Transcriptome profiling: methods and applications- A review

Global transcriptional profiling is a powerful tool that can expose expression patterns to define cellular states or to identify genes with similar expression patterns. In recent years, transcriptome profiling has been widely used to understand the genetic regulation of a particular cell type. Transcriptome is defined as a full range of messenger Ribonucleic acid (RNA) molecule expressed by an organism. In other words a transcriptome represents the small percentage of genetic code that is transcribed into RNA molecules. It can offer valuable information on the significant biological processes behind the maintenance of the functionality of the cell. Transcriptomics provides fundaments for more definitively designed studies and guidance to select the genes for functional studies. The technology for the study of the transcriptome is not dependent on any prior knowledge of the genes expressed in the cells. However, with regards to the administration and interpretation of the enormous data provided by transcriptome profiling challenges remain.. Four methods have been reviewed here that is, Microarray technology, Serial Analysis of Gene Expression (SAGE), RNA sequencing (RNA-Seq) and Massively Parallel Signature Sequencing (MPSS). The use of these technologies to analyse the expressed transcripts in several prokaryotic and eukaryotic genomes has revealed the high complexity of transcriptomes.

Identification and Characterization of In planta–Expressed Secreted Effector Proteins from Magnaporthe oryzae That Induce Cell Death in Rice

Interactions between rice and Magnaporthe oryzae involve the recognition of cellular components and the exchange of complex molecular signals from both partners. How these interactions occur in rice cells is still elusive. We employed robust-long serial analysis of gene expression, massively parallel signature sequencing, and sequencing by synthesis to examine transcriptome profiles of infected rice leaves. A total of 6,413 in planta–expressed fungal genes, including 851 genes encoding predicted effector proteins, were identified. We used a protoplast transient expression system to assess 42 of the predicted effector proteins for the ability to induce plant cell death. Ectopic expression assays identified five novel effectors that induced host cell death only when they contained the signal peptide for secretion to the extracellular space. Four of them induced cell death in Nicotiana benthamiana. Although the five effectors are highly diverse in their sequences, the physiological basis of cell death induced by each was similar. This study demonstrates that our integrative genomic approach is effective for the identification of in planta–expressed cell death–inducing effectors from M. oryzae that may play an important role facilitating colonization and fungal growth during infection.

MPSS profiling of embryonic gonad and primordial germ cells in chicken

The massively parallel signature sequencing (MPSS) provides a greater depth of coverage than expressed sequence tag scan or microarray and provides a comprehensive expression profile. We used the MPSS technology to uncover gene expression profiling in the early embryonic gonads and primordial germ cells (PGCs) in the chicken. Total numbers of sequenced signatures were 1,012,533 and 995,676 for the PGCs and gonad, respectively. Using a noise distribution model, we found that 1.67% of all signatures are expressed at a higher level in PCGs and 2.81% of all signatures are expressed at a higher level in the gonad. The MPSS data are presented via an interactive web interface available at http://snugenome.snu.ac.kr/MPSS . The MPSS data have been submitted to the Gene Expression Omnibus of the National Center for Biotechnology Information (accession number GSM137300 and GSM137301 for PGCs and gonad, respectively).