A digital 3D reference atlas reveals cellular growth patterns shaping the Arabidopsis ovule

AbstractA fundamental question in biology is how morphogenesis integrates the multitude of distinct processes that act at different scales, ranging from the molecular control of gene expression to cellular coordination in a tissue. Investigating morphogenesis of complex organs strongly benefits from three-dimensional representations of the organ under study. Here, we present a digital analysis of ovule development from Arabidopsis thaliana as a paradigm for a complex morphogenetic process. Using machine-learning-based image analysis we generated a three-dimensional atlas of ovule development with cellular resolution. It allows quantitative stage- and tissue-specific analysis of cellular patterns. Exploiting a fluorescent reporter enabled precise spatial determination of gene expression patterns, revealing subepidermal expression of WUSCHEL. Underlying the power of our approach, we found that primordium outgrowth progresses evenly, discovered a novel mode of forming a new cell layer, and detected a new function of INNER NO OUTER in restricting cell proliferation in the nucellus. Moreover, we identified two distinct subepidermal cell populations that make crucial contributions to ovule curvature. Our work demonstrates the expedience of a three-dimensional digital representation when studying the morphogenesis of an organ of complex cellular architecture and shape that eventually consists of 1,900 cells.

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A digital 3D reference atlas reveals cellular growth patterns shaping the Arabidopsis ovule

eLife ◽

10.7554/elife.63262 ◽

2021 ◽

Vol 10 ◽

Author(s):

Athul Vijayan ◽

Rachele Tofanelli ◽

Sören Strauss ◽

Lorenzo Cerrone ◽

Adrian Wolny ◽

...

Keyword(s):

Gene Expression ◽

Expression Patterns ◽

Three Dimensional ◽

Temporal Analysis ◽

Growth Patterns ◽

Cellular Growth ◽

Nucellar Cell ◽

Control Of Gene Expression ◽

Molecular Control ◽

Spatio Temporal

A fundamental question in biology is how morphogenesis integrates the multitude of processes that act at different scales, ranging from the molecular control of gene expression to cellular coordination in a tissue. Using machine-learning-based digital image analysis, we generated a three-dimensional atlas of ovule development in Arabidopsis thaliana, enabling the quantitative spatio-temporal analysis of cellular and gene expression patterns with cell and tissue resolution. We discovered novel morphological manifestations of ovule polarity, a new mode of cell layer formation, and previously unrecognized subepidermal cell populations that initiate ovule curvature. The data suggest an irregular cellular build-up of WUSCHEL expression in the primordium and new functions for INNER NO OUTER in restricting nucellar cell proliferation and the organization of the interior chalaza. Our work demonstrates the analytical power of a three-dimensional digital representation when studying the morphogenesis of an organ of complex architecture that eventually consists of 1900 cells.

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Cellular-resolution gene expression profiling in the neonatal marmoset brain reveals dynamic species- and region-specific differences

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2020125118 ◽

2021 ◽

Vol 118 (18) ◽

pp. e2020125118

Author(s):

Yoshiaki Kita ◽

Hirozumi Nishibe ◽

Yan Wang ◽

Tsutomu Hashikawa ◽

Satomi S. Kikuchi ◽

...

Keyword(s):

Gene Expression ◽

Gene Expression Profiling ◽

Expression Profiling ◽

Large Scale ◽

Molecular Mechanisms ◽

Neural Circuit ◽

Expression Patterns ◽

Three Dimensional ◽

Control Of Gene Expression ◽

Cellular Resolution

Precise spatiotemporal control of gene expression in the developing brain is critical for neural circuit formation, and comprehensive expression mapping in the developing primate brain is crucial to understand brain function in health and disease. Here, we developed an unbiased, automated, large-scale, cellular-resolution in situ hybridization (ISH)–based gene expression profiling system (GePS) and companion analysis to reveal gene expression patterns in the neonatal New World marmoset cortex, thalamus, and striatum that are distinct from those in mice. Gene-ontology analysis of marmoset-specific genes revealed associations with catalytic activity in the visual cortex and neuropsychiatric disorders in the thalamus. Cortically expressed genes with clear area boundaries were used in a three-dimensional cortical surface mapping algorithm to delineate higher-order cortical areas not evident in two-dimensional ISH data. GePS provides a powerful platform to elucidate the molecular mechanisms underlying primate neurobiology and developmental psychiatric and neurological disorders.

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Compendium of Methods to Uncover RNA-Protein Interactions In Vivo

Methods and Protocols ◽

10.3390/mps4010022 ◽

2021 ◽

Vol 4 (1) ◽

pp. 22

Author(s):

Mrinmoyee Majumder ◽

Viswanathan Palanisamy

Keyword(s):

Gene Expression ◽

Protein Interactions ◽

Rna Binding ◽

Rna Binding Proteins ◽

Expression Patterns ◽

Control Of Gene Expression ◽

Regulatory Pathways ◽

Advantages And Disadvantages ◽

Protein Nucleic Acid

Control of gene expression is critical in shaping the pro-and eukaryotic organisms’ genotype and phenotype. The gene expression regulatory pathways solely rely on protein–protein and protein–nucleic acid interactions, which determine the fate of the nucleic acids. RNA–protein interactions play a significant role in co- and post-transcriptional regulation to control gene expression. RNA-binding proteins (RBPs) are a diverse group of macromolecules that bind to RNA and play an essential role in RNA biology by regulating pre-mRNA processing, maturation, nuclear transport, stability, and translation. Hence, the studies aimed at investigating RNA–protein interactions are essential to advance our knowledge in gene expression patterns associated with health and disease. Here we discuss the long-established and current technologies that are widely used to study RNA–protein interactions in vivo. We also present the advantages and disadvantages of each method discussed in the review.

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Global Analysis of Cell Type-Specific Gene Expression

Comparative and Functional Genomics ◽

10.1002/cfg.281 ◽

2003 ◽

Vol 4 (2) ◽

pp. 208-215 ◽

Cited By ~ 16

Author(s):

David W. Galbraith

Keyword(s):

Gene Expression ◽

Fluorescent Protein ◽

Global Analysis ◽

Expression Patterns ◽

Three Dimensional ◽

Global Gene Expression ◽

Cell Types ◽

Reasonable Assumption ◽

Specific Gene ◽

Different Cell Types

The tissues and organs of multicellular eukaryotes are frequently observed to comprise complex three-dimensional interspersions of different cell types. It is a reasonable assumption that different global patterns of gene expression are found within these different cell types. This review outlines general experimental strategies designed to characterize these global gene expression patterns, based on a combination of methods of transgenic fluorescent protein (FP) expression and targeting, of flow cytometry and sorting and of high-throughput gene expression analysis.

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Spatial organization of different sigma factor activities and c-di-GMP signalling within the three-dimensional landscape of a bacterial biofilm

Open Biology ◽

10.1098/rsob.180066 ◽

2018 ◽

Vol 8 (8) ◽

pp. 180066 ◽

Cited By ~ 24

Author(s):

Gisela Klauck ◽

Diego O. Serra ◽

Alexandra Possling ◽

Regine Hengge

Keyword(s):

Gene Expression ◽

Extracellular Matrix ◽

Stationary Phase ◽

Sigma Factor ◽

Spatial Organization ◽

Expression Patterns ◽

Three Dimensional ◽

Biomechanical Properties ◽

Ribosomal Gene ◽

Bacterial Biofilm

Bacterial biofilms are large aggregates of cells embedded in an extracellular matrix of self-produced polymers. In macrocolony biofilms of Escherichia coli , this matrix is generated in the upper biofilm layer only and shows a surprisingly complex supracellular architecture. Stratified matrix production follows the vertical nutrient gradient and requires the stationary phase σ S (RpoS) subunit of RNA polymerase and the second messenger c-di-GMP. By visualizing global gene expression patterns with a newly designed fingerprint set of Gfp reporter fusions, our study reveals the spatial order of differential sigma factor activities, stringent control of ribosomal gene expression and c-di-GMP signalling in vertically cryosectioned macrocolony biofilms. Long-range physiological stratification shows a duplication of the growth-to-stationary phase pattern that integrates nutrient and oxygen gradients. In addition, distinct short-range heterogeneity occurs within specific biofilm strata and correlates with visually different zones of the refined matrix architecture. These results introduce a new conceptual framework for the control of biofilm formation and demonstrate that the intriguing extracellular matrix architecture, which determines the emergent physiological and biomechanical properties of biofilms, results from the spatial interplay of global gene regulation and microenvironmental conditions. Overall, mature bacterial macrocolony biofilms thus resemble the highly organized tissues of multicellular organisms.

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Collagen gene expression patterns by normal and keloid fibroblasts in the three-dimensional culture

Journal of Dermatological Science ◽

10.1016/s0923-1811(98)83763-8 ◽

1998 ◽

Vol 16 ◽

pp. S128

Author(s):

Madoka Sato ◽

Osamu Ishikawa ◽

Yoshiki Miyachi

Keyword(s):

Gene Expression ◽

Expression Patterns ◽

Three Dimensional ◽

Gene Expression Patterns ◽

Collagen Gene ◽

Collagen Gene Expression ◽

Three Dimensional Culture ◽

Keloid Fibroblasts

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A multiscale analysis of early flower development in Arabidopsis provides an integrated view of molecular regulation and growth control

10.1101/2020.09.25.313312 ◽

2020 ◽

Author(s):

Yassin Refahi ◽

Argyris Zardilis ◽

Gaël Michelin ◽

Raymond Wightman ◽

Bruno Leggio ◽

...

Keyword(s):

Flower Development ◽

Computational Models ◽

Fundamental Problem ◽

Expression Patterns ◽

Growth Control ◽

Cell Lineage ◽

Time Lapse ◽

Growth Patterns ◽

Cellular Growth ◽

Early Flower

Abstract The link between gene regulation and morphogenesis of multicellular organisms is a fundamental problem in biology. We address this question in the floral meristem of Arabidopsis, which generates new tissues and organs through complex changes in growth patterns. Starting from high-resolution time-lapse images, we generated a comprehensive 4-D atlas of early flower development including cell lineage, cellular growth rates and the expression patterns of 28 regulatory genes. This information was introduced in MorphoNet, a web-based open-access platform. The application of mechanistic computational models indicated that the molecular network based on the literature only explained a minority of the expression patterns. This was substantially improved by adding single regulatory hypotheses for individual genes. We next used the integrated information to correlate growth with the combinatorial expression of multiple genes. This led us to propose a set of hypotheses for the action of individual genes in morphogenesis, not visible by simply correlating gene expression and growth. This identified the central transcription factor LEAFY as a potential regulator of heterogeneous growth, which was supported by quantifying growth patterns in a leafy mutant. By providing an integrated, multiscale view of flower development, this atlas should represent a fundamental step towards mechanistic multiscale-scale models of flower development.

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Three‐dimensional reconstruction of Prdm family gene expression patterns during mouse development stage by tissue clearing technique

The FASEB Journal ◽

10.1096/fasebj.2019.33.1_supplement.lb189 ◽

2019 ◽

Vol 33 (S1) ◽

Author(s):

Jiwon Woo ◽

Haewon Kang ◽

Yong‐Eun Cho

Keyword(s):

Gene Expression ◽

Expression Patterns ◽

Three Dimensional ◽

Development Stage ◽

Gene Expression Patterns ◽

Three Dimensional Reconstruction ◽

Mouse Development ◽

Dimensional Reconstruction ◽

Clearing Technique ◽

Family Gene

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Differential Gene Expression Patterns and Interaction Networks in BCR-ABL–Positive and –Negative Adult Acute Lymphoblastic Leukemias

Journal of Clinical Oncology ◽

10.1200/jco.2006.09.3534 ◽

2007 ◽

Vol 25 (11) ◽

pp. 1341-1349 ◽

Cited By ~ 75

Author(s):

Dejan Juric ◽

Norman J. Lacayo ◽

Meghan C. Ramsey ◽

Janis Racevskis ◽

Peter H. Wiernik ◽

...

Keyword(s):

Gene Expression ◽

System Development ◽

Lymphoblastic Leukemia ◽

Expression Patterns ◽

Eastern Cooperative Oncology Group ◽

Cellular Growth ◽

Interaction Networks ◽

Gene Expression Patterns ◽

Interaction Patterns ◽

Molecular Features

Purpose To identify gene expression patterns and interaction networks related to BCR-ABL status and clinical outcome in adults with acute lymphoblastic leukemia (ALL). Patients and Methods DNA microarrays were used to profile a set of 54 adult ALL specimens from the Medical Research Council UKALL XII/Eastern Cooperative Oncology Group E2993 trial (21 p185BCR-ABL–positive, 16 p210BCR-ABL–positive and 17 BCR-ABL–negative specimens). Results Using supervised and unsupervised analysis tools, we detected significant transcriptomic changes in BCR-ABL–positive versus –negative specimens, and assessed their validity in an independent cohort of 128 adult ALL specimens. This set of 271 differentially expressed genes (including GAB1, CIITA, XBP1, CD83, SERPINB9, PTP4A3, NOV, LOX, CTNND1, BAALC, and RAB21) is enriched for genes involved in cell death, cellular growth and proliferation, and hematologic system development and function. Network analysis demonstrated complex interaction patterns of these genes, and identified FYN and IL15 as the hubs of the top-scoring network. Within the BCR-ABL–positive subgroups, we identified genes overexpressed (PILRB, STS-1, SPRY1) or underexpressed (TSPAN16, ADAMTSL4) in p185BCR-ABL–positive ALL relative to p210BCR-ABL–positive ALL. Finally, we constructed a gene expression- and interaction-based outcome predictor consisting of 27 genes (including GRB2, GAB1, GLI1, IRS1, RUNX2, and SPP1), which correlated with overall survival in BCR-ABL–positive adult ALL (P = .0001), independent of age (P = .25) and WBC count at presentation (P = .003). Conclusion We identified prominent molecular features of BCR-ABL–positive adult ALL, which may be useful for developing novel therapeutic targets and prognostic markers in this disease.

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