Different Transcriptional Profiles of RAW264.7 Infected with Mycobacterium tuberculosis H37Rv and BCG Identified via Deep Sequencing

Pan, Fengguang; Zhao, Yaya; Zhu, Seng; Sun, Changjiang; Lei, Liancheng; Feng, Xin; Han, Wen Y.

doi:10.1371/journal.pone.0051988

Cited by 10 publications

(9 citation statements)

References 49 publications

(54 reference statements)

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“…Only one gene (Pbr000187.1) did not show consistent expression between accurate quantification of expression and digital transcript abundance measurements (Additional file 5). Pearson’s correlation coefficient (r) showed that both the digital transcript abundance measurements and qRT-PCR data were highly correlated, with the r-value ranging from 0.656 (Pbr036692.1) to 0.934 (Pbr001279.1), which was in agreement with previous report [52]. The qRT-PCR further demonstrated that genes related to photosystem reaction (Pbr041327.1), hormone-related transcripts (Pbr036692.1), carbohydrate metabolism (Pbr021608.1, Pbr008092.1, and Pbr001279.1) and other differentially regulated genes (Pbr027181.1) showed significant difference between treatments and participated in the process of calyx abscission or persistent processes.…”

Section: Resultssupporting

confidence: 91%

Identifying the candidate genes involved in the calyx abscission process of 'Kuerlexiangli’ (Pyrus sinkiangensis Yu) by digital transcript abundance measurements

Wang

et al. 2013

BMC Genomics

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Background'Kuerlexiangli’ (Pyrus sinkiangensis Yu), a native pear of Xinjiang, China, is an important agricultural fruit and primary export to the international market. However, fruit with persistent calyxes affect fruit shape and quality. Although several studies have looked into the physiological aspects of the calyx abscission process, the underlying molecular mechanisms remain unknown. In order to better understand the molecular basis of the process of calyx abscission, materials at three critical stages of regulation, with 6000 × Flusilazole plus 300 × PBO treatment (calyx abscising treatment) and 50 mg.L-1GA3 treatment (calyx persisting treatment), were collected and cDNA fragments were sequenced using digital transcript abundance measurements to identify candidate genes.ResultsDigital transcript abundance measurements was performed using high-throughput Illumina GAII sequencing on seven samples that were collected at three important stages of the calyx abscission process with chemical agent treatments promoting calyx abscission and persistence. Altogether more than 251,123,845 high quality reads were obtained with approximately 8.0 M raw data for each library. The values of 69.85%-71.90% of clean data in the digital transcript abundance measurements could be mapped to the pear genome database. There were 12,054 differentially expressed genes having Gene Ontology (GO) terms and associating with 251 Kyoto Encyclopedia of Genes and Genomes (KEGG) defined pathways. The differentially expressed genes correlated with calyx abscission were mainly involved in photosynthesis, plant hormone signal transduction, cell wall modification, transcriptional regulation, and carbohydrate metabolism. Furthermore, candidate calyx abscission-specific genes, e.g. Inflorescence deficient in abscission gene, were identified. Quantitative real-time PCR was used to confirm the digital transcript abundance measurements results.ConclusionsWe identified candidate genes that showed highly dynamic changes in expression during the calyx abscission process. These genes are potential targets for future functional characterization and should be valuable for exploration of the mechanisms of calyx abscission, and eventually for developing methods based on small molecule application to induce calyx abscission in fruit production.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-14-727) contains supplementary material, which is available to authorized users.

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Section: Resultssupporting

confidence: 91%

Identifying the candidate genes involved in the calyx abscission process of 'Kuerlexiangli’ (Pyrus sinkiangensis Yu) by digital transcript abundance measurements

Wang

et al. 2013

BMC Genomics

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“…The results showed that although the exact fold changes for the selected genes at three stages varied between digital gene expression and qRT-PCR analysis, the trend of gene expression changes detected by the two different approaches were largely consistent (Figure 5 ). Pearson's correlation coefficients showed that the digital transcript abundance measurements and qRT-PCR data were highly correlated (Table 7 ), with R 2 -values ranging from 0.639 ( Pbr027485.1 ) to 0.998 ( Pbr004885.1 ), which was in agreement with previous reports (Pan et al, 2012 ).…”

Section: Resultssupporting

confidence: 91%

Transcriptome profiling reveals differential gene expression in proanthocyanidin biosynthesis associated with red/green skin color mutant of pear (Pyrus communis L.)

et al. 2015

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Anthocyanin concentration is the key determinant for red skin color in pear fruit. However, the molecular basis for development of red skin is complicated and has not been well-understood thus far. “Starkrimson” (Pyrus communis L.), an introduced red pear cultivated in the north of China and its green mutant provides a desirable red/green pair for identification of candidate genes involved in color variation. Here, we sequenced and annotated the transcriptome for the red/green color mutant at three stages of development using Illumina RNA-seq technology. The total number of mapped reads ranged from 26 to 46 million in six libraries. About 70.11–71.95% of clean reads could be mapped to the reference genome. Compared with green colored fruit, a total of 2230 differentially expressed genes (DEGs) were identified in red fruit. Gene Ontology (GO) terms were defined for 4886 differential transcripts involved in 15 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Three DEGs were identified as candidate genes in the flavonoid pathway, LAR, ANR, and C3H. Tellingly, higher expression was found for genes encoding ANR and LAR in the green color mutant, promoting the proanthocyanidin (PA) pathway and leading to lower anthocyanin. MYB-binding cis-motifs were identified in the promoter region of LAR and ANR. Based on these findings, we speculate that the regulation of PA biosynthesis might be a key factor for this red/green color mutant. Besides the known MYB and MADS transcription families, two new families, AP2 and WRKY, were identified as having high correlation with anthocyanin biosynthesis in red skinned pear. In addition, qRT-PCR was used to confirm the transcriptome results for 17 DEGs, high correlation of gene expression, further proved that AP2 and WARK regulated the anthocyanin biosynthesis in red skinned “Starkrimson,” and ANR and LAR promote PA biosynthesis and contribute to the green skinned variant. This study can serve as a valuable new resource laying a solid foundation for functional gene identification in the anthocyanin pathway of red-skinned pear and provide a good reference for relevant research on molecular mechanisms of color variation in other pear species.

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“…To date, however, the molecular mechanism of Sp110-mediated macrophage resistance to Mtb remains unknown, and the downstream genes involved in Sp110-mediated pathways are unexplored. Most recently, high-throughput sequencing and microarray technologies have been introduced to analyse the mammalian host response to mycobacterial pathogens, the results of which have greatly enhanced scientific understanding of the interactions occurring between host species and pathogens 2 28 29 30 31 32 . Because macrophages are the main host cells for Mtb , efficient genetic manipulation of them is required to investigate innate immunity to this pathogen, but achieving this is especially difficult in primary macrophages.…”

Section: Discussionmentioning

confidence: 99%

The Transcriptional Foundations of Sp110-mediated Macrophage (RAW264.7) Resistance to Mycobacterium tuberculosis H37Ra

Guo

Yao

et al. 2016

Sci Rep

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Human tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a leading global health problem, causing 1.3 million deaths each year. The nuclear body protein, Sp110, has been linked to TB resistance and previous work showed that it enhances macrophage apoptosis upon Mtb infection. Here, we report on the role of Sp110 in transcriptional regulation of macrophage responses to Mtb through integrated transcriptome and mechanistic studies. Transcriptome analysis revealed that Sp110 regulates genes involved in immune responses, apoptosis, defence responses, and inflammatory responses. Detailed investigation revealed that, in addition to apoptosis-related genes, Sp110 regulates cytokines, chemokines and genes that regulate intracellular survival of Mtb. Moreover, Sp110 regulates miRNA expression in macrophages, with immune and apoptosis-related miRNAs such as miR-125a, miR-146a, miR-155, miR-21a and miR-99b under Sp110 regulation. Additionally, our results showed that Sp110 upregulates BCL2 modifying factor (Bmf) by inhibiting miR-125a, and forced expression of Bmf induces macrophage apoptosis. These findings not only reveal the transcriptional basis of Sp110-mediated macrophage resistance to Mtb, but also suggest potential regulatory roles for Sp110 related to inflammatory responses, miRNA profiles, and the intracellular growth of Mtb.

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Different Transcriptional Profiles of RAW264.7 Infected with Mycobacterium tuberculosis H37Rv and BCG Identified via Deep Sequencing

Cited by 10 publications

References 49 publications

Identifying the candidate genes involved in the calyx abscission process of 'Kuerlexiangli’ (Pyrus sinkiangensis Yu) by digital transcript abundance measurements

Identifying the candidate genes involved in the calyx abscission process of 'Kuerlexiangli’ (Pyrus sinkiangensis Yu) by digital transcript abundance measurements

Transcriptome profiling reveals differential gene expression in proanthocyanidin biosynthesis associated with red/green skin color mutant of pear (Pyrus communis L.)

The Transcriptional Foundations of Sp110-mediated Macrophage (RAW264.7) Resistance to Mycobacterium tuberculosis H37Ra

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