HyeongJin Yun Homework

RNA Sequencing (RNA-seq)

RNA Sequencing (RNA-seq) is a powerful technology used to analyze the transcriptome of cells, tissues, or entire organisms. The transcriptome includes all RNA molecules expressed within a cell at a specific time and under specific conditions. RNA-seq determines the quantity and sequences of RNA molecules, generating gene expression profiles. The process involves the following steps:

RNA Extraction:

1. • Total RNA is extracted from the cells or tissues of interest. Total RNA typically includes mRNA, tRNA, rRNA, etc., but RNA-seq mainly focuses on mRNA.

cDNA Synthesis:

1. • The extracted RNA is converted into complementary DNA (cDNA) using reverse transcriptase. cDNA is stable and suitable for sequencing.

Library Preparation:

1. • Adapter sequences are attached to the cDNA fragments to prepare a sequencing library. Adapter sequences enable the sequencing machine to recognize and read the DNA fragments.

Sequencing:

1. • The prepared cDNA library is sequenced using next-generation sequencing (NGS) technology. This process generates millions of short DNA sequence reads.

Data Analysis:

1. • The generated sequence data are aligned to a reference genome. This step quantifies gene expression levels, detects novel transcripts, splicing variants, gene fusions, and more.

Applications:

• Gene Expression Analysis: Compare gene expression levels under different conditions or disease states.
• Discovery of New Transcripts: Identify previously unknown RNA molecules.
• Splicing Variant Analysis: Analyze different splicing forms and variants.
• Gene Fusion Detection: Detect gene fusion events, often associated with cancers.

Advantages:

• High sensitivity and accuracy: Can detect low-abundance RNA.
• Broad applicability: Suitable for various biological questions and sample types.

Limitations:

• Complexity of data processing: Requires advanced computational biology skills to process and interpret large amounts of data.
• Cost: High-quality RNA-seq analysis can still be relatively expensive.

RNA-seq is an essential tool in biological and medical research, helping to understand disease mechanisms, discover biomarkers, develop new drugs, and more.