functional genomics Flashcards
lecture 16
What is functional genomics?
Functional genomics involves experiments that describe gene functions and interactions, including studies on protein/DNA interactions, DNA methylation, gene expression, protein-protein interactions, and loss-of-function.
What are the types of functional genomics experiments?
Types include protein/DNA interactions, DNA methylation, gene expression, protein-protein interactions, and loss-of-function studies.
What is the role of microarrays in functional genomics?
Microarrays are used for measuring hybridization between sample DNA/RNA and probes, allowing for experiments like gene expression, ChIP, SNP detection, and methylation analysis.
How do microarrays work in functional genomics?
Samples are hybridized to probes on a microarray chip, washed, and then detected using fluorescence to measure expression or other interactions.
How does high-throughput sequencing (NGS) improve on microarrays?
NGS provides higher resolution and accuracy than microarrays by directly sequencing DNA, overcoming the limitations of hybridization-based approaches.
What are the basic steps in Illumina sequencing?
DNA is fragmented, adaptors are ligated, clonal clusters are formed, and sequencing proceeds with reversible termination to identify bases in cycles.
What is RNA-Seq and how does it differ from microarrays?
RNA-Seq uses direct sequencing to measure RNA content, providing greater resolution, dynamic range, and the ability to distinguish isoforms compared to microarrays.
What are some key advantages of RNA-Seq over microarrays?
RNA-Seq has higher resolution (single base), a greater dynamic range (>8000-fold), the ability to distinguish isoforms, and lower background noise.
What is the process of RNA-Seq?
RNA is converted into cDNA, which is fragmented, adapted, and then amplified for sequencing. The resulting sequences represent the RNA population in the sample.
What considerations are important when performing RNA-Seq?
RNA-Seq requires careful experimental design, handling large data sets, controlling for confounding factors, and using appropriate statistical models to manage noise.
What is ChIP-Seq used for?
ChIP-Seq (Chromatin Immunoprecipitation Sequencing) identifies protein-DNA interactions by cross-linking proteins to DNA, isolating and sequencing the DNA bound by a specific protein.
How does ATAC-Seq work?
ATAC-Seq (Assay for Transposase-Accessible Chromatin) uses transposase to cut exposed DNA, allowing sequencing of accessible chromatin regions, similar to DNAse-Seq.
What is bisulphite sequencing used for?
Bisulphite sequencing determines DNA methylation by converting unmethylated cytosines to thymine, with methylated cytosines remaining unchanged.
What is reduced representation bisulphite sequencing (RRBS)?
RRBS enriches for CpG sites using the MspI restriction enzyme, allowing for efficient sequencing of a small portion of the genome, which is ideal for studying DNA methylation.
How important is bioinformatics in functional genomics?
Bioinformatics is essential for processing and analyzing the large and complex datasets generated by high-throughput sequencing, enabling the interpretation of functional genomics experiments.
