Dynamic Transcriptional Regulation Research Articles

Predicting RNA polymerase II transcriptional elongation pausing and associated histone code.

RNA Polymerase II (Pol II) transcriptional elongation pausing is an integral part of the dynamic regulation of gene transcription in the genome of metazoans. It plays a pivotal role in many vital biological processes and disease progression. However, experimentally measuring genome-wide Pol II pausing is technically challenging and the precise governing mechanism underlying this process is not fully understood. Here, we develop RP3 (RNA Polymerase II Pausing Prediction), a network regularized logistic regression machine learning method, to predict Pol II pausing events by integrating genome sequence, histone modification, gene expression, chromatin accessibility, and protein-protein interaction data. RP3 can accurately predict Pol II pausing in diverse cellular contexts and unveil the transcription factors that are associated with the Pol II pausing machinery. Furthermore, we utilize a forward feature selection framework to systematically identify the combination of histone modification signals associated with Pol II pausing. RP3 is freely available at https://github.com/AMSSwanglab/RP3.

3D genomic alterations during development of skeletal muscle in chicken1

The development of skeletal muscle are complicated processes involving genes responsible for proper muscle morphology, contractility, cell proliferation, differentiation, interactions, migration, and death. The three-dimensional chromatin architecture of skeletal muscle development has not been studied intensively although dynamic transcriptional regulation during differentiation of muscle cells is one of the most deeply studied processes. The RNA-seq was used to analyze the transcriptome pattern during chicken muscle development across 12 stages. Hi-C was used to build a chromatin architectures during four representative stages. ChIP-seq was conducted to identify enhancers in these four stages, which are occupied by histone H3K27ac and H3K4me3 peaks. Results show that large-scale genome architecture changes are mostly unidirectional, and coupled by complex on/off dynamic patterns of gene expression. Specifically, we observed 258.30 Mb of the genome undergoing A/B compartment switching. Notable alterations (316.57 Mb) of interaction frequencies within TADs were observed. Substantial aging-associated genes exhibited ascending connectivity with the compartment transition from repressive to active status during muscle development. Some muscle-related gene promoters that interacted with active enhancers during development, and some myopathy/aging-associated genes that were activated in aging muscle were founded. These results provide key insights into skeletal muscle development in vivo, and offer a valuable resource that allows in-depth functional characterization of candidate genes.

PlantPAN 4.0: updated database for identifying conserved non-coding sequences and exploring dynamic transcriptional regulation in plant promoters.

PlantPAN 4.0 (http://PlantPAN.itps.ncku.edu.tw/) is an integrative resource for constructing transcriptional regulatory networks for diverse plant species. In this release, the gene annotation and promoter sequences were expanded to cover 115 species. PlantPAN 4.0 can help users characterize the evolutionary differences and similarities among cis-regulatory elements; furthermore, this system can now help in identification of conserved non-coding sequences among homologous genes. The updated transcription factor binding site repository contains 3428 nonredundant matrices for 18305 transcription factors; this expansion helps in exploration of combinational and nucleotide variants of cis-regulatory elements in conserved non-coding sequences. Additionally, the genomic landscapes of regulatory factors were manually updated, and ChIP-seq data sets derived from a single-cell green alga (Chlamydomonas reinhardtii) were added. Furthermore, the statistical review and graphical analysis components were improved to offer intelligible information through ChIP-seq data analysis. These improvements included easy-to-read experimental condition clusters, searchable gene-centered interfaces for the identification of promoter regions' binding preferences by considering experimental condition clusters and peak visualization for all regulatory factors, and the 20 most significantly enriched gene ontology functions for regulatory factors. Thus, PlantPAN 4.0 can effectively reconstruct gene regulatory networks and help compare genomic cis-regulatory elements across plant species and experiments.

Transcriptome Analyses Reveal the Mechanism of Changes in the Sugar Constituents of Jujube Fruits under Saline–Alkali Stress

Saline–alkali stress is an important environmental factor affecting the growth and development of plants. Plants affected by saline–alkali stress can mitigate the damage by regulating the content of osmoregulatory substances such as soluble sugars. Elucidating the regulatory mechanism of the changes in sugar fractions in jujube fruits under saline–alkali stress is crucial for the development of the jujube fruit industry in saline areas. In this study, we investigated the effects of saline–alkali stress on the development and sugar contents of jujube fruits by subjecting jujube trees to low- and high-saline–alkali stress treatments. The result showed that low saline–alkali stress increased the content of each sugar component and total sugar, whereas high saline–alkali stress suppressed their contents. In the early developmental stage, the fruit mainly accumulated fructose and glucose, whereas in the late stage, it accumulated mainly sucrose. We screened various genes, namely trehalose 6-phosphate phosphatase gene (LOC107418410), α-amylase gene (LOC107428855), α-glucosidase gene (LOC107418468), sucrose synthase gene (LOC107416188), and β-amylase gene (LOC107430415, LOC107406235), all of which were highly correlated with sucrose content in saline–alkali stress, indicating that the starch and sucrose metabolic pathways of jujube fruit are the key pathways regulating sugar accumulation in response to saline–alkali stress. To summarize, this study provides a system-level perspective on the dynamic transcriptional regulation of jujube fruits under saline–alkali stress. Additionally, the study preliminarily screened key differentially expressed genes that affect sugar accumulation in response to saline–alkali stress, providing a theoretical basis for the scientific regulation of jujube fruit quality.

O-207 zp1 mutation affects oocyte energy metabolism and leads to oocyte apoptosis

Abstract Study question How does the zp1 variation leads to apoptosis oocytes in antral follicular and infertility in females? Summary answer Mutant zp1 induces abnormal pyruvate transport leading to the accumulation of reactive oxygen species (ROS), which activates the mitochondria-mediated apoptosis pathway leading to oocytes apoptosis. What is known already Previous research reported a zp1 mutation in human infertility, and we develop a homologous rat strain to investigate the pathogenic effect. The ovaries of homozygous rat posses growing and fully grown oocytes, the oocytes completely lack a zona pellucida. Only 1-2 eggs were recovered from oviducts of per superovulated homozygous rat, and were not surrounded by a zona pellucida thus lost their fertilization capacity in vitro.Further studies showed that the homozygous female rats not only lacked ZP but also TZPs (an important communication bridge between granulosa cells and oocytes), and the caval follicles showed obvious apoptotic signals. Study design, size, duration In this study, 10 Sprague-Dawley rats were used at 8 weeks of age (5 wild-type and 5 mutant respectively). Participants/materials, setting, methods We used CRISPR/Cas 9-mediated genomic editing technology to develop a rat model carrying the homologous 8bp deleted mutation in Zp1 gene(Zp1mt/mt). The rats were sacrificed by cervical vertebra dislocation and their ovaries were isolated immediately. Then using bulk RNA sequencing of ovaries from Zp1mt/mt and wild-type female rats to identify the differential expression gene between the two groups.The differentially expressed genes enriched from KEGG were verified by qRT-PCR and in vitro functional experiments. Main results and the role of chance Total of 293 DEGs were obtained, of which 144 were up-regulated and 149 were down-regulated. The results of biological process showed that up-regulated genes were mainly involved in redox reaction and negative regulation of cell migration.Down-regulated genes are mainly involved in the follicular growth and development,and related to oocyte energy metabolism. In order to verify the DEG results obtained from RNA sequencing, the differentially expressed gene Gcgr, Plcβ2, Aox3 and Hpgd enriched from KEGG in cell metabolism were verified by qRT-PCR. The results showed that the differentially expressed gene results were consistent with the expression trend of sequencing data.The results showed that there was no significant difference in the expression of Pkm in granulosa cells, while there was a significant difference in the expression of Pdk4 in Zp1mt/mt oocytes. For ROS detection, 52 eggs of 4 Zp1mt/mt rats and 48 eggs of 6 wide-type rats were analyzed for reactive oxygen species. The results showed that the IOD of mutant eggs was significantly higher than that of wild-type,indicating that ROS content in mutant eggs was significantly increased, which was statistically significant.The detection of apoptotic protein expression in eggs shows that the apoptosis probability of Zp1mt/mt eggs is significantly higher than that ofwild-type. Limitations, reasons for caution This study provides more experimental basis and data support for the involvement of ZP in oogenesis, but the effect of ZP deficiency on the dynamic transcriptional regulation of developing oocytes-granulosa cells and the specific molecular mechanism remain to be further explored. Wider implications of the findings The work provides key insights into the crucial features of the transcriptional regulation in Zp1 mutant animal ovaries, and offers important clues for exploring the potential mechanism of abnormal oocyte development due to ZP deficiency. Trial registration number none

Network Biology Analyses and Dynamic Modeling of Gene Regulatory Networks under Drought Stress Reveal Major Transcriptional Regulators in Arabidopsis.

Drought is one of the most serious abiotic stressors in the environment, restricting agricultural production by reducing plant growth, development, and productivity. To investigate such a complex and multifaceted stressor and its effects on plants, a systems biology-based approach is necessitated, entailing the generation of co-expression networks, identification of high-priority transcription factors (TFs), dynamic mathematical modeling, and computational simulations. Here, we studied a high-resolution drought transcriptome of Arabidopsis. We identified distinct temporal transcriptional signatures and demonstrated the involvement of specific biological pathways. Generation of a large-scale co-expression network followed by network centrality analyses identified 117 TFs that possess critical properties of hubs, bottlenecks, and high clustering coefficient nodes. Dynamic transcriptional regulatory modeling of integrated TF targets and transcriptome datasets uncovered major transcriptional events during the course of drought stress. Mathematical transcriptional simulations allowed us to ascertain the activation status of major TFs, as well as the transcriptional intensity and amplitude of their target genes. Finally, we validated our predictions by providing experimental evidence of gene expression under drought stress for a set of four TFs and their major target genes using qRT-PCR. Taken together, we provided a systems-level perspective on the dynamic transcriptional regulation during drought stress in Arabidopsis and uncovered numerous novel TFs that could potentially be used in future genetic crop engineering programs.

Overcoming the cytoplasmic retention of GDOWN1 modulates global transcription and facilitates stress adaptation.

Dynamic regulation of transcription is crucial for the cellular responses to various environmental or developmental cues. Gdown1 is a ubiquitously expressed, RNA polymerase II (Pol II) interacting protein, essential for the embryonic development of metazoan. It tightly binds Pol II in vitro and competitively blocks the binding of TFIIF and possibly other transcriptional regulatory factors, yet its cellular functions and regulatory circuits remain unclear. Here, we show that human GDOWN1 strictly localizes in the cytoplasm of various types of somatic cells and exhibits a potent resistance to the imposed driving force for its nuclear localization. Combined with the genetic and microscope-based approaches, two types of the functionally coupled and evolutionally conserved localization regulatory motifs are identified, including the CRM1-dependent nucleus export signal (NES) and a novel Cytoplasmic Anchoring Signal (CAS) that mediates its retention outside of the nuclear pore complexes (NPC). Mutagenesis of CAS alleviates GDOWN1's cytoplasmic retention, thus unlocks its nucleocytoplasmic shuttling properties, and the increased nuclear import and accumulation of GDOWN1 results in a drastic reduction of both Pol II and its associated global transcription levels. Importantly, the nuclear translocation of GDOWN1 occurs in response to the oxidative stresses, and the ablation of GDOWN1 significantly weakens the cellular tolerance. Collectively, our work uncovers the molecular basis of GDOWN1's subcellular localization and a novel cellular strategy of modulating global transcription and stress-adaptation via controlling the nuclear translocation of GDOWN1.

ATM-mediated ELL phosphorylation enhances its self-association through increased EAF1 interaction and inhibits global transcription during genotoxic stress.

Mammalian cells immediately inhibit transcription upon exposure to genotoxic stress to avoid fatal collision between ongoing transcription and newly recruited DNA repair machineries to protect genomic integrity. However, mechanisms of this early transcriptional inhibition are poorly understood. In this study, we decipher a novel role of human EAF1, a positive regulator of ELL-dependent RNA Polymerase II-mediated transcription in vitro, in regulation of temporal inhibition of transcription during genotoxic stress. Our results show that, besides Super Elongation Complex (SEC) and Little Elongation Complex (LEC), human ELL (aka ELL1) also forms a complex with EAF1 alone. Interestingly, contrary to the in vitro studies, EAF1 inhibits ELL-dependent RNA polymerase II-mediated transcription of diverse target genes. Mechanistically, we show that intrinsic self-association property of ELL leads to its reduced interaction with other SEC components. EAF1 enhances ELL self-association and thus reduces its interaction with other SEC components leading to transcriptional inhibition. Physiologically, we show that upon exposure to genotoxic stress, ATM-mediated ELL phosphorylation-dependent enhanced EAF1 association results in reduced ELL interaction with other SEC components that lead to global transcriptional inhibition. Thus, we describe an important mechanism of dynamic transcriptional regulation during genotoxic stress involving post-translational modification of a key elongation factor.

C/EBPδ-induced epigenetic changes control the dynamic gene transcription of S100a8 and S100a9.

The proinflammatory alarmins S100A8 and S100A9 are among the most abundant proteins in neutrophils and monocytes but are completely silenced after differentiation to macrophages. The molecular mechanisms of the extraordinarily dynamic transcriptional regulation of S100a8 and S100a9 genes, however, are only barely understood. Using an unbiased genome-wide CRISPR/Cas9 knockout (KO)-based screening approach in immortalized murine monocytes, we identified the transcription factor C/EBPδ as a central regulator of S100a8 and S100a9 expression. We showed that S100A8/A9 expression and thereby neutrophil recruitment and cytokine release were decreased in C/EBPδ KO mice in a mouse model of acute lung inflammation. S100a8 and S100a9 expression was further controlled by the C/EBPδ antagonists ATF3 and FBXW7. We confirmed the clinical relevance of this regulatory network in subpopulations of human monocytes in a clinical cohort of cardiovascular patients. Moreover, we identified specific C/EBPδ-binding sites within S100a8 and S100a9 promoter regions, and demonstrated that C/EBPδ-dependent JMJD3-mediated demethylation of H3K27me3 is indispensable for their expression. Overall, our work uncovered C/EBPδ as a novel regulator of S100a8 and S100a9 expression. Therefore, C/EBPδ represents a promising target for modulation of inflammatory conditions that are characterized by S100a8 and S100a9 overexpression.

Programmable Synthetic Upstream Activating Sequence Library for Fine-Tuning Gene Expression Levels in Saccharomyces cerevisiae.

A wide dynamic range of promoters is necessary for fine-tuning transcription levels. However, weak intensity and narrow dynamic range limit transcriptional regulation via constitutive promoters. The upstream activation sequence (UAS) located upstream of the core promoter is a crucial region that could obviously enhance promoter strength. Herein, we created a random mutagenesis library consisting of 330 different variants based on the UAS of the TDH3 promoter with an ∼37-fold dynamic range by error-prone polymerase chain reaction (PCR) and obtained strong intensity mutant UAS, which was ∼12-fold greater than the wild-type UASTDH3. Analysis of the mutant library revealed 15 strength-enhancing sites and their corresponding bases of the UASTDH3 regions, which provided the impetus for a synthetic library. The resulting 32 768 mutant UAS library was constructed by permutation and combination of the bases of the 15 enhancing sites. To characterize the library, a strength prediction model was built by correlating DNA structural features and UAS strength, which provided a model between UAS sequence and intensity. Following characterization, the UAS library was applied to precisely regulate gene expression in the production of β-carotene, proving that the UAS library would be a useful tool for gene tuning in metabolic engineering. In summary, we designed, constructed, and characterized a UAS library that facilitated precise tuning of transcription levels of target proteins.

Architecture and Dynamics of the Wounding-Induced Gene Regulatory Network During the Oolong Tea Manufacturing Process (Camellia sinensis).

Understanding extensive transcriptional reprogramming events mediated by wounding during the oolong tea manufacturing process is essential for improving oolong tea quality. To improve our comprehension of the architecture of the wounding-induced gene regulatory network, we systematically analyzed the high-resolution transcriptomic and metabolomic data from wounding-treated (after turnover stage) tea leaves at 11 time points over a 220-min period. The results indicated that wounding activates a burst of transcriptional activity within 10 min and that the temporal expression patterns over time could be partitioned into 18 specific clusters with distinct biological processes. The transcription factor (TF) activity linked to the TF binding motif participated in specific biological processes within different clusters. A chronological model of the wounding-induced gene regulatory network provides insight into the dynamic transcriptional regulation event after wounding treatment (the turnover stage). Time series data of wounding-induced volatiles reveal the scientific significance of resting for a while after wounding treatment during the actual manufacturing process of oolong tea. Integrating information-rich expression data with information on volatiles allowed us to identify many high-confidence TFs participating in aroma formation regulation after wounding treatment by using weighted gene co-expression network analysis (WGCNA). Collectively, our research revealed the complexity of the wounding-induced gene regulatory network and described wounding-mediated dynamic transcriptional reprogramming events, serving as a valuable theoretical basis for the quality formation of oolong tea during the post-harvest manufacturing process.

Dynamic formation and transcriptional regulation mediated by phytohormones during chalkiness formation in rice

BackgroundRice (Oryza sativa L.) Chalkiness, the opaque part in the kernel endosperm formed by loosely piled starch and protein bodies. Chalkiness is a complex quantitative trait regulated by multiple genes and various environmental factors. Phytohormones play important roles in the regulation of chalkiness formation but the underlying molecular mechanism is still unclear at present.ResultsIn this research, Xiangzaoxian24 (X24, pure line of indica rice with high-chalkiness) and its origin parents Xiangzaoxian11 (X11, female parent, pure line of indica rice with high-chalkiness) and Xiangzaoxian7 (X7, male parent, pure line of indica rice with low-chalkiness) were used as materials. The phenotype, physiological and biochemical traits combined with transcriptome analysis were conducted to illustrate the dynamic process and transcriptional regulation of rice chalkiness formation. Impressively, phytohormonal contents and multiple phytohormonal signals were significantly different in chalky caryopsis, suggesting the involvement of phytohormones, particularly ABA and auxin, in the regulation of rice chalkiness formation, through the interaction of multiple transcription factors and their downstream regulators.ConclusionThese results indicated that chalkiness formation is a dynamic process associated with multiple genes, forming a complex regulatory network in which phytohormones play important roles. These results provided informative clues for illustrating the regulatory mechanisms of chalkiness formation in rice.

Multiple Modes of Regulation Control Dynamic Transcription Patterns During the Mitosis-G1 Transition

Following cell division, genomes must reactivate gene expression patterns that reflect the identity of the cell. Here, we use PRO-seq to examine the mechanisms that reestablish transcription patterns after mitosis. We uncover regulation of transcription cycle at multiple steps including initiation, promoter-proximal pause positioning and escape, poly-A site cleavage and termination during the mitotic-G1 transition. During mitosis, RNA polymerase activity is retained at initiation sites, albeit shifted in position relative to non-mitotic cells. This activity is strongly linked to maintenance of local chromatin architecture during mitosis and is more predictive of rapid gene reactivation than histone modifications previously associated with bookmarking. These molecular bookmarks, combined with sequence-specific transcription factors, direct expression of select cell growth and cell specific genes during mitosis followed by reactivation of functional gene groups with distinct kinetics after mitosis. This study details how dynamic regulation of transcription at multiple steps contributes to gene expression during the cell cycle.

175 Dynamic transcriptional and epigenetic regulation through vitamin D receptor and p63/p53 signaling in epidermal keratinocytes

175 Dynamic transcriptional and epigenetic regulation through vitamin D receptor and p63/p53 signaling in epidermal keratinocytes

Phase separation, transcriptional elongation control, and human diseases.

Precise regulation of gene transcription is of great importance to development and diseases. Promoter-proximal transcriptional pause is a key and general mechanism to precisely control transcription in metazoans. Subsequent to transcription initiation and synthesis of a short RNA, RNA polymerase II (Pol II) usually pauses at the promoter-proximal regions, standing by for further signals to be released into the productive elongation stage. Fine regulation of Pol II pausing and release is achieved by the concerted action of many negative and positive elongation factors, including the super elongation complex (SEC). Recent studies suggested that phase-separated assemblies of transcription regulatory complexes could provide a general biophysical basis for the dynamic regulation of transcription in response to various cellular needs, though direct evidence at endogenous level in living cells is still largely lacking. Here, we summarize and discuss latest advances in understanding how phase separation contributes to RNA polymerase II-mediated transcription, with a focus on transcriptional pause and release.

Chromatin accessibility of kidney tubular cells under stress reveals key transcription factor mediating acute and chronic kidney disease.

Cellular injury caused by stimuli plays an important role in the progression of various diseases including acute and chronic kidney diseases. The dynamic transcriptional regulation responding to stimuli underlies the important mechanism of injury. In this study, we investigated the regulatory elements and their dynamic activities in kidney tubular epithelial cells. We captured the chromatin accessibility and gene expression with ATAC-seq and RNA sequencing under a variety of extracellular stimuli including H2 O2 , TGF-β1, and FG4592 which is an agonist of hypoxia-inducible factor. Our results revealed both condition-specific and condition-shared transcription regulation. Interestingly, the shared regulation program revealed that the key transcription factor HNF1B-mediated cellular reprogramming leads to a common change among the stimuli. We found the HNF1B regulatory network was significantly disrupted in various kidney diseases.

TET1 promotes RXRα expression and adipogenesis through DNA demethylation

Adipose tissue is important for systemic metabolic homeostasis in response to environmental changes, and adipogenesis involves dynamic transcriptional regulation. Ten-eleven translocation (TET) enzymes (TET1, 2 and 3) oxidize the 5-methylcytosine (5mC) in DNA to 5-hydroxylmethylcytosine (5hmC), which associates with transcriptional activation. Step by step, 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) are further generated by TETs and the cytosine can be restored through base-excision repair. It is still unclear how DNA demethylation is involved in adipogenesis. Through a phenotypic screen, we found TET inhibition decreased adipocyte differentiation from mesenchymal stem cells (MSCs). Comparing with the undifferentiated MSCs, the differentiated adipocytes exhibited much higher levels of 5hmC and slightly increased 5fC and 5caC. Higher 5hmC was associated with better differentiation at single-cell level by image analysis. TET1 is upregulated in differentiation and depletion of it significantly impaired the gain of 5hmC. Furthermore, Tet1 depletion significantly hampered the adipocyte differentiation. Using RNA-seq, 5mC and 5hmC-DNA immunoprecipitation, we found that Tet1 knockout led to lower expression of genes associated with lipid metabolism and fat cell differentiation. Genes with loss of 5mC or gain of 5hmC in adipocytes include Lipe, Bmp4 and Rxra, etc. RXRα agonist partially rescued the inhibitory effect of Tet1 knockout for adipogenesis. So, Rxra is one of the critical TET1 modulated genes. Together, TET1-mediated active DNA demethylation plays an important role in adipogenesis.

Solid tumours hijack the histone variant network.

Cancer is a complex disease characterized by loss of cellular homeostasis through genetic and epigenetic alterations. Emerging evidence highlights a role for histone variants and their dedicated chaperones in cancer initiation and progression. Histone variants are involved in processes as diverse as maintenance of genome integrity, nuclear architecture and cell identity. On a molecular level, histone variants add a layer of complexity to the dynamic regulation of transcription, DNA replication and repair, and mitotic chromosome segregation. Because these functions are critical to ensure normal proliferation and maintenance of cellular fate, cancer cells are defined by their capacity to subvert them. Hijacking histone variants and their chaperones is emerging as a common means to disrupt homeostasis across a wide range of cancers, particularly solid tumours. Here we discuss histone variants and histone chaperones as tumour-promoting or tumour-suppressive players in the pathogenesis of cancer.

Transcriptional modulation patterns of abalone Haliotis discus hannai hypoxia inducible factor-1α (HIF-1α) in interdependent crosstalk between hypoxia, infection, and environmental stresses

Hypoxia-inducible factor-1α (HIF-1α) is a key transcription factor for regulating oxygen-dependent homeostasis. Here, we characterized HIF-1α in Pacific abalone (Haliotis discus hannai), an aquaculture-relevant mollusk species, and its transcriptional regulation patterns in response to oxygen-dependent and oxygen-independent stimuli were investigated. The molecular cloning and sequence analysis revealed that the abalone HIF-1α shared conversed features in its domain organization such as basic helix–loop–helix (bHLH) domain, Per-Arnt-Sim (PAS) domain, oxygen-dependent degradation domains (ODDDs), and C-terminal transactivation domain (C-TAD) with metazoan orthologs. The abalone HIF-1α was proven to be transcriptionally active in multiple tissues according to dissolved oxygen contents, with the most sensitive responsiveness in the gill. Under non-hypoxic conditions, the tissue-dependent transcriptional regulation patterns of the abalone HIF-1α were closely correlated and intertwined with those of HSP90 and MT in response to thermal challenge and heavy metal exposure, respectively. The abalone HIF-1α expression was significantly modulated under normoxic conditions in response to immune challenges with lipopolysaccharide and Vibrio harveyi with the highest upregulation in the hemocytes. However, the combined treatment of hypoxia and immune stimulation exhibited no synergistic activation for the induction of HIF-1α mRNA. Collectively, dynamic transcriptional regulation of the abalone HIF-1α with the tissue specificity in response to oxygen-dependent and oxygen-independent stimulatory challenges suggests that HIF-1α plays crucial roles in interdependent crosstalk between hypoxia, innate immunity, and environmental stresses, which can be a useful basis to investigate cellular and physiological responses of farmed abalones to oxygen depletion and other-related stress factors.

Phosphate-Starvation-Inducible S-Like RNase Genes in Rice Are Involved in Phosphate Source Recycling by RNA Decay.

The fine-tuning of inorganic phosphate (Pi) for enhanced use efficiency has long been a challenging subject in agriculture, particularly in regard to rice as a major crop plant. Among ribonucleases (RNases), the RNase T2 family is broadly distributed across kingdoms, but little has been known on its substrate specificity compared to RNase A and RNase T1 families. Class I and class II of the RNase T2 family are defined as the S-like RNase (RNS) family and have showed the connection to Pi recycling in Arabidopsis. In this study, we first carried out a phylogenetic analysis of eight rice and five Arabidopsis RNS genes and identified mono-specific class I and dicot-specific class I RNS genes, suggesting the possibility of functional diversity between class I RNS family members in monocot and dicot species through evolution. We then compared the in silico expression patterns of all RNS genes in rice and Arabidopsis under normal and Pi-deficient conditions and further confirmed the expression patterns of rice RNS genes via qRT-PCR analysis. Subsequently, we found that most of the OsRNS genes were differentially regulated under Pi-deficient treatment. Association of Pi recycling by RNase activity in rice was confirmed by measuring total RNA concentration and ribonuclease activity of shoot and root samples under Pi-sufficient or Pi-deficient treatment during 21 days. The total RNA concentrations were decreased by < 60% in shoots and < 80% in roots under Pi starvation, respectively, while ribonuclease activity increased correspondingly. We further elucidate the signaling pathway of Pi starvation through upregulation of the OsRNS genes. The 2-kb promoter region of all OsRNS genes with inducible expression patterns under Pi deficiency contains a high frequency of P1BS cis-acting regulatory element (CRE) known as the OsPHR2 binding site, suggesting that the OsRNS family is likely to be controlled by OsPHR2. Finally, the dynamic transcriptional regulation of OsRNS genes by overexpression of OsPHR2, ospho2 mutant, and overexpression of OsPT1 lines involved in Pi signaling pathway suggests the molecular basis of OsRNS family in Pi recycling via RNA decay under Pi starvation.