An expression of interest

Bonetta, Laura

doi:10.1038/4401233a

Cited by 5 publications

(3 citation statements)

References 36 publications

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“…Solexa SAGE produced more initial SAGE tags than the previous SAGE libraries because it has much deeper coverage. Note that the Illumina Solexa Genome Analyzer produced a SAGE library that is about 20 times more sensitive than a normal SAGE library [26]. …”

Section: Resultsmentioning

confidence: 99%

Identifying novel genes in C. elegans using SAGE tags

2010

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BackgroundDespite extensive efforts devoted to predicting protein-coding genes in genome sequences, many bona fide genes have not been found and many existing gene models are not accurate in all sequenced eukaryote genomes. This situation is partly explained by the fact that gene prediction programs have been developed based on our incomplete understanding of gene feature information such as splicing and promoter characteristics. Additionally, full-length cDNAs of many genes and their isoforms are hard to obtain due to their low level or rare expression. In order to obtain full-length sequences of all protein-coding genes, alternative approaches are required.ResultsIn this project, we have developed a method of reconstructing full-length cDNA sequences based on short expressed sequence tags which is called sequence tag-based amplification of cDNA ends (STACE). Expressed tags are used as anchors for retrieving full-length transcripts in two rounds of PCR amplification. We have demonstrated the application of STACE in reconstructing full-length cDNA sequences using expressed tags mined in an array of serial analysis of gene expression (SAGE) of C. elegans cDNA libraries. We have successfully applied STACE to recover sequence information for 12 genes, for two of which we found isoforms. STACE was used to successfully recover full-length cDNA sequences for seven of these genes.ConclusionsThe STACE method can be used to effectively reconstruct full-length cDNA sequences of genes that are under-represented in cDNA sequencing projects and have been missed by existing gene prediction methods, but their existence has been suggested by short sequence tags such as SAGE tags.

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Section: Resultsmentioning

confidence: 99%

Identifying novel genes in C. elegans using SAGE tags

2010

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“…Human beings are developed from a fertilized egg into a complete individual; during the whole process, a series of precise regulations on the development are included, such as gene expression and gene silence [ 1 ], transcriptional regulation [ 2 ], posttranscriptional regulation [ 3 ], hormone regulation [ 4 ], chromosome behavior regulation [ 5 ], and apoptosis [ 6 ]. For these different regulative pathways, their target cells are embryonic stem cells (ESCs).…”

Section: Introductionmentioning

confidence: 99%

Epigenetic Regulations in Neural Stem Cells and Neurological Diseases

Zhou

Wang

Sun

et al. 2018

Stem Cells International

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Among the regulatory mechanisms of the renewal and differentiation of neural stem cells, recent evidences support that epigenetic modifications such as DNA methylation, histone modification, and noncoding RNAs play critical roles in the regulation on the proliferation and differentiation of neural stem cells. In this review, we discussed recent advances of DNA modifications on the regulative mechanisms of neural stem cells. Among these epigenetic modifications, DNA 5-hydroxymethylcytosine (5hmC) modification is emerging as an important modulator on the proliferation and differentiation of neural stem cells. At the same time, Ten-eleven translocation (Tet) methylcytosine dioxygenases, the rate-limiting enzyme for the 5-hydroxymethylation reaction from 5-methylcytosine to 5-hydroxymethylcytosine, play a critical role in the tumorigenesis and the proliferation and differentiation of stem cells. The functions of 5hmC and TET proteins on neural stem cells and their roles in neurological diseases are discussed.

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“…Many miRNA profiling platforms and techniques have been used to assay the miRNA repertoire of biological samples. Platforms have incorporated cloning, microarrays, PCR, highthroughput Northern blots, nanoscale technologies, and other modalities [2][3][4][12][13][14][15][16][17][18][19][20][21][22][23][24][25][26][27][28][29]. Each technique presumably entails specific strengths and weaknesses, including sensitivity, specificity, and cost-related considerations.…”

Section: Introductionmentioning

confidence: 99%

Focus on RNA isolation: Obtaining RNA for microRNA (miRNA) expression profiling analyses of neural tissue

Wang

Wilfred

Baldwin

et al. 2008

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanism

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MicroRNAs (miRNAs) are present in all known plant and animal tissues and appear to be somewhat concentrated in the mammalian nervous system. Many different miRNA expression profiling platforms have been described. However, relatively little research has been published to establish the importance of 'upstream' variables in RNA isolation for neural miRNA expression profiling. We tested whether apparent changes in miRNA expression profiles may be associated with tissue processing, RNA isolation techniques, or different cell types in the sample. RNA isolation was performed on a single brain sample using eight different RNA isolation methods, and results were correlated using a conventional miRNA microarray and then cross-referenced to Northern blots. Differing results were seen between samples obtained using different RNA isolation techniques and between microarray and Northern blot results. Another complication of miRNA microarrays is tissue-level heterogeneity of cellular composition. To investigate this phenomenon, miRNA expression profiles were determined and compared between highly-purified primary cerebral cortical cell preparations of rat primary E15-E18 neurons versus rat primary E15-E18 astrocytes. Finally, to assess the importance of dissecting human brain gray matter from subjacent white matter in cerebral cortical studies, miRNA expression profiles were compared between gray matter and immediately contiguous white matter. The results suggest that for microarray studies, cellular composition is important, and dissecting white matter from gray matter improves the specificity of the results. Based on these data, recommendations for miRNA expression profiling in neural tissues, and considerations worthy of further study, are discussed.

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An expression of interest

Cited by 5 publications

References 36 publications

Identifying novel genes in C. elegans using SAGE tags

Identifying novel genes in C. elegans using SAGE tags

Epigenetic Regulations in Neural Stem Cells and Neurological Diseases

Focus on RNA isolation: Obtaining RNA for microRNA (miRNA) expression profiling analyses of neural tissue

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