Transcriptome analysis identifies genes involved in the somatic embryogenesis of Eucalyptus

Abstract Background: Eucalyptus, a highly diverse genus of the Myrtaceae family, is the most widely planted hardwood in the world due to its increasing importance for fiber and energy. Somatic embryogenesis (SE) is one large-scale method to provide commercial use of the vegetative propagation of Eucalyptus and dedifferentiation is a key step for plant cells to become meristematic. However, little is known about the molecular changes during the Eucalyptus SE.Results: We compared the transcriptome profiles of the differentiated and dedifferentiated tissues of two Eucalyptus species – E. camaldulensis (high embryogenetic potential) and E. grandis x urophylla (low embryogenetic potential). Initially, we identified 18,777 to 20,240 genes in all samples. Compared to the differentiated tissues, we identified 9,229 and 8,989 differentially expressed genes (DEGs) in the dedifferentiated tissues of E. camaldulensis and E. grandis x urophylla, respectively, and 2,687 up-regulated and 2,581 down-regulated genes shared. Next, we identified 2,003 up-regulated and 1,958 down-regulated genes only in E. camaldulensis, including 6 somatic embryogenesis receptor kinase, 17 ethylene, 12 auxin, 83 ribosomal protein, 28 zinc finger protein, 10 heat shock protein, 9 histone, 122 cell wall related and 98 transcription factor genes. Genes from other families like ABA, arabinogalactan protein and late embryogenesis abundant protein were also found to be specifically dysregulated in the dedifferentiation process of E. camaldulensis. Further, we identified 48,447 variants (SNPs and small indels) specific to E. camaldulensis, including 13,434 exonic variants from 4,723 genes (e.g., annexin, GN, ARF and AP2-like ethylene-responsive transcription factor). qRT-PCR was used to confirm the gene expression patterns in both E. camaldulensis and E. grandis x urophylla. Conclusions: This is the first time to study the somatic embryogenesis of Eucalyptus using transcriptome sequencing. It will improve our understanding of the molecular mechanisms of somatic embryogenesis and dedifferentiation in Eucalyptus. Our results provide a valuable resource for future studies in the field of Eucalyptus and will benefit the Eucalyptus breeding program.

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Transcriptome analysis identifies genes involved in the somatic embryogenesis of Eucalyptus

BMC Genomics ◽

10.1186/s12864-020-07214-5 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Yufei Xiao ◽

Junji Li ◽

Ye Zhang ◽

Xiaoning Zhang ◽

Hailong Liu ◽

...

Keyword(s):

Transcription Factor ◽

Somatic Embryogenesis ◽

Large Scale ◽

Molecular Mechanisms ◽

Zinc Finger Protein ◽

Expression Patterns ◽

Late Embryogenesis Abundant ◽

Arabinogalactan Protein ◽

Late Embryogenesis Abundant Protein ◽

Eucalyptus Species

Abstract Background Eucalyptus, a highly diverse genus of the Myrtaceae family, is the most widely planted hardwood in the world due to its increasing importance for fiber and energy. Somatic embryogenesis (SE) is one large-scale method to provide commercial use of the vegetative propagation of Eucalyptus and dedifferentiation is a key step for plant cells to become meristematic. However, little is known about the molecular changes during the Eucalyptus SE. Results We compared the transcriptome profiles of the differentiated and dedifferentiated tissues of two Eucalyptus species – E. camaldulensis (high embryogenetic potential) and E. grandis x urophylla (low embryogenetic potential). Initially, we identified 18,777 to 20,240 genes in all samples. Compared to the differentiated tissues, we identified 9229 and 8989 differentially expressed genes (DEGs) in the dedifferentiated tissues of E. camaldulensis and E. grandis x urophylla, respectively, and 2687 up-regulated and 2581 down-regulated genes shared. Next, we identified 2003 up-regulated and 1958 down-regulated genes only in E. camaldulensis, including 6 somatic embryogenesis receptor kinase, 17 ethylene, 12 auxin, 83 ribosomal protein, 28 zinc finger protein, 10 heat shock protein, 9 histone, 122 cell wall related and 98 transcription factor genes. Genes from other families like ABA, arabinogalactan protein and late embryogenesis abundant protein were also found to be specifically dysregulated in the dedifferentiation process of E. camaldulensis. Further, we identified 48,447 variants (SNPs and small indels) specific to E. camaldulensis, including 13,434 exonic variants from 4723 genes (e.g., annexin, GN, ARF and AP2-like ethylene-responsive transcription factor). qRT-PCR was used to confirm the gene expression patterns in both E. camaldulensis and E. grandis x urophylla. Conclusions This is the first time to study the somatic embryogenesis of Eucalyptus using transcriptome sequencing. It will improve our understanding of the molecular mechanisms of somatic embryogenesis and dedifferentiation in Eucalyptus. Our results provide a valuable resource for future studies in the field of Eucalyptus and will benefit the Eucalyptus breeding program.

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Transcriptome analysis identifies genes involved in the somatic embryogenesis of Eucalyptus

10.21203/rs.3.rs-47390/v2 ◽

2020 ◽

Author(s):

Yufei Xiao ◽

Junji Li ◽

Ye Zhang ◽

Xiaoning Zhang ◽

Hailong Liu ◽

...

Keyword(s):

Transcription Factor ◽

Somatic Embryogenesis ◽

Large Scale ◽

Molecular Mechanisms ◽

Zinc Finger Protein ◽

Expression Patterns ◽

Late Embryogenesis Abundant ◽

Arabinogalactan Protein ◽

Late Embryogenesis Abundant Protein ◽

Eucalyptus Species

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Transcriptome Analysis Identifies Genes Involved in the Somatic Embryogenesis of Eucalyptus

10.21203/rs.3.rs-47390/v1 ◽

2020 ◽

Author(s):

Yufei Xiao ◽

Junji Li ◽

Ye Zhang ◽

Xiaoning Zhang ◽

Hailong Liu ◽

...

Keyword(s):

Transcription Factor ◽

Somatic Embryogenesis ◽

Large Scale ◽

Molecular Mechanisms ◽

Zinc Finger Protein ◽

Expression Patterns ◽

Late Embryogenesis Abundant ◽

Arabinogalactan Protein ◽

Late Embryogenesis Abundant Protein ◽

Transcriptional Level

Abstract Background: Eucalyptus, a highly diverse genus of the Myrtaceae family, is the most widely planted hardwood due to its increasing importance for fiber and energy in the word. Somatic embryogenesis is one method to provide large-scale commercial use for the vegetative propagation of Eucalyptus and dedifferentiation is a key step for plant cells to become meristematic. However, little is known about the molecular changes during the SE of Eucalyptus on transcriptional level.Results: We compared the transcriptome profiles of the differentiated and dedifferentiated tissues of two Eucalyptus cultivars – E. camaldulensis (high embryogenetic potential) and E. grandis x urophylla (low embryogenetic potential). In total, we identified 18,777 to 20,240 genes in all samples. Compared to the differentiated tissues, we identified 9,229 and 8,989 differentially expressed genes (DEGs) in the dedifferentiated tissues of E. camaldulensis and E. grandis x urophylla, respectively. Comparison of DEGs showed that they shared 2,687 up-regulated and 2,581 down-regulated genes. Next, we found 2,003 up-regulated and 1,958 down-regulated genes specifically identified in E. camaldulensis, including 6 somatic embryogenesis receptor kinase, 17 ethylene, 12 auxin, 83 ribosomal protein, 28 zinc finger protein, 10 heat shock protein, 9 histone and 98 transcription factor genes. Genes from other families like ABA, arabinogalactan protein and late embryogenesis abundant protein were also found to be specifically dysregulated in E. camaldulensis. Further, we identified 48,447 variants (SNPs and small indels) specific to E. camaldulensis, including 13,434 exonic variants from 4,723 genes (e.g., annexin, GN, ARF and AP2-like ethylene-responsive transcription factor). qRT-PCR was used to confirm the gene expression patterns in both E. camaldulensis and E. grandis x urophylla. Conclusions: This is the first time to study the somatic embryogenesis of Eucalyptus using transcriptome sequencing. Our results will improve our understanding of the molecular mechanisms of somatic embryogenesis and dedifferentiation in Eucalyptus. Our results provide a valuable resource for future studies in the field of Eucalyptus and will benefit the Eucalyptus breeding program.

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Gene expression programs during callus development in tissue culture of two Eucalyptus species

BMC Plant Biology ◽

10.1186/s12870-021-03391-x ◽

2022 ◽

Vol 22 (1) ◽

Cited By ~ 1

Author(s):

Ye Zhang ◽

Junji Li ◽

Changrong Li ◽

Shengkan Chen ◽

Qinglan Tang ◽

...

Keyword(s):

Gene Expression ◽

Tissue Culture ◽

Transcription Factor ◽

Shoot Regeneration ◽

Molecular Mechanisms ◽

Stomatal Closure ◽

Expression Patterns ◽

Specific Protein ◽

Eucalyptus Species ◽

Embryogenic Potential

Abstract Background Eucalyptus is a highly diverse genus of the Myrtaceae family and widely planted in the world for timber and pulp production. Tissue culture induced callus has become a common tool for Eucalyptus breeding, however, our knowledge about the genes related to the callus maturation and shoot regeneration is still poor. Results We set up an experiment to monitor the callus induction and callus development of two Eucalyptus species - E. camaldulensis (high embryogenic potential) and E. grandis x urophylla (low embryogenic potential). Then, we performed transcriptome sequencing for primary callus, mature callus, shoot regeneration stage callus and senescence callus. We identified 707 upregulated and 694 downregulated genes during the maturation process of the two Eucalyptus species and most of them were involved in the signaling pathways like plant hormone and MAPK. Next, we identified 135 and 142 genes that might play important roles during the callus development of E. camaldulensis and E. grandis x urophylla, respectively. Further, we found 15 DEGs shared by these two Eucalyptus species during the callus development, including Eucgr.D00640 (stem-specific protein TSJT1), Eucgr.B00171 (BTB/POZ and TAZ domain-containing protein 1), Eucgr.C00948 (zinc finger CCCH domain-containing protein 20), Eucgr.K01667 (stomatal closure-related actinbinding protein 3), Eucgr.C00663 (glutaredoxin-C10) and Eucgr.C00419 (UPF0481 protein At3g47200). Interestingly, the expression patterns of these genes displayed “N” shape in the samples. Further, we found 51 genes that were dysregulated during the callus development of E. camaldulensis but without changes in E. grandis x urophylla, such as Eucgr.B02127 (GRF1-interacting factor 1), Eucgr.C00947 (transcription factor MYB36), Eucgr.B02752 (laccase-7), Eucgr.B03985 (transcription factor MYB108), Eucgr.D00536 (GDSL esterase/lipase At5g45920) and Eucgr.B02347 (scarecrow-like protein 34). These 51 genes might be associated with the high propagation ability of Eucalyptus and 22 might be induced after the dedifferentiation. Last, we performed WGCNA to identify the co-expressed genes during the callus development of Eucalyptus and qRT-PCR experiment to validate the gene expression patterns. Conclusions This is the first time to globally study the gene profiles during the callus development of Eucalyptus. The results will improve our understanding of gene regulation and molecular mechanisms in the callus maturation and shoot regeneration.

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Molecular regulation of Snai2 in development and disease

Journal of Cell Science ◽

10.1242/jcs.235127 ◽

2019 ◽

Vol 132 (23) ◽

Author(s):

Wenhui Zhou ◽

Kayla M. Gross ◽

Charlotte Kuperwasser

Keyword(s):

Transcription Factor ◽

Cell Biology ◽

Molecular Mechanisms ◽

Epithelial To Mesenchymal Transition ◽

Zinc Finger Protein ◽

Main Role ◽

Biological Processes ◽

Developmental Defects ◽

Mesenchymal Transition ◽

Damage Repair

ABSTRACT The transcription factor Snai2, encoded by the SNAI2 gene, is an evolutionarily conserved C2H2 zinc finger protein that orchestrates biological processes critical to tissue development and tumorigenesis. Initially characterized as a prototypical epithelial-to-mesenchymal transition (EMT) transcription factor, Snai2 has been shown more recently to participate in a wider variety of biological processes, including tumor metastasis, stem and/or progenitor cell biology, cellular differentiation, vascular remodeling and DNA damage repair. The main role of Snai2 in controlling such processes involves facilitating the epigenetic regulation of transcriptional programs, and, as such, its dysregulation manifests in developmental defects, disruption of tissue homeostasis, and other disease conditions. Here, we discuss our current understanding of the molecular mechanisms regulating Snai2 expression, abundance and activity. In addition, we outline how these mechanisms contribute to disease phenotypes or how they may impact rational therapeutic targeting of Snai2 dysregulation in human disease.

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Multimodal bioinformatic analyses of the neurodegenerative disease-associated TECPR2 gene reveal its diverse roles

Journal of Medical Genetics ◽

10.1136/jmedgenet-2021-108193 ◽

2021 ◽

pp. jmedgenet-2021-108193

Author(s):

Ido Shalev ◽

Judith Somekh ◽

Alal Eran

Keyword(s):

Protein Interactions ◽

Large Scale ◽

Molecular Mechanisms ◽

Neurological Diseases ◽

Treatment Options ◽

Expression Patterns ◽

Population Variation ◽

Functional Enrichment ◽

Phylogenetic Profiling ◽

Developing Neurons

BackgroundLoss of tectonin β-propeller repeat-containing 2 (TECPR2) function has been implicated in an array of neurodegenerative disorders, yet its physiological function remains largely unknown. Understanding TECPR2 function is essential for developing much needed precision therapeutics for TECPR2-related diseases.MethodsWe leveraged considerable amounts of functional data to obtain a comprehensive perspective of the role of TECPR2 in health and disease. We integrated expression patterns, population variation, phylogenetic profiling, protein-protein interactions and regulatory network data for a minimally biased multimodal functional analysis. Genes and proteins linked to TECPR2 via multiple lines of evidence were subject to functional enrichment analyses to identify molecular mechanisms involving TECPR2.ResultsTECPR2 was found to be part of a tight neurodevelopmental gene expression programme that includes KIF1A, ATXN1, TOM1L2 and FA2H, all implicated in neurological diseases. Functional enrichment analyses of TECPR2-related genes converged on a role in late autophagy and ribosomal processes. Large-scale population variation data demonstrated that this role is non-redundant.ConclusionsTECPR2 might serve as an indicator for the energy balance between protein synthesis and autophagy, and a marker for diseases associated with their imbalance, such as Alzheimer’s disease and Huntington’s disease. Specifically, we speculate that TECPR2 plays an important role as a proteostasis regulator during synaptogenesis, highlighting its importance in developing neurons. By advancing our understanding of TECPR2 function, this work provides an essential stepping stone towards the development of precision diagnostics and targeted treatment options for TECPR2-related disorders.

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Integrative functional analyses of the neurodegenerative disease-associated TECPR2 gene reveal its diverse roles

10.21203/rs.2.22274/v1 ◽

2020 ◽

Author(s):

Ido Shalev ◽

Judith Somekh ◽

Alal Eran

Keyword(s):

Protein Interactions ◽

Large Scale ◽

Molecular Mechanisms ◽

Neurological Diseases ◽

Treatment Options ◽

Expression Patterns ◽

Population Variation ◽

Functional Enrichment ◽

Phylogenetic Profiling ◽

Developing Neurons

Abstract BackgroundLoss of tectonin β-propeller repeat-containing 2 (TECPR2) function has been implicated in an array of neurodegenerative disorders, yet its physiological function remains largely unknown. Understanding TECPR2 function is essential for developing much needed precision therapeutics for TECPR2-related diseases. MethodsWe leveraged the considerable amounts of functional data to obtain a comprehensive perspective of the role of TECPR2 in health and disease. We integrated expression patterns, population variation, phylogenetic profiling, protein-protein interactions, and regulatory network data for a minimally biased multimodal functional analysis. Genes and proteins linked to TECPR2 via multiple lines of evidence were subject to functional enrichment analyses to identify molecular mechanisms involving TECPR2.ResultsTECPR2 was found to be part of a tight neurodevelopmental gene expression program that includes KIF1A, ATXN1, TOM1L2, and FA2H, all implicated in neurological diseases. Functional enrichment analyses of TECPR2-related genes converged on a role in late autophagy and ribosomal processes. Large-scale population variation data demonstrated that this role is nonredundant. ConclusionsTECPR2 might serve as an indicator for the energy balance between protein synthesis and autophagy, and a marker for diseases associated with their imbalance, such as Alzheimer’s disease, Huntington’s disease, and various cancers. Our work further suggests that TECPR2 plays a role as a synaptic proteostasis regulator during synaptogenesis, highlighting its importance in developing neurons. By advancing our understanding of TECPR2 function, this work provides an essential stepping stone towards the development of precision diagnostics and targeted treatment options for TECPR2-related disorders.

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Gene Expression Patterns Underlying the Reinstatement of Plasticity in the Adult Visual System

Neural Plasticity ◽

10.1155/2013/605079 ◽

2013 ◽

Vol 2013 ◽

pp. 1-8 ◽

Cited By ~ 11

Author(s):

Ettore Tiraboschi ◽

Ramon Guirado ◽

Dario Greco ◽

Petri Auvinen ◽

Jose Fernando Maya-Vetencourt ◽

...

Keyword(s):

Gene Expression ◽

Visual Cortex ◽

Large Scale ◽

Molecular Mechanisms ◽

Expression Patterns ◽

Monocular Deprivation ◽

Adult Brain ◽

Gene Expression Patterns ◽

Postnatal Life ◽

Critical Periods

The nervous system is highly sensitive to experience during early postnatal life, but this phase of heightened plasticity decreases with age. Recent studies have demonstrated that developmental-like plasticity can be reactivated in the visual cortex of adult animals through environmental or pharmacological manipulations. These findings provide a unique opportunity to study the cellular and molecular mechanisms of adult plasticity. Here we used the monocular deprivation paradigm to investigate large-scale gene expression patterns underlying the reinstatement of plasticity produced by fluoxetine in the adult rat visual cortex. We found changes, confirmed with RT-PCRs, in gene expression in different biological themes, such as chromatin structure remodelling, transcription factors, molecules involved in synaptic plasticity, extracellular matrix, and excitatory and inhibitory neurotransmission. Our findings reveal a key role for several molecules such as the metalloproteases Mmp2 and Mmp9 or the glycoprotein Reelin and open up new insights into the mechanisms underlying the reopening of the critical periods in the adult brain.

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Transcription Factor Erg Variants and Functional Diversification of Chondrocytes during Limb Long Bone Development

The Journal of Cell Biology ◽

10.1083/jcb.150.1.27 ◽

2000 ◽

Vol 150 (1) ◽

pp. 27-40 ◽

Cited By ~ 50

Author(s):

Masahiro Iwamoto ◽

Yoshinobu Higuchi ◽

Eiki Koyama ◽

Motomi Enomoto-Iwamoto ◽

Kojiro Kurisu ◽

...

Keyword(s):

Transcription Factor ◽

Limb Development ◽

Matrix Protein ◽

Molecular Mechanisms ◽

Articular Chondrocytes ◽

Bone Cells ◽

Expression Patterns ◽

Extracellular Matrix Protein ◽

Long Bone ◽

Chondrocyte Maturation

During limb development, chondrocytes located at the epiphyseal tip of long bone models give rise to articular tissue, whereas the more numerous chondrocytes in the shaft undergo maturation, hypertrophy, and mineralization and are replaced by bone cells. It is not understood how chondrocytes follow these alternative pathways to distinct fates and functions. In this study we describe the cloning of C-1-1, a novel variant of the ets transcription factor ch-ERG. C-1-1 lacks a short 27–amino acid segment located ∼80 amino acids upstream of the ets DNA binding domain. We found that in chick embryo long bone anlagen, C-1-1 expression characterizes developing articular chondrocytes, whereas ch-ERG expression is particularly prominent in prehypertrophic chondrocytes in the growth plate. To analyze the function of C-1-1 and ch-ERG, viral vectors were used to constitutively express each factor in developing chick leg buds and cultured chondrocytes. We found that virally driven expression of C-1-1 maintained chondrocytes in a stable and immature phenotype, blocked their maturation into hypertrophic cells, and prevented the replacement of cartilage with bone. It also induced synthesis of tenascin-C, an extracellular matrix protein that is a unique product of developing articular chondrocytes. In contrast, virally driven expression of ch-ERG significantly stimulated chondrocyte maturation in culture, as indicated by increases in alkaline phosphatase activity and deposition of a mineralized matrix; however, it had modest effects in vivo. The data show that C-1-1 and ch-ERG have diverse biological properties and distinct expression patterns during skeletogenesis, and are part of molecular mechanisms by which limb chondrocytes follow alternative developmental pathways. C-1-1 is the first transcription factor identified to date that appears to be instrumental in the genesis and function of epiphyseal articular chondrocytes.

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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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