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What is Genomics?
Genomics is the branch of molecular biology focused on the structure, function, evolution, and mapping of genomes.
What is a Genome?
A genome refers to all the genetic information of an organism, including its DNA sequences.
Characteristics of the Genome
The genome contains genes that code for proteins, essential for various cellular functions and traits.
Gene Expression and Its Regulation
Gene expression is controlled by regulatory elements such as promoters, enhancers, and silencers.
Organization and Regulation of a Typical Eukaryotic Gene
A typical eukaryotic gene is organized with a promoter region, regulatory elements, coding sequences, untranslated regions, splice sites, and an open reading frame.
Loss and Gain of Function
Gene Inactivation (Loss of Function) includes techniques like RNA Interference (RNAi) and CRISPR-Cas9.
What is RNA Interference (RNAi)?
RNAi involves using small interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs) to silence specific genes.
What is CRISPR-Cas9?
CRISPR-Cas9 is a powerful genome-editing tool that can create targeted mutations in genes.
Gene Overexpression (Gain of Function)
Transgenic Models and Inducible Expression Systems help assess the effects of increased gene expression.
What is Next Generation Sequencing (NGS)?
NGS technologies allow for high-throughput sequencing of DNA and RNA.
General Workflow of NGS (Illumina)
The typical workflow includes sample preparation, library preparation, amplification, sequencing, and data analysis.
Gene Sequencing Applications
Applications include genome sequencing, mutation screening, studying gene regulation, transcriptome sequencing, and noninvasive cancer detection.
Techniques for Studying Genomes
Techniques include whole genome sequencing (WGS), RNA sequencing (RNA-seq), CRISPR-Cas9 gene editing, and microarray analysis.
What is the basic structure of a gene?
A gene is a segment of DNA that contains the necessary information to produce a functional product.
What is the coding sequence in a gene?
The coding sequence is the part of the gene that contains the actual information for building proteins.
What are exons?
Exons are sequences within a gene that remain in the final mRNA after splicing.
What are regulatory elements in a gene?
Regulatory elements are sequences that control the expression of the gene.
What is a promoter?
A promoter is a region where RNA polymerase binds to initiate transcription.
What are enhancers and silencers?
Enhancers increase transcription levels, while silencers decrease transcription levels.
What is the transcription start site (TSS)?
The transcription start site is the location on DNA where RNA polymerase begins synthesizing RNA.
What are introns?
Introns are non-coding regions that are transcribed into pre-mRNA but are removed during RNA processing.
What is the 5’ UTR (Untranslated Region)?
The 5’ UTR is located upstream of the coding sequence and is involved in regulating translation.
What is the 3’ UTR (Untranslated Region)?
The 3’ UTR is located downstream of the coding sequence and plays a role in regulating gene expression.
What is a termination sequence?
A termination sequence signals the end of transcription.
What is the Human Genome Project (HGP)?
The Human Genome Project is an international research initiative aimed at mapping and sequencing the entire human genome.
When was the Human Genome Project initiated?
The HGP was initiated in 1990.
What significant milestone occurred in June 2000?
A working draft of the entire human genome was completed in June 2000.
When were analyses of the working draft published?
Analyses of the working draft were published in February 2001.
When was the sequencing of the human genome completed?
The sequencing was completed in April 2003.
Who were the key leaders of the HGP?
Craig Venter and Francis Collins.
What were the main goals of the Human Genome Project?
To determine the sequences of approximately 3 billion base pairs in human DNA and to identify around 30,000 genes.
How does genome sequencing help in gene discovery?
It helps identify new genes and find gene regulatory sequences.
What bioinformatics challenges did the HGP address?
The project produced a completed human genome draft and insights into GC content variation.
What is genome assembly?
Genome assembly involves piecing together sequence fragments into chromosomes.
What is GC content variation?
GC content variation refers to differences in GC-rich regions across the genome.
What are CpG islands?
CpG islands are GC-rich regions where CG dinucleotides exceed 70%.
What is notable about human gene structure compared to other organisms?
Human exons are generally shorter than those in worms and flies.
How many chromosomes are in the human genome?
The human genome consists of 23 pairs of chromosomes.
What characteristics remain unknown after the HGP?
Many functional implications of identified genes remain unclear.
What is GC content?
GC content refers to the percentage of guanine (G) and cytosine (C) bases in a given DNA sequence.
Why is GC content significant?
GC content can influence gene density and the overall functionality of genomic regions.
What is GC bias?
GC bias occurs when sequencing data shows an uneven representation of reads from regions with varying GC content.
How does GC bias affect RNA-Seq data?
GC bias can significantly impact differential expression analysis in RNA-Seq experiments.
What are the implications of GC bias in genome assembly?
Strong GC bias can lower assembly completeness and increase fragmentation.
What are CpG islands?
CpG islands are regions of DNA that have a high frequency of CpG dinucleotides.
Where are CpG islands commonly found?
CpG islands are frequently located in the promoter regions of genes.
What role do CpG islands play in gene regulation?
CpG islands help regulate gene expression by making DNA more accessible to transcription factors.
How does methylation affect CpG islands?
Methylation of CpG islands can lead to gene silencing.
What is the relationship between CpG islands and cancer?
Hypermethylation of CpG islands can contribute to the inactivation of tumor suppressor genes.
How many CpG islands are estimated to exist in the human genome?
There are approximately 28,890 CpG islands in the human genome.
What are the structural components of a gene?
Structural components include promoter, enhancer/silencer, exons, introns, UTRs, and splice sites.
What is annotation in genomics?
Annotation is the process of assigning identities and functions to sequences within the genome.
What are SNPs?
Single Nucleotide Polymorphisms (SNPs) are a type of genetic variation where a single nucleotide differs between individuals.
How do SNPs contribute to genetic diversity?
SNPs can affect how genes function and influence disease susceptibility.
What is a mutation?
A mutation is a change in the DNA sequence that can affect one or more nucleotides.
How do SNPs differ from mutations?
SNPs are a specific type of mutation that occurs at a single nucleotide position.
What are some applications of studying SNPs and mutations?
Applications include identifying genetic markers for diseases and developing personalized medicine approaches.
What is the HapMap Project?
The HapMap Project is an international effort to develop a haplotype map of the human genome.
What is a haplotype?
A haplotype is a group of alleles at multiple loci that are transmitted together on the same chromosome.
Why are haplotypes important in genetics?
Haplotypes help identify associations between genetic variations and phenotypes.
What are tag SNPs?
Tag SNPs are representative SNPs used to represent other nearby SNPs in a haplotype block.
How does the HapMap Project aid in disease association studies?
The HapMap provides a resource for researchers to find genes associated with health and disease.
What was achieved in Phase I of the HapMap Project?
Phase I identified over 1 million accurate SNP genotypes from 269 individuals.
What advancements were made in Phase II of the HapMap Project?
Phase II added over 2.1 million additional SNPs.
What role do phenotypes play in relation to haplotypes?
Phenotypes reflect observable traits influenced by genetic variations.
What is meant by ‘multiple haplotypes’?
Multiple haplotypes refer to different combinations of alleles at multiple loci.
