scholarly journals Chicken sperm transcriptome profiling by microarray analysis

Genome ◽  
2016 ◽  
Vol 59 (3) ◽  
pp. 185-196 ◽  
Author(s):  
R.P. Singh ◽  
C.M. Shafeeque ◽  
S.K. Sharma ◽  
R. Singh ◽  
J. Mohan ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Embryonic Development ◽  
Microarray Analysis ◽  
Cell Structure ◽  
Transcriptome Profiling ◽  
Rt Pcr ◽  
Mammalian Sperm ◽  
Functional Rnas ◽  
Rna Contamination ◽  
Pcr Microarray

It has been confirmed that mammalian sperm contain thousands of functional RNAs, and some of them have vital roles in fertilization and early embryonic development. Therefore, we attempted to characterize transcriptome of the sperm of fertile chickens using microarray analysis. Spermatozoal RNA was pooled from 10 fertile males and used for RNA preparation. Prior to performing the microarray, RNA quality was assessed using a bioanalyzer, and gDNA and somatic cell RNA contamination was assessed by CD4 and PTPRC gene amplification. The chicken sperm transcriptome was cross-examined by analysing sperm and testes RNA on a 4 × 44K chicken array, and results were verified by RT-PCR. Microarray analysis identified 21 639 predominantly nuclear-encoded transcripts in chicken sperm. The majority (66.55%) of the sperm transcripts were shared with the testes, while surprisingly, 33.45% transcripts were detected (raw signal intensity greater than 50) only in the sperm and not in the testes. The greatest proportion of up-regulated transcripts were responsible for signal transduction (63.20%) followed by embryonic development (56.76%) and cell structure (56.25%). Of the 20 most abundant transcripts, 18 remain uncharacterized, whereas the least abundant genes were mostly associated with the ribosome. These findings lay a foundation for more detailed investigations on sperm RNAs in chickens to identify sperm-based biomarkers for fertility.

scholarly journals Expression profile of microRNAs in gastrointestinal stromal tumors revealed by high throughput quantitative RT-PCR microarray

2015 ◽  
Vol 21 (19) ◽  
pp. 5843-5855 ◽  
Author(s):  
Han-Xing Tong ◽  
Yu-Hong Zhou ◽  
Ying-Yong Hou ◽  
Yong Zhang ◽  
Yuan Huang ◽  
...  
Keyword(s):  
Expression Profile ◽  
High Throughput ◽  
Gastrointestinal Stromal Tumors ◽  
Rt Pcr ◽  
Stromal Tumors ◽  
Pcr Microarray

Comparative transcriptome profiling reveals the reprogramming of gene networks under arsenic stress in Indian mustard

Genome ◽  
2019 ◽  
Vol 62 (12) ◽  
pp. 833-847
Author(s):  
Sapna Thakur ◽  
Shruti Choudhary ◽  
Preeti Dubey ◽  
Pankaj Bhardwaj
Keyword(s):  
Signal Transduction ◽  
Gene Networks ◽  
Large Scale ◽  
Indian Mustard ◽  
Transcriptome Profiling ◽  
Dry Weight ◽  
Control Measures ◽  
Glutathione Metabolism ◽  
Adverse Health Effects ◽  
Arsenic Accumulation

Arsenic is a widespread toxic metalloid that is classified as a class I carcinogen known to cause adverse health effects in humans. In the present study, we investigated arsenic accumulation potential and comparative gene expression in Indian mustard. The amount of arsenic accumulated in shoots varied in the range of 15.99–1138.70 mg/kg on a dry weight basis among five cultivars. Comparative expression analysis revealed 10 870 significantly differentially expressed genes mostly belonging to response to stress, metabolic processes, signal transduction, transporter activity, and transcription regulator activity to be up-regulated, while most of the genes involved in photosynthesis, developmental processes, and cell growth were found to be down-regulated in arsenic-treated tissues. Further, pathway analysis using the KEGG Automated Annotation server (KAAS) revealed a large-scale reprogramming of genes involved in genetic and environmental information processing pathways. Top pathways with maximum KEGG orthology hits included carbon metabolism (2.5%), biosynthesis of amino acids (2.1%), plant hormone signal transduction (1.4%), and glutathione metabolism (0.6%). A transcriptomic investigation to understand the arsenic accumulation and detoxification in Indian mustard will not only help to improve its phytoremediation efficiency but also add to the control measures required to check bioaccumulation of arsenic in the food chain.

scholarly journals Transcriptional Dynamics of Grain Development in Barley (Hordeum vulgare L.)

2019 ◽  
Vol 20 (4) ◽  
pp. 962 ◽  
Author(s):  
Jianxin Bian ◽  
Pingchuan Deng ◽  
Haoshuang Zhan ◽  
Xiaotong Wu ◽  
Mutthanthirige Nishantha ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Rna Editing ◽  
Signal Transduction Pathway ◽  
Sugar Metabolism ◽  
Transcriptome Profiling ◽  
Barley Grain ◽  
Grain Development ◽  
Hordeum Vulgare L ◽  
Functional Studies ◽  
Transcriptional Dynamics

Grain development, as a vital process in the crop’s life cycle, is crucial for determining crop quality and yield. However, the molecular basis and regulatory network of barley grain development is not well understood at present. Here, we investigated the transcriptional dynamics of barley grain development through RNA sequencing at four developmental phases, including early prestorage phase (3 days post anthesis (DPA)), late prestorage or transition phase (8 DPA), early storage phase (13 DPA), and levels off stages (18 DPA). Transcriptome profiling found that pronounced shifts occurred in the abundance of transcripts involved in both primary and secondary metabolism during grain development. The transcripts’ activity was decreased during maturation while the largest divergence was observed between the transitions from prestorage phase to storage phase, which coincided with the physiological changes. Furthermore, the transcription factors, hormone signal transduction-related as well as sugar-metabolism-related genes, were found to play a crucial role in barley grain development. Finally, 4771 RNA editing events were identified in these four development stages, and most of the RNA editing genes were preferentially expressed at the prestore stage rather than in the store stage, which was significantly enriched in “essential” genes and plant hormone signal transduction pathway. These results suggested that RNA editing might act as a ‘regulator’ to control grain development. This study systematically dissected the gene expression atlas of barley grain development through transcriptome analysis, which not only provided the potential targets for further functional studies, but also provided insights into the dynamics of gene regulation underlying grain development in barley and beyond.

scholarly journals Expression of taste signal transduction molecules in the caecum of common marmosets

2013 ◽  
Vol 9 (4) ◽  
pp. 20130409 ◽  
Author(s):  
Sae Gonda ◽  
Shuichi Matsumura ◽  
Shoichiro Saito ◽  
Yasuhiro Go ◽  
Hiroo Imai
Keyword(s):  
Signal Transduction ◽  
Immunohistochemical Analysis ◽  
Common Marmoset ◽  
Rt Pcr ◽  
Common Marmosets ◽  
Plant Exudates ◽  
The Common ◽  
Signal Transduction Proteins ◽  
First Time ◽  
Human Primate

The extraoral presence of taste signal transduction proteins has recently been reported in rodents and humans. Here, we report for the first time the presence of these signal transduction proteins in the caecum of a non-human primate, the common marmoset. Quantitative RT-PCR data on the gene expression of taste signal transduction molecules (gustducin and TRPM5) in common marmosets suggested high expression in the caecum, which was not observed in other non-human primates. Immunohistochemical analysis confirmed the specific presence of gustducin and taste receptors in marmoset caecal cells. These results may relate to the specific feeding behaviour of marmosets, which consume plant exudates, primarily gums.

Identification of Genes Induced by Taxol Application Using a Combination of Differential Display RT-PCR and DNA Microarray Analysis

2001 ◽  
Vol 56 (9-10) ◽  
pp. 814-819 ◽  
Author(s):  
Ei-ichiro Fukusaki ◽  
Takashi Oishi ◽  
Hozumi Tanaka ◽  
Shin-ichiro Kajiyama ◽  
Akio Kobayashi
Keyword(s):  
Microarray Analysis ◽  
Dna Microarray ◽  
Differential Display ◽  
Gene Expression Pattern ◽  
Cdna Clones ◽  
Rt Pcr ◽  
Dna Microarray Analysis ◽  
Glass Slides ◽  
Polymerase Chain ◽  
Cdna Fragments

Abstract The differential display reverse transcriptional polymerase chain reaction (DD-RT-PCR) was used to hunt for cDNA fragments specifically expressed by taxol treatment of HeLa cells. Forty-eight cDNA clones were differentially displayed through the experiments. The cDNA fragments obtained were separately spotted onto glass slides to prepare a tailor-made DNA chip. The gene expression pattern of differentially displayed cDNA fragments were checked by DNA microarray analysis.

Muscle transcriptome profiling in divergent phenotype swine breeds during growth using microarray and RT-PCR tools

2011 ◽  
Vol 42 (5) ◽  
pp. 501-509 ◽  
Author(s):  
M. D’Andrea ◽  
S. Dal Monego ◽  
A. Pallavicini ◽  
M. Modonut ◽  
R. Dreos ◽  
...  
Keyword(s):  
Transcriptome Profiling ◽  
Rt Pcr

scholarly journals Cytokine-mediated increases in fetal hemoglobin are associated with globin gene histone modification and transcription factor reprogramming

Blood ◽  
2009 ◽  
Vol 114 (11) ◽  
pp. 2299-2306 ◽  
Author(s):  
Orapan Sripichai ◽  
Christine M. Kiefer ◽  
Natarajan V. Bhanu ◽  
Toshihiko Tanno ◽  
Seung-Jae Noh ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Protein Expression ◽  
Histone Modification ◽  
Globin Gene ◽  
Expression Patterns ◽  
Fetal Hemoglobin ◽  
Transcriptome Profiling ◽  
Globin Genes

Abstract Therapeutic regulation of globin genes is a primary goal of translational research aimed toward hemoglobinopathies. Signal transduction was used to identify chromatin modifications and transcription factor expression patterns that are associated with globin gene regulation. Histone modification and transcriptome profiling were performed using adult primary CD34+ cells cultured with cytokine combinations that produced low versus high levels of gamma-globin mRNA and fetal hemoglobin (HbF). Embryonic, fetal, and adult globin transcript and protein expression patterns were determined for comparison. Chromatin immunoprecipitation assays revealed RNA polymerase II occupancy and histone tail modifications consistent with transcriptional activation only in the high-HbF culture condition. Transcriptome profiling studies demonstrated reproducible changes in expression of nuclear transcription factors associated with high HbF. Among the 13 genes that demonstrated differential transcript levels, 8 demonstrated nuclear protein expression levels that were significantly changed by cytokine signal transduction. Five of the 8 genes are recognized regulators of erythropoiesis or globin genes (MAFF, ID2, HHEX, SOX6, and EGR1). Thus, cytokine-mediated signal transduction in adult erythroid cells causes significant changes in the pattern of globin gene and protein expression that are associated with distinct histone modifications as well as nuclear reprogramming of erythroid transcription factors.

The Identification and Genomic Analysis of microRNAs in Human Erythrocytes in Sickle Cell Diseases.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 3400-3400
Author(s):  
Shao-Yin Chen ◽  
Yulei Wang ◽  
Marilyn I. Telen ◽  
Jen-Tsan A. Chi
Keyword(s):  
Microarray Analysis ◽  
Target Gene ◽  
Terminal Differentiation ◽  
Genomic Analysis ◽  
Microrna Expression ◽  
Rt Pcr ◽  
Northern Blots ◽  
Disease Phenotypes ◽  
Differentiated Cells ◽  
The Poor

Abstract Erythrocytes are circulating blood cells responsible for efficient gas exchange in human body. Since mature erythrocytes are terminally differentiated cells without nuclei and organelles, it is commonly thought that they do not contain nucleic acids. In this study, we re-examined this issue and found that human mature erythrocytes, while lacking ribosomal and large-sized RNAs, possess abundant small-sized RNAs. Using a combination of microarray analysis, real-time RT-PCR and Northern blots we found that mature erythrocytes contained abundant and diverse microRNAs which were distinct from microRNAs observed in reticulocytes/leukocytes and contributed to the majority of the microRNA expression in whole blood. When we used microarrays to analyze erythrocytes from normal (HbAA) and homozygous sickle (HbSS) individulas, we noted dramatic a difference in their microRNA expression pattern. To investigate how this difference is associated with erythrocyte disease phenotypes, we found that the poor expression of miR-320 was responsible for the defective downregulation of its target gene CD71 in HbSS cells during terminal differentiation. Collectively, we have discovered significant microRNA expression in human mature erythrocytes, which enables the microarray analysis of erythrocyte property to provide insights into the human erythrocyte diseases.

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