Biology subjects

Takahashi, H.

Publications and source records attributed to Takahashi, H..

At least 73 records · Page 4Linked to original sources

bioRxiv2023

Evaluating drought tolerance stability in soybean by theresponse of irrigation change captured from time-seriesmultispectral data

This study investigated a method to evaluate the drought tolerance stability of a genotype in a single environmental trial by capturing the plant response to irrigation changes. Genotypes that exhibit stable phenotypes under various drought stress conditions are required for stable crop production. However, considerable time and money are required to evaluate the environmental stability of a genotype through multiple environmental trials. As an index of drought tolerance stability, we calculated the coefficient of variation (CV) of shoot fresh weight of 178 soybean (Glycine max (L.) Merr.) accessions in a total of nine types of drought treatments, including changing irrigation treatments (every five or ten days) over 3-year trials. To capture the plant responses to irrigation changes, time-series multispectral (MS) data were collected, including the timings of the irrigation/non-irrigation switch in the changing irrigation treatments. We built a random regression model (RRM) for each of the nine treatments using the time-series MS data. We built a genomic prediction model (MTRRM model) using the genetic random regression coefficients of RRM as secondary traits and evaluated the accuracy of each model for predicting CV. In two out of the three years, the prediction accuracy of MTRRM models built in the changing irrigation treatment was higher than that in the continuous drought treatment in the same year. When the CV was predicted using the MTRRM model across years in the changing irrigation treatment, the prediction accuracy was 61% higher than that of the simple genomic prediction model. These results suggest that drought tolerance stability can be evaluated in a single environmental trial, which may reduce the time and cost of selecting genotypes with high drought tolerance stability.

genetics↗

bioRxiv2023

Generalizable neuromarker for autism spectrum disorder across imaging sites and developmental stages: A multi-site study

Autism spectrum disorder (ASD) is a lifelong condition, and its underlying biological mechanisms remain elusive. The complexity of various factors, including inter-site and development-related differences, makes it challenging to develop generalizable neuroimaging-based biomarkers for ASD. This study used a large-scale, multi-site dataset of 730 Japanese adults to develop a generalizable neuromarker for ASD across independent sites (U.S., Belgium, and Japan) and different developmental stages (children and adolescents). Our adult ASD neuromarker achieved successful generalization for the US and Belgium adults (area under the curve [AUC] = 0.70) and Japanese adults (AUC = 0.81). The neuromarker demonstrated significant generalization for children (AUC = 0.66) and adolescents (AUC = 0.71; all P<0.05, family-wise-error corrected). We identified 141 functional connections (FCs) important for discriminating individuals with ASD from TDCs. These FCs largely centered on social brain regions such as the amygdala, hippocampus, dorsomedial and ventromedial prefrontal cortices, and temporal cortices. Finally, we mapped schizophrenia (SCZ) and major depressive disorder (MDD) onto the biological axis defined by the neuromarker and explored the biological continuity of ASD with SCZ and MDD. We observed that SCZ, but not MDD, was located proximate to ASD on the biological dimension defined by the ASD neuromarker. The successful generalization in multifarious datasets and the observed relations of ASD with SCZ on the biological dimensions provide new insights for a deeper understanding of ASD.

neuroscience↗

bioRxiv2023

Functional and long-lived melanocytes from human pluripotent stem cells with transient ectopic expression of JMJD3

BackgroundMelanocytes are an essential part of the epidermis, and their regeneration has received much attention because propagation of human adult melanocytes in vitro is too slow for clinical use. Differentiation from human pluripotent stem cells to melanocytes has been reported, but the protocols to produce them require multiple and complex differentiation steps. MethodWe differentiated human embryonic stem cells (hESCs) that transiently express JMJD3 to pigmented cells. We investigated whether the pigmented cells have melanocytic characteristics and functions by qRT-PCR, immunocytochemical analysis and flow cytometry. We also investigated their biocompatibility by injecting the cells into immunodeficient mice for clinical use. ResultWe successfully differentiated and established a pure culture of melanocytes. The melanocytes maintained their growth rate for a long time, approximately 200 days, and were functional. They exhibited melanogenesis and transfer of melanin to peripheral keratinocytes. Moreover, melanocytes simulated the developmental processes from melanoblasts to melanocytes. The melanocytes had high engraftability and biocompatibility in the immunodeficient mice. ConclusionThe robust generation of functional and long-lived melanocytes are key to developing clinical applications for the treatment of pigmentary skin disorders.

cell biology↗

bioRxiv2023

Raman spectral analysis of microbial pigment compositions in vegetative cells and heterocysts of multicellular cyanobacterium

The one-dimensional multicellular cyanobacterium, Anabaena sp. PCC 7120, exhibits a simple topology consisting of two types of cells under the nitrogen-depleted conditions. Although the differentiated (heterocyst) and undifferentiated cells (vegetative cells) were distinguished by their cellular shapes, we found that their internal states, that is, microbial pigment compositions, were distinguished by using a Raman microscope. Almost of Raman bands of the cellular components were assigned to vibrations of the pigments; chlorophyll a, {beta}-carotene, phycocyanin, and allophycocyanin. We found that the Raman spectral measurement can detect the decomposition of both phycocyanin and allophycocyanin, which are components of the light-harvesting phycobilisome complex in the photosystem II. We observed that the Raman bands of phycocyanin and allophycocyanin exhibited more remarkable decrease in the heterocysts when compared to those of chlorophyll a and {beta}-carotene. This result indicated the prior decomposition of phycobilisome in the heterocysts. Moreover, the Raman bands of allophycocyanin were more decreased in heterocysts when compared to those of phycocyanin, suggesting that the decomposition of phycocyanin was more strongly suppressed than allophycocyanin in heterocysts. We show that the Raman measurement is useful to detect the change of pigment composition in the cell differentiation.

microbiology↗

bioRxiv2023

α-synuclein preformed fibrils bind to β-neurexins and impair β-neurexin-mediated presynaptic organization

Synucleinopathies form a group of neurodegenerative diseases defined by misfolding and aggregation of alpha-synuclein (-syn). Abnormal accumulation and spreading of -syn aggregates lead to synapse dysfunction and neuronal cell death. Yet, little is known about synaptic mechanisms underlying -syn pathology. Here we identified {beta}-isoforms of neurexins ({beta}-NRXs) as presynaptic organizing proteins that interact with -syn preformed fibrils (-syn PFFs), toxic -syn aggregates, but not -syn monomers. Our cell surface protein binding assays and surface plasmon resonance assays reveal that -syn PFFs bind directly to {beta}-NRX through their N-terminal histidine-rich domain (HRD) at nanomolar range (Kd: ~500 nM monomer equivalent). Furthermore, our artificial synapse formation assays show that -syn PFFs diminish excitatory and inhibitory presynaptic organization induced by a specific isoform of neuroligin 1 that binds only {beta}-NRXs, but not -isoforms of neurexins. Thus, our data suggest that -syn PFFs interact with {beta}-NRXs to inhibit {beta}-NRX-mediated presynaptic organization, providing novel molecular insight into how -syn PFFs induce synaptic pathology in synucleinopathies such as Parkinsons disease and dementia with Lewy bodies.

neuroscience↗

bioRxiv2022

Reduced progranulin increases tau and alpha-synuclein inclusions and alters phenotypes of tauopathy mice via glucocerebrosidase

Comorbid proteinopathies are observed in many neurodegenerative disorders including Alzheimers disease (AD), increase with age, and influence clinical outcomes, yet the mechanisms remain ill-defined. Here, we show that reduction of progranulin (PGRN), a lysosomal protein associated with TDP-43 proteinopathy, also increases tau inclusions, causes concomitant accumulation of -synuclein and worsens mortality and disinhibited behaviors in tauopathy mice. The increased inclusions paradoxically protect against spatial memory deficit and hippocampal neurodegeneration. PGRN reduction with tau pathology attenuates activity of {beta}-glucocerebrosidase (GCase), a protein previously associated with synucleinopathy, while increasing glucosylceramide (GlcCer)-positive tau inclusions. In neuronal culture, GCase inhibition enhances tau aggregation induced by AD-tau. Furthermore, purified GlcCer directly promotes tau aggregation in vitro. Neurofibrillary tangles in human tauopathies are also GlcCer-immunoreactive. Thus, in addition to TDP-43, PGRN regulates tau- and synucleinopathies via GCase and GlcCer. A lysosomal PGRN-GCase pathway may be a common therapeutic target for age-related comorbid proteinopathies.

neuroscience↗

bioRxiv2022

Identification of basic helix-loop-helix transcription factors that activate betulinic acid biosynthesis by RNA-sequencing of hydroponically cultured Lotus japonicus

Although triterpenes are ubiquitous in plant kingdom, their biosynthetic regulatory mechanisms are limitedly understood. Here, we found that hydroponic culture dramatically activated betulinic acid (BA) biosynthesis in the model Fabaceae Lotus japonicus, and investigated its transcriptional regulation. Fabaceae plants develop secondary aerenchyma (SA) on the surface of hypocotyls and roots during flooding for root air diffusion. Hydroponic culture induced SA in L. japonicus and simultaneously increased the accumulation of BA and the transcript levels of its biosynthetic genes. RNA-sequencing of soil-grown and hydroponically cultured plant tissues, including SA collected by laser microdissection, revealed that several transcription factor genes were co-upregulated with BA biosynthetic genes. Overexpression of LjbHLH32 and LjbHLH50 in L. japonicus transgenic hairy roots upregulated the expression of BA biosynthesis genes, resulting in enhanced BA accumulation. However, transient luciferase reporter assays in Arabidopsis mesophyll cell protoplasts showed that LjbHLH32 transactivated promoters of biosynthetic genes in the soyasaponin pathway but not the BA pathway, like its homolog GubHLH3, a soyasaponin biosynthesis regulator in Glycyrrhiza uralensis. This suggested the evolutionary origin and complex regulatory mechanisms of BA biosynthesis in Fabaceae. This study sheds light on the unrevealed biosynthetic regulatory mechanisms of triterpenes in Fabaceae plants. HighlightHydroponic culture enhanced betulinic acid synthesis in Lotus japonicus. RNA-sequencing and functional characterization experiments suggest that LjbHLH32 and LjbHLH50 are the transcription factors activating betulinic acid biosynthesis.

plant biology↗

bioRxiv2022

DOTA chelation through click chemistry enables favorable biodistribution of 89Zr-radiolabeled antibodies: A comparison with DFO chelation

Currently, the DFO chelator is commonly used to conjugate monoclonal antibodies (mAbs) and 89Zr, whereas the DOTA chelator is commonly used to conjugate mAbs and alpha- and beta-emitting metal radionuclides. However, if the degradation of [89Zr]Zr-DFO-mAb is not negligible, the in vivo biodistribution of 89Zr might not reflect that of metal radionuclides conjugated with DOTA-mAb. We hypothesized that [89Zr]Zr-DOTA-mAb as a new imaging counterpart would accurately predict the biodistribution of therapeutic metal radionuclides delivered by DOTA-mAb. In this study, we prepared [89Zr]Zr-DOTA-trastuzumab for the first time by a two-step reaction using click chemistry and then investigated the differences in biodistribution profiles between two chelating approaches for 89Zr. MethodsWe prepared [89Zr]Zr-DOTA-trastuzumab from DOTA-tetrazine conjugates (DOTA-Tz) and transcyclooctene-trastuzumab conjugates (TCO-trastuzumab). We first radiolabeled DOTA-Tz with 89Zr in a reaction solution of MeOH and HEPES buffer and then used a click reaction to obtain [89Zr]Zr-DOTA-Tz/TCO-trastuzumab. We performed biodistribution studies and PET imaging with [89Zr]Zr-DOTA-trastuzumab in a mouse model of HER2-positive ovarian cancer, SKOV3 xenograft mice at 24, 72, and 144 hours post-injection and compared these data with those of [89Zr]Zr-DFO-trastuzumab. ResultsTCO-trastuzumab was radiolabeled with [89Zr]Zr-DOTA-Tz in the two-step reaction in good radiochemical yield (57.8 {+/-} 17.6%). HER2-positive tumors were clearly visualized with [89Zr]Zr-DOTA-trastuzumab in PET imaging studies. The temporal profile changes of 89Zr radioactivity in SKOV3 tumors and bone marrow were sufficiently different between [89Zr]Zr-DOTA-trastuzumab and [89Zr]Zr-DFO-trastuzumab (P < 0.05). Conclusion: [89Zr]Zr-DOTA-trastuzumab can be produced by the two-step radiolabeling reaction based on the Tz/TCO click reaction. Presumably, 89Zr released from DFO is not negligible. In contrast, [89Zr]Zr-DOTA-mAb would better predict the biodistribution of [177Lu]Lu- or [225Ac]Ac-DOTA-mAb than [89Zr]Zr-DFO-mAb, thus avoiding the use of different chelator for 89Zr at the expense of the click chemistry step. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/507067v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@d7256borg.highwire.dtl.DTLVardef@d9d3d5org.highwire.dtl.DTLVardef@e24d97org.highwire.dtl.DTLVardef@1541bf0_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2022

Paradoxical tumor suppressive role of the musculoaponeurotic fibrosarcoma gene in colorectal cancer

Somatic cell reprogramming using the microRNAs miR200c, miR-302s, and miR-369s leads to increased expression of cyclin-dependent kinase inhibitors in human colorectal cancer (CRC) cells and suppressed tumor growth. Here, we investigated whether these microRNAs inhibit colorectal tumorigenesis in CPC;Apc mice, which are prone to colon and rectal polyps. Repeated administration of microRNAs inhibited polyp formation. Microarray analysis indicated that c-MAF, which reportedly shows oncogene-like behavior in multiple myeloma and T-cell lymphoma, decreased in tumor samples but increased in microRNA-treated normal mucosa. Immunohistochemistry identified downregulation of c-MAF as an early tumorigenesis event in CRC, with low c-MAF expression associated with poor prognosis. Of note, c-MAF expression and p53 protein levels were inversely correlated in CRC samples. c-MAF knockout led to enhanced tumor formation in azoxymethane/dextran sodium sulfate-treated mice, with activation of cancer-promoting genes. c-MAF may play a tumor-suppressive role in CRC development.

molecular biology↗

bioRxiv2022

SorCS1 inhibits amyloid-β binding to neurexin and rescues amyloid-β-induced synaptic pathology

Amyloid-{beta} oligomers (A{beta}Os), toxic peptide aggregates found in Alzheimers disease (AD), cause synapse pathology. A{beta}Os interact with Neurexins (NRXs), key synaptic organizers, and this interaction dampens normal trafficking and function of NRXs. Axonal trafficking of NRX is in part regulated by its interaction with SorCS1, a protein sorting receptor, but the impact of SorCS1 regulation of NRXs in A{beta} pathology was previously unstudied. Here, we show competitive interaction of SorCS1 and A{beta}Os with {beta}-NRXs and rescue effects of SorCS1 on A{beta}O-induced synaptic pathology. Like A{beta}Os, SorCS1 binds to NRX1{beta} through the histidine-rich-domain (HRD) of NRX1{beta}, and SorCS1 and A{beta}Os compete for NRX1{beta} binding. In cultured hippocampal neurons, SorCS1 colocalizes with NRX1{beta} on the axon surface, and axonal expression of SorCS1 rescues A{beta}O-induced impairment of NRX-mediated presynaptic organization and presynaptic vesicle recycling as well as A{beta}O-induced structural defects in excitatory synapses. Thus, we reveal a role of SorCS1 in the rescue of A{beta}O-induced NRX dysfunction and synaptic pathology, providing the basis for a novel potential therapeutic strategy for AD.

neuroscience↗

bioRxiv2022

Structure of a LRRC8 chimera with physiologically relevant properties reveals heptameric assembly and pore-blocking lipids

Volume-regulated anion channels (VRACs) mediate Cl- and organic solute efflux from vertebrate cells and are essential for cell volume homeostasis. VRACs are heteromeric assemblies of LRRC8A-E proteins with unknown stoichiometries. Homomeric LRRC8A and LRRC8D channels have a hexameric structure. However, these channels are either non-functional or exhibit abnormal functional properties limiting their utility for structure-function analyses. We circumvented these limitations by developing novel homomeric LRRC8 chimeric channels with physiologically relevant functional properties. We demonstrate here that the LRRC8C-LRRC8A(IL125) chimera comprising LRRC8C and 25 amino acids unique to the first intracellular loop (IL1) of LRRC8A has a heptameric structure like that of homologous pannexin channels. Membrane lipids are a key structural element of the channel and are located between subunits and occluding the channel pore. Our results suggest that native VRAC/LRRC8 channels are heptamers and that associated lipids are likely essential for normal channel gating and regulation.

biophysics↗

bioRxiv2022

Glutamine synthetase mRNA releases sRNA from its 3'UTR to regulate carbon/nitrogen metabolic balance

Glutamine synthetase is the key enzyme of nitrogen assimilation, which is encoded in the first cistron of glnALG operon and is induced under nitrogen limiting conditions through transcriptional activation by NtrBC in Salmonella and E. coli. 2-oxoglutarate serves as the carbon skeleton of glutamate and glutamine, but how 2-oxoglutarate fluctuation is controlled in response to nitrogen availability remained unknown. We show that the glnA mRNA produces an Hfq-dependent GlnZ sRNA from its 3 sUTR through RNase E-mediated cleavage. Through a base-pairing mechanism, GlnZ primarily regulates sucA, encoding the E1o component of 2-oxoglutarate dehydrogenase. In the cells grown on glutamine as the nitrogen source, the endogenous GlnZ represses the expression of SucA to redirect the carbon flow from the TCA cycle to the nitrogen assimilation pathway. This study also clarifies that the release of GlnZ sRNA from the glnA mRNA by RNase E is essential for the post-transcriptional regulation of sucA, and thus the mRNA coordinates the two independent functions to balance the supply and demand of the fundamental metabolites.

microbiology↗

bioRxiv2022

Genetic architectures of postmating isolation and morphology of two highly diverged rockfishes (genus Sebastes)

Postmating isolation is thought to be an important driver of the late stages of speciation. However, relatively little is empirically known about the process compared to other isolating mechanisms that drive the early stages of speciation, especially in non-model organisms. We characterized the genetic architecture of postmating isolation between two rockfishes, Sebastes schlegelii and S. trivittatus, whose reproductive isolation is complete. We examined transmission ratio distortion (TRD) patterns of genetic markers in two reciprocal backcross populations. Markers showing either of the two types of TRD was widespread across the genome, with some of the distorted markers forming extensive clusters around the recombination coldspots. These suggest that the postmating isolation effectively prevents gene flow across the genome and the recombination landscape contributes to the genetic architecture. Comparisons between two backcross families and two developmental stages showed little similarity in the distorted markers, suggesting asymmetry and stage-specificity of the isolation. This may be due to hybrid incompatibility involving maternal factors or extrinsic selection. The lack of sex-ratio distortion in the mapping families suggested that Haldanes rule in terms of hybrid inviability does not hold. Additionally, QTL mapping detected significant QTLs for sex and the morphological traits relevant to speciation and convergence of rockfishes, including body coloration. Genes in the melanocortin system, including agouti-signaling protein 1 (asip1) and melanocortin 1 receptor (mc1r), might underlie the horizontal and vertical color patterns on the body, respectively. These findings constitute an essential step towards a comprehensive understanding of speciation and morphological diversification of rockfishes.

evolutionary biology↗

bioRxiv2022

Abnormal Tibia Translation leads Directly the Surface Cartilage Degeneration with Molecular Biological Response using a Novel Non-Invasive ACL ruptured Mice Model

ObjectiveThe ACL-deficient model helps to clarify the mechanism of knee OA; however, the conventional ACL injury model could have included concurrent onset factors such as direct compression stress to cartilage and subchondral bone. In this study, we established a novel Non-invasive ACL-Ruptured mouse model without concurrent injuries and elucidated the relationship between OA progression and joint instability. DesignWe induced the ACL-Rupture non-invasively in twelve-week-old C57BL/6 male mice and evaluated histological, macroscopical, and morphological analysis at 0 days. Next, we created the ACL-R, controlled abnormal tibial translation (CATT), and Sham groups. Then, the joint stability and OA pathophysiology were analyzed at 2, 4, and 8 weeks. ResultsNo intra-articular injuries, except for ACL rupture, were observed in the ACL-R model. ACL-R mice increased anterior tibial displacement compared to the Sham group (p<0.001, 95% CI [-1.509 to -0.966]) and CATT group (p<0.001, 95% CI [-0.841 to -0.298]) at 8 weeks. All mice in the ACL-R group caused cartilage degeneration. The degree of cartilage degeneration in the ACL-R group was higher than in the CATT group (p=0.006) at 8 weeks. The MMP-3-positive cell rate of chondrocytes increased in the ACL-R group than CATT group from 4 weeks (p=0.043; 95% CI [-28.32 to -0.364]) while that of synovial cells increased at 8 weeks (p=0.031; 95% CI [-23.398 to -1.021]). ConclusionWe successfully established a Non-invasive ACL-R model without intra-articular damage. Our model revealed that chondrocytes might react to abnormal mechanical stress prior to synovial cells while the knee OA onset.

molecular biology↗

bioRxiv2021

OTUD1 deubiquitylase regulates NF-κB- and KEAP1-mediated inflammatory responses and reactive oxygen species-associated cell death pathways

Deubiquitylating enzymes (DUBs) regulate numerous cellular functions by removing ubiquitin modifications. We examined the effects of 88 human DUBs on linear ubiquitin chain assembly complex (LUBAC)-induced NF-{kappa}B activation, and identified OTUD1 as a potent suppressor. OTUD1 regulates the canonical NF-{kappa}B pathway by hydrolysing K63-linked ubiquitin chains from NF-{kappa}B signalling factors, including LUBAC. OTUD1 negatively regulates the canonical NF-{kappa}B activation, apoptosis, and necroptosis, whereas OTUD1 upregulates the interferon (IFN) antiviral pathway. The N-terminal intrinsically disordered region of OTUD1, which contains an EGTE motif, is indispensable for KEAP1-binding and NF-{kappa}B suppression. OTUD1 is involved in the KEAP1-mediated antioxidant response and reactive oxygen species (ROS)-induced cell death, oxeiptosis. In Otud1-/--mice, inflammation, oxidative damage, and cell death were enhanced in inflammatory bowel disease, acute hepatitis, and sepsis models. Thus, OTUD1 is a crucial regulator for the inflammatory, innate immune, and oxidative stress responses and ROS-associated cell death pathways.

cell biology↗

bioRxiv2021

Structural basis for activation and gating of IP3 receptors

Calcium (Ca2+) is a universal and versatile cellular messenger used to regulate numerous cellular processes in response to external or internal stimuli. A pivotal component of the Ca2+ signaling toolbox in cells is the inositol 1,4,5-triphosphate (IP3) receptors (IP3Rs), which mediate Ca2+ release from the endoplasmic reticulum (ER), controlling cytoplasmic and organellar Ca2+ concentrations1-3. IP3Rs are activated by IP3 and Ca2+, inhibited by Ca2+ at high concentrations, and potentiated by ATP1-3. However, the underlying molecular mechanisms are unclear due to the lack of structures in the active conformation. Here we report cryo-electron microscopy (cryo-EM) structures of human type-3 IP3R in multiple gating conformations; IP3-ATP bound pre-active states with closed channels, IP3-ATP-Ca2+ bound active state with an open channel, and IP3-ATP-Ca2+ bound inactive state with a closed channel. The structures demonstrate how IP3-induced conformational changes prime the receptor for activation by Ca2+, how Ca2+ binding leads to channel opening, and how ATP modulates the activity, providing insights into the long-sought questions regarding the molecular mechanism of the receptor activation and gating.

biophysics↗

bioRxiv2021

Time-series Multi-spectral Imaging in Soybean for Improving Biomass and Genomic Prediction Accuracy

Multi-spectral (MS) imaging enables the measurement of characteristics important for increasing the prediction accuracy of genotypic and phenotypic values for yield-related traits. In this study, we evaluated the potential application of temporal MS imaging for the prediction of above-ground biomass (AGB) and determined which developmental stages should be used for accurate prediction in soybean. Field experiments with 198 accessions of soybean were conducted with four different irrigation levels. Five vegetation indices (VIs) were calculated using MS images from soybean canopies from early to late growth stages. To predict the genotypic values of AGB, VIs at the different growth stages were used as secondary traits in a multi-trait genomic prediction. The accuracy of the prediction model increased starting at an early stage of growth (31 days after sowing). To predict phenotypic values of AGB, we employed multi-kernel genomic prediction. Consequently, the prediction accuracy of phenotypic values reached a maximum at a relatively early growth stage (38 days after sowing). Hence, the optimal timing for MS imaging may depend on the irrigation levels.

plant biology↗

bioRxiv2021

Identification of transcription termination defects at DNA hypomethylated transcription termination sites in DNA methyltransferase 3a-deficient vertebrates.

CpG methylation in genomic DNA is well known as a repressive epigenetic marker in eukaryotic transcription, and DNA methylation of the promoter regions is correlated with silencing of gene expression. In contrast to the promoter regions, the function of DNA methylation during transcription termination remains to be elucidated. A recent study has revealed that mouse DNA methyltransferase 3a (Dnmt3a) mainly functions in de novo methylation in the promoter and gene body regions (including transcription termination sites (TTSs)) during development. To investigate the relationship between DNA methylation overlapping the TTSs and transcription termination, we employed two strategies: informatic analysis using already deposited datasets of Dnmt3a-/- mouse cells and the zebrafish model system. Bioinformatic analysis using methylome and transcriptome data showed that hypomethylated differentially methylated regions overlapping the TTSs were associated with increased read counts and chimeric transcripts downstream of TTSs in Dnmt3a-/- Agouti-related protein neurons, but not in Dnmt3a-/- embryonic stem cells and mouse embryonic fibroblasts. We experimentally detected increased read-through and chimeric transcripts downstream of hypomethylated TTSs in zebrafish maternal-zygotic dnmt3aa-/- mutant. This study is the first to identify transcription termination defects in DNA hypomethylated TTSs in Dnmt3a-/- vertebrates.

genomics↗