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Annoroad and its cooperative partners have published six SCIs in a month

2017-12-12


Recently, Annoroad has many article achievements in tumor, stem cell, germ cell and other aspects, with six articles published in journals within last month and a total impact factor of 33.632.  The editor is filled with admiration to the research strength of all cooperative teachers and at the same time, silently gives likes to the effective and high-quality technologies of our Annoroad.


Then, the editor will make a brief introduction to these six articles, convenient for all readers to know about the progresses and technical applications of relevant researches. After all, speaking through the literatures is consistent with a science researcher’s style that is simple and unadorned.


I.     scRNA-seq interprets the mechanism of mouse X-chromosome reactivation [1]


Annoroad's scRNA-seq technology contributes to the research of chromosome reactivation mechanism

Journal Published: Nature Communications

Cooperation Unit: Institute Curie

Research Results: The scientists carried out the principal component analysis (PCA) to the data obtained by carrying out the scRNA-seq to mouse E3.5 and E4.0 inner cell mass and the transcriptome data of trophectoderm (TE) cells and primitive endoderm (PrE) cells which has been published, and found that there is an obvious heterogeneity between E3.5 and E4.0 cells and either early or metaphase cells can be differentiated into two cell subsets. While based on the expression of pluripotent differentiation factor, E4.0 inner cell mass was obviously differentiated into two kinds, i.e. primitive endoderm cells and trophectoderm cells. The clustering analysis based on the differentially expressed genes also obtained a consistent result.

Figure 1 Clustering analysis based on the single cell transcriptome data


II.    Passive DNA demethylation may up regulate the expression of totipotent genes and promote the generation of iPSC [2]


Annoroad WGBS and RRBS technologies contributes to the functional research of passive DNA demethylation

Journal Published: Journal of Biological Chemistry

Cooperation Unit: Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences

Research Results: The author researched and found that the hereditary DNA methylation during the cell proliferation not only conducts in the S-phase of cell cycle but also completes in the G2/M-phase and G1-phase. This phenomenon is more obvious in fast cell proliferation rare and when Dnmt1 is silenced, causing the whole genome methylation level of cells in G1-phase is obviously higher than that in G2/M-phase. The author showed, through a further whole genome bisulfite sequencing (WGBS), that such methylation difference is intensively reflected in the totipotent gene promoter region. In addition, promoting the cell proliferation or repressing the expression of DNMT1 and p53 can induce the passive DNA demethylation, to induce the demethylation in relevant totipotent gene, to further promote the somatic reprogramming.

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Figure 2 Passive DNA methylation may up regulate the expression of totipotent gene

III.   The deletion of polycomb protein Pcgf1 will seriously impact the normal differentiation of embryonic stem cell [3]


Annoroad RNA-seq technology contributes to the research of stem cell differentiation

Journal Published: Scientific Reports

Cooperation Unit: Nanjing University

Research Results: The author used the RNA-seq to analyze the mRNA from the Pcgf1 defective cells, found that the Pcgf1 up-regulation involves the expression of basic transcription factors of ectoderm and mesoderm differentiation and revealed the function of Pcgf1 in gene activation during the ES cell lineage specification. The research confirmed that Pcgf1 has an important function in gene activation during the ES cell maintenance.

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Figure 3 RNA-seq analyzes the transcriptional activator function of Pcgf1


IV.  Pcgf 3/5 interacts with the pluripotent factors in embryonic stem cells to activate the transcription [4]


Annoroad RNA-seq technology contributes to the research of pluripotent factors of embryonic stem cells

Journal Published: Journal of Biological Chemistry

Cooperation Unit: Nanjing University

Research Results: The author researched and found that a subset of PcG protein participates in the transcription activation in some cellular environments, but how to realize this function is still unknown. Through the RNA-Seq analysis to these treated cells, he found that comparing with the effect of polycomb repressive complex 1 (PRC1) in gene repression, Pcgf3/5 mainly participates in the expression of many genes during the mesoderm differentiation as the transcription activation factor.

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Figure 4 Analysis of differential expression genes of ES cells with the deletion of Pcgf3/5


V.   Sequencing reveals GSK3 is the key determinant of lung cancer cell apoptosis mediated by p53 [5]


Annoroad RNA-seq technology contributes to the new programme research of lung cancer treatment

Journal Published: Cellular Physiology and Biochemistry

Cooperation Unit: Northeast Agricultural University

Research Results: The author used the RNA-seq to test the transcriptional level of human non-small cell lung cancer (A549) cells treated by nutlin and RITA, two compounds activated by p53. The analysis result showed that nutlin and RITA can induce 66 pathway differential regulations, and by combining the shRNA deep analysis, there were 2 approaches, i.e. “adhesin junction” and “axon guidance”, that cause the P53 reactivation, where GSK3 plays a key role in A549 cell apoptosis mediated by p53. This research provides a new understanding for the mechanism of A549 cell apoptosis mediated by p53 and lays a foundation for the treatment of lung cancer.

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Figure 5 Analysis of RNA sequencing data reveals the different transcription profiles of RITA and nutlin in A549 cells


VI.  Tolerance of plants mediated by Cd stress response gene AtFC1 to Cd toxicity [6]


Annoroad RNA-seq technology contributes to the research of plant stress response mechanism

Journal Published: Cellular Physiology and Biochemistry

Cooperation Unit: Nanjing Agricultural University

Research Results: The scholar researched and found that the AtFC1 over-expression strain shows Cd stress tolerance, and AtFC1 deficiency shows Cd stress sensitivity. The transcriptome sequencing analysis results of fc1 mutant plants after Cd stress shows that the dysfunction of AtFC1 may cause differential expressions of a large number of genes. The result shows AtFC1 can be a positive regulator of plants to the Cd stress tolerance, thus the action mechanism of FC1 in mediated plants to Cd stress response was found, which provides a foundation for further exploring its downstream genes.

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Figure 6 Gene differential expression analyses of Arabidopsis fc1 mutant strains and field strains under Cd stress

I hope the literature summary above can help you understand current progress of RNA-seq and other researches and our core technologies, and welcome teachers to contact us for consulting and advising. May the results of our efforts fuse with your scientific researches to produce different sparks!


Reference


[1] Borensztein, M., Okamoto, I., Syx, L., Guilbaud, G., Picard, C., Ancelin,K., Galupa, R., Diabangouaya, P., Servant, N., Chen, C.J., et al. Contribution of epigenetic landscapes and transcription factors to X-chromosome reactivation in the inner cell mass [J]. Nature Communications, 2017, 8, 1297.

[2] He S, Sun H, Lin L, et al. Passive DNA demethylation preferentially up-regulates pluripotency-related genes and facilitates the generation of induced pluripotent stem cells[J]. Journal of Biological Chemistry, 2017:jbc.M117.810457.

[3] Yan Y, Zhao W, Huang Y, et al. Loss of Polycomb Group Protein Pcgf1 Severely Compromises Proper Differentiation of Embryonic Stem Cells[J]. Scientific Reports, 2017, 7:46276.

[4] Zhao Wukui, Huang Yikai, Zhang Jingzi, et al. Polycomb group RING finger protein 3/5 activate transcription via an interaction with the pluripotency factor Tex10 in embryonic stem cells[J]. J.Biol. Chem., 2017.

[5] Zhang Yu, Zhu Chenyang, SunBangyao et al. Integrated High Throughput Analysis IdentifiesGSK3 as a Crucial Determinant of p53-Mediated Apoptosis in Lung Cancer Cells[J]. Cell. Physiol. Biochem., 2017, 42(3): 1177-1191.

[6] Song Jun, Feng Sheng Jun, Chen Jian et al. A cadmium stress-responsive gene AtFC1 confers plant tolerance to cadmium toxicity[J]. BMC Plant Biol., 2017, 17(1):187.


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