Intron Research Articles

RNA-First Approach Identifies Deep Intronic PHEX Variants in X-Linked Hypophosphatemic Rickets.

Up to 20% of patients with X-linked hypophosphatemic rickets (XLH) have no causative variant identified on routine molecular diagnostic testing. To identify intronic variants causing PHEX mis-splicing in patients with XLH. The metabolic bone clinic of a paediatric orthopedic hospital. Four patients (age 6 to 12 years; 3 girls) with clinically diagnosed XLH and no PHEX variant on routine testing. RNA and DNA sequence analysis of PHEX. Urine-derived cells were cultured, and mRNA was extracted and transcribed to cDNA. PHEX cDNA was amplified by PCR, followed by sequencing of PCR products. Sequencing of PHEX intronic DNA regions was performed to identify variants causing mis-splicing observed on RNA analysis. PHEX mis-splicing was identified in 3 of the 4 participants, and an intronic variant was identified in all 3 cases. In a 12-year-old boy, transcript analysis showed skipping of PHEX exon 13, while sequencing of PHEX intronic regions revealed a de novo 18 bp deletion in intron 13. In a 7-year-old girl, a pseudoexon in PHEX intron 17 was found, associated with a de novo deep intronic variant (c.1768+173A>G) that activated a cryptic splice donor site. Finally, an 84 bp pseudoexon in PHEX intron 21 caused by a recurrent de novo deep intronic variant (c.2147+1197A>G) was identified in an 11-year-old girl. Analysis of RNA from urine-derived cells combined with sequencing of PHEX introns can identify deep intronic variants in individuals with XLH without a detectable PHEX variant in routine exon-centric molecular diagnosis.

Population-wide DNA methylation polymorphisms at single-nucleotide resolution in 207 cotton accessions reveal epigenomic contributions to complex traits.

DNA methylation plays multiple regulatory roles in crop development. However, the relationships of methylation polymorphisms with genetic polymorphisms, gene expression, and phenotypic variation in natural crop populations remain largely unknown. Here, we surveyed high-quality methylomes, transcriptomes, and genomes obtained from the 20-days-post-anthesis (DPA) cotton fibers of 207 accessions and extended the classical framework of population genetics to epigenetics. Over 287 million single methylation polymorphisms (SMPs) were identified, 100 times more than the number of single nucleotide polymorphisms (SNPs). These SMPs were significantly enriched in intragenic regions while depleted in transposable elements. Association analysis further identified a total of 5,426,782 cis-methylation quantitative trait loci (cis-meQTLs), 5078 cis-expression quantitative trait methylation (cis-eQTMs), and 9157 expression quantitative trait loci (eQTLs). Notably, 36.39% of cis-eQTM genes were not associated with genetic variation, indicating that a large number of SMPs associated with gene expression variation are independent of SNPs. In addition, out of the 1715 epigenetic loci associated with yield and fiber quality traits, only 36 (2.10%) were shared with genome-wide association study (GWAS) loci. The construction of multi-omics regulatory networks revealed 43 cis-eQTM genes potentially involved in fiber development, which cannot be identified by GWAS alone. Among these genes, the role of one encoding CBL-interacting protein kinase 10 in fiber length regulation was successfully validated through gene editing. Taken together, our findings prove that DNA methylation data can serve as an additional resource for breeding purposes and can offer opportunities to enhance and expedite the crop improvement process.

Mapping the epigenomic landscape of post-traumatic stress disorder in human cortical neurons.

The study conducted a comprehensive genome-wide analysis of differential 5mC and 5hmC modifications at both CpG and non-CpG sites in postmortem orbitofrontal neurons from 25 PTSD cases and 13 healthy controls. It was observed that PTSD patients exhibit a greater number of differential 5hmC sites compared to 5mC sites. Specifically, individuals with PTSD tend to show hyper-5mC/5hmC at CpG sites, particularly within CpG islands and promoter regions, and hypo-5mC/5hmC at non-CpG sites, especially within intragenic regions. Functional enrichment analysis indicated distinct yet interconnected roles for 5mC and 5hmC in PTSD. The 5mC marks primarily regulate cell-cell adhesion processes, whereas 5hmC marks are involved in embryonic morphogenesis and cell fate commitment. By integrating published PTSD findings from central and peripheral tissues through multi-omics approaches, several biological mechanisms were prioritized, including developmental processes, HPA axis regulation, and immune responses. Based on the consistent enrichment in developmental processes, we hypothesize that if epigenetic changes occur during early developmental stages, they may increase the risk of developing PTSD following trauma exposure. Conversely, if these epigenetic changes occur in adulthood, they may influence neuronal apoptosis and survival mechanisms.

G-quadruplex forming regions in GCK and TM6SF2 are targets for differential DNA methylation in metabolic disease and hepatocellular carcinoma patients

The alarming increase in global rates of metabolic diseases (MetDs) and their association with cancer risk renders them a considerable burden on our society. The interplay of environmental and genetic factors in causing MetDs may be reflected in DNA methylation patterns, particularly at non-canonical (non-B) DNA structures, such as G-quadruplexes (G4s) or R-loops. To gain insight into the mechanisms of MetD progression, we focused on DNA methylation and functional analyses on intragenic regions of two MetD risk genes, the glucokinase (GCK) exon 7 and the transmembrane 6 superfamily 2 (TM6SF2) intron 2-exon 3 boundary, which harbor non-B DNA motifs for G4s and R-loops.Pyrosequencing of 148 blood samples from a nested cohort study revealed significant differential methylation in GCK and TM6SF2 in MetD patients versus healthy controls. Furthermore, these regions harbor hypervariable and differentially methylated CpGs also in hepatocellular carcinoma versus normal tissue samples from The Cancer Genome Atlas (TCGA). Permanganate/S1 nuclease footprinting with direct adapter ligation (PDAL-Seq), native polyacrylamide DNA gel electrophoresis and circular dichroism (CD) spectroscopy revealed the formation of G4 structures in these regions and demonstrated that their topology and stability is affected by DNA methylation. Detailed analyses including histone marks, chromatin conformation capture data, and luciferase reporter assays, highlighted the cell-type specific regulatory function of the target regions. Based on our analyses, we hypothesize that changes in DNA methylation lead to topological changes, especially in GCK exon 7, and cause the activation of alternative regulatory elements or potentially play a role in alternative splicing.Our analyses provide a new view on the mechanisms underlying the progression of MetDs and their link to hepatocellular carcinomas, unveiling non-B DNA structures as important key players already in early disease stages.

Development of DNA Insertion-specific Markers Based on the Intron Region of Oplegnathus punctatus itih4b for Genetic Sex Identification.

Spotted knifejaw (Oplegnathus punctatus) is a significant marine fish species that exhibits pronounced sexual dimorphism, with males generally exhibiting greater weight and growth rates than females. Therefore, the farming of O. punctatus with a high proportion of males is beneficial for improving the quality and efficiency of the O. punctatus aquaculture industry. Furthermore, the development of a rapid technique in sexing O. punctatus fry will facilitate the selection and breeding of superior male varieties of O. punctatus. In this study, genome-wide scanning, comparative genomics, and structural variation analysis methods were employed to identify and extract the homologous region of the inter-alpha-trypsin inhibitor heavy chain 4 (itih4b) gene on the X and Y chromosomes from the complete genome sequence of O. punctatus. This analysis revealed the presence of a large segment of DNA insertion markers on the Y chromosome in the region. Itih4b plays an important role in the mechanisms that regulate inflammatory and immune responses in multicellular organisms. The method described here involved the design of a pair of primers to amplify two bands of 532bp and 333bp in males (individuals with DNA insertion variants in the intron of the itih4b gene). In females (individuals without DNA insertion), only one band of 333bp could be distinguished by agarose gel electrophoresis. This method shortened the time required to accurately characterize intronic DNA insertion variants and genetic sexes in O. punctatus, thereby improving detection efficiency. This study has significant value for the large-scale breeding of O. punctatus all-male seedlings and provides a reference point for the study of intron variation regulation and RNA shearing in the itih4b gene.

R2R3-MYB transcription factor CsMYB60 controls mature fruit skin color by regulating flavonoid accumulation in cucumber.

Skin color is an important trait that determines the cosmetic appearance and quality of fruits. In cucumber, the skin color ranges from white to brown in mature fruits. However, the genetic basis for this important trait remains unclear. We conducted a genome-wide association study of natural cucumber populations, along with map-based cloning techniques, on an F2 population resulting from a cross between Pepino (with yellow-brown fruit skin) and Zaoer-N (with creamy fruit skin). We identified CsMYB60 as a candidate gene responsible for skin coloration in mature cucumber fruits. In cucumber accessions with white to pale yellow skin color, a premature stop mutation (C to T) was found in the second exon region of CsMYB60, whereas light yellow cucumber accessions exhibited splicing premature termination caused by an intronic mutator-like element insertion in CsMYB60. Transgenic CsMYB60c cucumber plants displayed a yellow-brown skin color by promoting accumulation of flavonoids, especially hyperoside, a yellow-colored flavonol. CsMYB60c encodes a nuclear protein that primarily acts as a transcriptional activator through its C-terminal activation motif. RNA sequencing and DNA affinity purification sequencing assays revealed that CsMYB60c promotes skin coloration by directly binding to the YYTACCTAMYT motif in the promoter regions of flavonoid biosynthetic genes, including CsF3'H, which encodes flavonoid 3'-hydroxylase. The findings of our study not only offer insight into the function of CsMYB60 as dominantly controlling fruit coloration, but also highlight that intronic DNA mutations can have a similar phenotypic impact as exonic mutations, which may be valuable in future cucumber breeding programs.

Histone proteoform analysis reveals epigenetic changes in adult mouse brown adipose tissue in response to cold stress

BackgroundRegulation of the thermogenic response by brown adipose tissue (BAT) is an important component of energy homeostasis with implications for the treatment of obesity and diabetes. Our preliminary analyses of RNA-Seq data uncovered many nodes representing epigenetic modifiers that are altered in BAT in response to chronic thermogenic activation. Thus, we hypothesized that chronic thermogenic activation broadly alters epigenetic modifications of DNA and histones in BAT.ResultsMotivated to understand how BAT function is regulated epigenetically, we developed a novel method for the first-ever unbiased top-down proteomic quantitation of histone modifications in BAT and validated our results with a multi-omic approach. To test our hypothesis, wildtype male C57BL/6J mice were housed under chronic conditions of thermoneutral temperature (TN, 28°C), mild cold/room temperature (RT, 22°C), or severe cold (SC, 8°C) and BAT was analyzed for DNA methylation and histone modifications. Methylation of promoters and intragenic regions in genomic DNA decrease in response to chronic cold exposure. Integration of DNA methylation and RNA expression datasets suggest a role for epigenetic modification of DNA in regulation of gene expression in response to cold. In response to cold housing, we observe increased bulk acetylation of histones H3.2 and H4, increased histone H3.2 proteoforms with di- and trimethylation of lysine 9 (K9me2 and K9me3), and increased histone H4 proteoforms with acetylation of lysine 16 (K16ac) in BAT.ConclusionsOur results reveal global epigenetically-regulated transcriptional “on” and “off” signals in murine BAT in response to varying degrees of chronic cold stimuli and establish a novel methodology to quantitatively study histones in BAT, allowing for direct comparisons to decipher mechanistic changes during the thermogenic response. Additionally, we make histone PTM and proteoform quantitation, RNA splicing, RRBS, and transcriptional footprint datasets available as a resource for future research.

Andean uplift, climatic events, and rainforest bridges determined the spatiotemporal evolution of the cumaru and tonka beans (Dipterygeae: Leguminosae)

Abstract Historical climatic and geological events are largely known to have impacted biome evolution across the Neotropics and their associated rich biodiversity. However, a clear understanding of dispersal and biome shifts between neotropical biomes over time is still lacking for many ecologically important plant clades. We investigated the timing and ancestral species movements within the early branching papilionoid legume Dipterygeae lineage of neotropical tree species, some of which are among the most ecologically dominant across Amazonian rainforests and Brazilian savannas, to understand how dispersal and evolutionary trajectories in biome predilection have led to their modern distribution. We also estimated the evolution of fruit types and discuss their potential roles in the colonization of non-Amazonian rainforest habitats. To address these questions, we used one nuclear (ITS/5.8S) and two plastid (matK and trnL intron) DNA regions of the Dipterygeae clade to estimate divergence times with a Bayesian relaxed-clock approach, ancestral area distribution, and evolutionary shifts in biome and morphological traits. All currently recognized species of this clade were sampled, covering its full geographical range. Dipterygeae originated in the Amazonia during the Middle Eocene, where it has undergone a long history of in situ diversification, particularly over the last 15 Myr. Dispersal events into the rainforests of the Brazilian Coastal Atlantic Forest and Chocó + Central America, the fire-prone savannas of the Cerrado, and the Caatinga seasonally dry tropical forest occurred independently. Most lineages ecologically associated with rainforests are dispersed by animals (zoochory), whereas shifts to open habitats generally coincide with wind dispersal (anemochory). Our study highlights the significance of geological events, climatic factors, and shifts in fruit type as crucial contributors to the diversification of Dipterygeae.

Transcription and splicing variations of SR genes accompany with genome-wide accumulation of long-introns in pine

Most of mRNAs in Eukaryote were matured after the removal of introns in their pre-mRNA transcripts. Serine/arginine-rich (SR) proteins are a group of splicing regulators regulating the splicing processes globally. Expressions of SR proteins themselves were extensively regulated, at both transcription and splicing levels, under different environmental conditions, specially heat stress conditions. The pine genome is characterized by super-long and easily methylated introns in a large number of genes that derived from the extensive accumulation of transposons (TEs). Here, we identified and analyzed the phylogenetic characteristics of 24 SR proteins and their encoding genes from the pine genome. Then we explored transcription and pre-mRNA splicing expression patterns of SR genes in P. massoniana seedlings under normal and heat stress temperature conditions. Our results showed that the transcription patterns of SR genes in pine exhibited significant changes compared to other plant species, and these changes were not strictly correlated with the intron length and DNA methylation intensity of the SR genes. Interestingly, none of the long introns of SR genes underwent alternative splicing (AS) in our experiment. Furthermore, the intensity of AS regulation may be related to the potential DNA methylation intensity of SR genes. Taken together, this study explores for the first time the characteristics of significant variations in the transcription and splicing patterns of SR proteins in a plant species with an over-accumulation of super-long introns.

Juveniles, young adults, and infants with hepatitis B virus infection: A genomic study.

Integration of hepatitis B virus (HBV) DNA into the human genome is recognized as an oncogenic factor and a barrier to hepatitis B cure. In the study, biopsy liver tissues were collected from adolescents and young adults with acute HBV infection younger than or equal to 35 years of age and from HBV-infected infant patients younger than or equal to 6 months of age. A high-throughput sequencing method was used to detect HBV DNA integration. Totally, 12 adolescents, young adults, and 6 infants were included. Among the 12 patients with acute HBV infection, immunohistochemical staining of intrahepatic hepatitis B surface antigen for all displayed negative results, and no HBV DNA integrants in the hepatocyte DNA were confirmed. All infant patients had elevated levels of alanine aminotransferase and high levels of serum HBV DNA. Numerous gene sites of hepatocyte DNA were integrated by HBV DNA for each infant patient, ranging from 120 to 430 integration sites. The fragile histidine triad gene was the high-frequency integrated site in the intragenic region for infant patients. In conclusion, hepatocyte DNA is integrated by HBV DNA in babies with active hepatitis B but seems seldom affected among adolescents and young adults with acute HBV infection. Infantile hepatitis B should be taken seriously considering abundant HBV DNA integration events.

Multi-locus genome-wide association study reveal genomic regions underlying root system architecture traits in Ethiopian sorghum germplasm.

The identification of genomic regions underlying the root system architecture (RSA) is vital for improving crop abiotic stress tolerance. To improve sorghum (Sorghum bicolor L. Moench) for environmental stress tolerance, information on genetic variability and genomic regions linked to RSA traits is paramount. The aim of this study was, therefore, to investigate common quantitative trait nucleotides (QTNs) via multiple methodologies and identify genomic regions linked to RSA traits in a panel of 274 Ethiopian sorghum accessions. Multi-locus genome-wide association study was conducted using 265,944 high-quality single nucleotide polymorphism markers. Considering the QTN detected by at least three different methods, a total of 17 reliable QTNs were found to be significantly associated with root angle, number, length, and dry weight. Four QTNs were detected on chromosome SBI-05, followed by SBI-01 and SBI-02 with three QTNs each. Among the 17 QTNs, 11 are colocated with previously identified root traits quantitative trait loci and the remaining six are genome regions with novel genes. A total of 118 genes are colocated with these up- and down-streams of the QTNs. Moreover, five QTNs were found intragenic. These QTNs are S5_8994835 (number of nodal roots), S10_55702393 (number of nodal roots), S1_56872999 (nodal root angle), S9_1212069 (nodal root angle), and S5_5667192 (root dry weight) intragenic regions of Sobic.005G073101, Sobic.010G198000, Sobic.001G273000, Sobic.009G013600, and Sobic.005G054700, respectively. Particularly, Sobic.005G073101, Sobic.010G198000, and Sobic.009G013600 were found responsible for the plant growth hormone-induced RSA. These genes may regulate root development in the seedling stage. Further analysis on these genes might be important to explore the genetic structure of RSA of sorghum.

Common mutation analysis of beta-thalassemia carriers by amplification refractory mutation system-polymerase chain reaction in cases diagnosed by capillary zone electrophoresis at National Public Health Laboratory, Nepal

Abstract BACKGROUND: Beta (β)-thalassemia is a globally prevalent genetic disorder with over 350 known mutations in the β-globin gene. Intervening-sequence (IVS) 1–5 (G→C), 619 bp deletion, IVS 1–1 (G →T), C-15 (G→A), frameshift (FS) 41/42 (−CTTT), FS 8/9 (+G), codon 19, A-G, and codon 17 (A→T) are some common mutations in β-thalassemia. This study aimed to identify and analyze the common mutation by amplification refractory mutation system polymerase chain reaction in β-thalassemia carriers diagnosed by capillary zone electrophoresis (CZE) at National Public Health Laboratory. MATERIALS AND METHODS: On the basis of archived data, the CZE performed on 781 samples between June 2019 and July 2022 was analyzed. Without regard to age, gender, race, or address, 121 samples were ultimately selected for mutation analysis during this time because they were identified as positive for the β-thalassemia traits based on high HbA2 levels of more than 3.5%. RESULTS: IVS 1–5 (G→C) was the most common mutation followed by 619 bp deletion. Five mutations namely IVS 1–5 (G→C), 619 bp deletion, FS 41/42 (−TTCT), FS 8/9 (+G), and codon 15 (G→A) accounted for 84.3% of cases. A single mutation was seen in 87 cases (71.9%), more than one mutation in 15 cases (12.4%) whereas 19 cases (15.7%) did not show any of the mutations tested. CONCLUSION: IVS 1–5 (G-C) is the most prevalent mutation in Southeast Asian nations, with the 619 bp deletion predominant in the Tharu community. Further research is needed to understand diverse ethnic groups and regions, enabling prenatal diagnostics and genetic counseling for β-thalassemia prevention.

Intragenic Agrobacterium-mediated gene transfer mimics micro-translocations without foreign DNA

Main conclusionAgrobacterium-mediated transformation of Nicotiana tabacum, using an intragenic T-DNA region derived entirely from the N. tabacum genome, results in the equivalence of micro-translocations within genomes.Intragenic Agrobacterium-mediated gene transfer was achieved in Nicotiana tabacum using a T-DNA composed entirely of N. tabacum DNA, including T-DNA borders and the acetohydroxyacid synthase gene conferring resistance to sulfonylurea herbicides. Genomic analysis of a resulting plant, with single locus inheritance of herbicide resistance, identified a single insertion of the intragenic T-DNA on chromosome 5. The insertion event was composed of three N. tabacum DNA fragments from other chromosomes, as assembled on the T-DNA vector. This validates that intragenic transformation of plants can mimic micro-translocations within genomes, with the absence of foreign DNA.

Drug resistance markers in Plasmodium vivax isolates from a Kanchanaburi province, Thailand between January to May 2023.

Plasmodium vivax has become the predominant species in the border regions of Thailand. The emergence and spread of antimalarial drug resistance in P. vivax is one of the significant challenges for malaria control. Continuous surveillance of drug resistance is therefore necessary for monitoring the development of drug resistance in the region. This study aims to investigate the prevalence of the mutation in the P. vivax multidrug resistant 1 (Pvmdr1), dihydrofolate reductase (Pvdhfr), and dihydropteroate synthetase (Pvdhps) genes conferred resistance to chloroquine (CQ), pyrimethamine (P) and sulfadoxine (S), respectively. 100 P. vivax isolates were obtained between January to May 2023 from a Kanchanaburi province, western Thailand. Nucleotide sequences of Pvmdr1, Pvdhfr, and Pvdhps genes were amplified and sequenced. The frequency of single nucleotide polymorphisms (SNPs)-haplotypes of drug-resistant alleles was assessed. The linkage disequilibrium (LD) tests were also analyzed. In Pvmdr1, T958M, Y976F, and F1076L, mutations were detected in 100%, 21%, and 23% of the isolates, respectively. In Pvdhfr, the quadruple mutant allele (I57R58M61T117) prevailed in 84% of the samples, followed by (L57R58M61T117) in 11%. For Pvdhps, the double mutant allele (G383G553) was detected (48%), followed by the triple mutant allele (G383M512G553) (47%) of the isolates. The most prevalent combination of Pvdhfr (I57R58M61T117) and Pvdhps (G383G553) alleles was sextuple mutated haplotypes (48%). For LD analysis, the association in the SNPs pairs was found between the intragenic and intergenic regions of the Pvdhfr and Pvdhps genes. The study has recently updated the high prevalence of three gene mutations associated with CQ and SP resistance. Genetic monitoring is therefore important to intensify in the regions to further assess the spread of drug resistant. Our data also provide evidence on the distribution of drug resistance for the early warning system, thereby threatening P. vivax malaria treatment policy decisions at the national level.

Brain methylome remodeling selectively regulates neuronal activity genes linking to emotional behaviors in mice exposed to maternal immune activation

How early life experience is translated into storable epigenetic information leading to behavioral changes remains poorly understood. Here we found that Zika virus (ZIKV) induced-maternal immune activation (MIA) imparts offspring with anxiety- and depression-like behavior. By integrating bulk and single-nucleus RNA sequencing (snRNA-seq) with genome-wide 5hmC (5-hydroxymethylcytosine) profiling and 5mC (5-methylcytosine) profiling in prefrontal cortex (PFC) of ZIKV-affected male offspring mice, we revealed an overall loss of 5hmC and an increase of 5mC levels in intragenic regions, associated with transcriptional changes in neuropsychiatric disorder-related genes. In contrast to their rapid initiation and inactivation in normal conditions, immediate-early genes (IEGs) remain a sustained upregulation with enriched expression in excitatory neurons, which is coupled with increased 5hmC and decreased 5mC levels of IEGs in ZIKV-affected male offspring. Thus, MIA induces maladaptive methylome remodeling in brain and selectively regulates neuronal activity gene methylation linking to emotional behavioral abnormalities in offspring.

Genome-Wide Methylation Sensitive Elements Demarcate Targetable Regulatory Elements for Controllable Gene Activation

There are multiple published studies correlating DNA methylation with gene expression, but to date, most are associative in nature without precise localization of causal elements. Multiple CpG destinations have been described with inconsistent evidence supporting their causal association with transcription. This has hampered adoption and use of methylation signatures as biomarkers or for targeted therapies. This has had consequent effects in hindering mechanistic understanding in how global demethylation agents lead to responses in some patients, but not others. With this state of the literature in mind, we set out to better understand and locate causal methylation regulatory loci genome-wide. We hypothesized that causal methylation regulatory elements possess heightened sensitivity to regulatory signals such as “demethylate”; signals that can be introduced using hypo-methylating agents (HMAs) typically used in treatment of Myelodysplastic syndromes and Acute Myeloid Leukemia. We thus analyzed 19 whole-genomic bisulfite sequenced sample pairs (pre/post-demethylation in patients, cell lines, and in murine in vivo samples) and identified previously undescribed DNA methylation sensitive elements throughout the genome, which we call Methylation Mesas (MMs) based on the profile shape observed in naïve and post-HMA treated sample. These narrow-width MMs range typically between 45-300bp wide and are present throughout the genome with greater abundance in noncoding and intragenic regions than in promoter-CpG islands. We also demonstrate that MM show an up to 90% concordant overlap with primed and active histone marks by means of a compiled histone mark footprint map using 60 human and 59 murine ENCODE datasets for each respective species, suggesting a functional role for MMs as regulatory elements with transcriptional potential. While HMA's enable identification of MM's genome-wide, their mode of action renders them unsuitable for ascertaining the direct transcriptional potential of any singular locus. Therefore, in order to ascertain the causal role of MM for transcriptional regulation, we developed a fine-resolution targeted demethylation technology(CRISPR-DiR), leveraging our previously published findings that DNA methyltransferase I (DNMT1) can be blocked by DNMT1-interacting RNAs (DiR). Compared with other targeted demethylation technologies with wider effect windows (eg. CRISPR-TET1), CRISPR-DiR shows superior locus specificity thus serving as an ideal tool to identify causal regulatory elements. Using tumor suppressor p16 as an example, we elucidated that demethylation of a single MM in the first exon is sufficient to trigger locus and distal chromatin rewiring events that natively initiate expression to a significantly greater extent than promoter CpG island targeting alone. Similar CRISPR-DiR activation is also observed in four additional, natively silenced tumor suppressor genes, one of which has no annotated CpG island. In summary, we have identified a previously undescribed narrow-width DNA methylation sensitive regulatory element, consistent across all epigenomes investigated, located largely independent of the promoter CpG island dogma, yet initiating gene transcription more potently. Identification of said elements paves the way for future studies to better understand the mechanisms of how mutations in DNA methyltransferases lead to disease, how global hypomethylating agents can lead to a response in diseases such as MDS and AML but can also activate oncogenes, and finally development of targeted therapies.

Metagenomic binning of PacBio HiFi data prior to assembly reveals a complete genome of Cosmopolites sordidus (Germar) (Coleopterea: Curculionidae, Dryophthorinae) the most damaging arthropod pest of bananas and plantains.

PacBio HiFi sequencing was employed in combination with metagenomic binning to produce a high-quality reference genome of Cosmopolites sordidus. We compared k-mer and alignment reference based pre-binning and post-binning approaches to remove contamination. We were also interested to know if the post-binning approach had interspersed bacterial contamination within intragenic regions of Arthropoda binned contigs. Our analyses identified 3,433 genes that were composed with reads identified as of putative bacterial origins. The pre-binning approach yielded a C. sordidus genome of 1.07 Gb genome composed of 3,089 contigs with 98.6% and 97.1% complete and single copy genome and protein BUSCO scores respectively. In this article we demonstrate that in this case the pre-binning approach does not sacrifice assembly quality for more stringent metagenomic filtering. We also determine post-binning allows for increased intragenic contamination increased with increasing coverage, but the frequency of gene contamination increased with lower coverage. Future work should focus on developing reference free pre-binning approaches for HiFi reads produced from eukaryotic based metagenomic samples.

A molecular phylogeny of the early-branching Genistoid lineages of papilionoid legumes reveals a new Amazonian genus segregated from Clathrotropis

Abstract Molecular phylogenetic studies focused on the early-branching papilionoid legumes have revealed many new clades and supported several generic realignments, yet the monophyly of some of the constituent genera has remained unassessed. This is the case for the Amazonian genus Clathrotropis of the tribe Ormosieae. The genus, as traditionally circumscribed, comprises seven species of trees, including some of the most ecologically hyper dominant taxa across the Amazonian terra firme and seasonally flooded forests. Here we employed a Bayesian analysis of densely sampled nuclear ribosomal ITS/5.8S and plastid matK and trnL intron DNA sequences to evaluate the monophyly of Clathrotropis. All individual and concatenated analyses concurred in showing the non-monophyletic nature of Clathrotropis, whose species fall into three distantly related lineages: one, comprised of C. brachypetala, C. brunnea, C. glaucophylla and the ecologically dominant C. macrocarpa, is circumscribed here as the new genus Cabari; the two others, comprising C. paradoxa and the widespread C. nitida, are more closely related to Spirotropis of the tribe Ormosieae. Such phylogeny-based dismemberment of Clathrotropis is further supported by vegetative, floral, fruit, and seed characters. Although the genes analysed in this study have provided phylogenetically informative data supporting the need for a new circumscription of Clathrotropis, we suggest that future phylogenomic studies should seek to better resolve the relationships of the newly described genus Cabari across the phylogenetically recalcitrant early-branching nodes of the Genistoid clade.

Arginine Methylation of BRD4 By CARM1 Regulates Its Function in AML

Acute myeloid leukemia (AML) is generally an aggressive and lethal malignancy characterized by the accumulation of immature myeloid cells in the bone marrow and peripheral blood. We have previously shown the dependence of AML, but not normal hematopoiesis, on the presence of coactivator associated arginine methyltransferase 1 (CARM1), which suggests that targeting CARM1 could be useful in the treatment of AML. In preclinical studies, we and others have shown promising effects of CARM1 inhibitors on the growth of hematologic malignancies 1. In order to unearth a potential mechanism for the strong efficacy of CARM1 inhibition or knockdown (KD) in the AML1-ETO (AE+) driven AML mouse model, we employed the BioID system in an AE+ human cell line, SKNO-1, to identify novel substrates and interacting partners of CARM1 that could drive the pathogenesis of the disease. We identified over 500 interactors of CARM1, many of which are novel, including one particularly promising therapeutic target, bromodomain-containing protein 4 (BRD4). When examining the mechanism of action of CARM1 inhibitors, we observed significant overlap between the gene expression changes induced by CARM1 inhibition or KD and BRD4 inhibition or KD. Given evidence that both the histone reader, BRD4, and a histone writer, CARM1, play active roles in AML generation, we examined the relationship between these two proteins in AML. We observed a direct physical interaction between these proteins, using immunoprecipitation and two AE+ AML cell lines. Furthermore, using an overexpression system and tagged fragments of BRD4, we identified the particular interacting regions of BRD4 with CARM1. We also identified BRD4 as a substrate of CARM1 and used mass spectrometry to map the sites of CARM1-dependent BRD4 asymmetric dimethylation, implicating four specific arginine residues in the C-terminus of the protein. This crucial information led us to generate antibodies towards these specific CARM1-dependent methylated arginine residues. Using these novel antibodies, we have shown that small molecule inhibition or KD of CARM1 reduces the methylation of BRD4 while also affecting its intracellular localization. In AE+ leukemia cells, exposure to CARM1 inhibitor results in the reduced chromatin localization of BRD4, while in normal CD34+ HSPCs, under the same conditions, we do not see this effect. These findings suggest a selective effect of CARM1 inhibitors for AML therapy, that may not significantly impair normal hematopoiesis. To identify which BRD4-dependent genes are affected by CARM1 inhibition we utilized chromatin-immunoprecipitation and sequencing (ChIP-seq) coupled with RNA-seq and found the loss of BRD4 from promoters and intragenic regions of several oncogenes, together with loss of RNA expression. Given the importance of CARM1 and BRD4 in the development of AML, we are currently investigating the biological and transcriptional activities present in BRD4 mutants that cannot be methylated by CARM1. While methylation of the N-terminus of BRD4 by PRMTs has been reported 2; we have focused our efforts on the C-terminus of the protein, given the re-localization of BRD4 that occurs when CARM1 is inhibited or knocked down. We continue to define the biological effects of a CARM1-BRD4 signaling axis, to assess the importance of this axis in the pathogenesis of oncogene-driven AML. This study also suggests that inhibiting bromodomain containing proteins like BRD4 can be accomplished by targeting the enzymes that post-translationally modify their function. Further insights will be provided by pre-clinical animal and other studies that are ongoing. 1. Greenblatt SM, Man N, Hamard PJ, et al. CARM1 is essential for myeloid leukemogenesis but dispensable for normal hematopoiesis. Cancer Cell. 2019;35(1):156. doi:10.1016/j.ccell.2018.12.008 2. Liu L, Lin B, Yin S, et al. Arginine methylation of BRD4 by PRMT2/4 governs transcription and DNA repair. Sci Adv. 2022;8(49):eadd8928. doi:10.1126/sciadv.add8928

Phylogenetic analysis of the endemic Bornmuellera Hausskn. spp. (Brassicaceae) in Türkiye based on nuclear ITS and chloroplast trnL intron, trnL-F, rbcL and trnQ-rps16 DNA sequences

Phylogenetic analysis of the endemic Bornmuellera Hausskn. spp. (Brassicaceae) in Türkiye based on nuclear ITS and chloroplast trnL intron, trnL-F, rbcL and trnQ-rps16 DNA sequences