Serial analysis of gene expression (SAGE): unraveling the bioinformatics tools

Tuteja, Renu; Tuteja, Narendra

doi:10.1002/bies.20070

Cited by 37 publications

(10 citation statements)

References 39 publications

(48 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Eight were up-regulated (Pou5f1 , Zp2 , Ivns1abp , Vbp1 , Padi6 , Rbpms2 , Genbank:EG626058, 6430591E23Rik) and three were down-regulated ( Sp3 , Hdac2 , Ogt ) in newborn normal ovaries. Because alternative statistical analyses [24-26] may be useful for the comparison of these data sets, we have made the original microarray and SAGE data available at Gene Expression Omnibus [27] under accession GSE5558 and GSE5802, respectively.…”

Section: Resultsmentioning

confidence: 99%

Ovarian gene expression in the absence of FIGLA, an oocyte-specific transcription factor

et al. 2007

View full text Add to dashboard Cite

Background: Ovarian folliculogenesis in mammals is a complex process involving interactions between germ and somatic cells. Carefully orchestrated expression of transcription factors, cell adhesion molecules and growth factors are required for success. We have identified a germ-cell specific, basic helix-loop-helix transcription factor, FIGLA (Factor In the GermLine, Alpha) and demonstrated its involvement in two independent developmental processes: formation of the primordial follicle and coordinate expression of zona pellucida genes.

show abstract

Section: Resultsmentioning

confidence: 99%

Ovarian gene expression in the absence of FIGLA, an oocyte-specific transcription factor

et al. 2007

View full text Add to dashboard Cite

show abstract

“…Previous studies have sequence barcoded up to 6,200 yeast (39,40) or viral (39,40) strains for competition experiments and analyzed the barcodes by deep sequencing (Bar-seq) or microarrays. As we were competing a relatively small number of viral strains (nine), we identified the barcodes using an approach based on the principles of serial analysis of gene expression (SAGE) (41). The sequence barcodes were fused into concatemers in a simple two-step PCR, cloned, and identified by Sanger sequencing.…”

Section: Discussionmentioning

confidence: 99%

Evasion of Superinfection Exclusion and Elimination of Primary Viral RNA by an Adapted Strain of Hepatitis C Virus

Webster

Ott

Greene

2013

J Virol

View full text Add to dashboard Cite

Cells that are productively infected by hepatitis C virus (HCV) are refractory to a second infection by HCV via a block in viral replication known as superinfection exclusion. The block occurs at a postentry step and likely involves translation or replication of the secondary viral RNA, but the mechanism is largely unknown. To characterize HCV superinfection exclusion, we selected for an HCV variant that could overcome the block. We produced a high-titer HC-J6/JFH1 (Jc1) viral genome with a fluorescent reporter inserted between NS5A and NS5B and used it to infect Huh7.5 cells containing a Jc1 replicon. With multiple passages of these infected cells, we isolated an HCV variant that can superinfect cells at high levels. Notably, the superinfectious virus rapidly cleared the primary replicon from superinfected cells. Viral competition experiments, using a novel strategy of sequencebarcoding viral strains, as well as superinfection of replicon cells demonstrated that mutations in E1, p7, NS5A, and the poly(U/ UC) tract of the 3= untranslated region were important for superinfection. Furthermore, these mutations dramatically increased the infectivity of the virus in naive cells. Interestingly, viruses with a shorter poly(U/UC) and an NS5A domain II mutation were most effective in overcoming the postentry block. Neither of these changes affected viral RNA translation, indicating that the major barrier to postentry exclusion occurs at viral RNA replication. The evolution of the ability to superinfect after less than a month in culture and the concomitant exclusion of the primary replicon suggest that superinfection exclusion dramatically affects viral fitness and dynamics in vivo. In superinfection exclusion, a cell productively infected with a specific virus becomes resistant to infection with a homologous virus. This process has been described for several viruses, including human immunodeficiency virus (HIV) (1), Sindbis virus (2), duck hepatitis B virus (3), and citrus tristeza virus (4), in a broad range of hosts. Cells infected with or actively replicating hepatitis C virus (HCV) also become refractory to further HCV infection (5, 6). The superinfection block occurs at the level of translation or replication of the incoming secondary viral RNA (5-7), which is similar to the case of the related pestivirus bovine diarrhea virus (8). The exact mechanism is unclear. Since HCV RNA levels quickly plateau in infected cells in vitro, a superinfection block at the level of RNA translation or replication suggests that access to the necessary host factor(s) is rate limiting. This has clear implications for HCV treatment. By definition, a rate-limiting host factor is critical for the replication of the virus and may be a unique target in future therapies.Superinfection exclusion itself also has clear implications for treating HCV infection. Since viral recombination requires a host cell to be productively replicating two genomes, superinfection exclusion would be expected to effectively prevent viral recombination. If, howeve...

show abstract

“…Such global gene expression patterns can be represented by a "transcriptome", which reveals the identity and the level of expression of each expressed gene in a deWned population of cells (Velculescu et al 1997;Tuteja and Tuteja 2004). The transcriptome can be modulated by both external and internal factors, and thereby provide not only a wealth of basic biological insights but also a global view of biological responses to environmental stimuli.…”

Section: Introductionmentioning

confidence: 99%

LongSAGE analysis of the early response to cold stress in Arabidopsis leaf

Byun

Kim

Lee

2009

Planta

View full text Add to dashboard Cite

The initial events involved in signal transduction generated by cold exposure are poorly known in plants. We were interested in the characterization of early response to cold stress in Arabidopsis leaves. So we examined plants exposed to 0 degrees C for 1 h. Using LongSAGE at the level of transcription, a total of 27,612 tags, including 11,089 unique tags were sequenced and analyzed. By adopting LongSAGE methods, the ambiguity of tag identification was reduced by about 10%. Only 46% of identified tags in the 1-h cold-stressed plants matched existing Arabidopsis UniGene entries. A comparison of the tags derived from the cold-treated leaves with those identified in the non-treated leaves revealed 315 differentially expressed genes (P < 0.01). Functional classification of expressed genes during the early cold response indicated that genes were involved in light harvesting, the Calvin cycle, and photorespiration were expressed at relatively low levels compared to their presence in non-cold-stressed plants. On other hand, genes involved in mitochondrial electron transport and ATP synthesis showed an increased expression. Some orphan LongSAGE tags uniquely matched pri-miRNA, suggesting the existence of miRNA in our SAGE library. These findings suggest that diverse protection strategies appear in the early response of leaves exposed to cold stress. First of all, several genes included in signal transduction through calcium mediated signal sensing, and cascades of several kinases, and transcription factors, were distinguished in the early cold response. Furthermore, genes affecting the synthesis of salicylic acid, nitrate assimilation, ammonia assimilation, the gluconeogenesis pathway, and glucosinolate biosynthesis were newly detected in relationship with cold stress. Finally, our results in the present work provide new insights into the molecular mechanisms involved in transcriptional regulation in response to cold exposure in plants.

show abstract

Serial analysis of gene expression (SAGE): unraveling the bioinformatics tools

Cited by 37 publications

References 39 publications

Ovarian gene expression in the absence of FIGLA, an oocyte-specific transcription factor

Ovarian gene expression in the absence of FIGLA, an oocyte-specific transcription factor

Evasion of Superinfection Exclusion and Elimination of Primary Viral RNA by an Adapted Strain of Hepatitis C Virus

LongSAGE analysis of the early response to cold stress in Arabidopsis leaf

Contact Info

Product

Resources

About