scholarly journals A New Insight into Flowering Regulation: Molecular Basis of Flowering Initiation in Magnolia × soulangeana ‘Changchun’

Genes ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 15 ◽  
Author(s):  
Zheng Jiang ◽  
Liyong Sun ◽  
Qiang Wei ◽  
Ye Ju ◽  
Xuan Zou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Molecular Basis ◽  
Woody Plants ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Flower Buds ◽  
Flowering Initiation ◽  
Specific Regulation ◽  
Flowering Process

Magnolia × soulangeana ‘Changchun’ are trees that bloom in spring and summer respectively after flower bud differentiation. Here, we use phenological and morphological observation and RNA-seq technology to study the molecular basis of flowering initiation in ‘Changchun’. During the process of flowering initiation in spring and summer, the growth of expanded flower buds increased significantly, and their shape was obviously enlarged, which indicated that flowering was initiated. A total of 168,120 expressed genes were identified in spring and summer dormant and expanded flower buds, of which 11,687 genes showed significantly differential expression between spring and summer dormant and expanded flower buds. These differentially expressed genes (DEGs) were mainly involved in plant hormone signal transduction, metabolic processes, cellular components, binding, and catalytic activity. Analysis of differential gene expression patterns revealed that gibberellin signaling, and some transcription factors were closely involved in the regulation of spring and summer flowering initiation in ‘Changchun’. A qRT-PCR (quantitative Real Time Polymerase Chain Reaction) analysis showed that BGISEQ-500 sequencing platform could truly reflect gene expression patterns. It also verified that GID1B (GIBBERELLIN INSENSITIVE DWARF1 B), GID1C, SPL8 (SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 8), and GASA (GIBBERELLIC ACID-STIMULATED ARABIDOPSIS) family genes were expressed at high levels, while the expression of SPY (SPINDLY) was low during spring and summer flowering initiation. Meanwhile, the up- and down-regulated expression of, respectively, AGL6 (AGAMOUS-LIKE 6) and DREB3 (DEHYDRATION-RESPONSIVE ELEMENT-BINDING PROTEIN 3), AG15, and CDF1 (CYCLIC DOF FACTOR 1) might also be involved in the specific regulation of spring and summer flowering initiation. Obviously, flowering initiation is an important stage of the flowering process in woody plants, involving the specific regulation of relevant genes and transcription factors. This study provides a new perspective for the regulation of the flowering process in perennial woody plants.

scholarly journals Evaluating the Molecular Basis for Acute Mountain Sickness: Hypoxia Response Gene Expression Patterns in Warfighters and Murine Populations

2013 ◽  
Vol 178 (11) ◽  
pp. 1256-1263 ◽  
Author(s):  
Jeremy L. Goodin ◽  
Jose M. Pizarro-Matos ◽  
Balakrishna M. Prasad ◽  
Thomas J. Seiter ◽  
Courtney R. Weaver ◽  
...  
Keyword(s):  
Gene Expression ◽  
Molecular Basis ◽  
Expression Patterns ◽  
Acute Mountain Sickness ◽  
Gene Expression Patterns ◽  
Response Gene ◽  
Hypoxia Response ◽  
Mountain Sickness

scholarly journals Genomic DNA microarray comparison of gene expression patterns in Paracoccidioides brasiliensis mycelia and yeasts in vitro

Microbiology ◽  
2009 ◽  
Vol 155 (8) ◽  
pp. 2795-2808 ◽  
Author(s):  
Jomar Patrício Monteiro ◽  
Karl V. Clemons ◽  
Laurence F. Mirels ◽  
John A. Coller ◽  
Thomas D. Wu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Genomic Dna ◽  
Paracoccidioides Brasiliensis ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Protein Catabolism ◽  
Time Points ◽  
Over Time

Paracoccidioides brasiliensis is a thermally dimorphic fungus, and causes the most prevalent systemic mycosis in Latin America. Infection is initiated by inhalation of conidia or mycelial fragments by the host, followed by further differentiation into the yeast form. Information regarding gene expression by either form has rarely been addressed with respect to multiple time points of growth in culture. Here, we report on the construction of a genomic DNA microarray, covering approximately 25 % of the genome of the organism, and its utilization in identifying genes and gene expression patterns during growth in vitro. Cloned, amplified inserts from randomly sheared genomic DNA (gDNA) and known control genes were printed onto glass slides to generate a microarray of over 12 000 elements. To examine gene expression, mRNA was extracted and amplified from mycelial or yeast cultures grown in semi-defined medium for 5, 8 and 14 days. Principal components analysis and hierarchical clustering indicated that yeast gene expression profiles differed greatly from those of mycelia, especially at earlier time points, and that mycelial gene expression changed less than gene expression in yeasts over time. Genes upregulated in yeasts were found to encode proteins shown to be involved in methionine/cysteine metabolism, respiratory and metabolic processes (of sugars, amino acids, proteins and lipids), transporters (small peptides, sugars, ions and toxins), regulatory proteins and transcription factors. Mycelial genes involved in processes such as cell division, protein catabolism, nucleotide biosynthesis and toxin and sugar transport showed differential expression. Sequenced clones were compared with Histoplasma capsulatum and Coccidioides posadasii genome sequences to assess potentially common pathways across species, such as sulfur and lipid metabolism, amino acid transporters, transcription factors and genes possibly related to virulence. We also analysed gene expression with time in culture and found that while transposable elements and components of respiratory pathways tended to increase in expression with time, genes encoding ribosomal structural proteins and protein catabolism tended to sharply decrease in expression over time, particularly in yeast. These findings expand our knowledge of the different morphological forms of P. brasiliensis during growth in culture.

scholarly journals Patterns of gene expression in the sheep heart during the perinatal period revealed by transcriptomic modeling

2015 ◽  
Vol 47 (9) ◽  
pp. 407-419 ◽  
Author(s):  
Elaine M. Richards ◽  
M. Belen Rabaglino ◽  
Andrew Antolic ◽  
Charles E. Wood ◽  
Maureen Keller-Wood
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Expression Patterns ◽  
Perinatal Period ◽  
Gene Expression Patterns ◽  
Acid Oxidation ◽  
Expression Of Genes ◽  
Development And Differentiation ◽  
Near Term ◽  
Coexpressed Genes

Septa from sheep hearts at 130 days gestation, term, and 14-day-old lambs were used to model the changes in gene expression patterns during the perinatal period using Agilent 15k ovine microarrays. We used Bioconductor for R to model five major patterns of coexpressed genes. Gene ontology and transcription factor analyses using Webgestalt modeled the biological significances and transcription factors of the gene expression patterns. Modeling indicated a decreased expression of genes associated with anatomical development and differentiation during this period, whereas those associated with increased protein synthesis and growth associated with maturation of the endoplasmic reticulum rose to term but did not further increase from the near term expression. Expression of genes associated with cell responsiveness, for example, immune responses, decreased at term but expression returned by postnatal day 14. Changes in genes related to metabolism showed differential substrate-associated patterns: those related to carbohydrate metabolism rose to term and remained stable thereafter, whereas those associated with fatty acid oxidation facility rose throughout the period. The timing of many of these maturational processes was earlier in relation to birth than in the rodent. The importance of the transcription factors, estrogen-related receptors, and v-myc avian myelocytomatosis viral oncogene homolog was also highlighted in the pattern of gene expression during development of the perinatal sheep heart.

Modelling Barrett's oesophagus

2010 ◽  
Vol 38 (2) ◽  
pp. 321-326 ◽  
Author(s):  
Jianping Kong ◽  
Douglas B. Stairs ◽  
John P. Lynch
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Epithelial Cells ◽  
Expression Patterns ◽  
Dominant Negative ◽  
Barrett’S Oesophagus ◽  
Columnar Epithelium ◽  
Gene Expression Patterns ◽  
Barrett's Oesophagus ◽  
Normal Oesophagus

Barrett's oesophagus is the replacement of normal squamous oesophageal epithelium with an intestinalized columnar epithelium. Although some insight has been gained as to what Barrett's oesophagus is, how this columnar epithelium emerges from within a stratified squamous epithelium remains an unanswered question. We have sought to determine whether oesophageal keratinocytes can be trans-differentiated into Barrett's oesophagus cells. Using an Affymetrix microarray, we found unexpectedly that gene-expression patterns in the Barrett's oesophagus were only slightly more similar to the normal small intestine than they were to the normal oesophagus. Thus gene-expression patterns suggest significant molecular similarities remain between Barrett's oesophagus cells and normal squamous oesophageal epithelium, despite their histological resemblance with intestine. We next determined whether directed expression of intestine-specific transcription factors could induce intestinalization of keratinocytes. Retroviral-mediated Cdx2 (Caudal-type homeobox 2) expression in immortalized human oesophageal keratinocytes engineered with human telomerase reverse transcriptase (EPC2-hTERT cells) could be established transiently, but not maintained, and was associated with a reduction in cell proliferation. Co-expression of cyclin D1 rescued proliferation in the Cdx2-expressing cells, but co-expression of dominant-negative p53 did not. Cdx2 expression in the EPC2-hTERT.D1 cells did not induce intestinalization. However, when combined with treatments that induce chromatin remodelling, there was a significant induction of Barrett's oesophagus-associated genes. Studies are ongoing to determine whether other intestinal transcription factors, either alone or in combination, can provoke greater intestinalization of oesophageal keratinocytes. We conclude that, on the basis of gene-expression patterns, Barrett's oesophagus epithelial cells may represent an intermediate between oesophageal keratinocytes and intestinal epithelial cells. Moreover, our findings suggest that it may be possible to induce Barrett's oesophagus epithelial cells from oesophageal keratinocytes by altering the expression of certain critical genes.

scholarly journals Algorithmic Reconstruction of GBM Network Complexity

2021 ◽  
Author(s):  
Abicumaran Uthamacumaran ◽  
Morgan Craig
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Single Cell ◽  
Cell Fate ◽  
Data Science ◽  
Expression Patterns ◽  
State Transitions ◽  
Gene Expression Patterns ◽  
Cell Fate Decisions ◽  
Study Gene Expression

Glioblastoma (GBM) is a complex disease that is difficult to treat. Establishing the complex genetic interactions regulating cell fate decisions in GBM can help to shed light on disease aggressivity and improved treatments. Networks and data science offer novel approaches to study gene expression patterns from single-cell datasets, helping to distinguish genes associated with control of differentiation and thus aggressivity. Here, we applied a host of data theoretic techniques, including clustering algorithms, Waddington landscape reconstruction, trajectory inference algorithms, and network approaches, to compare gene expression patterns between pediatric and adult GBM, and those of adult GSCs (glioma-derived stem cells) to identify the key molecular regulators of the complex networks driving GBM/GSC and predict their cell fate dynamics. Using these tools, we identified critical genes and transcription factors coordinating cell state transitions from stem-like to mature GBM phenotypes, including eight transcription factors (OLIG1/2, TAZ, GATA2, FOXG1, SOX6, SATB2, YY1) and four signaling genes (ATL3, MTSS1, EMP1, and TPT1) as clinically targetable novel putative function interactions differentiating pediatric and adult GBMs from adult GSCs. Our study is among the first to provide strong evidence of the applicability of complex systems approaches for reverse-engineering gene networks from patient-derived single-cell datasets and inferring their complex dynamics, bolstering the search for new clinically- relevant targets in GBM.

scholarly journals Identification of a modular super-enhancer in murine retinal development

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
Victoria Honnell ◽  
Jackie L. Norrie ◽  
Anand G. Patel ◽  
Cody Ramirez ◽  
Jiakun Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Proliferation ◽  
Transcription Factors ◽  
Progenitor Cell ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Retinal Progenitor Cell ◽  
Retinal Progenitor ◽  
Super Enhancer ◽  
Progenitor Cell Proliferation

AbstractSuper-enhancers are expansive regions of genomic DNA comprised of multiple putative enhancers that contribute to the dynamic gene expression patterns during development. This is particularly important in neurogenesis because many essential transcription factors have complex developmental stage– and cell–type specific expression patterns across the central nervous system. In the developing retina, Vsx2 is expressed in retinal progenitor cells and is maintained in differentiated bipolar neurons and Müller glia. A single super-enhancer controls this complex and dynamic pattern of expression. Here we show that deletion of one region disrupts retinal progenitor cell proliferation but does not affect cell fate specification. The deletion of another region has no effect on retinal progenitor cell proliferation but instead leads to a complete loss of bipolar neurons. This prototypical super-enhancer may serve as a model for dissecting the complex gene expression patterns for neurogenic transcription factors during development. Moreover, it provides a unique opportunity to alter expression of individual transcription factors in particular cell types at specific stages of development. This provides a deeper understanding of function that cannot be achieved with traditional knockout mouse approaches.

scholarly journals Intake of Watermelon and Watermelon Byproducts in Male Mice Fed a Western-Style Obesogenic Diet Alters Hepatic Gene Expression Patterns, as Determined by RNA Sequencing

2020 ◽  
Vol 4 (8) ◽  
Author(s):  
Mariana Buranelo Egea ◽  
Gavin Pierce ◽  
Alexandra R Becraft ◽  
Marlena Sturm ◽  
Wesley Yu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Rna Sequencing ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Control Group ◽  
Peroxisome Proliferator ◽  
Hepatic Gene Expression ◽  
Peroxisome Proliferator Activated Receptor ◽  
Expression Levels

ABSTRACT Background Consumption of watermelon has been associated with beneficial effects on metabolism, including reductions in systolic blood pressure, improved fasting blood glucose levels, and changes in hepatic metabolite accumulation. Objectives In the present study, we investigated the impact of consumption of watermelon flesh (WF), watermelon rind (WR), and watermelon skin (WS) on hepatic gene expression patterns in an obesogenic mouse model. Methods Hepatic RNA was isolated and RNA sequencing was performed following a 10-week feeding trial during which C57BL/6 J mice were provided either a low-fat diet (LF), high-fat diet (HF; controls), or HF plus either WS, WR, or WF. Bioinformatic approaches were used to determine changes in the canonical pathways and gene expression levels for lipid- and xenobiotic-regulating nuclear hormone receptors and other related transcription factors, including the aryl hydrocarbon receptor (AhR), constitutive androstane receptor (CAR), farnesyl X receptor, peroxisome proliferator–activated receptor alpha (PPARα), peroxisome proliferator–activated receptor gamma, liver X receptor, pregnane X receptor, and nuclear factor erythroid 2–related factor 2. Results There were 9394 genes that had unchanged expression levels between all 5 diet groups, and 247, 58, and 34 genes were uniquely expressed in the WF, WR, and WS groups, respectively. The relative levels of mRNAs regulated by AhR, CAR, and PPARα were upregulated in mice in the WF group, as compared to the HF control mice; in comparison, mRNAs regulated mainly by CAR were upregulated in mice in the WR and WS groups, compared to those in the HF control group. Conclusions At modest levels of intake reflective of typical human consumption, mice in the WF, WS, and WR groups exhibited hepatic gene expression profiles that were altered when compared to mice in the HF control group. Several of these changes involve genes regulated by ligand-responsive transcription factors implicated in xenobiotic and lipid metabolisms, suggesting that the modulation of these transcription factors occurred in response to the consumption of WS, WR, and WF. Some of these changes are likely due to nuclear hormone receptor–mediated changes involved in lipid and xenobiotic metabolisms.

Transcriptome analysis reveals hybridization-induced genome shock in an interspecific F1 hybrid from Camellia

Genome ◽  
2018 ◽  
Vol 61 (7) ◽  
pp. 477-485 ◽  
Author(s):  
Min Zhang ◽  
Xin-Kai Liu ◽  
Wen Fan ◽  
Dan-Feng Yan ◽  
Nai-Sheng Zhong ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Histone Methylation ◽  
Flower Development ◽  
Woody Plants ◽  
Genome Stability ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Rna Seq ◽  
F1 Hybrid

The combination of two divergent genomes during hybridization can result in “genome shock”. Although genome shock has been reported in the hybrids of some herbaceous plants, the pattern and the principle it follows are far from understood, especially in woody plants. Here, the gene expression patterns were remodeled in the F1 hybrid from the crossing of Camellia azalea × Camellia amplexicaulis compared with the parents as revealed by RNA-seq. About 54.5% of all unigenes were differentially expressed between the F1 hybrid and at least one of the parents, including 6404 unigenes with the highest expression level in the F1 hybrid. A series of genes, related to flower development, essential for RNA-directed DNA methylation and histone methylation, as well as 223 transposable elements, were enriched; and most of them exhibited a higher level of expression in the F1 hybrid. These results indicated that the genome shock induced by interspecific hybridization in Camellia could indeed result in changes of gene expression patterns, potentially through regulating DNA methylation and histone methylation which may be helpful for the maintaining of genome stability and even related to the unique phenotype of the F1 hybrid.

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