Spatial-temporal Regulation Research Articles

Spatial-temporal regulation of the prostanoid receptor EP2 co-ordinates PGE2-mediated cAMP signaling in decidualizing human endometrium

Spatial-temporal regulation of the prostanoid receptor EP2 co-ordinates PGE2-mediated cAMP signaling in decidualizing human endometrium

Scar/WAVE drives actin protrusions independently of its VCA domain using proline-rich domains

Cell migration requires the constant modification of cellular shape by reorganization of the actin cytoskeleton. Fine-tuning of this process is critical to ensure new actin filaments are formed only at specific times and in defined regions of the cell. The Scar/WAVE complex is the main catalyst of pseudopod and lamellipodium formation during cell migration. It is a pentameric complex highly conserved through eukaryotic evolution and composed of Scar/WAVE, Abi, Nap1/NCKAP1, Pir121/CYFIP, and HSPC300/Brk1. Its function is usually attributed to activation of the Arp2/3 complex through Scar/WAVE's VCA domain, while other parts of the complex are expected to mediate spatial-temporal regulation and have no direct role in actin polymerization. Here, we show in both B16-F1 mouse melanoma and Dictyostelium discoideum cells that Scar/WAVE without its VCA domain still induces the formation of morphologically normal, actin-rich protrusions, extending at comparable speeds despite a drastic reduction of Arp2/3 recruitment. However, the proline-rich regions in Scar/WAVE and Abi subunits are essential, though either is sufficient for the generation of actin protrusions in B16-F1 cells. We further demonstrate that N-WASP can compensate for the absence of Scar/WAVE's VCA domain and induce lamellipodia formation, but it still requires an intact WAVE complex, even if without its VCA domain. We conclude that the Scar/WAVE complex does more than directly activating Arp2/3, with proline-rich domains playing a central role in promoting actin protrusions. This implies a broader function for the Scar/WAVE complex, concentrating and simultaneously activating many actin-regulating proteins as a lamellipodium-producing core.

Transformer-based spatial–temporal detection of apoptotic cell death in live-cell imaging

Intravital microscopy has revolutionized live-cell imaging by allowing the study of spatial–temporal cell dynamics in living animals. However, the complexity of the data generated by this technology has limited the development of effective computational tools to identify and quantify cell processes. Amongst them, apoptosis is a crucial form of regulated cell death involved in tissue homeostasis and host defense. Live-cell imaging enabled the study of apoptosis at the cellular level, enhancing our understanding of its spatial–temporal regulation. However, at present, no computational method can deliver robust detection of apoptosis in microscopy timelapses. To overcome this limitation, we developed ADeS, a deep learning-based apoptosis detection system that employs the principle of activity recognition. We trained ADeS on extensive datasets containing more than 10,000 apoptotic instances collected both in vitro and in vivo, achieving a classification accuracy above 98% and outperforming state-of-the-art solutions. ADeS is the first method capable of detecting the location and duration of multiple apoptotic events in full microscopy timelapses, surpassing human performance in the same task. We demonstrated the effectiveness and robustness of ADeS across various imaging modalities, cell types, and staining techniques. Finally, we employed ADeS to quantify cell survival in vitro and tissue damage in mice, demonstrating its potential application in toxicity assays, treatment evaluation, and inflammatory dynamics. Our findings suggest that ADeS is a valuable tool for the accurate detection and quantification of apoptosis in live-cell imaging and, in particular, intravital microscopy data, providing insights into the complex spatial–temporal regulation of this process.

Transformer-based spatial-temporal detection of apoptotic cell death in live-cell imaging.

Intravital microscopy has revolutionized live-cell imaging by allowing the study of spatial-temporal cell dynamics in living animals. However, the complexity of the data generated by this technology has limited the development of effective computational tools to identify and quantify cell processes. Amongst them, apoptosis is a crucial form of regulated cell death involved in tissue homeostasis and host defense. Live-cell imaging enabled the study of apoptosis at the cellular level, enhancing our understanding of its spatial-temporal regulation. However, at present, no computational method can deliver robust detection of apoptosis in microscopy timelapses. To overcome this limitation, we developed ADeS, a deep learning-based apoptosis detection system that employs the principle of activity recognition. We trained ADeS on extensive datasets containing more than 10,000 apoptotic instances collected both in vitro and in vivo, achieving a classification accuracy above 98% and outperforming state-of-the-art solutions. ADeS is the first method capable of detecting the location and duration of multiple apoptotic events in full microscopy timelapses, surpassing human performance in the same task. We demonstrated the effectiveness and robustness of ADeS across various imaging modalities, cell types, and staining techniques. Finally, we employed ADeS to quantify cell survival in vitro and tissue damage in mice, demonstrating its potential application in toxicity assays, treatment evaluation, and inflammatory dynamics. Our findings suggest that ADeS is a valuable tool for the accurate detection and quantification of apoptosis in live-cell imaging and, in particular, intravital microscopy data, providing insights into the complex spatial-temporal regulation of this process.

Supply Restoration of Data Centers in Flexible Distribution Networks With Spatial-Temporal Regulation

The reliable operation of Internet data centers (IDCs) is crucial to digitization transformation of society. However, the extreme fault on the IDC-located distribution network is fatal to IDC operation. The evolution of flexible distribution networks (FDNs) can satisfy the deep de-pendence of IDC on high-quality and reliable power supply. In FDNs, AC/DC feeders with multiple voltage levels can be flexibly interconnected and adjusted by flexible stations (FSs). It is promising to flexibly enhance operation per-formance of crucial IDCs after fault isolation in FDNs. In this paper, a coordinated supply restoration method of IDCs in FDNs with spatial-temporal regulation is proposed to minimize IDC data-dropping loss under complex faults. First, a spatial-temporal transfer strategy of IDC work-loads is precisely formulated and an FS-based network reconfiguration strategy is proposed. Then, a mixed-integer second-order conic programming model is established for efficient solving. Spatial-temporal coordination among the source, network, storage, and demand sides can be realized without violating physical feasibility. Finally, the proposed method is validated on the modified IEEE 33-node and modified IEEE 123-node test cases. Case studies show that total outage loss is effectively reduced with sufficient utili-zation of available power. Operational performance of FDN is also enhanced under extreme faults.

HiCAR: Analysis of Open Chromatin Associated Long-range Chromatin Interaction Using Low-Input Materials.

Cis-regulatory elements (cREs) and their long-range interactions are crucial for spatial-temporal gene regulation. While cREs can be characterized as accessible chromatin sequences, comprehensively identifying their spatial interactions remains a challenge. We recently developed a method, HiCAR (Hi-C on Accessible Regulatory DNA), which combines Tn5 transposase and chromatin proximity ligation to analyze open chromatin-anchored interactions in low-input cells. Application of HiCAR in human embryonic stem cells and lymphoblastoid cells reveals high-resolution chromatin contacts with efficiency comparable to in situ Hi-C across various distance ranges. Moreover, HiCAR was successfully applied to 30,000 primary human muscle stem cells, showcasing its potential for analyzing chromatin accessibility and looping in low-input primary cells and clinical samples. Here, we provide a detailed step-by-step protocol to perform the updated HiCAR experiments. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Tn5 Transposase Assembly Basic Protocol 2: HiCAR Library Preparation.

A loss-of-function mutation in human Oxidation Resistance 1 disrupts the spatial–temporal regulation of histone arginine methylation in neurodevelopment

BackgroundOxidation Resistance 1 (OXR1) gene is a highly conserved gene of the TLDc domain-containing family. OXR1 is involved in fundamental biological and cellular processes, including DNA damage response, antioxidant pathways, cell cycle, neuronal protection, and arginine methylation. In 2019, five patients from three families carrying four biallelic loss-of-function variants in OXR1 were reported to be associated with cerebellar atrophy. However, the impact of OXR1 on cellular functions and molecular mechanisms in the human brain is largely unknown. Notably, no human disease models are available to explore the pathological impact of OXR1 deficiency.ResultsWe report a novel loss-of-function mutation in the TLDc domain of the human OXR1 gene, resulting in early-onset epilepsy, developmental delay, cognitive disabilities, and cerebellar atrophy. Patient lymphoblasts show impaired cell survival, proliferation, and hypersensitivity to oxidative stress. These phenotypes are rescued by TLDc domain replacement. We generate patient-derived induced pluripotent stem cells (iPSCs) revealing impaired neural differentiation along with dysregulation of genes essential for neurodevelopment. We identify that OXR1 influences histone arginine methylation by activating protein arginine methyltransferases (PRMTs), suggesting OXR1-dependent mechanisms regulating gene expression during neurodevelopment. We model the function of OXR1 in early human brain development using patient-derived brain organoids revealing that OXR1 contributes to the spatial–temporal regulation of histone arginine methylation in specific brain regions.ConclusionsThis study provides new insights into pathological features and molecular underpinnings associated with OXR1 deficiency in patients.

Guanidinium manipulated interfacial polymerization for polyamide nanofiltration membranes with ultra-high permselectivity

Polyamide (PA) nanofiltration (NF) membranes with excellent permeability and selectivity have always been the ultimate pursuit of desalination technology. Herein, we present a guanidinium manipulated interfacial polymerization strategy to develop guanidyl-integrated PA NF membranes with ultra-high permselectivity. A nylon microfiltration membrane is utilized as the support to conduct spatial-temporal regulation of amine monomers along with controllable diffusion reaction. Through introducing 1,3-diaminoguanidine (DAG) or triaminoguanidine (TAG) into the aqueous piperazine solution, the free volumes of PA membranes could be well modulated at the sub-angstrom scale. Consequently, the TAG-integrated PA membrane exhibited high water permeance of 33.1 LMH bar−1 and superior Na2SO4 rejection of 99.2%. Meanwhile, this membrane achieved outstanding anion sieving capability (Cl−/SO42− ∼ 343) and nearly 100% tetracycline removal, which is superior to the “state-of-the-art” PA NF membranes. The DAG-integrated PA membrane attained ultra-high water permeance of 46.5 LMH bar−1 due to its relatively large free volume. In addition, the nylon composite PA membranes displayed desirable anti-pressure and organic solvent-resistant abilities. This study provides a convenient and scalable preparation strategy for highly permselective NF membranes, which holds great application potential in desalination and resource recovery.

Single particle tracking reveals SARS-CoV-2 regulating and utilizing dynamic filopodia for viral invasion

Although severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entry mechanism has been explored, little is known about how SARS-CoV-2 regulates the subcellular structural remodeling to invade multiple organs and cell types. Here, we unveil how SARS-CoV-2 boosts and utilizes filopodia to enter the target cells by real-time imaging. Using SARS-CoV-2 single virus-like particle (VLP) tracking in live cells and sparse deconvolution algorithm, we uncover that VLPs utilize filopodia to reach the entry site in two patterns, “surfing” and “grabbing”, which avoid the virus from randomly searching on the plasma membrane. Moreover, combining mechanical simulation, we elucidate that the formation of virus-induced filopodia and the retraction speed of filopodia depend on cytoskeleton dynamics and friction resistance at the substrate surface caused by loading-virus gravity, respectively. Further, we discover that the entry process of SARS-CoV-2 via filopodia depends on Cdc42 activity and actin-associated proteins fascin, formin, and Arp2/3. Together, our results highlight that the spatial–temporal regulation of actin cytoskeleton by SARS-CoV-2 infection makes filopodia as a highway for virus entry and potentiates it as an antiviral target.

Diverse p120RasGAP interactions with doubly phosphorylated partners EphB4, p190RhoGAP, and Dok1

RasGAP (p120RasGAP), the founding member of the GTPase-activating protein (GAP) family, is one of only nine human proteins to contain two SH2 domains and is essential for proper vascular development. Despite its importance, its interactions with key binding partners remains unclear. In this study we provide a detailed viewpoint of RasGAP recruitment to various binding partners and assess their impact on RasGAP activity. We reveal the RasGAP SH2 domains generate distinct binding interactions with three well-known doubly phosphorylated binding partners: p190RhoGAP, Dok1, and EphB4. Affinity measurements demonstrate a 100-fold weakened affinity for RasGAP-EphB4 binding compared to RasGAP-p190RhoGAP or RasGAP-Dok1 binding, possibly driven by single versus dual SH2 domain engagement with a dominant N-terminal SH2 interaction. Small-angle X-ray scattering reveals conformational differences between RasGAP-EphB4 binding and RasGAP-p190RhoGAP binding. Importantly, these interactions do not impact catalytic activity, implying RasGAP utilizes its SH2 domains to achieve diverse spatial-temporal regulation of Ras signaling in a previously unrecognized fashion.

Multi-copper oxidases SKU5 and SKS1 coordinate cell wall formation using apoplastic redox-based reactions in roots.

The primary cell wall is a fundamental plant constituent that is flexible but sufficiently rigid to support the plant cell shape. Although many studies have demonstrated that reactive oxygen species (ROS) serve as important signaling messengers to modify the cell wall structure and affect cellular growth, the regulatory mechanism underlying the spatial-temporal regulation of ROS activity for cell wall maintenance remains largely unclear. Here, we demonstrate the role of the Arabidopsis (Arabidopsis thaliana) multicopper oxidase-like protein skewed 5 (SKU5) and its homolog SKU5-similar 1 (SKS1) in root cell wall formation through modulating ROS homeostasis. Loss of SKU5 and SKS1 function resulted in aberrant division planes, protruding cell walls, ectopic deposition of iron, and reduced nicotinamide adeninedinucleotide phosphate (NADPH) oxidase-dependent ROS overproduction in the root epidermis-cortex and cortex-endodermis junctions. A decrease in ROS level or inhibition of NADPH oxidase activity rescued the cell wall defects of sku5 sks1 double mutants. SKU5 and SKS1 proteins were activated by iron treatment, and iron over-accumulated in the walls between the root epidermis and cortex cell layers of sku5 sks1. The glycosylphosphatidylinositol-anchored motif was crucial for membrane association and functionality of SKU5 and SKS1. Overall, our results identified SKU5 and SKS1 as regulators of ROS at the cell surface for regulation of cell wall structure and root cell growth.

Bradykinin promotes murine melanoma cell migration and invasion through endogenous production of superoxide and nitric oxide

Spatial confinement and temporal regulation of signaling by nitric oxide (NO) and reactive oxygen species (ROS) occurs in cancer cells. Signaling mediated by NO and ROS was investigated in two sub clones of the murine melanoma B16F10-Nex2 cell line, Nex10C and Nex8H treated or not with bradykinin (BK). The sub clone Nex10C, similar to primary site cells, has a low capacity for colonizing the lungs, whereas the sub clone Nex8H, similar to metastatic cells, corresponds to a highly invasive melanoma. BK-treated Nex10C cells exhibited a transient increase in NO and an inhibition in basal O2− levels. Inhibition of endogenous NO production by l-NAME resulted in detectable levels of O2−. l-NAME promoted Rac1 activation and enhanced Rac1–PI3K association. l-NAME in the absence of BK resulted in Nex10C cell migration and invasion, suggesting that NO is a negative regulator of O2− mediated cell migration and cell invasion. BK-treated Nex8H cells sustained endogenous NO production through the activation of NOS3. NO activated Rac1 and promoted Rac1–PI3K association. NO stimulated cell migration and cell invasion through a signaling axis involving Ras, Rac1 and PI3K. In conclusion, a role for O2− and NO as positive regulators of Rac1–PI3K signaling associated with cell migration and cell invasion is proposed respectively for Nex10C and Nex8H murine melanoma cells.

Spatial–temporal regulation of fatty alcohol biosynthesis in yeast

BackgroundConstruction of efficient microbial cell factories is one of the core steps for establishing green bio-manufacturing processes. However, the complex metabolic regulation makes it challenging in driving the metabolic flux toward the product biosynthesis. Dynamically coupling the biosynthetic pathways with the cellular metabolism at spatial–temporal manner should be helpful for improving the production with alleviating the cellular stresses.ResultsIn this study, we observed the mismatch between fatty alcohol biosynthesis and cellular metabolism, which compromised the fatty alcohol production in Saccharomyces cerevisiae. To enhance the fatty alcohol production, we spatial-temporally regulated fatty alcohol biosynthetic pathway by peroxisomal compartmentalization (spatial) and dynamic regulation of gene expression (temporal). In particular, fatty acid/acyl-CoA responsive promoters were identified by comparative transcriptional analysis, which helped to dynamically regulate the expression of acyl-CoA reductase gene MaFAR1 and improved fatty alcohol biosynthesis by 1.62-fold. Furthermore, enhancing the peroxisomal supply of acyl-CoA and NADPH further improved fatty alcohol production to 282 mg/L, 2.52 times higher than the starting strain.ConclusionsThis spatial–temporal regulation strategy partially coordinated fatty alcohol biosynthesis with cellular metabolism including peroxisome biogenesis and precursor supply, which should be applied for production of other products in microbes.

A spatial-temporal optimal allocation method of irrigation water resources considering groundwater level

The healthy and sustainable development of irrigation area not only serves as the guarantee of national food production security, but also shoulders the important task of regional ecological security, in which maintaining groundwater level plays an important role. Due to the close relationship between groundwater level and irrigation recharge groundwater, realizing rational use of water resources under strictly implementing the total limit of water use and holding reasonable groundwater level is of great significance to the healthy development of irrigated areas. Therefore, this study established a spatial-temporal optimal allocation regulation method of irrigation water resources by coupling groundwater numerical technology and the characteristics of hydrological cycle with comprehensively considering the dual constraints between total water consumption and reasonable groundwater depth. Besides, taking Helan County, a typical area of Qingtongxia Irrigation district in Ningxia as an example, a case study on optimal allocation of irrigation water resources was carried out. The results show that compared with the actual current water use situation, the total irrigation water shortage rate of Helan County Irrigation District (HCID) decreases from 21.61% to 21%. Under the combined control of total available water and groundwater depths, it is realized the fairness and balance of water use in different regions and periods by the allocation of water resources in spatial and temporal. Meanwhile, the area located in the reasonable groundwater depth range increased by 1.65% after optimization. Overall, the balanced and optimal allocation method of irrigation water resources with both total water use and groundwater depth control is not only improving the efficient and rational utilization of limited water resources, but also can regulate groundwater depth to guarantee regional ecological health and sustainable development.

IL7Rα and TSLPR expression on Langerhans cells in response to inflammatory stimulation

Abstract A key component of immune barriers are innate immune cells localized in the epithelium responsible for sensing local signals such as foreign antigens and cytokines. In the skin, specialized antigen presenting cells (APC) known as Langerhans cells (LC) can integrate these signals influencing downstream T cell activation and polarization. Thymic stromal lymphopoietin (TSLP) is a proinflammatory mediator released by keratinocytes that promotes LC to enhance type 2 immune response (Th2). When Th2 response becomes unbalanced, it induces type 2 inflammation as seen in atopic dermatitis. TSLP signaling is regulated by two cell surface receptor chains: TSLP receptor (TSLPR) and IL7Rα. Interestingly, IL7Rα is not commonly expressed in murine conventional APC such as dendritic cells (DC). Our previous findings have shown that IL7Rα expression regulates TSLP sensitivity of splenic DCs (sDC) ex vivo. However, the receptor expression dynamic in tissue resident LC and its biological implications has not yet been elucidated. In this study we enriched LC from healthy mice B6 mice using MACS magnetic beads. Cytokine surface receptors and pospho-STAT5 activation were assessed using flow cytometry. Moreover, topic administration of vitamin analog MC903 will be used to evaluate TSLPR and IL7Rα dynamic. Our current results indicate that IL7Rα is expressed on unstimulated LC contrary to sDC. Furthermore, TSLPR was not differently expressed between LC and sDC. Functional assessment of p-STAT5 ex vivo and the dynamic of these receptors in the context of MC903 treatment in vivo is yet to be measured. Our results suggest that tissue resident APC regulate differently cytokines receptors enabling spatial-temporal regulation of proinflammatory signals. Academy of Finland (IJ: grants: 25013080481 and 25013142041), The Competitive State Research Financing of the Expert Responsibility Area of Fimlab Laboratories (grant X51409 to IJ), Tampere University Hospital Support Foundation (IJ) and Tampere Tuberculosis Foundation (IJ).

Quantitative live imaging of floral organ initiation and floral meristem termination in Aquilegia.

In-depth investigation of any developmental process in plants requires knowledge of both the underpinning molecular networks and how they directly determine patterns of cell division and expansion over time. Floral meristems (FMs) produce floral organs, after which they undergo floral meristem termination (FMT); precise control of organ initiation and FMT is crucial to the reproductive success of any flowering plant. Using live confocal imaging, we characterized developmental dynamics during floral organ primordia initiation and FMT in Aquilegia coerulea (Ranunculaceae). Our results uncover distinct patterns of primordium initiation between stamens and staminodes compared with carpels, and provide insight into the process of FMT, which is discernable based on cell division dynamics that precede carpel initiation. To our knowledge, this is the first quantitative live imaging of meristem development in a system with numerous whorls of floral organs, as well as an apocarpous gynoecium. This study provides crucial information for our understanding of how the spatial-temporal regulation of floral meristem behavior is achieved in both evolutionary and developmental contexts. This article has an associated 'The people behind the papers' interview.

Dendritic Cell Subsets: The Next Target for Pregnant Complications?

Dendritic cells (DCs) are professional antigen-presenting cells with both immune stimulatory and regulatory functions. DCs are critical players in pregnancy, whose dysregulation is associated with multiple pregnancy-related complications. According to recently reported findings, this review aimed to elaborate the effects of subsets of DCs on gestation, including plasmacytoid DCs (pDCs), conventional DCs (cDCs), immature DCs (iDCs), and mature DCs (mDCs). The present review clearly illustrate that the subsets of DCs, the spatial-temporal regulation of DCs during pregnancy, the balance of pDCs/cDCs ratio influenced the pregnancy outcomes, and the balance of iDCs/mDCs ratio influenced the pregnancy outcomes.  The possibility of targeting DC subsets for the treatment of pregnancy-related complications and eliminating the remaining gaps were discussed. A deeper understanding of DC subsets regulation during pregnancy can significantly contribute to the clinical application of these cells.

Inside Cover: Red‐ and Far‐Red‐Emitting Zinc Probes with Minimal Phototoxicity for Multiplexed Recording of Orchestrated Insulin Secretion (Angew. Chem. Int. Ed. 49/2021)

Insulin secretion from β-cells in intact islets can now be recorded together with calcium signal and organelles. In their Research Article on page 25846, Zhixing Chen and co-workers developed a new class of red- and far-red-emitting Zn2+ probes with minimal phototoxicity. Tailored for 4D, long-term, and multiple-color recording of Zn2+/insulin co-secretion in β-cells and islets, the new probes promise to unveil the spatial-temporal regulation of islet endocrinology.

Correlation of cellular traction forces and dissociation kinetics of adhesive protein zyxin revealed by multi-parametric live cell microscopy.

Cells exert traction forces on the extracellular matrix to which they are adhered through the formation of focal adhesions. Spatial-temporal regulation of traction forces is crucial in cell adhesion, migration, cellular division, and remodeling of the extracellular matrix. By cultivating cells on polyacrylamide hydrogels of different stiffness we were able to investigate the effects of substrate stiffness on the generation of cellular traction forces by Traction Force Microscopy (TFM), and characterize the molecular dynamics of the focal adhesion protein zyxin by Fluorescence Correlation Spectroscopy (FCS) and Fluorescence Recovery After Photobleaching (FRAP). As the rigidity of the substrate increases, we observed an increment of both, cellular traction generation and zyxin residence time at the focal adhesions, while its diffusion would not be altered. Moreover, we found a positive correlation between the traction forces exerted by cells and the residence time of zyxin at the substrate elasticities studied. We found that this correlation persists at the subcellular level, even if there is no variation in substrate stiffness, revealing that focal adhesions that exert greater traction present longer residence time for zyxin, i.e., zyxin protein has less probability to dissociate from the focal adhesion.

LCM and RNA-seq analyses revealed roles of cell cycle and translational regulation and homoeolog expression bias in cotton fiber cell initiation

BackgroundCotton fibers provide a powerful model for studying cell differentiation and elongation. Each cotton fiber is a singular and elongated cell derived from epidermal-layer cells of a cotton seed. Efforts to understand this dramatic developmental shift have been impeded by the difficulty of separation between fiber and epidermal cells.ResultsHere we employed laser-capture microdissection (LCM) to separate these cell types. RNA-seq analysis revealed transitional differences between fiber and epidermal-layer cells at 0 or 2 days post anthesis. Specifically, down-regulation of putative cell cycle genes was coupled with upregulation of ribosome biosynthesis and translation-related genes, which may suggest their respective roles in fiber cell initiation. Indeed, the amount of fibers in cultured ovules was increased by cell cycle progression inhibitor, Roscovitine, and decreased by ribosome biosynthesis inhibitor, Rbin-1. Moreover, subfunctionalization of homoeologs was pervasive in fiber and epidermal cells, with expression bias towards 10% more D than A homoeologs of cell cycle related genes and 40–50% more D than A homoeologs of ribosomal protein subunit genes. Key cell cycle regulators were predicted to be epialleles in allotetraploid cotton. MYB-transcription factor genes displayed expression divergence between fibers and ovules. Notably, many phytohormone-related genes were upregulated in ovules and down-regulated in fibers, suggesting spatial-temporal effects on fiber cell development.ConclusionsFiber cell initiation is accompanied by cell cycle arrest coupled with active ribosome biosynthesis, spatial-temporal regulation of phytohormones and MYB transcription factors, and homoeolog expression bias of cell cycle and ribosome biosynthesis genes. These valuable genomic resources and molecular insights will help develop breeding and biotechnological tools to improve cotton fiber production.