (AQP3C1) in the Spiny Dogfish, Squalus acanthias

The previously available coding region for the spiny dogfish (Squalus acanthias) AQP3-2 gene was amplified from cDNAs using PCR. Agarose gel electrophoresis gave a band of the AQP3-2 coding region, as well as multiple smaller splice variant bands. The main AQP3-2 band and the largest and most fluorescently intense pair of these splice variant bands were cloned and sequenced. Amplifications were performed on a range of tissue cDNAs, but AQP3-2 was only expressed in the kidney and brain. Quantitative PCR amplifications using pre-existing kidney cDNA from an environmental salinity acclimation experiment showed that the abundance of mRNA from both the main AQP3-2 transcript and the largest splice variant (Splice Variant 1) was lower in 120% seawater (SW) acclimated fish, although only the values for Splice Variant 1 were statistically significant. A custom-made affinity-purified rabbit polyclonal AQP3-2 antibody was produced, and this gave four bands of around the correct sizes (which were 27 and 32 kDa) for the complete AQP3-2 and Splice Variant 1 proteins. Two of the bands may have been N-glycosylated forms of these proteins. Other bands were also present on the Western blot. No bands were present when the antibody was pre-blocked by the peptide antigen. In tissue sections of the dogfish kidney, immunohistochemical localization experiments showed that AQP3-2 was expressed in the early distal tubule (EDT) and late distal tubule (LDT) nephron segments. The results suggest that AQP3-2 may be involved in cell volume regulation in the EDT and water and urea absorption in the LDT nephron segment.

Cell-free supernatant of Lactobacillus gasseri 1A-TV shows a promising activity to eradicate carbapenem-resistant Klebsiella pneumoniae colonization.

The use of beneficial bacteria like Lactobacillus spp. is a potential innovative approach to fight antibiotic-resistant pathogens. Klebsiella pneumoniae is one of the most concerning multi drug-resistant (MDR) pathogens, and its ability to colonize the human gut is considered to be the main reason for recurrent infections in critically ill patients. In this study, Lactobacillus gasseri 1A-TV, already described for its probiotic activity, was characterized at the genomic level. Moreover, its cell-free supernatant (CFS) was tested for antimicrobial activity against extended-spectrum β-lactamase (ESBL)- and carbapenemase (KPC)-producing K. pneumoniae clinical isolates. Whole-genome sequencing showed that the L. gasseri 1A-TV genome was of 2,018,898 bp in size with 34.9% GC content, containing 1,937 putative protein coding sequences, 55 tRNA, and 4 rRNA detected by RAST and classified in 20 functional groups by Cluster of Orthologous Genes (COG). BAGEL4 (BActeriocin GEnome minimal tooL) and the antiSMASH 7.0 pipeline identified two bacteriocin biosynthetic gene clusters (BBGCs), namely, BBGC1 that comprises two class IIc bacteriocins including gassericin A-like bacteriocin, and BBGC2 carrying the class III bacteriocin helveticin J. Strikingly, 1A-TV CFS inhibited the growth of all K. pneumoniae isolates only after 8 h of incubation, showing a bactericidal effect at 24 h and interfering, even at lower concentrations, with the biofilm production of biofilm-producer strains independently of a bactericidal effect. NMR analysis of CFS identified and quantified several metabolites involved in carbohydrate metabolism and amino acid metabolism, and organic acids like ethanol, lactate, acetate, and succinate. Finally, in vitro assays of 1A-TV showed significant co-aggregation effects against carbapenem-resistant K. pneumoniae, namely, strains 1, 2, 3, and 7. Our findings highlight the antimicrobial activity of 1A-TV as a probiotic candidate or its CFS as a natural bioproduct active against MDR K. pneumoniae strains, underlining the importance of novel therapeutic strategies for prevention and control of ESBL- and carbapenemase-producing K. pneumoniae colonization.

A Comparative Analysis of Mitogenomes in Species of the Tapinoma nigerrimum Complex and Other Species of the Genus Tapinoma (Formicidae, Dolichoderinae)

Using next-generation sequencing data, the complete mitogenomes of six species from the genus Tapinoma were assembled. This study explores the mitochondrial genomes of Tapinoma species, among them the five species from the Tapinoma nigerrimum complex, comparing them with each other and with other species from Dolichoderinae subfamily to understand their evolutionary relationships and evolution. Tapinoma mitochondrial genomes contain the typical set of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and the A + T-rich control region. A phylogenetic analysis using the protein-coding gene sequences from available Dolichoderinae mitogenomes supports the monophyletic nature of the genus Tapinoma, with the T. nigerrimum complex forming a well-supported clade. Key findings include genetic traits unique to the T. nigerrimum complex, such as a start codon in the atp8 gene and a complete stop codon in cox1, distinguishing them from other Tapinoma species. Additionally, a gene rearrangement involving tRNA-Trp, tRNA-Cys, and tRNA-Tyr was found exclusively in the Tapinoma species, suggesting a potential phylogenetic marker for the genus.

Positive Selection of TLR2 and MyD88 Genes Provides Insights Into the Molecular Basis of Immunological Adaptation in Amphibians.

The transition from water to land of amphibians is evolutionarily significant in the history of vertebrates, and immunological adaptation is an important challenge for amphibians to respond to the dramatic changes of the environmental pathogens during their origin and diversification. Toll-like receptors (TLRs) are important pattern recognition receptors for the innate immune response and TLRs signaling pathway play essential roles in the immune responses to pathogens and inflammatory reaction. However, the evolutionary patterns and molecular mechanisms underlying their adaptation in amphibians are poorly documented to date. Here, we determined the coding regions, expression patterns of TLR2 and Myeloid differentiation factor 88 (MyD88) in the large treefrog (Zhangixalus dennysi), and explored the evolutionary patterns of these two genes in amphibians. Quantitative Real-time PCR analyses showed that the TLR2 and MyD88 mRNA were expressed in all the organs/tissues examined, both with the highest levels in the heart and the lowest levels in the body fat for TLR2 and lung for MyD88. The highly conservation and functional significance of these two genes in amphibians were supported based on the sequence characteristics and evolutionary analyses. Significantly positive selection was found to be acting on TLR2 and MyD88 in amphibians based on different site models. Strong signal of positive selection among different amphibian lineages for these two genes was also detected and a series of positively selected sites were identified based on the branch-site analysis. Our results suggest that amphibians have adapted to different pathogenic microorganisms during their transition from the aquatic to terrestrial environment and diversification into various habitats. The present study will provide new insights into the evolutionary process and molecular basis underlying the immunological adaptation in vertebrates.

Transcriptional and post-transcriptional regulation of whiB6 by a response regulator PhoP and a small noncoding RNA MTS1338 in Mycobacterium tuberculosis

WhiB6 in pathogenic mycobacteria is highly upregulated during NO stress, hypoxia, and macrophage infection. Its expression primarily results from transcriptional control by a two-component response regulator PhoP in response to the various stresses exerted on mycobacterial cells inside phagosomes. Herein, we investigated the transcriptional and posttranscriptional regulatory mechanism of whiB6 expression. We found that PhoP binds to the PhoP-signature sequences located upstream to the core promoter region of whiB6 gene and controls its expression at the transcriptional level. Phosphorylation of PhoP is obligatory for binding to whiB6 promoter. A dormancy regulatory factor DosR, although doesn’t bind to whiB6 gene, can bind to the PhoP-bound whiB6 gene implicating its potential role in whiB6 expression. A virulence-associated sRNA MTS1338 directly binds to the coding region of whiB6 gene presumably protecting it from cellular ribonucleases. Induction of MTS1338 in response to low pH and oxidative stress increases whiB6 accumulation likely through the stabilization of whiB6 transcript at the posttranscriptional level. This study substantially increases our knowledge of the regulation of whiB6 expression in M. tuberculosis.

An electrochemical biosensor for mercury(II) detection based on DNA-Au bio-bar codes coupled with enzymatic dual signal amplification

Mercury ion (Hg2+) is one of the most toxic heavy metal pollutants, which not only causes enormous damage and pollution to environment, but also results in numerous irreversible impairments to the human health. Herein, a novel amperometric DNA biosensor was constructed for Hg2+ detection based on DNA-Au bio-bar codes coupled with enzymatic dual signal amplification. Carboxylated graphene oxide (GO − COOH) was selected as electrode modified material to provide anchoring sites for attachment DNA oligonucleotides. Substrate DNA was attached on the GO − COOH surface via covalent coupling interaction between amine (–NH2) groups on DNA and carboxyl (–COOH) groups on GO. AuNPs co-linked with bio-bar code DNA and target DNA via Au-S bonds were utilized as DNA-Au bio-bar codes, which labeled with HRP through avidin/biotin interaction. In the presence of object Hg2+, the target DNA on HRP-labeled DNA-Au bio-bar codes (HRP-DNA-Au bio-bar codes) hybridized with substrate DNA on GO − COOH via thymine-Hg2+-thymine (T-Hg2+-T) coordination chemistry. HRP-DNA-Au bio-bar codes catalyze hydroquinone oxidation to benzoquinone in presence of by hydrogen peroxide, generating an enhanced amperometric response signal. The current signal of biosensor is proportional to the logarithm of Hg2+ concentrations ranging from 25 pM to 10 μM with a detection limit of 10 pM (S/N = 3). Furthermore, without the need for target amplification, the prepared electrochemical DNA biosensor exhibited superior selectivity against other interfering metal ions, providing a facile and sensitive platform for Hg2+ detection in real environmental samples.

Initiation of molecular testing of endometrial carcinomas in a population-based setting: practical considerations and pitfalls.

Since the publication of The Cancer Genome Atlas (TCGA) molecular Classification of endometrial carcinomas in 2013, multiple studies have demonstrated the prognostic and therapeutic importance of this. However, there is great variability on whether and how this is undertaken in different institutions, and this is often dependent on resources and availability of molecular testing. Points of controversy include whether molecular classification is needed on all endometrial carcinomas and whether pure molecular testing is undertaken or a surrogate such as the ProMisE (Proactive Molecular Risk Classifier for Endometrial Cancer) Classifier. Herein we report our experience instigating molecular classification of endometrial carcinomas in Northern Ireland. From 1st March 2023, all endometrial carcinomas diagnosed on biopsy in the four pathology laboratories in Northern Ireland were referred to the central molecular pathology laboratory for genomic analysis using a custom next-generation sequencing (NGS) panel; the NGS panel included the entire coding regions of polymerase epsilon (POLE) and TP53 genes, as well as microsatellite instability (MSI) analysis. All cases also underwent immunohistochemical staining with oestrogen receptor (ER), p53, and the mismatch repair (MMR) proteins MLH1, PMS2, MSH2, and MSH6. The molecular results were available by the time of surgery (if a hysterectomy was performed) allowing integration into the final pathology report where a TCGA molecular type was assigned. Two hundred and sixty-seven endometrial carcinomas underwent molecular testing; in five cases, there was insufficient material for testing, leaving 262 cases. The TCGA groups were POLEmut (19; 7.3%), MMRd (63; 24%), p53abn (62; 23.7%), and no specific molecular profile (NSMP) 118 (45%). Seventeen tumours (6.5%) were "multiple-classifiers": five POLEmut-p53abn, two POLEmut-MMRd, one POLE-MMRd-p53abn (all included in the POLEmut TCGA group), and nine MMRd-p53abn (included in the MMRd group). This represents one of the first population-based studies investigating the prevalence of the different TCGA molecular groups of endometrial carcinomas in an unselected population. Performing molecular testing on biopsies enables management to be tailored to the molecular group and allows integration of the TCGA group into the report of the final resection specimen. We hope our experience will facilitate other laboratories in undertaking TCGA molecular classification.

ANN-based chaotic PRNG in the novel jerk chaotic system and its application for the image encryption via 2-D Hilbert curve

In this paper, we introduce a category of Novel Jerk Chaotic (NJC) oscillators featuring symmetrical attractors. The proposed jerk chaotic system has three equilibrium points. We show that these equilibrium points are saddle-foci points and unstable. We have used traditional methods such as bifurcation diagrams, phase portraits, and Lyapunov exponents to analyze the dynamic properties of the proposed novel jerk chaotic system. Moreover, simulation results using Multisim, based on an appropriate electronic implementation, align with the theoretical investigations. Additionally, the NJC system is solved numerically using the Dormand Prince algorithm. Subsequently, the Jerk Chaotic System is modeled using a multilayer Feed-Forward Neural Network (FFNN), leveraging its nonlinear mapping capability. This involved utilizing 20,000 values of x1, x2, and x3 for training (70%), validation (15%), and testing (15%) processes, with the target values being their iterative values. Various network structures were experimented with, and the most suitable structure was identified. Lastly, a chaos-based image encryption algorithm is introduced, incorporating scrambling technique derived from a dynamic DNA coding and an improved Hilbert curve. Experimental simulations confirm the algorithm’s efficacy in enduring numerous attacks, guaranteeing strong resiliency and robustness.

Complete genome sequence of "Candidatus Dehalogenimonas loeffleri" strain W, a highly salt-tolerant chlorinated alkane-dechlorinating bacterium isolated from estuarine sediments.

"Candidatus Dehalogenimonas loeffleri" strain W, isolated from estuarine sediments, can dechlorinate 1,2-dichloroethane under high salinity. Its genome consists of a circular 1,772,240-bp chromosome with a G + C content of 52.5% and encompasses 1,763 protein-coding sequences, including 28 genes encoding reductive dehalogenases.

Genome assembly of wisent (Bison bonasus) uncovers a deletion that likely inactivates the THRSP gene

The wisent (Bison bonasus) is Europe’s largest land mammal. We produced a HiFi read-based wisent assembly with a contig N50 value of 91 Mb containing 99.7% of the highly conserved single copy mammalian genes which improves contiguity a thousand-fold over an existing assembly. Extended runs of homozygosity in the wisent genome compromised the separation of the HiFi reads into parental-specific read sets, which resulted in inferior haplotype assemblies. A bovine super-pangenome built with assemblies from wisent, bison, gaur, yak, taurine and indicine cattle identified a 1580 bp deletion removing the protein-coding sequence of THRSP encoding thyroid hormone-responsive protein from the wisent and bison genomes. Analysis of 725 sequenced samples across the Bovinae subfamily showed that the deletion is fixed in both Bison species but absent in Bos and Bubalus. The THRSP transcript is abundant in adipose, fat, liver, muscle, and mammary gland tissue of Bos and Bubalus, but absent in bison. This indicates that the deletion likely inactivates THRSP in bison. We show that super-pangenomes can reveal potentially trait-associated variation across phylogenies, but also demonstrate that haplotype assemblies from species that went through population bottlenecks warrant scrutiny, as they may have accumulated long runs of homozygosity that complicate phasing.

Evaluation of Heterogeneity in the Coding Region of BRAF, MAP2K1, and MAP2K2 Genes in Primary and Metastatic Melanomas.

The incidence of melanoma has been increasing in recent decades. BRAF mutations appear in 50%-70% of melanomas. The BRAF-targeted therapy increased the disease-free survival of patients with metastatic melanoma, but this response may be short, due to several resistance mechanisms, such as the presence of other subclones with mutations. Evaluation of mutations and heterogeneity in the coding region of the BRAF, MAP2K1, and MAP2K2 genes in primary and metastatic melanomas. Twenty-seven samples of primary and metastatic superficial spreading melanoma (SSM) and acral lentiginous melanoma (ALM) were analyzed for BRAF, MAP2K1, and MAP2K2 mutations using the next-generation sequencing technique. In ALM, the mutation rate found was 50% in the BRAF and MAP2K1 genes and 28.6% in MAP2K2. In the SSM, BRAF was mutated in 76.9%, MAP2K1 in 30.8%, and MAP2K2 in 23.2% of the cases. All samples were formed by distinct tumor subclones in the same lesion. Intertumoral heterogeneity was present between primary and metastatic lesions of ALM in BRAF, MAP2K1, and MAP2K2; the cases of SSM were heterogeneous for BRAF and MAP2K1. We sought to evaluate the mutations in the BRAF, MAP2K1, and MAP2K2 genes, revealing a heterogeneous mutation profile in samples of ALM and SSM.

Transcriptomic analysis of codon usage patterns and gene expression characteristics in leafy spurge

Leafy spurge (Euphorbia esula) is an important herb and potential energy source with medicinal value. Codon usage bias (CUB) is a static feature of genes and genomes that results from adaptation and selection during long-term evolution and facilitates molecular breeding in transgenic plants. Here, we used TransDecoder to identify candidate coding regions from the downloaded leafy spurge transcriptome and generate coding region annotation files based on reference genomes. The whole genome showed A/T bias, especially at terminal positions, and seven high-frequency codons were identified. We compared codon usage frequencies to identify candidate exogenous expression receptor systems for leafy spurge. The identified factors affecting leafy spurge CUB included natural selection and other factors, mutation pressure and base composition, with natural selection and other factors being dominant. The observed CUB was significantly positively correlated with the gene expression levels. Systematic analysis of whole-genome leafy spurge revealed that highly expressed protein-coding genes presented greater CUB than did less expressed protein-coding genes. Furthermore, the highly expressed genes tended to have terminal G/C bases. In summary, we conducted a series of related studies based on the leafy spurge whole-genome sequence and laid a foundation for selecting suitable exogenous expression receptor systems and improving gene expression levels.

Identification of qTGW2, a Minor-Effect QTL Controlling Grain Weight in Rice

Grain weight and grain shape are key traits affecting grain yield and quality in rice. In this research, a quantitative trait locus (QTL), qTGW2, that controls 1000-grain weight (TGW), grain length (GL), and grain width (GW) in rice, was fine-mapped within an 84.7 kb region on chromosome 2 using three sets of near isogenic lines (NILs) originated from the indica rice cross, Teqing (TQ)/IRBB52. In the NIL populations, the TGW, GL, and GW of the IRBB52 homozygous lines increased by 0.22 g, 0.020 mm, and 0.009 mm compared with the TQ homozygous lines. Four annotated genes showed nucleotide polymorphisms between the two parental lines in the qTGW2 region. Only one annotated gene, LOC_Os02g57660, exhibited significant expression differences between NILTQ and NILIRBB52 in the young panicles performed by RNA sequencing and the quantitative real-time polymerase chain reaction. These results indicated that LOC_Os02g57660, which encodes phosphatidylinositol-4-phosphate 5-kinase (PIP5K), was the candidate gene of qTGW2. Then, one insertion-deletion (InDel) was found in the LOC_Os02g57660 coding region. The haplotype analysis was performed based on the phenotypic data of 4720 rice accessions from RiceVarMap V2.0. Two haplotypes, Hap1 (TQ-type) and Hap2 (IRBB52-type), were classified according to one InDel. Significant differences in grain weight traits were identified between Hap1 and Hap2. Hap2 has greater GL and RLW but lower GW, thus exhibiting potential to simultaneously improve grain yield and quality.

JC virus small tumor antigen promotes S phase entry and cell cycle progression

The early coding region of JC virus (JCV) encodes several regulatory proteins including large T antigen (LT-Ag), small t antigen (Sm t-Ag) and T’ proteins because of the alternative splicing of the pre-mRNA. LT-Ag plays a critical role in cell transformation by targeting the key cell cycle regulatory proteins including p53 and pRb, however, the role of Sm t-Ag in this process remains elusive. Here, we investigated the effect of Sm t-Ag on the cell cycle progression and demonstrated that it facilitates S phase entry and exit when cells are released from G0/G1 growth arrest. Examination of the cell cycle stage specific expression profiles of the selected cyclins and cyclin-dependent kinases, including those active at the G1/S and G2/M transition state, demonstrated a higher level of early expression of these regulators such as cyclin B, cycling E, and Cdk2. In addition, analysis of the effect of Sm t-Ag on the growth promoting pathways including those active in the PI3K/Akt/mTOR axis showed substantially higher levels of the phosphorylated-Akt, -Gsk3-β and -S6K1 in Sm t-Ag-positive cells. Collectively, our results demonstrate that Sm t-Ag promotes cell cycle progression by activating the growth promoting pathways through which it may contribute to LT-Ag-mediated cell transformation.

Long-read DNA sequencing reveals the organization of the mitochondrial genome in the early-branching dinoflagellate Oxyrrhis marina.

The mitochondrial genomes of dinoflagellate protists are remarkable for their highly fragmented and heterogeneous organization. Early attempts to determine their structure without ‘next-generation’ DNA sequencing failed to recover a defined genome. Still, it coincided in showing that the proteins coding genes, three in total, and parts of the ribosomal RNA genes were spread across a diffuse assortment of small linear fragments. In contrast, a recent study employed Illumina sequencing to assemble a 326 kbp long single-molecule, circular mitochondrial genome in the symbiotic dinoflagellate Breviolum minutum. Here, we used a combination of short- and long-read massively-parallel DNA sequencing to analyze further the mitochondrial DNA of the early-branching dinoflagellate Oxyrrhis marina. We found that the mitochondrial genome of O. marina consists of 3 linear chromosomes sized 15.9, 33.8 and 40.6 kbp for a total of 90.3 kbp. It contains the cox1, cox3 and cob genes, the same three proteins encoded in the mitochondrion of all myzozoans (Apicomplexa and Dinophyceae), some fragments of ribosomal RNA genes as well as many non-functional gene fragments and extensive noncoding DNA. Our analysis unveiled segments syntenic patterns and rearrangements encompassing coding and non-coding regions, suggesting that recombination is a pervasive process driving the evolution of these genomes.