Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation.

Nucleosomes block access to DNA methyltransferase, unless they are remodeled by DECREASE in DNA METHYLATION 1 (DDM1LSH/HELLS), a Snf2-like master regulator of epigenetic inheritance. We show that DDM1 promotes replacement of histone variant H3.3 by H3.1. In ddm1 mutants, DNA methylation is partly restored by loss of the H3.3 chaperone HIRA, while the H3.1 chaperone CAF-1 becomes essential. The single-particle cryo-EM structure at 3.2 Å of DDM1 with a variant nucleosome reveals engagement with histone H3.3 near residues required for assembly and with the unmodified H4 tail. An N-terminal autoinhibitory domain inhibits activity, while a disulfide bond in the helicase domain supports activity. DDM1 co-localizes with H3.1 and H3.3 during the cell cycle, and with the DNA methyltransferase MET1Dnmt1, but is blocked by H4K16 acetylation. The male germline H3.3 variant MGH3/HTR10 is resistant to remodeling by DDM1 and acts as a placeholder nucleosome in sperm cells for epigenetic inheritance.

DNA methylation biomarkers distinguishing early-stage prostate cancer from benign prostatic hyperplasia.

Background: DNA methylation markers are considered robust diagnostic features in various cancer types, as epigenetic marks are commonly altered during cancer progression. Differentiation between benign prostatic hyperplasia (BPH) and early-stage prostate cancer (PCa) is clinically difficult, relying on the information of the patient's symptoms or levels of prostate-specific antigen. Methods: A total of 42 PCa patients and 11 BPH patients were recruited. Genomic DNA was purified from tissues and used for the library preparation of the target-enriched methylome with enzymatic conversion and a Twist 85 Mbp EM-seq panel. Paired-end sequencing (150 bp) was performed using NovaSeq 6000 or NextSeq 550. After quality control, including adapter trimming and de-duplication of raw sequencing data, differential methylation patterns were analyzed between the BPH and PCa groups. Results: We report DNA methylation patterns existing between BPH and PCa. The major finding is that broad hypermethylation occurred at genic loci in PCa tissues as compared to the BPH. Gene ontology analysis suggested that hypermethylation of genic loci involved in chromatin and transcriptional regulation is involved in cancer progression. We also compared PCa tissues with high Gleason scores to tissues with low Gleason scores. The high-Gleason PCa tissues showed hundreds of focal differentially methylated CpG sites corresponding to genes functioning in cancer cell proliferation or metastasis. This suggests that dissecting early-to-advanced-grade cancer stages requires an in-depth analysis of differential methylation at the single CpG site level. Conclusions: Our study reports that enzymatic methylome sequencing data can be used to distinguish PCa from BPH and advanced PCa from early-stage PCa. The stage-specific methylation patterns in this study will be valuable resources for diagnostic purposes as well as further development of liquid biopsy approaches for the early detection of PCa.

Chromatin remodeling of histone H3 variants underlies epigenetic inheritance of DNA methylation.

Epigenetic inheritance refers to the faithful replication of DNA methylation and histone modification independent of DNA sequence. Nucleosomes block access to DNA methyltransferases, unless they are remodeled by DECREASE IN DNA METHYLATION1 (DDM1 Lsh/HELLS ), a Snf2-like master regulator of epigenetic inheritance. We show that DDM1 activity results in replacement of the transcriptional histone variant H3.3 for the replicative variant H3.1 during the cell cycle. In ddm1 mutants, DNA methylation can be restored by loss of the H3.3 chaperone HIRA, while the H3.1 chaperone CAF-1 becomes essential. The single-particle cryo-EM structure at 3.2 Å of DDM1 with a variant nucleosome reveals direct engagement at SHL2 with histone H3.3 at or near variant residues required for assembly, as well as with the deacetylated H4 tail. An N-terminal autoinhibitory domain binds H2A variants to allow remodeling, while a disulfide bond in the helicase domain is essential for activity in vivo and in vitro . We show that differential remodeling of H3 and H2A variants in vitro reflects preferential deposition in vivo . DDM1 co-localizes with H3.1 and H3.3 during the cell cycle, and with the DNA methyltransferase MET1 Dnmt1 . DDM1 localization to the chromosome is blocked by H4K16 acetylation, which accumulates at DDM1 targets in ddm1 mutants, as does the sperm cell specific H3.3 variant MGH3 in pollen, which acts as a placeholder nucleosome in the germline and contributes to epigenetic inheritance.

Regulation of retrotransposition in Arabidopsis.

Plant genomes are largely comprised of retrotransposons which can replicate through 'copy and paste' mechanisms. Long terminal repeat (LTR) retrotransposons are the major class of retrotransposons in plant species, and importantly they broadly affect the expression of nearby genes. Although most LTR retrotransposons are non-functional, active retrotranspositions have been reported in plant species or mutants under normal growth condition and environmental stresses. With the well-defined reference genome and numerous mutant alleles, Arabidopsis studies have significantly expanded our understanding of retrotransposon regulation. Active LTR retrotransposon loci produce virus-like particles to perform reverse transcription, and their complementary DNA can be inserted into new genomic loci. Due to the detrimental consequences of retrotransposition, plants like animals, have developed transcriptional and post-transcriptional silencing mechanisms. Recently several different genome-wide techniques have been developed to understand LTR retrotransposition in Arabidopsis and different plant species. Transposome, methylome, transcriptome, translatome and small RNA sequencing data have revealed how host silencing mechanisms can affect multiple steps of retrotransposition. These recent advances shed light on future mechanistic studies of retrotransposition as well as retrotransposon diversity.

Autophagy-Related Protein MAP1LC3C Plays a Crucial Role in Odontogenic Differentiation of Human Dental Pulp Cells

BACKGROUND@#Autophagy plays important roles in odontogenic differentiation of dental pulp cells (DPCs) in the developmental stage of tooth bud. Few studies have reported the role of autophagy during reparative dentin formation process. The objective of this study was to discover gene expression pattern correlated to autophagy and their role during odontogenic differentiation process in DPCs. @*METHODS@#After tooth cavities were prepared on the mesial surface of lower first molar crown of rats. Odontogenic differentiation and reparative dentin formation were assessed based on detection of morphology change with hematoxylin and eosin staining. @*RESULTS@#After tooth cavities were prepared on the mesial surface of lower first molar crown of rats, odontogenic differentiation and reparative dentin formation were assessed based on detection of morphology change with hematoxylin and eosin staining and dentin sialophosphoprotein (DSPP), whereas autophagy inhibitor 3-methyladenine (3MA) reversed. @*Results@#of quantitative polymerized chain reaction array of autophagosome formation related genes revealed that GABARAPL2 was prominently upregulated while expression of other ATG8 family members were moderately increased after tooth cavity preparation. In addition, human DPCs incubated in differentiation medium predominantly upregulated MAP1LC3C, which selectively decreased by 3MA but not by autophagy enhancer trehalose. Knock-down of MAP1LC3C using shRNA resulted in strong downregulation of dentin matrix protein 1 and DSPP as well-known odontogenic marker compared to knock-down of MAP1LC3B during odontogenic differentiation process of human DPCs. @*CONCLUSION@#Our results suggest that MAP1LC3C plays a crucial role in odontogenic differentiation of human DPCs via regulating autophagic flux.

Autophagy-Related Protein MAP1LC3C Plays a Crucial Role in Odontogenic Differentiation of Human Dental Pulp Cells

BACKGROUND@#Autophagy plays important roles in odontogenic differentiation of dental pulp cells (DPCs) in the developmental stage of tooth bud. Few studies have reported the role of autophagy during reparative dentin formation process. The objective of this study was to discover gene expression pattern correlated to autophagy and their role during odontogenic differentiation process in DPCs. @*METHODS@#After tooth cavities were prepared on the mesial surface of lower first molar crown of rats. Odontogenic differentiation and reparative dentin formation were assessed based on detection of morphology change with hematoxylin and eosin staining. @*RESULTS@#After tooth cavities were prepared on the mesial surface of lower first molar crown of rats, odontogenic differentiation and reparative dentin formation were assessed based on detection of morphology change with hematoxylin and eosin staining and dentin sialophosphoprotein (DSPP), whereas autophagy inhibitor 3-methyladenine (3MA) reversed. @*Results@#of quantitative polymerized chain reaction array of autophagosome formation related genes revealed that GABARAPL2 was prominently upregulated while expression of other ATG8 family members were moderately increased after tooth cavity preparation. In addition, human DPCs incubated in differentiation medium predominantly upregulated MAP1LC3C, which selectively decreased by 3MA but not by autophagy enhancer trehalose. Knock-down of MAP1LC3C using shRNA resulted in strong downregulation of dentin matrix protein 1 and DSPP as well-known odontogenic marker compared to knock-down of MAP1LC3B during odontogenic differentiation process of human DPCs. @*CONCLUSION@#Our results suggest that MAP1LC3C plays a crucial role in odontogenic differentiation of human DPCs via regulating autophagic flux.

Arabidopsis retrotransposon virus-like particles and their regulation by epigenetically activated small RNA.

In Arabidopsis, LTR retrotransposons are activated by mutations in the chromatin gene DECREASE in DNA METHYLATION 1 (DDM1), giving rise to 21- to 22-nt epigenetically activated siRNA (easiRNA) that depend on RNA DEPENDENT RNA POLYMERASE 6 (RDR6). We purified virus-like particles (VLPs) from ddm1 and ddm1rdr6 mutants in which genomic RNA is reverse transcribed into complementary DNA. High-throughput short-read and long-read sequencing of VLP DNA (VLP DNA-seq) revealed a comprehensive catalog of active LTR retrotransposons without the need for mapping transposition, as well as independent of genomic copy number. Linear replication intermediates of the functionally intact COPIA element EVADE revealed multiple central polypurine tracts (cPPTs), a feature shared with HIV in which cPPTs promote nuclear localization. For one member of the ATCOPIA52 subfamily (SISYPHUS), cPPT intermediates were not observed, but abundant circular DNA indicated transposon "suicide" by auto-integration within the VLP. easiRNA targeted EVADE genomic RNA, polysome association of GYPSY (ATHILA) subgenomic RNA, and transcription via histone H3 lysine-9 dimethylation. VLP DNA-seq provides a comprehensive landscape of LTR retrotransposons and their control at transcriptional, post-transcriptional, and reverse transcriptional levels.

Two-Stage Total Knee Arthroplasty for Prosthetic Joint Infection

PURPOSE: This retrospective review was conducted to identify prognostic factors for two-stage reimplantation for infected total knee arthroplasty (TKA) and the rate of reinfection following revision TKA. MATERIALS AND METHODS: Out of 88 patients diagnosed with post-TKA infection between 1998 and 2011, 76 underwent two-stage reimplantation and were reviewed in this study. The 76 patients were divided into two groups-those who experienced reinfection and those who did not. Comorbidities, culture results, and inflammation indices were analyzed and compared between the two groups. RESULTS: Of the 76 patients who underwent a two-stage reimplantation, 18 (23.7%) experienced reinfection. Patients with more than three comorbidities had significantly higher reinfection rates than those with less than three comorbidities (47.1% vs. 4.8%, p=0.032). The reinfection rate between the culture positive prosthetic joint infection group and the culture negative prosthetic joint infection group was not significantly different (p=0.056). Inflammation indices (erythrocyte sedimentation rate [ESR] and C-reactive protein [CRP]) showed a statistically significant difference between patients with reinfection and those without reinfection at 4 weeks after the first-stage surgery. CONCLUSIONS: Reimplantation must be carefully performed when the risk of reinfection is high, particularly in patients with more than three systemic or local comorbidities and higher inflammation indices (ESR and CRP) prior to revision TKA.

A trihelix DNA binding protein counterbalances hypoxia-responsive transcriptional activation in Arabidopsis.

Transcriptional activation in response to hypoxia in plants is orchestrated by ethylene-responsive factor group VII (ERF-VII) transcription factors, which are stable during hypoxia but destabilized during normoxia through their targeting to the N-end rule pathway of selective proteolysis. Whereas the conditionally expressed ERF-VII genes enable effective flooding survival strategies in rice, the constitutive accumulation of N-end-rule-insensitive versions of the Arabidopsis thaliana ERF-VII factor RAP2.12 is maladaptive. This suggests that transcriptional activation under hypoxia that leads to anaerobic metabolism may need to be fine-tuned. However, it is presently unknown whether a counterbalance of RAP2.12 exists. Genome-wide transcriptome analyses identified an uncharacterized trihelix transcription factor gene, which we named HYPOXIA RESPONSE ATTENUATOR1 (HRA1), as highly up-regulated by hypoxia. HRA1 counteracts the induction of core low oxygen-responsive genes and transcriptional activation of hypoxia-responsive promoters by RAP2.12. By yeast-two-hybrid assays and chromatin immunoprecipitation we demonstrated that HRA1 interacts with the RAP2.12 protein but with only a few genomic DNA regions from hypoxia-regulated genes, indicating that HRA1 modulates RAP2.12 through protein-protein interaction. Comparison of the low oxygen response of tissues characterized by different levels of metabolic hypoxia (i.e., the shoot apical zone versus mature rosette leaves) revealed that the antagonistic interplay between RAP2.12 and HRA1 enables a flexible response to fluctuating hypoxia and is of importance to stress survival. In Arabidopsis, an effective low oxygen-sensing response requires RAP2.12 stabilization followed by HRA1 induction to modulate the extent of the anaerobic response by negative feedback regulation of RAP2.12. This mechanism is crucial for plant survival under suboptimal oxygenation conditions. The discovery of the feedback loop regulating the oxygen-sensing mechanism in plants opens new perspectives for breeding flood-resistant crops.

Efficacy and Safety of Stem Cell Therapies for Patients with Stroke: a Systematic Review and Single Arm Meta-Analysis

BACKGROUND AND OBJECTIVES: Stem cell-based therapy is a potential new approach in the treatment of stroke. However, the efficacy and safety of these treatments are not yet fully understood. Therefore, we performed a meta-analysis of available single-arm studies using stem cell-based therapy in patients with stroke. METHODS: We searched MEDLINE, EMBASE, and the Cochrane database for studies of stem cell therapy in patients with stroke from its inception through July 2014. The articles included in the search were restricted to the English language, studies with at least 5 patients, and those using cell-based therapies for treating stroke. RESULTS: Fourteen studies included in the meta-analysis. The pooled mean difference in National Institutes of Health Stroke Scale (NIHSS) scores from baseline to follow-up points was 5.7 points (95%CI: -8.2 to -3.2, I2=91.5%) decreased. Also the pooled mean difference in modified Bathel index (BI) score was increased by 31.5 points (95%CI: 35.6~14.9, I2=52.7%) and the pooled incidence rate to achieve on modified Rankin score (mRS)< or =2 was 40% (95% CI: 30%~51%, I2=35.4%) at follow-up points. The pooled incidence rates of death, seizure, and infection were 13% (95%CI, 8~23%), 15% (95%CI, 8~25%), and 15% (95%CI, 8~23%), respectively. CONCLUSIONS: The published data suggest that stem cell-based therapy for patients with stroke can be judged as effective based on single arm clinical studies. However, clinical benefits of stem cell therapy for patients with stroke need further investigation and reevaluation to test the clinical efficacy.

Linking genes of unknown function with abiotic stress responses by high-throughput phenotype screening.

Over 13% of all genes in the Arabidopsis thaliana genome encode for proteins classified as having a completely unknown function, with the function of >30% of the Arabidopsis proteome poorly characterized. Although empirical data in the form of mRNA and proteome profiling experiments suggest that many of these proteins play an important role in different biological processes, their functional characterization remains one of the major challenges in modern biology. To expand the annotation of genes with unknown function involved in the response of Arabidopsis to different environmental stress conditions, we selected 1007 such genes and tested the response of their corresponding homozygous T-DNA insertional mutants to salinity, oxidative, osmotic, heat, cold and hypoxia stresses. Depending on the specific abiotic stresses tested, 12-31% of mutants had an altered stress-response phenotype. Interestingly, 832 out of 1007 mutants showed tolerance or sensitivity to more than one abiotic stress treatment, suggesting that genes of unknown function could play an important role in abiotic stress-response signaling, or general acclimation mechanisms. Further analysis of multiple stress-response phenotypes within different populations of mutants revealed interesting links between acclimation to heat, cold and oxidative stresses, as well as between sensitivity to ABA, osmotic, salinity, oxidative and hypoxia stresses. Our findings provide a significant contribution to the biological characterization of genes with unknown function in Arabidopsis and demonstrate that many of these genes play a key role in the response of plants to abiotic stresses.

Association Between Work Conditions and Smoking in South Korea

BACKGROUND: A variety of sociodemographic factors, such as gender, age, household income, and educational level, influence individuals' likelihood of smoking. Work-related factors may also be linked to smoking behavior. We sought to investigate the relationship between smoking and work environment in South Korea. METHODS: We analyzed data from the Fifth Korean National Health and Nutrition Examination Survey to determine whether there was an association between smoking and occupation type (e.g., manual, nonmanual, or service work), night-shift work, and hours worked/week (e.g., 60 hours) for 4,685 workers. Regression models were adjusted for sociodemographic variables such as age, recent alcohol consumption, hours slept, educational level, and household income. RESULTS: The prevalence of smoking was 50.1% in men and 7.2% in women. For women, manual workers had 2.34 times [95% confidence interval (CI): 1.02-5.36] greater odds of smoking compared with nonmanual workers, whereas service workers had 2.37 times greater odds (95% CI: 1.28-4.40). Furthermore, women who worked 49-60 hours had 2.21 times greater odds of smoking (95% CI: 1.10-3.75) as compared with women who worked 40-48 hours. CONCLUSION: Women who work long hours or who are employed in service or manual positions are more likely to smoke. These results indicate a need in South Korea to target these specific groups when creating nonsmoking policies.

Making sense of low oxygen sensing.

Plant-specific group VII Ethylene Response Factor (ERF) transcription factors have emerged as pivotal regulators of flooding and low oxygen responses. In rice (Oryza sativa), these proteins regulate contrasting strategies of flooding survival. Recent studies on Arabidopsis thaliana group VII ERFs show they are stabilized under hypoxia but destabilized under oxygen-replete conditions via the N-end rule pathway of targeted proteolysis. Oxygen-dependent sequestration at the plasma membrane maintains at least one of these proteins, RAP2.12, under normoxia. Remarkably, SUB1A, the rice group VII ERF that enables prolonged submergence tolerance, appears to evade oxygen-regulated N-end rule degradation. We propose that the turnover of group VII ERFs is of ecological relevance in wetland species and might be manipulated to improve flood tolerance of crops.

The Effect of Water Exercise Program for Treating the Gestational Edema / 대한주산의학회잡지

PURPOSE: To confirm the effect of water exercise program for treating the gestational edema. METHODS: Both low leg volume, body weight and urine specific gravity were measured in thirty women with gestational edema before and after water exercise program. Fetal heart rate, maternal heart rate and maternal blood pressure were measured before and after water exercise program. RESULTS: Right leg volume was decreased by 286 ml from 1714 to 1428 mL (P<.0001), left leg volume was decreased by 267 mL from 1,644 to 1,377 mL (P<0.0001), and total leg volume was decreased by 553 mL from 3,359 to 2,805 mL (P<0.0001). Urine specific gravity was decreased by 0.0047 from 1.0197 to 1.0150 (P=0.004). Maternal body weight, heart rate, blood pressure, and fetal heart rate were showed no significant change. CONCLUSION: Water exercise program is effective and safe method for treating the gestational edema.

Comparisons of Oxidative Stress during Laparoscopic Cholecystectomy and Open Cholecystectomy

PURPOSE: During oxidative stress, the levels of oxygen free radical increase dramatically, which plays a role in apoptosis, aging and is chemic injury, but also leads to positive effects such as induction of host defense genes and mobilization of ion transport systems. It has been suggested that the advantages of laparoscopic surgery are closely related to the reduced oxidative stress that occurs during laparoscopic cholecystectomy (LC) when compared to open cholecystectomy (OC). This study was conducted to compare oxidative stress markers including total antioxidant status (TAS), superoxide dismutase (SOD) and gluthathione reductase (GR) between the LC group and OC group to determine if these surgical procedures result in different patterns of oxidative stress. METHODS: Our prospective study included fifty patients with symptomatic cholelithiasis and cholecystitis, of whom 25 underwent LC and 25 underwent OC. The plasma levels of oxidative stress markers (TAS, SOD, and GR) were measured preoperatively and on the 1st, 2nd and 3rd postoperative days. RESULTS: The postoperative hospitalization days differed significantly between the two groups (p0.05). An acceptable postoperative decrease in SOD was observed in the OC group, especially after the 2nd postoperative day (p0.05) upon analysis of covariance. A significant postoperative decrease in the level of SOD was observed in the OC group, especially after the 2nd postoperative day (p<0.01), and there was also a significant difference in the serial change in SOD between groups (p=0.020). The level of GR in the OC group decreased significantly on the 2nd postoperative day (p=0.022). Moreover, ANCOVA revealed a significant difference in the serial changes in thelevel of GR between the two groups (p=0.039). CONCLUSION: Our study compared oxidative stress between LC and OC groups based on the levels of TAS, SOD, and GR. We found that minimally invasive surgery, such as laparoscopic cholecystectomy, produced less oxidative stress than open surgery.

A Case of Sarcoidosis in a Stonemason Exposed to Crystalline Silica / 대한산업의학회지

BACKGROUND: Sarcoidosis is a systemic granulomatous disease that can affect any organ, the exact cause of which is uncertain. Currently, investigations of crystalline silica improve the mechanism how it works the course of autoimmune diseases and some hypothesis supports that it also can attribute to sarcoidosis. CASE REPORT: The patient was a 53-year-old male, who works as a stonemason for 30 years. Sarcoidosis was suspected based on his chest X-ray and CT(Computed tomography). A biopsy was performed and he was indeed diagnosed with sarcoidosis. CONCLUSION: It is thought that sarcoidosis is more prevalent in the people who work at places with a risk of exposure to crystalline silica. This case suggests that if a patient gets sarcoidosis after being exposed to crystalline silica, or after once being diagnosed with silicosis, his or her sarcoidosis may have occurred due to exposure to crystalline silica.

Homeostatic response to hypoxia is regulated by the N-end rule pathway in plants.

Plants and animals are obligate aerobes, requiring oxygen for mitochondrial respiration and energy production. In plants, an unanticipated decline in oxygen availability (hypoxia), as caused by roots becoming waterlogged or foliage submergence, triggers changes in gene transcription and messenger RNA translation that promote anaerobic metabolism and thus sustain substrate-level ATP production. In contrast to animals, oxygen sensing has not been ascribed to a mechanism of gene regulation in response to oxygen deprivation in plants. Here we show that the N-end rule pathway of targeted proteolysis acts as a homeostatic sensor of severe low oxygen levels in Arabidopsis, through its regulation of key hypoxia-response transcription factors. We found that plants lacking components of the N-end rule pathway constitutively express core hypoxia-response genes and are more tolerant of hypoxic stress. We identify the hypoxia-associated ethylene response factor group VII transcription factors of Arabidopsis as substrates of this pathway. Regulation of these proteins by the N-end rule pathway occurs through a characteristic conserved motif at the amino terminus initiating with Met-Cys. Enhanced stability of one of these proteins, HRE2, under low oxygen conditions improves hypoxia survival and reveals a molecular mechanism for oxygen sensing in plants via the evolutionarily conserved N-end rule pathway. SUB1A-1, a major determinant of submergence tolerance in rice, was shown not to be a substrate for the N-end rule pathway despite containing the N-terminal motif, indicating that it is uncoupled from N-end rule pathway regulation, and that enhanced stability may relate to the superior tolerance of Sub1 rice varieties to multiple abiotic stresses.

Molecular characterization of the submergence response of the Arabidopsis thaliana ecotype Columbia.

• A detailed description of the molecular response of Arabidopsis thaliana to submergence can aid the identification of genes that are critical to flooding survival. • Rosette-stage plants were fully submerged in complete darkness and shoot and root tissue was harvested separately after the O(2) partial pressure of the petiole and root had stabilized at c. 6 and 0.1 kPa, respectively. As controls, plants were untreated or exposed to darkness. Following quantitative profiling of cellular mRNAs with the Affymetrix ATH1 platform, changes in the transcriptome in response to submergence, early darkness, and O(2)-deprivation were evaluated by fuzzy k-means clustering. This identified genes co-regulated at the conditional, developmental or organ-specific level. Mutants for 10 differentially expressed HYPOXIA-RESPONSIVE UNKNOWN PROTEIN (HUP) genes were screened for altered submergence tolerance. • The analysis identified 34 genes that were ubiquitously co-regulated by submergence and O(2) deprivation. The biological functions of these include signaling, transcription, and anaerobic energy metabolism. HUPs comprised 40% of the co-regulated transcripts and mutants of seven of these genes were significantly altered in submergence tolerance. • The results define transcriptomic adjustments in response to submergence in the dark and demonstrate that the manipulation of HUPs can alter submergence tolerance.