Comparison of a proteomic approach with a microarray-based approach to detect exons in the mouse genome

Sheng, Quanhu; Wang, Lian-Shui; Dai, Jie; Jiang, Xueying; Li, Rong Xia; Ma, Dongzhu; Li, Yixue; Zeng, Rong; Wu, Jiarui

doi:10.1038/ng1106-1223

Cited by 4 publications

(1 citation statement)

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“…For example, Gygi et al detected a 20 fold-increase in protein expression for some genes that were unaltered at the mRNA level by microarray analysis [16], [54]. Clearly, a twofold differential expression of genes may not necessarily result in a twofold change in protein expression [55]. In addition, several mRNA molecules are not translated and may act as transcription regulators or may decay before protein is synthesized [56], [57] leading to a differential expression of genes, but not proteins.…”

Section: Discussionmentioning

confidence: 99%

Genomic and Proteomic Analysis of the Impact of Mitotic Quiescence on the Engraftment of Human CD34+ Cells

2011

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It is well established that in adults, long-term repopulating hematopoietic stem cells (HSC) are mitotically quiescent cells that reside in specialized bone marrow (BM) niches that maintain the dormancy of HSC. Our laboratory demonstrated that the engraftment potential of human HSC (CD34+ cells) from BM and mobilized peripheral blood (MPB) is restricted to cells in the G0 phase of cell cycle but that in the case of umbilical cord blood (UCB) -derived CD34+ cells, cell cycle status is not a determining factor in the ability of these cells to engraft and sustain hematopoiesis. We used this distinct in vivo behavior of CD34+ cells from these tissues to identify genes associated with the engraftment potential of human HSC. CD34+ cells from BM, MPB, and UCB were fractionated into G0 and G1 phases of cell cycle and subjected in parallel to microarray and proteomic analyses. A total of 484 target genes were identified to be associated with engraftment potential of HSC. System biology modeling indicated that the top four signaling pathways associated with these genes are Integrin signaling, p53 signaling, cytotoxic T lymphocyte-mediated apoptosis, and Myc mediated apoptosis signaling. Our data suggest that a continuum of functions of hematopoietic cells directly associated with cell cycle progression may play a major role in governing the engraftment potential of stem cells. While proteomic analysis identified a total of 646 proteins in analyzed samples, a very limited overlap between genomic and proteomic data was observed. These data provide a new insight into the genetic control of engraftment of human HSC from distinct tissues and suggest that mitotic quiescence may not be the requisite characteristic of engrafting stem cells, but instead may be the physiologic status conducive to the expression of genetic elements favoring engraftment.

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Section: Discussionmentioning

confidence: 99%

Genomic and Proteomic Analysis of the Impact of Mitotic Quiescence on the Engraftment of Human CD34+ Cells

2011

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Human and Chimpanzee Transcriptomes: Comparative Evolution

Khaitovich¹,

Kehrer-Sawatzko

Cooper

2008

Encyclopedia of Life Sciences

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The biological basis of the uniqueness of human abilities is one of the most fascinating research topics of all time. Evolutionary studies now allow us, at least in principle, to identify the underlying functional genetic elements which are specific to humans. However, despite enormous progress in the biosciences over recent years, which has resulted in the complete sequencing of the human genome as well as the genomes of two closely related primate species – chimpanzee and rhesus macaque – the molecular mechanisms underlying human‐specific abilities remain unknown. Gene expression studies now provide us with a powerful tool to identify the functional differences distinguishing humans from chimpanzees, our closest living relatives. From the evolutionary and functional perspective, however, the interpretation of the observed expression differences is almost never as straightforward as we would ideally like.

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Membrane subproteomic analysis of Mycobacterium bovis bacillus Calmette‐Guérin

et al. 2007

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Mycobacterium bovis bacillus Calmette-Guérin (BCG) vaccine has been known for a long time to prevent tuberculosis (TB) worldwide since 1921. Nonetheless, we know little about BCG membrane proteome. In the present study, we utilized alkaline incubation and Triton X-114-based methods to enrich BCG membrane proteins and subsequently digested them using proteolytic enzyme. The recovered peptides were further separated by 2-D LC and identified by ESI-MS/MS. As a result, total 474 proteins were identified, including 78 integral membrane proteins (IMPs). Notably, 18 BCG IMPs were described for the first time in mycobacterium. Further analysis of the 78 IMPs indicated that the theoretical molecular mass distribution of them ranged from 8.06 to 167.86 kDa and pI scores ranged from 4.40 to 11.60. Functional classification revealed that a large proportion of the identified IMPs (67.9%, 53 out of 78) were involved in cell wall and cell processes functional group. In conclusion, here we reported a comprehensive profile of the BCG membrane subproteome. The present investigation may allow the identification of some valuable vaccine and drug target candidates and thus provide basement for future designing of preventive, diagnostic, and therapeutic strategies against TB.

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Comparison of a proteomic approach with a microarray-based approach to detect exons in the mouse genome

Cited by 4 publications

References 4 publications

Genomic and Proteomic Analysis of the Impact of Mitotic Quiescence on the Engraftment of Human CD34+ Cells

Genomic and Proteomic Analysis of the Impact of Mitotic Quiescence on the Engraftment of Human CD34+ Cells

Human and Chimpanzee Transcriptomes: Comparative Evolution

Membrane subproteomic analysis of Mycobacterium bovis bacillus Calmette‐Guérin

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