Biology subjects

Sakamoto, T.

Publications and source records attributed to Sakamoto, T..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

The metabolic ability of swallowtails results in the production of bioactive substances from plant components

Host plant selection may depend on the metabolic system in herbivorous insects. Although oligophagous insects take up specific host plant components, how host plant components and their biological activities are altered through their metabolic systems remains unknown. Here, by examining gene expression of metabolic enzymes and components in the larval frass, we investigated the metabolic ability of Papilio memnon larvae fed with Citrus x paradisi (grapefruit) against host plant components. The gene expression levels of some metabolic enzymes were fluctuated between the larval midgut and the larval fat bodies. Furthermore, the chloroform extract from the larval frass, but not that from grapefruit leaves, inhibited cell viability of human pancreatic cancer cell line, MIA PaCa2. Finally, we identified two chlorophyll catabolites, pheophorbide-a and pyropheophorbide-a, in the larval frass extract. Pyropheophorbide-a reduces cell viability of and induces morphological changes in cells of MIA PaCa2; in addition, pheophorbide-a and pyropheophorbide-a inhibit the aggregation of amyloid {beta}-protein (human, 1-42). Therefore, the chemical structure and biological activity of host plant components are affected by the P. memnon metabolic system. Our findings may contribute to the development of a bioprocess for the production of pheophorbide-a and pyrophephorbide-a from chlorophyll via the metabolic functions of P. memnon larvae.

biochemistry↗

bioRxiv2025

Evolutionary History of Treponema pallidum subsp. pertenue: Insights into Host Ancestry and Cross-Species Transmission

Treponema pallidum, a bacterium from the Spirochaetota phylum, is responsible for treponematoses, such as syphilis, yaws, bejel, and pinta. Different subspecies of this bacterium cause each of these diseases. This study focuses on Treponema pallidum subsp. pertenue (TPE), which causes yaws in humans and is primarily transmitted through direct contact with skin lesions, mainly affecting children and preadolescents. If untreated, it can progress to severe deformities in bones and cartilage. During the 20th century, significant progress was made in the eradication and control of this disease. However, in recent decades, there has been an increase in the number of reported cases. Until recently, it was believed that this subspecies affected only humans, but recent studies have identified that non-human primates (NHPs) have also been naturally infected with TPE. Considering the impacts of this disease on both humans and other species, TPE has become a focus of surveillance and scientific investigation. This study aims to clarify the relationship between infection in humans and other primate species, contributing to a better understanding of transmission dynamics and potential control and prevention strategies. To achieve this, we used genome sequences from 58 TPE strains (24 from humans and 19 from NHPs) available in public repositories and applied phylogenetic analyses and computational tools for recombinant region detection. The phylonetic analysis demonstrated a rapid expansion of the subspecies at the base of the tree and clustered the samples into nine groups. No groups contained both human and NHP samples, indicating that interactions between the two sample groups are rare or nonexistent. Recombination analyses detected only one region where an NHP sample may have recombined with a human sample. The application of the molecular clock in phylogenetic inference indicated a recent origin of TPE in 1885. The study of trait evolution further suggests that the host of the most recent common ancestor of TPE was humans. The analyses conducted in this study provided deeper insights into the spread of the disease and its interaction across different species.

evolutionary biology↗

bioRxiv2025

Autism-Associated Genes and Neighboring lncRNAs Converge on Key Gene Regulatory Networks

Autism spectrum disorder (ASD) is highly heritable, and mutations in hundreds of genes have been implicated as individually rare causes of ASD1-3. Understanding how disruptions to these functionally diverse genes lead to the core features of ASD remains a major challenge4. Moreover, ASD is three- to four-fold more common in males than females5, and autistic females tend to carry more autosomal risk alleles for ASD compared to autistic males6,7, but the biological basis of this "female protective effect" (FPE) is unknown8,9. Here we show that individual perturbations of 18 ASD genes in human neural progenitor cells converge on shared effects on gene expression, including widespread downregulation of other ASD genes. De novo reconstruction of a gene regulatory network (GRN) enabled the identification of central transcriptional regulators, including the prominent ASD gene CHD8 as well as novel candidates such as REST, that drive this transcriptomic convergence. Furthermore, the X-linked transcription factor ZFX, which is expressed from both the active and the inactive X chromosomes in females10, emerged as a key activator of many ASD genes: we propose that the higher ZFX expression level observed in female brain can buffer damaging mutations in diverse ASD genes, contributing to the FPE. Together, these results reveal how key GRNs can become broadly and similarly dysregulated upon disruption of individual ASD genes and provide molecular insight into the female protective effect in ASD.

genetics↗

bioRxiv2024

Establishment of a locally adaptive allele in multidimensional continuous space

Local adaptation is widely seen when species adapt to spatially heterogeneous environments. Although many theoretical studies have investigated the dynamics of local adaptation using two-population models, there remains a need to extend the theoretical framework to continuous space settings, reflecting the real habitats of species. In this study, we use a multidimensional continuous space model and mathematically analyze the establishment process of local adaptation, with a specific emphasis on the relative roles of mutation and migration. First, the role of new mutations is evaluated by deriving the establishment probability of a locally adapted mutation using a branching process and a diffusion approximation. Next, the contribution of immigrants from a neighboring region with similar environmental conditions is considered. Theoretical predictions of the local adaptation rate agreed with the results of Wright-Fisher simulations in both mutation-driven and migration-driven cases. Evolutionary dynamics depend on several factors, including the strength of migration and selection, population density, habitat size, and spatial dimensions. These results offer a theoretical framework for assessing whether mutation or migration predominantly drives convergent local adaptation in spatially continuous environments in the presence of patchy regions with similar environmental conditions.

evolutionary biology↗

bioRxiv2024

PREDICTION OF SINGLE NUCLEOTIDE VARIANT EFFECTS RELATED TO SEX DETERMINATION IN Carica papaya (Caricaceae)

Papaya (Carica papaya) produces one of the most consumed fruits worldwide, holding great economic importance, especially in tropical regions. Papaya trade mainly involves gynodioecious cultivars with a ratio of 1:1 or 2:1 of hermaphrodites to females. For commercial reasons and also inherent to cultivation, it is preferable to have as many hermaphrodites as possible. In general, it is still not possible to produce only hermaphrodite seeds, so the sex of the plant is usually identified by conventional methods after the first flowering of the papaya plant. This occurs about 4-6 months after planting the seedling, with the females typically being discarded at the end. To avoid wasting resources and achieve higher harvest yields, producers may also resort to molecular methods using sex markers. However, this alternative also has its limitations, including high costs. Given these challenges, many researchers have focused on studying the process of sex determination in C. papaya, but the factors directly influencing this process remain unknown. The elucidation of this mechanism is not only of great agronomic interest, but also represents a significant opportunity for C. papaya to establish itself as a model organism for studying sexual chromosomes of recent evolutionary origin. Therefore, in this work, a bioinformatics strategy was used to address the topic. A genotype-phenotype association study was conducted to find possible genetic factors involved in sex determination using resequencing data from 36 individuals (24 male papaya plants and 12 hermaphrodites) obtained from public databases. The association study was preceded by a variant calling performed with BCFTOOLS, which found 75,607 variants, leaving 37,027 after filtering. Association studies were then carried out using the PLINK program with the filtered variants, and among these, 251 of the most statistically significant variants were applied to the SnpEff program for variant annotation, returning 449 effects, including 402 with a modifier level of impact, 22 with a low impact, and 25 with a moderate effect. Inferences and gene annotations were also performed using the Augustus software and BLASTP alignments with the gene sequences that had moderate effects predicted by SnpEff, as well as de novo genome assemblies of a male sample and its alignment with the hermaphrodite sex-determining region. These results were recorded and compared with previous studies in the literature. This allowed for the conclusion that the specific results obtained serve as a starting point for more robust studies to understand the molecular mechanisms of sex determination in C. papaya.

genomics↗

bioRxiv2024

Revisiting the taxonomy of Enterococcus casseliflavus and related species

Enterococcus casseliflavus is a commensal bacterium that can occasionally cause human infections. A concern is that all strains of this species carry the vanC operon on their chromosomes, which reduces susceptibility to vancomycin. Aside from that, the classification of E. casseliflavus remains challenging because it shares up to 99% 16S rRNA sequence identity with other enterococci species. Here, we reassess the taxonomy and genomic diversity of E. casseliflavus and closely related taxa by comprehensively analyzing publicly available genomes to clarify their evolutionary relationships, ecological distributions, and clinical relevance. We retrieved 156 genomes of clinical and non-clinical isolates that showed ANI >90% with E. casseliflavus from public databases. Using ANI, core genome-based phylogeny, and pangenome reconstruction, we consistently identified three well-defined clusters corresponding to E. casseliflavus, E. entomosocium, and E. innesii. Our results indicate that a higher ANI threshold (>96.6%) is required to accurately discriminate between species within this group, as many strains showed more than 95% ANI with multiple species. Our results also support that E. flavescens and E. casseliflavus represent a single species and should be treated as synonyms. Genes related to biocide resistance, metal tolerance, and virulence were identified across the three species. E. casseliflavus exhibited the greatest diversity of resistance determinants. All species harbored the vanC operon associated with intrinsic vancomycin resistance, while two genomes additionally carried the vanD operon linked to high-level glycopeptide resistance. Overall, our findings refine species boundaries and highlight the importance of genome-based approaches for accurate classification and surveillance within the Enterococcus genus.

bioinformatics↗

bioRxiv2024

The persistence of locally adapted polymorphisms under mutation swamping

Locally adapted traits can exhibit a wide range of genetic architectures, from pronounced divergence at a few loci to small allele frequency shifts at many loci. The type of architecture that evolves depends strongly on migration rate, as weakly selected loci experience swamping and do not make stable contributions to divergence. Simulations from previous studies showed that even when mutations are strongly selected and should resist migration swamping, the architecture of adaptation can collapse and become transient at high mutation rates. Here, we use an analytical two-population model to study how this "mutation swamping" phenomenon depends upon population size, strength of selection, and parameters determining mutation effects. To do this, we developed a mathematical theory based on the diffusion approximation to predict the threshold mutation rate above which swamping occurs, and find that this performs well across wide range of parameter space, based on comparisons with individual-based simulations. The mutation swamping threshold depends most strongly on the average effect size of mutations, and weakly on the strength of selection, but is only minimally affected by population size. Across a wide range of parameter space, we observe that mutation swamping occurs when the trait-wide mutation rate is 10-3-10-2, suggesting that this phenomenon is potentially relevant to complex traits with a large mutational target. On the other hand, based on the apparent stability of genetic architecture in many classic examples of local adaptation, our theory suggests that per-trait mutation rates are often relatively low.

evolutionary biology↗

bioRxiv2024

Development of the 12-base short dimeric myogenetic oligodeoxynucleotide that induces myogenic differentiation

A myogenetic oligodeoxynucleotide (myoDN), iSN04 (5-AGA TTA GGG TGA GGG TGA-3), is a single-stranded 18-base telomeric DNA that serves as an anti-nucleolin aptamer and induces myogenic differentiation, which is expected to be a nucleic acid drug for the prevention of disease-associated muscle wasting. To improve the drug efficacy and synthesis cost of myoDN, shortening the sequence while maintaining its structure-based function is a major challenge. Here, we report the novel 12-base non-telomeric myoDN, iMyo01 (5-TTG GGT GGG GAA-3), which has comparable myogenic activity to iSN04. iMyo01 as well as iSN04 promoted myotube formation of primary-cultured human myoblasts with upregulation of myogenic gene expression. Both iMyo01 and iSN04 interacted with nucleolin, but iMyo01 did not bind to berberine, the isoquinoline alkaloid that stabilizes iSN04. Nuclear magnetic resonance revealed that iMyo01 forms a G-quadruplex structure despite its short sequence. Native polyacrylamide gel electrophoresis and computational molecular dynamics simulation indicated that iMyo01 forms a homodimer to generate a G-quadru-plex. These results provide new insights into the aptamer truncation technology that preserves aptamer conformation and bioactivity for the development of efficient nucleic acid drugs. Key ContributionThis study reports the structure-based shortening of a myogenetic oligodeox-ynucleotide, iSN04, as an anti-nucleolin aptamer that induces myogenesis. The shortening technology of aptamers while maintaining their conformation and activity improves their potency of drug function and synthesis cost.

cell biology↗

bioRxiv2024

Comparative analyses of adsorbed circulating proteins in the PMMA and PES hemodiafilters in patients on predilution online hemodiafiltration

Acute and chronic inflammation are common in patients with end-stage kidney disease (ESKD). So, the adsorption of pro-inflammatory cytokines by the hollow fiber has been expected to modify the inflammatory dysregulation in ESKD patients. However, it remains to be determined in detail what molecules of fiber materials can preferably adsorb proteins from the circulating circuit. We aimed this study to analyze directly the adsorbed proteins in the polymethyl methacrylate (PMMA) and polyethersulfone (PES) membranes in patients on predilution online hemodiafiltration (OL-HDF). To compare the adsorbed proteins in the PMMA and PES hemodiafilters membrane, we initially performed predilution OL-HDF using the PES (MFX-25Seco) membrane while then switched to the PMMA (PMF-A) membrane under the same condition in three patients. We extracted proteins from the collected hemodiafilters by extraction, then SDS-PAGE of the extracted sample, protein isolation, in-gel tryptic digestion, and nano-LC MS/MS analyses. The concentrations of adsorbed proteins from the PMMA and PES membrane extracts were 35.6{+/-}7.9 {micro}g/{micro}L and 26.1{+/-}9.2 {micro}g/{micro}L. SDS-PAGE analysis revealed distinct variations of adsorbed proteins mainly in the molecular weight between 10 to 25 kDa. By tryptic gel digestion and mass spectrometric analysis, the PMMA membrane exhibited higher adsorptions of {beta}2 microglobulin, dermcidin, retinol-binding protein-4, and lambda-1 light chain than those from the PES membrane. In contrast, amyloid A-1 protein was adsorbed more potently in the PES membrane. Western blot analyses revealed that the PMMA membrane adsorbed interleukin-6 (IL-6) approximately 5 to 118 times compared to the PES membrane. These findings suggest that PMMA-based OL-HDF therapy may be useful in controlling inflammatory status in ESKD patients.

pathology↗

bioRxiv2024

CAP peptide artificially induces insect gall

Galls caused by gall-inducing insects in their host plants clearly illustrate the concept of extended phenotype, which refers to traits expressed in a host organism when manipulated by a parasite. Candidate effector molecules involved in gall formation, such as phytohormones, amino acids, and proteins, have been reported in numerous studies. However, to date, no attempts to artificially regenerate gall structures using effector candidates have been reported. In this study, we tested the peptide from Cysteine-rich secretory proteins, Antigen 5, and Pathogenesis-related 1 proteins, CAP peptide as a gall-inducing effector candidate obtained from transcripts isolated from the horned gall aphid, (Schlechtendalia chinensis) through in silico screening and the Arabidopsis-based gall-forming assay, which is a bioassay system for analysing the molecular mechanisms of gall formation. Furthermore, we succeeded in generating an artificial gall in the host plant Veronica peregrina, without any insect parasitism, using three minimal effector elements: CAP peptide, auxin, and cytokinin. Given the strong similarities observed in organ structure with a central cavity and three types of tissue and gene expression patterns between the native and artificial galls, we concluded that CAP peptide is a general gall-inducing effector peptide secreted by gall-inducing insects.

molecular biology↗

bioRxiv2023

Non-contact respiratory measurements of outdoor-housed rhesus macaques (Macaca mulatta) using millimeter-wave radars

Respiration is an invaluable signal that facilitates the real-time observation of physiological dynamics. In recent years, the advancement of non-contact measurement technology has gained momentum in capturing physiological dynamics in natural settings. This technology is anticipated to find utility in healthcare, not only in humans but also in captive animals, to enhance animal welfare. Currently, the predominant non-contact approach for captive animals involves measuring vital signs through subtle variations in skin color. However, this approach is limited when dealing with body regions covered with hair or outdoor environments under fluctuating sunlight. In contrast, millimeter-wave radar systems, which employ millimeter waves that can penetrate animal fur, exhibit minimal susceptibility to sunlight interference. Thus, this method holds promise for non-contact vital measurements in natural and outdoor settings. In this study, we validated a millimeter-wave radar methodology for capturing respiration in outdoor-housed rhesus macaques (Macaca mulatta). The radar was positioned beyond the captive enclosure and maintained at a distance of > 5 m from the target. Millimeter waves were transmitted to the target, and the reflected waves were used to estimate skin surface displacement associated with respiration. The results revealed periodic skin surface displacement, and the estimated respiratory rate was within the reported range of respiratory rates for rhesus macaques. This result suggests the potential applicability of millimeter-wave radar for non-contact respiration monitoring in outdoor-housed macaques. The continued advancement of non-contact vital measurement technology will contribute to the mental and physical monitoring of captive animals to establish comfortable captive environments. Research HighlightsMillimeter-wave radar systems succeeded in the non-contact measurement of respiration in outdoor-housed rhesus macaques from > 5 m. Our results demonstrate the feasibility of radar-based remote monitoring to assess the welfare of zoo-housed animals.

zoology↗

bioRxiv2023

Long-read genome assembly of the Japanese parasitic wasp Copidosoma floridanum (Hymenoptera: Encyrtidae)

Copidosoma floridanum is a cosmopolitan species and an egg-larval parasitoid of the Plusiine moth. C. floridanum has a unique development mode called polyembryony, in which thousands of genetically identical embryos are produced from a single egg. Some embryos develop into sterile soldier larvae, and their developmental patterns differ between the US and Japanese C. floridanum strains. Genome sequencing can accelerate our understanding of the molecular bases underlying polyembryony, including the production of soldier castes. However, only the genome sequence of the US strain has been reported. In the present study, we determined the genome sequence of the Japanese strain using Pacific Biosciences high-fidelity reads and generating a highly contiguous assembly (552.7 Mb, N50: 17.9 Mb). Gene prediction and annotation identified 13,886 transcripts derived from 10,786 gene models. We searched the genomic differences between US and Japanese strains. Among gene models predicted in this study, 100 gene loci in the Japanese strain had extremely different gene structure from those in the US strain. This was accomplished through the functional annotation (GGSEARCH) and long-read sequencing. Genomic differences between strains were also reflected to amino acid sequences of vasa that plays a central role in caste determination in this species. The genome assemblies constructed in this study will facilitate the genomic comparisons between Japanese and US strains, leading to our understanding of detail genomic regions responsible for the ecological and physiological characters of C. floridanum.

genomics↗

bioRxiv2023

Phylogenetic Analysis of the rfb Locus Genes of the Genus Leptospira of Serogroups Serjoe, Mini and Hebdomadis

Leptospirosis is a zoonosis of great impact on public health since it is considered a notifiable disease occurring mainly in tropical regions with poor sanitation and vulnerable socioeconomic conditions. It is caused by bacteria of the genus Leptospira and phylum Spirochaetes and contamination occurs through direct or indirect contact with the contaminating agent. In addition to taxonomic classification, which is performed through sequencing and the analysis of some marker genes, such as 16S rRNA and secY, they are usually classified based on their antigenic characteristics into serogroups and serovars. This kind of classification is largely applied in epidemiological studies and vaccine development. Despite its importance, few studies have been conducted to understand the evolutionary dynamics of the emergence or change of serology in this genus. In view of this, we applied phylogenetic methods in order to understand the evolutionary processes involving the serology of the genus. To this end, sequences of genes comprising the rfb locus from samples of serogroups Sejroe, Mini, and Hebdomadis (34 samples) were extracted and submitted to the phylogenetic pipeline, resulting in the inference of 75 maximum likelihood trees. Topology tests showed that most of the gene trees are significantly different from the species tree. We could depict the occurrence of lateral gene transfer between L. borgpetersenii and L. kirschneri; and L. interrogans and L. weilli. In this analysis, no evidence was found for the lateral gene transfer between samples of the Hardjo serovar of L. interrogans and L. borgpetersenii. Thus, it is also suggested that the occurrence of horizontal transfer of genes from the rfb locus between distinct species is less frequent than expected.

evolutionary biology↗

bioRxiv2023

The evolution of RNA interference among Metazoa

In animals, three main RNA interference mechanisms have been described so far, which respectively maturate three types of small noncoding RNAs (sncRNAs): miRNAs, piRNAs and endo-siRNAs. The diversification of these mechanisms is deeply linked with the evolution of the Argonaute gene superfamily since each type of sncRNA is loaded by a specific Argonaute homolog protein. Moreover, other protein families play pivotal roles in the maturation of sncRNAs, like the DICER ribonuclease family, whose DICER1 and DICER2 paralogs maturate respectively miRNAs and endo-siRNAs. Among Metazoa, the distribution of these families has been only studied in major groups, and there are very few data for clades like Lophotrochozoa. Thus, we here inferred the evolutionary history of the animal Argonaute and DICER families including 43 lophotrochozoan species. Phylogenetic analyses along with newly sequenced sncRNA libraries depicted a loss of the endo-siRNA pathway along the Lophotrochozoa evolution, with the absence of DICER2 in Nematoda and Polyzoa, and with the absence of DICER2 and the Argonaute homolog in the rest of Trochozoa phyla. On the contrary, early diverging phyla, Platyhelminthes and Syndermata, showed a complete endo-siRNA pathway. On the other hand, miRNAs were revealed the most conserved and ubiquitous mechanism of the metazoan RNA interference machinery, confirming their pivotal role in animal cell regulation.

evolutionary biology↗

bioRxiv2023

Genetic structure and diversity of rfb locus of pathogenic species of genus Leptospira

Considered a globally important zoonotic bacterial disease, leptospirosis affects both humans and commercially important animals. It is transmitted through direct or indirect exposure to the urine of infected animals and is a major public health challenge in regions with heavy rainfall, floods, and poor socioeconomic conditions. The genus Leptospira has 67 species, which can be grouped into pathogenic and saprophytic groups. Serological classification based on antigenic characteristics is important in epidemiology and clinical analysis but is laborious, requires infrastructure and specialized labor, and takes days to obtain results. In this study, we aimed to find genetic patterns associated with the serological classification of Leptospira to propose molecular markers for classifying Leptospira samples at the serogroup level. For this, we used genomic data of 722 samples distributed in 67 species in public databases and compared the gene composition of their rfb locus. Clustering analysis was able to group samples into five major classes that share similarities in both the serological and genetic composition of the rfb locus. We also identified some syntenic blocks in the internal region of the rfb locus and patterns of presence and absence of these blocks which can be used to determine the serogroup of a sample. Our findings can assist the development of molecular strategies for the serological identification of Leptospira samples, which could be more rapid and accurate than the current method.

bioinformatics↗

bioRxiv2023

MBNL1 regulates programmed postnatal switching between regenerative and differentiated cardiac states.

Discovering determinants of cardiomyocyte maturity and the maintenance of differentiated states is critical to both understanding development and potentially reawakening endogenous regenerative programs in adult mammalian hearts as a therapeutic strategy. Here, the RNA binding protein Muscleblind-like 1 (MBNL1) was identified as a critical regulator of cardiomyocyte differentiated states and their regenerative potential through transcriptome-wide control of RNA stability. Targeted MBNL1 overexpression early in development prematurely transitioned cardiomyocytes to hypertrophic growth, hypoplasia, and dysfunction, whereas loss of MBNL1 function increased cardiomyocyte cell cycle entry and proliferation through altered cell cycle inhibitor transcript stability. Moreover, MBNL1-dependent stabilization of the estrogen-related receptor signaling axis was essential for maintaining cardiomyocyte maturity. In accordance with these data, modulating MBNL1 dose tuned the temporal window of cardiac regeneration, where enhanced MBNL1 activity arrested myocyte proliferation, and MBNL1 deletion promoted regenerative states with prolonged myocyte proliferation. Collectively these data suggest MBNL1 acts as a transcriptome-wide switch between regenerative and mature myocyte states postnatally and throughout adulthood.

cell biology↗

bioRxiv2022

Detecting remote homolog using structure alignment algorithms and machine learning

Remote homolog detection is a classic problem in Bioinformatics. It attempts to identify distantly related proteins sharing a similar structure. Methods that can accurately detect remote homologs benefit protein functional annotation. Recent computational advances in methods predicting the three-dimensional structure of a protein from amino acid sequences allow the massive use of structural data to develop new tools for identifying remote homologs. In this work, we created a discriminative SVM-based method based on structural alignment algorithms (FATCAT, TM-Align, and LovoAlign) to detect whether a protein is a remote homolog with any proteins in the SCOPe database. The final model showed a ROC AUC of 0.9191.

bioinformatics↗

bioRxiv2022

The plant nuclear lamina disassembles to regulate genome folding in stress conditions

The nuclear lamina (NL) is a complex network of nuclear lamins and lamin-associated nuclear membrane proteins, which scaffold the nucleus to maintain structural integrity. In Arabidopsis thaliana, Nuclear Matrix Constituent Proteins (NMCPs) are essential components of the NL and are required to maintain the structural integrity of the nucleus and specific perinuclear chromatin anchoring. At the nuclear periphery, suppressed chromatin overlapping with repetitive sequences and inactive protein coding genes are enriched. At a chromosomal level, plant chromatin organization in interphase nuclei displays flexibilities in response to various developmental cues and environmental stimuli. Based on these observations in Arabidopsis, and given the role of AtNMCP genes (CRWN1 and CRWN4) in organizing chromatin positioning at the nuclear periphery, one can expect considerable changes in chromatin-NL interactions when the global chromatin organization patterns are being altered in plants. Here, we report the highly flexible nature of plant nuclear lamina, which disassembles substantially under various stress conditions. Particularly, under heat stress, we reveal that chromatin domains, initially tethered to the nuclear envelope, remain largely associated with CRWN1 and become scattered in the inner nuclear space. Via investigating the three-dimensional chromatin contact network, we further reveal that CRWN1 proteins play a structural role in shaping the changes in genome folding under heat stress. Also, CRWN1 acts as a negative transcriptional co-regulator to modulate the shift of the plant transcriptome profile in response to heat stress.

genomics↗