Expression Profiles and Post-Translational Modifications of Phosphoenolpyruvate Carboxylase Isozymes of Bienertia sinuspersici during Leaf Development

Aberrations in histone post-translational modifications (PTMs), as well as in the histone modifying enzymes (HMEs) that catalyze their deposition and removal, have been reported in many tumors and many epigenetic inhibitors are currently under investigation for cancer treatment. Therefore, profiling epigenetic features in cancer could have important implications for the discovery of both biomarkers for patient stratification and novel epigenetic targets. In this study, we employed mass spectrometry-based approaches to comprehensively profile histone H3 PTMs in a panel of normal and tumoral tissues for different cancer types, identifying various changes, some of which appear to be a consequence of the increased proliferation rate of tumors, while others are cell-cycle independent. Histone PTM changes found in tumors partially correlate with alterations of the gene expression profiles of HMEs obtained from publicly available data and are generally lost in culture conditions. Through this analysis, we identified tumor- and subtype-specific histone PTM changes, but also widespread changes in the levels of histone H3 K9me3 and K14ac marks. In particular, H3K14ac showed a cell-cycle independent decrease in all the seven tumor/tumor subtype models tested and could represent a novel epigenetic hallmark of cancer.

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Estrogen Signaling and the Aging Brain: Context-Dependent Considerations for Postmenopausal Hormone Therapy

ISRN Endocrinology ◽

10.1155/2013/814690 ◽

2013 ◽

Vol 2013 ◽

pp. 1-16 ◽

Cited By ~ 10

Author(s):

Natasha N. Mott ◽

Toni R. Pak

Keyword(s):

Hormone Therapy ◽

Expression Profiles ◽

Critical Factor ◽

Brain Regions ◽

Receptor Expression ◽

Estrogen Signaling ◽

Aging Brain ◽

Post Translational Modifications ◽

Factors Affecting ◽

Estrogenic Effects

Recent clinical studies have spurred rigorous debate about the benefits of hormone therapy (HT) for postmenopausal women. Controversy first emerged based on a sharp increase in the risk of cardiovascular disease in participants of the Women’s Health Initiative (WHI) studies, suggesting that decades of empirical research in animal models was not necessarily applicable to humans. However, a reexamination of the data from the WHI studies suggests that the timing of HT might be a critical factor and that advanced age and/or length of estrogen deprivation might alter the body's ability to respond to estrogens. Dichotomous estrogenic effects are mediated primarily by the actions of two high-affinity estrogen receptors alpha and beta (ERα & ERβ). The expression of the ERs can be overlapping or distinct, dependent upon brain region, sex, age, and exposure to hormone, and, during the time of menopause, there may be changes in receptor expression profiles, post-translational modifications, and protein:protein interactions that could lead to a completely different environment for E2 to exert its effects. In this review, factors affecting estrogen-signaling processes will be discussed with particular attention paid to the expression and transcriptional actions of ERβ in brain regions that regulate cognition and affect.

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Logic-based Analysis of Gene Expression Data Predicts Pathway Crosstalk between TNF, TGFB1 and EGF in Basal-like Breast Cancer

10.1101/614933 ◽

2019 ◽

Author(s):

Kyuri Jo ◽

Beatriz Santos Buitrago ◽

Minsu Kim ◽

Sungmin Rhee ◽

Carolyn Talcott ◽

...

Keyword(s):

Breast Cancer ◽

Gene Expression ◽

Signaling Pathways ◽

Expression Profiles ◽

Formal System ◽

Gene Expression Profiles ◽

Breast Cancer Subtypes ◽

Post Translational Modifications ◽

Cancer Subtypes ◽

Pathway Crosstalk

AbstractFor breast cancer, clinically important subtypes are well characterised at the molecular level in terms of gene expression profiles. In addition, signaling pathways in breast cancer have been extensively studied as therapeutic targets due to their roles in tumor growth and metastasis. However, it is challenging to put signaling pathways and gene expression profiles together to characterise biological mechanisms of breast cancer subtypes since many signaling events result from post-translational modifications, rather than gene expression differences.We present a logic-based approach to explain the differences in gene expression profiles among breast cancer subtypes using Pathway Logic and transcriptional network information. Pathway Logic is a rewriting-logic-based formal system for modeling biological pathways including post-translational modifications. Proposed method demonstrated its utility by constructing subtype-specific path from key receptors (TNFR, TGFBR1 and EGFR) to key transcription factor (TF) regulators (RELA, ATF2, SMAD3 and ELK1) and identifying potential pathway crosstalk via TFs in basal-specific paths, which could provide a novel insight on aggressive breast cancer subtypes.AvailabilityAnalysis result is available at http://epigenomics.snu.ac.kr/PL/

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Genome-Wide Analysis of Spatiotemporal Expression Patterns During Rice Leaf Development

10.21203/rs.3.rs-103621/v1 ◽

2020 ◽

Author(s):

Masayuki Miya ◽

Takanori Yoshikawa ◽

Yutaka Sato ◽

Jun-Ichi Itoh

Keyword(s):

Leaf Development ◽

Leaf Blade ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Clusters ◽

Mature Stage ◽

Future Research ◽

Rice Leaf ◽

Genome Wide ◽

Rice Leaves

Abstract Background: Rice leaves consist of three distinct regions along a proximal-distal axis, namely the leaf blade, sheath, and blade-sheath boundary region. Each region has a unique morphology and function, but the genetic programs underlying the development of each region are poorly understood. To fully elucidate rice leaf development and discover genes with unique functions in rice and grasses, it is crucial to explore genome-wide transcriptional profiles during the development of the three regions.Results: In this study, we performed microarray analysis to profile the spatial and temporal patterns of gene expression in the rice leaf using dissected parts of leaves sampled in broad developmental stages. The dynamics in each region revealed that the transcriptomes changed dramatically throughout the progress of tissue differentiation, and those of the leaf blade and sheath differed greatly at the mature stage. Cluster analysis of expression patterns among leaf parts revealed groups of genes that may be involved in specific biological processes related to rice leaf development. Moreover, we found novel genes potentially involved in rice leaf development using a combination of transcriptome data and in situ hybridization, and analyzed their spatial expression patterns at high resolution. We successfully identified multiple genes that exhibit localized expression in tissues characteristic of rice or grass leaves.Conclusions: Although the genetic mechanisms of leaf development have been elucidated in several eudicots, direct application of that information to rice and grasses is not appropriate due to the morphological and developmental differences between them. Our analysis provides not only insights into the development of rice leaves but also expression profiles that serve as a valuable resource for gene discovery. The genes and gene clusters identified in this study may facilitate future research on the unique developmental mechanisms of rice leaves.

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Identifying TRKA and TRKB specific pathways in neuroblastoma through phosphoproteomic analysis.

Journal of Clinical Oncology ◽

10.1200/jco.2012.30.15_suppl.e20008 ◽

2012 ◽

Vol 30 (15_suppl) ◽

pp. e20008-e20008

Author(s):

Samuel Louis Volchenboum ◽

Kolbrun Kristjansdottir ◽

Ilana Bergelson ◽

Saira Khan ◽

Garrett M. Brodeur

Keyword(s):

Protein Expression ◽

Tyrosine Kinase ◽

Cell Lines ◽

Isotope Labeling ◽

Expression Profiles ◽

Protein Translation ◽

Great Promise ◽

Tyrosine Kinase Receptor ◽

Post Translational Modifications ◽

Trkb Receptors

e20008 Background: Neuroblastoma is the most common solid tumor found in children and is difficult to treat given its genetic and clinical heterogeneity. The tyrosine kinase receptor, TrkB, is often co-expressed with the MYCN oncogene in high-risk tumors, whereas the TrkA receptor is most often found expressed in low-risk, non-MYCN amplified samples. There are differences in the gene expression profiles of TrkB- and TrkA-over-expressing cell lines, but they do not explain the phenotypic variation. We hypothesize that differences in protein translation and post-translational modifications have profound downstream effects on cellular signaling and disease phenotype. Methods: We performed quantitative proteomics using stable isotope labeling, phosphopeptide enrichment, and tandem mass spectrometry on parental SY5Y neuroblastoma cells and cell lines stably transfected with either TrkA or TrkB. Receptors were activated with NGF or BDNF and activation was inhibited with CEP-701 (Lestaurtinib), a selective tyrosine kinase inhibitor, currently in clinical trials. Samples were separated by gel electrophoresis, digested with trypsin, and applied to the mass spectrometer for protein identification. Results: We have performed quantitative phosphoproteomic analysis and compared protein expression levels and patterns in TrkA overexpressing, TrkB overexpressing, and parental SY5Y cells. The TrkA and TrkB receptors were activated with NGF and BDNF ligands, respectively, as evidenced by increased phosphorylation of ERK and AKT, with inhibition by CEP-701. Changes in protein abundance and pathway activation following both ligand binding and inhibition are being determined by quantitative phosphoproteomic analysis, and TrkA-specific and TrkB-specific differences will be presented. Conclusions: As current genomic techniques may underestimate the differences in protein expression, proteomic profiling holds great promise for describing how post-translational modifications such as phosphorylation can affect tumor phenotype. Our work may reveal key elements of TRK signaling pathways important in neuroblastoma tumorigenesis, and may lead to the identification of novel targets for therapy development.

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Genome-wide analysis of spatiotemporal expression patterns during rice leaf development

BMC Genomics ◽

10.1186/s12864-021-07494-5 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Masayuki Miya ◽

Takanori Yoshikawa ◽

Yutaka Sato ◽

Jun-Ichi Itoh

Keyword(s):

Leaf Development ◽

Leaf Blade ◽

Expression Profiles ◽

Expression Patterns ◽

Gene Clusters ◽

Mature Stage ◽

Future Research ◽

Rice Leaf ◽

Genome Wide ◽

Rice Leaves

Abstract Background Rice leaves consist of three distinct regions along a proximal-distal axis, namely the leaf blade, sheath, and blade-sheath boundary region. Each region has a unique morphology and function, but the genetic programs underlying the development of each region are poorly understood. To fully elucidate rice leaf development and discover genes with unique functions in rice and grasses, it is crucial to explore genome-wide transcriptional profiles during the development of the three regions. Results In this study, we performed microarray analysis to profile the spatial and temporal patterns of gene expression in the rice leaf using dissected parts of leaves sampled in broad developmental stages. The dynamics in each region revealed that the transcriptomes changed dramatically throughout the progress of tissue differentiation, and those of the leaf blade and sheath differed greatly at the mature stage. Cluster analysis of expression patterns among leaf parts revealed groups of genes that may be involved in specific biological processes related to rice leaf development. Moreover, we found novel genes potentially involved in rice leaf development using a combination of transcriptome data and in situ hybridization, and analyzed their spatial expression patterns at high resolution. We successfully identified multiple genes that exhibit localized expression in tissues characteristic of rice or grass leaves. Conclusions Although the genetic mechanisms of leaf development have been elucidated in several eudicots, direct application of that information to rice and grasses is not appropriate due to the morphological and developmental differences between them. Our analysis provides not only insights into the development of rice leaves but also expression profiles that serve as a valuable resource for gene discovery. The genes and gene clusters identified in this study may facilitate future research on the unique developmental mechanisms of rice leaves.

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Genome-wide survey and identification of AP2/ERF genes involved in shoot and leaf development in Liriodendron chinense

BMC Genomics ◽

10.1186/s12864-021-08119-7 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Yaxian Zong ◽

Ziyuan Hao ◽

Zhonghua Tu ◽

Yufang Shen ◽

Chengge Zhang ◽

...

Keyword(s):

Stress Responses ◽

Leaf Development ◽

Developmental Stages ◽

Expression Profiles ◽

Leaf Primordia ◽

Response Factors ◽

Anatomic Structure ◽

Genome Wide ◽

Liriodendron Chinense ◽

Erf Family

Abstract Background Liriodendron chinense is a distinctive ornamental tree species due to its unique leaves and tulip-like flowers. The discovery of genes involved in leaf development and morphogenesis is critical for uncovering the underlying genetic basis of these traits. Genes in the AP2/ERF family are recognized as plant-specific transcription factors that contribute to plant growth, hormone-induced development, ethylene response factors, and stress responses. Results In this study, we identified 104 putative AP2/ERF genes in the recently released L. chinense genome and transcriptome database. In addition, all 104 genes were grouped into four subfamilies, the AP2, ERF, RAV, and Soloist subfamilies. This classification was further supported by the results of gene structure and conserved motif analyses. Intriguingly, after application of a series test of cluster analysis, three AP2 genes, LcERF 94, LcERF 96, and LcERF 98, were identified as tissue-specific in buds based on the expression profiles of various tissues. These results were further validated via RT-qPCR assays and were highly consistent with the STC analysis. We further investigated the dynamic changes of immature leaves by dissecting fresh shoots into seven discontinuous periods, which were empirically identified as shoot apical meristem (SAM), leaf primordia and tender leaf developmental stages according to the anatomic structure. Subsequently, these three candidates were highly expressed in SAM and leaf primordia but rarely in tender leaves, indicating that they were mainly involved in early leaf development and morphogenesis. Moreover, these three genes displayed nuclear subcellular localizations through the transient transformation of tobacco epidermal cells. Conclusions Overall, we identified 104 AP2/ERF family members at the genome-wide level and discerned three candidate genes that might participate in the development and morphogenesis of the leaf primordium in L. chinense.

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Light-regulated gene expression during maize leaf development.

The Journal of Cell Biology ◽

10.1083/jcb.98.2.558 ◽

1984 ◽

Vol 98 (2) ◽

pp. 558-564 ◽

Cited By ~ 101

Author(s):

T Nelson ◽

M H Harpster ◽

S P Mayfield ◽

W C Taylor

Keyword(s):

Gene Expression ◽

Chlorophyll A ◽

Phosphoenolpyruvate Carboxylase ◽

Leaf Development ◽

Light Harvesting ◽

Messenger Rnas ◽

Bisphosphate Carboxylase ◽

Maize Leaf ◽

Protein Gel ◽

Regulated Gene Expression

We have established schedules of expression during maize leaf development in light and darkness for the messenger RNAs (mRNAs) and polypeptides for ribulose 1,5-bisphosphate carboxylase (RuBPCase) subunits, phosphoenolpyruvate carboxylase (PEPCase), and the light-harvesting chlorophyll a/b-binding protein (LHCP). Levels of mRNAs were measured by hybridization with cloned probes, and proteins were measured by immunodetection on protein gel blots. The initial synthesis in leaves of all four mRNAs follows a light-independent schedule; illumination influences only the level to which each mRNA accumulates. The synthesis of RuBPCase small and large subunits and of PEPCase polypeptides also follows a light-independent schedule which is modified quantitatively by light. However, the accumulation of LHCP polypeptides absolutely requires illumination. The accumulation of each protein closely follows the accumulation of its mRNA during growth in light. Higher ratios of PEPCase and RuBPCase protein to mRNA occur during dark growth.

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SMYD3: a regulator of epigenetic and signaling pathways in cancer

Clinical Epigenetics ◽

10.1186/s13148-021-01021-9 ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Benjamin J. Bernard ◽

Nupur Nigam ◽

Kyunghee Burkitt ◽

Vassiliki Saloura

Keyword(s):

Expression Profiles ◽

Tissue Expression ◽

Post Translational Modifications ◽

Histone 3 ◽

Functional Implications ◽

Methylation Mark ◽

Cancer Types ◽

Basic Characteristics ◽

Exciting Area ◽

Chromatin Modifiers

AbstractChromatin modifiers and their implications in oncogenesis have been an exciting area of cancer research. These are enzymes that modify chromatin via post-translational modifications such as methylation, acetylation, sumoylation, phosphorylation, in addition to others. Depending on the modification, chromatin modifiers can either promote or repress transcription. SET and MYN-domain containing 3 (SMYD3) is a chromatin modifier that has been implicated in the development and progression of various cancer types. It was first reported to tri-methylate Histone 3 Lysine 4 (H3K4), a methylation mark known to promote transcription. However, since this discovery, other histone (H4K5 and H4K20, for example) and non-histone (VEGFR, HER2, MAP3K2, ER, and others) substrates of SMYD3 have been described, primarily in the context of cancer. This review aims to provide a background on basic characteristics of SMYD3, such as its protein structure and tissue expression profiles, discuss reported histone and non-histone substrates of SMYD3, and underscore prognostic and functional implications of SMYD3 in cancer. Finally, we briefly discuss ongoing efforts to develop inhibitors of SMYD3 for future therapeutic use. It is our hope that this review will help synthesize existing research on SMYD3 in an effort to propel future discovery.

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Regulatory networks of circRNAs related to transcription factors in Populus euphratica Oliv. heteromorphic leaves

Bioscience Reports ◽

10.1042/bsr20190540 ◽

2019 ◽

Vol 39 (12) ◽

Cited By ~ 1

Author(s):

Lianghong Bao ◽

Shaowei Qin ◽

CaiLin Li ◽

Zhongzhong Guo ◽

Lifeng Zhao

Keyword(s):

Transcription Factors ◽

Leaf Development ◽

Regulatory Networks ◽

Target Genes ◽

Expression Profiles ◽

Populus Euphratica ◽

Circular Rnas ◽

Leaf Morphogenesis ◽

Heteromorphic Leaves ◽

Populus Euphratica Oliv

Abstract Circular RNAs (circRNAs) are a novel class of non-coding RNAs that are characterized by a covalently closed circular structure. They have been widely found in Populus euphratica Oliv. heteromorphic leaves (P. hl). To study the role of circRNAs related to transcription factors (TFs) in the morphogenesis of P. hl, the expression profiles of circRNAs in linear, lanceolate, ovate, and broad-ovate leaves of P. euphratica were elucidated by strand-specific sequencing. We identified and characterized 22 circRNAs related to TFs in P. hl at the four developmental stages. Using the competing endogenous RNAs hypothesis as a guide, we constructed circRNA–miRNA–TF mRNA regulatory networks, which indicated that circRNAs antagonized microRNAs (miRNAs), thereby influencing the expression of the miRNA target genes and playing a significant role in transcriptional regulation. Gene ontology annotation of the target TF genes predicted that these circRNAs were associated mainly with the regulation of leaf development, leaf morphogenesis, signal transduction, and response to abiotic stress. These findings implied that the circRNAs affected the size and number of cells in P. hl by regulating the expression of TF mRNAs. Our results provide a basis for further studies of leaf development in poplar trees.

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