Q.1 What is the primary focus of functional genomics?
Sequencing DNA to identify gene order
Studying the structure of proteins
Understanding gene function and interaction
Designing electronic circuits for gene therapy
Explanation - Functional genomics aims to describe the activity of genes, how they are regulated, and how they interact within cellular networks, rather than just their sequences.
Correct answer is: Understanding gene function and interaction
Q.2 Which high-throughput technique is most commonly used to measure gene expression levels across the entire genome?
Western blot
RNA-seq
Chromatin immunoprecipitation
Electron microscopy
Explanation - RNA-seq sequences cDNA libraries to quantify transcript abundance genome-wide, providing a comprehensive view of gene expression.
Correct answer is: RNA-seq
Q.3 The process of removing introns from pre-mRNA transcripts is called:
Transcription
Translation
Splicing
Polyadenylation
Explanation - Splicing is performed by the spliceosome to excise introns and join exons, creating mature messenger RNA.
Correct answer is: Splicing
Q.4 What does ATAC-seq measure?
Protein-DNA interaction sites
Chromatin accessibility
DNA methylation patterns
RNA editing events
Explanation - ATAC-seq uses a transposase to insert sequencing adapters into open chromatin regions, indicating regulatory activity.
Correct answer is: Chromatin accessibility
Q.5 Which of the following is NOT a typical output of a transcriptomic analysis?
Differentially expressed genes
Gene co-expression networks
Protein tertiary structure
Alternative splicing events
Explanation - Transcriptomics focuses on RNA levels; protein structure is studied via proteomics and structural biology, not transcriptomics.
Correct answer is: Protein tertiary structure
Q.6 Which computational tool is commonly used to assemble short RNA-seq reads into transcripts?
BLAST
HISAT2
Cufflinks
PhyML
Explanation - Cufflinks assembles aligned RNA-seq reads into transcripts and estimates their abundances.
Correct answer is: Cufflinks
Q.7 In the context of functional genomics, what does the term 'epigenome' refer to?
The complete set of genes in a cell
DNA sequence variations that alter phenotype
Chemical modifications that affect gene expression without changing DNA sequence
The set of all proteins encoded by the genome
Explanation - Epigenetic marks such as DNA methylation or histone modifications regulate gene activity while leaving the underlying DNA unchanged.
Correct answer is: Chemical modifications that affect gene expression without changing DNA sequence
Q.8 What is the role of a transcription factor in gene regulation?
To degrade mRNA transcripts
To initiate RNA synthesis by binding DNA regulatory elements
To splice exons during transcription
To add a poly-A tail to mRNA
Explanation - Transcription factors bind promoters or enhancers to recruit RNA polymerase and control the initiation of transcription.
Correct answer is: To initiate RNA synthesis by binding DNA regulatory elements
Q.9 Which assay is used to identify protein-DNA interactions in vivo?
ChIP-seq
EMSA
qPCR
Northern blot
Explanation - Chromatin immunoprecipitation followed by sequencing (ChIP-seq) maps binding sites of DNA-associated proteins genome-wide.
Correct answer is: ChIP-seq
Q.10 What does a false discovery rate (FDR) threshold control in high-throughput data analysis?
The proportion of true positives detected
The proportion of false positives among declared significant results
The sample size needed for adequate power
The rate of sequencing errors
Explanation - FDR controls the expected proportion of incorrectly rejected null hypotheses within the set of significant findings.
Correct answer is: The proportion of false positives among declared significant results
Q.11 Which of the following best describes 'alternative splicing'?
The process of copying DNA into RNA
The removal of introns during RNA maturation
The selection of different exon combinations from the same pre-mRNA
The addition of a 5' cap to mRNA
Explanation - Alternative splicing produces multiple transcript variants by including or excluding specific exons, expanding proteomic diversity.
Correct answer is: The selection of different exon combinations from the same pre-mRNA
Q.12 Which type of RNA is most commonly used for CRISPR-Cas9 gene editing?
mRNA
tRNA
guide RNA (gRNA)
rRNA
Explanation - The guide RNA directs the Cas9 nuclease to a specific DNA sequence for targeted genome editing.
Correct answer is: guide RNA (gRNA)
Q.13 In the context of gene regulatory networks, a 'hub gene' is:
A gene that is never expressed
A gene with many regulatory connections
A gene that encodes a transcription factor
A gene that is only expressed in the brain
Explanation - Hub genes interact with numerous other genes or proteins, often playing central roles in regulatory networks.
Correct answer is: A gene with many regulatory connections
Q.14 Which metric is used to measure the relative expression of a gene between two conditions?
RPKM
FC (fold change)
P-value
GC content
Explanation - Fold change quantifies how many times a gene's expression differs between conditions; RPKM normalizes read counts but is not a comparative metric alone.
Correct answer is: FC (fold change)
Q.15 What is the main purpose of a 'knockout' experiment?
To overexpress a gene
To delete or inactivate a gene
To measure protein–protein interactions
To label DNA with fluorescent markers
Explanation - Gene knockout removes or disrupts a gene's function to study its role by observing resulting phenotypic changes.
Correct answer is: To delete or inactivate a gene
Q.16 Which database contains curated information on functional genomic annotations?
GenBank
UniProt
Ensembl
OMIM
Explanation - Ensembl provides comprehensive functional annotation of genomes, including gene models, regulatory elements, and expression data.
Correct answer is: Ensembl
Q.17 Which of the following best describes a 'gene ontology' term?
A measure of DNA methylation level
A standardized description of gene function, biological process, or cellular component
The DNA sequence of a promoter region
A statistical test for differential expression
Explanation - Gene Ontology (GO) provides a controlled vocabulary to describe gene products in terms of function, processes, and localization.
Correct answer is: A standardized description of gene function, biological process, or cellular component
Q.18 Which sequencing technology is best suited for detecting long repetitive sequences?
Sanger sequencing
Illumina short-read sequencing
PacBio SMRT sequencing
Microarray hybridization
Explanation - Single-molecule real-time (SMRT) sequencing produces long reads that can span repetitive regions better than short-read platforms.
Correct answer is: PacBio SMRT sequencing
Q.19 Which of the following is NOT a step in the RNA-seq workflow?
Library preparation
Read alignment
Protein purification
Differential expression analysis
Explanation - RNA-seq involves RNA extraction, library prep, sequencing, alignment, and expression analysis; protein purification is unrelated.
Correct answer is: Protein purification
Q.20 What does 'CRISPR' stand for in CRISPR-Cas9?
Clustered Regularly Interspaced Short Palindromic Repeats
Cutting Rapidly Induced Single Protein Response
Cytosine Regulator Inhibitor Sequence Pattern
Chromosomal Recombination Insertional Site Pattern
Explanation - CRISPR is an adaptive immune system in bacteria, consisting of short repeated sequences interspaced by spacers derived from viruses.
Correct answer is: Clustered Regularly Interspaced Short Palindromic Repeats
Q.21 Which type of analysis is performed to identify co-regulated gene modules in transcriptomic data?
Principal Component Analysis
Hierarchical Clustering
Weighted Gene Co-Expression Network Analysis (WGCNA)
Sequence Alignment
Explanation - WGCNA constructs networks based on gene co-expression to identify modules of functionally related genes.
Correct answer is: Weighted Gene Co-Expression Network Analysis (WGCNA)
Q.22 A 'cis-regulatory element' is:
A region in the genome that codes for a protein
An enhancer or silencer located on the same DNA molecule as the gene it regulates
A transcription factor that binds to promoters
A non-coding RNA that modulates gene expression
Explanation - Cis-regulatory elements are DNA sequences that influence transcription of adjacent genes, unlike trans factors which are proteins.
Correct answer is: An enhancer or silencer located on the same DNA molecule as the gene it regulates
Q.23 Which computational method is used to predict potential miRNA target sites in mRNA?
BLAST
miRanda
RPKM calculation
Flow cytometry
Explanation - miRanda aligns miRNA sequences to mRNA to find complementary seed regions and predict regulatory interactions.
Correct answer is: miRanda
Q.24 Which of the following best defines a 'transcript isoform'?
A different variant of a protein translated from the same mRNA
A distinct mRNA produced from the same gene due to alternative splicing
A type of DNA methylation mark
A spliceosome component
Explanation - Alternative splicing generates multiple transcript isoforms from a single gene, which may encode different protein products.
Correct answer is: A distinct mRNA produced from the same gene due to alternative splicing
Q.25 What is the primary advantage of single-cell RNA-seq (scRNA-seq)?
It measures DNA mutations directly
It profiles gene expression at the individual cell level
It sequences protein structures
It is cheaper than bulk RNA-seq
Explanation - scRNA-seq captures transcriptomes of individual cells, revealing cellular heterogeneity and rare cell types.
Correct answer is: It profiles gene expression at the individual cell level
Q.26 Which of the following best explains 'epitranscriptomics'?
Study of RNA modifications that influence gene expression
Analysis of DNA methylation patterns
Mapping protein-DNA interactions
Sequencing of entire genomes
Explanation - Epitranscriptomics examines chemical modifications (e.g., m6A) on RNA molecules that affect stability, translation, and splicing.
Correct answer is: Study of RNA modifications that influence gene expression
Q.27 Which software is commonly used for visualizing genome-wide chromatin interaction data such as Hi-C?
IGV
Juicebox
BLAST
MCL
Explanation - Juicebox allows interactive visualization of Hi-C contact maps and 3D chromatin structures.
Correct answer is: Juicebox
Q.28 What is the main purpose of a 'control sample' in functional genomic experiments?
To provide a baseline for comparison
To increase sequencing depth
To label DNA fragments
To amplify gene expression
Explanation - Controls help distinguish genuine biological signals from technical noise or artifacts.
Correct answer is: To provide a baseline for comparison
Q.29 Which type of assay would you use to identify DNA regions that bind to a specific transcription factor?
ChIP-seq
RNA-seq
ATAC-seq
Western blot
Explanation - ChIP-seq immunoprecipitates DNA fragments bound by the transcription factor, revealing its genomic binding sites.
Correct answer is: ChIP-seq
Q.30 In functional genomics, what is the 'phenotypic readout'?
The DNA sequence of a gene
The observable traits resulting from genetic manipulation
The structure of a protein
The alignment score of two sequences
Explanation - Phenotypic readouts are measurable characteristics (e.g., growth rate, fluorescence) that indicate gene function.
Correct answer is: The observable traits resulting from genetic manipulation
Q.31 Which of the following describes 'allele-specific expression'?
Expression of only one allele of a gene in a heterozygous individual
Expression of a gene in all alleles equally
Expression of a gene only in the presence of a mutation
Expression of genes exclusively on the X chromosome
Explanation - Allele-specific expression occurs when one allele is transcribed preferentially or exclusively, often due to epigenetic regulation.
Correct answer is: Expression of only one allele of a gene in a heterozygous individual
Q.32 Which sequencing approach is most suitable for detecting low-frequency mutations in a population?
Standard Illumina sequencing
Deep sequencing (high coverage)
Sanger sequencing
Microarray profiling
Explanation - High sequencing depth increases sensitivity to detect rare variants that might be present at low allele frequencies.
Correct answer is: Deep sequencing (high coverage)
Q.33 What does a 'heatmap' typically represent in gene expression studies?
The 3D structure of DNA
A visual representation of expression levels across samples
The frequency of SNPs in a population
The sequence of a promoter region
Explanation - Heatmaps color-code gene expression values, allowing quick visual assessment of patterns and clusters.
Correct answer is: A visual representation of expression levels across samples
Q.34 Which of the following is a key advantage of using CRISPR interference (CRISPRi) over gene knockouts?
It permanently deletes the gene
It provides reversible, tunable gene suppression
It enhances gene expression
It is easier to design primers
Explanation - CRISPRi uses a deactivated Cas9 fused to a repressor domain to transiently reduce transcription without cutting DNA.
Correct answer is: It provides reversible, tunable gene suppression
Q.35 What is the 'gold standard' for validating gene function discovered via high-throughput screens?
Computational prediction
Literature review
Targeted loss- or gain-of-function assays
Protein crystallography
Explanation - Functional validation confirms a gene's role through precise genetic manipulation in a controlled context.
Correct answer is: Targeted loss- or gain-of-function assays
Q.36 Which of these is NOT a typical type of functional genomics data?
RNA-seq
ChIP-seq
SNP array genotyping
Methylation profiling
Explanation - While SNP arrays map genetic variation, functional genomics focuses on expression, regulation, and epigenetics.
Correct answer is: SNP array genotyping
Q.37 Which of the following best describes 'transcriptional noise'?
Random fluctuations in gene expression levels
Noise introduced by sequencing errors
Background fluorescence in imaging
Unpredictable promoter activity in bacteria
Explanation - Transcriptional noise refers to stochastic variability in mRNA production among identical cells.
Correct answer is: Random fluctuations in gene expression levels
Q.38 In a differential expression analysis, a gene with a log2 fold change of 2 has:
Half the expression in treated versus control
Four times the expression in treated versus control
No change in expression
Zero expression in both conditions
Explanation - A log2 fold change of 2 corresponds to 2^2 = 4-fold upregulation.
Correct answer is: Four times the expression in treated versus control
Q.39 Which of the following best characterizes 'cis-regulatory modules'?
Groups of genes located on the same chromosome
Clusters of transcription factor binding sites that jointly regulate a gene
Protein complexes that modify histones
Non-coding RNAs that act in trans
Explanation - Cis-regulatory modules comprise multiple binding sites that coordinate transcriptional regulation of a gene.
Correct answer is: Clusters of transcription factor binding sites that jointly regulate a gene
Q.40 What does the 'coverage' metric refer to in sequencing data?
The number of unique reads aligning to a genome
The average number of times each base is sequenced
The proportion of the genome that is repetitive
The GC content of a library
Explanation - Coverage indicates how many times each base is represented on average, influencing confidence in variant calls.
Correct answer is: The average number of times each base is sequenced
Q.41 Which type of genetic screen uses RNA interference to silence genes across the genome?
CRISPR knockout screen
siRNA library screen
Yeast two-hybrid screen
Transposon mutagenesis screen
Explanation - siRNA libraries systematically knock down genes, revealing phenotypes associated with loss of function.
Correct answer is: siRNA library screen
Q.42 What is the main purpose of using a 'housekeeping gene' in gene expression experiments?
To serve as a positive control for sequencing
To normalize for variations in RNA input or cDNA synthesis efficiency
To identify cell-type specific markers
To measure DNA methylation levels
Explanation - Housekeeping genes are expressed consistently across conditions, allowing data normalization.
Correct answer is: To normalize for variations in RNA input or cDNA synthesis efficiency
Q.43 Which of these best explains 'gene silencing' by DNA methylation?
Methyl groups added to cytosine residues inhibit transcription factor binding
Methyl groups increase the rate of RNA polymerase transcription
Methylation removes histone tails from DNA
DNA methylation occurs only in prokaryotes
Explanation - DNA methylation often blocks transcription factor access or recruits repressive proteins, reducing gene expression.
Correct answer is: Methyl groups added to cytosine residues inhibit transcription factor binding
Q.44 Which computational approach is used to infer the functional relationship between two genes based on their expression patterns?
Pearson correlation analysis
Sequence homology search
Mass spectrometry
DNA barcoding
Explanation - High correlation between gene expression profiles suggests co-regulation or functional linkage.
Correct answer is: Pearson correlation analysis
Q.45 Which of the following best describes a 'transgene'?
A gene naturally present in an organism's genome
A foreign gene introduced into an organism
A silent mutation in a gene
A type of non-coding RNA
Explanation - Transgenes are externally sourced genes integrated into an organism to study expression or confer new traits.
Correct answer is: A foreign gene introduced into an organism
Q.46 Which technique can identify the spatial localization of RNA molecules within cells?
Fluorescence in situ hybridization (FISH)
CRISPR-Cas9 editing
Western blotting
Mass spectrometry
Explanation - FISH uses fluorescent probes to bind specific RNA sequences, revealing their subcellular distribution.
Correct answer is: Fluorescence in situ hybridization (FISH)
Q.47 In a 'dual-luciferase reporter assay', the Renilla luciferase is used as:
The experimental gene of interest
A normalizing control for transfection efficiency
An inhibitor of firefly luciferase
A fluorescent marker for cell sorting
Explanation - Renilla activity provides an internal standard to account for variations in assay conditions.
Correct answer is: A normalizing control for transfection efficiency
Q.48 Which of the following is NOT a common source of batch effect in RNA-seq experiments?
Different library preparation kits
Sequencing run date
RNA extraction protocol
Gene coding sequence
Explanation - Batch effects arise from technical variation, not biological sequence differences.
Correct answer is: Gene coding sequence
Q.49 What is the role of the 'splicing factor' in mRNA processing?
To remove introns from pre-mRNA
To add a 5' cap to mRNA
To initiate DNA replication
To degrade mature mRNA
Explanation - Splicing factors assist the spliceosome in accurately excising introns and ligating exons.
Correct answer is: To remove introns from pre-mRNA
Q.50 Which type of data is generated by a proteogenomics workflow?
Protein mass spectra matched to a genome
DNA sequence reads from whole-genome sequencing
Gene expression counts from RNA-seq
Chromatin accessibility peaks
Explanation - Proteogenomics combines proteomics and genomics to validate novel proteins and refine gene models.
Correct answer is: Protein mass spectra matched to a genome
Q.51 Which of the following best describes 'RNA velocity' analysis?
Predicting the future transcriptional state of individual cells
Measuring the speed of RNA polymerase during transcription
Assessing the rate of mRNA degradation
Quantifying the movement of RNA in the cytoplasm
Explanation - RNA velocity uses unspliced vs spliced reads to infer the direction and speed of cellular differentiation trajectories.
Correct answer is: Predicting the future transcriptional state of individual cells
Q.52 Which of the following is a key feature of a 'promoter'?
A DNA sequence upstream of a gene that initiates transcription
A protein that degrades mRNA
An enhancer located downstream of a gene
A non-coding RNA involved in gene silencing
Explanation - Promoters contain binding sites for RNA polymerase and general transcription factors to start transcription.
Correct answer is: A DNA sequence upstream of a gene that initiates transcription
Q.53 Which of these best describes a 'single-nucleotide polymorphism (SNP)'?
A large deletion of a chromosome segment
A variation involving a single base pair in the DNA sequence
A rearrangement of entire chromosomes
A change in the amino acid sequence of a protein
Explanation - SNPs are the most common type of genetic variation, representing a single base change.
Correct answer is: A variation involving a single base pair in the DNA sequence
Q.54 In CRISPR-Cas9 genome editing, what is the role of the protospacer adjacent motif (PAM)?
It guides the gRNA to the target DNA
It is required for Cas9 binding and cleavage
It marks the DNA for repair
It acts as a nuclear localization signal
Explanation - PAM sequences (e.g., NGG for SpCas9) are necessary for Cas9 recognition and enzymatic activity.
Correct answer is: It is required for Cas9 binding and cleavage
Q.55 Which of the following best characterizes a 'regulon'?
A set of genes regulated by the same transcription factor
A cluster of genes located on the same chromosome
A group of proteins that physically interact
A DNA segment containing multiple promoters
Explanation - Regulons group genes sharing a common regulatory mechanism, often controlled by a single TF.
Correct answer is: A set of genes regulated by the same transcription factor
Q.56 Which computational approach is used to predict the effect of a missense mutation on protein stability?
BLAST alignment
SIFT
RPKM calculation
Mass spectrometry
Explanation - SIFT predicts whether an amino acid substitution is tolerated based on sequence homology and physicochemical properties.
Correct answer is: SIFT
Q.57 What does a 'q-value' represent in multiple hypothesis testing?
The raw p-value of a test
The probability that a hypothesis is true
The adjusted p-value controlling FDR
The fold change in expression
Explanation - Q-values are p-values corrected for multiple testing, representing the expected proportion of false discoveries.
Correct answer is: The adjusted p-value controlling FDR
Q.58 Which of the following best describes 'cis-acting regulatory variation'?
A mutation in a transcription factor protein
A polymorphism affecting a regulatory element on the same DNA molecule as the gene
A mutation in an intergenic enhancer on a different chromosome
A variation in microRNA expression
Explanation - Cis-acting variants alter regulatory sequences near the gene they influence, affecting its expression.
Correct answer is: A polymorphism affecting a regulatory element on the same DNA molecule as the gene
Q.59 Which of the following is a major challenge in single-cell RNA-seq data analysis?
High sequencing depth needed per cell
Large amount of technical noise and dropout events
Difficulty in mapping reads to the genome
Limited availability of computational resources
Explanation - scRNA-seq suffers from stochastic gene dropout and high variability, complicating downstream interpretation.
Correct answer is: Large amount of technical noise and dropout events
Q.60 What does the 'peak calling' step in ATAC-seq or ChIP-seq analysis refer to?
Identifying high-frequency SNPs
Detecting regions of increased read coverage indicating open chromatin or protein binding
Selecting the best sequencing read length
Calculating the GC content across the genome
Explanation - Peak calling algorithms identify significant enrichments of reads that correspond to accessible chromatin or DNA-bound proteins.
Correct answer is: Detecting regions of increased read coverage indicating open chromatin or protein binding
Q.61 In a gene expression heatmap, what does a cluster of genes in the same row typically indicate?
These genes are located on the same chromosome
These genes have similar expression patterns across samples
These genes encode proteins of similar size
These genes have identical promoter sequences
Explanation - Clustering groups genes with correlated expression profiles, often reflecting shared regulation.
Correct answer is: These genes have similar expression patterns across samples
Q.62 What is the purpose of the 'RPKM' metric in RNA-seq analysis?
To normalize read counts by gene length and library size
To measure protein abundance
To estimate DNA methylation levels
To determine the number of exons per gene
Explanation - RPKM (Reads Per Kilobase Million) adjusts for transcript length and total sequencing depth.
Correct answer is: To normalize read counts by gene length and library size
Q.63 Which of the following describes the 'three-tier' model of gene expression regulation?
Chromatin remodeling, transcription initiation, mRNA splicing
DNA replication, RNA transcription, protein translation
Protein folding, post-translational modification, protein degradation
Signal reception, second messenger, transcription factor activation
Explanation - The three-tier model refers to chromatin accessibility, transcription factor binding, and splicing decisions.
Correct answer is: Chromatin remodeling, transcription initiation, mRNA splicing
Q.64 Which technique allows the simultaneous profiling of mRNA and chromatin accessibility from the same cell?
scRNA-seq
scATAC-seq
CITE-seq
SNARE-seq
Explanation - SNARE-seq captures both transcriptome and chromatin accessibility in single cells, linking epigenetic state to transcription.
Correct answer is: SNARE-seq
Q.65 In a differential expression analysis, a p-value of 0.001 is considered:
Highly significant before multiple testing correction
Not significant
The same as a q-value
A measure of expression fold change
Explanation - A low p-value indicates strong evidence against the null hypothesis, but must be adjusted for multiple comparisons.
Correct answer is: Highly significant before multiple testing correction
Q.66 What is the main function of the 'RNA polymerase II' enzyme?
To transcribe ribosomal RNA
To transcribe messenger RNA from DNA
To splice introns from pre-mRNA
To catalyze DNA replication
Explanation - RNA polymerase II synthesizes mRNA, which is then processed into mature transcripts.
Correct answer is: To transcribe messenger RNA from DNA
Q.67 Which of the following best describes 'chromatin looping'?
The continuous stretching of chromatin fibers
The folding of chromatin to bring distant regulatory elements close to promoters
The process of DNA replication fork progression
The degradation of histones during apoptosis
Explanation - Chromatin loops bring enhancers and promoters into spatial proximity, facilitating gene regulation.
Correct answer is: The folding of chromatin to bring distant regulatory elements close to promoters
Q.68 In functional genomics, what is the advantage of using an 'inducible promoter'?
It permanently turns on gene expression
It allows controlled activation or repression of a target gene
It eliminates the need for transgenic animals
It provides a higher expression level than constitutive promoters
Explanation - Inducible promoters respond to specific stimuli, enabling temporal regulation of gene expression.
Correct answer is: It allows controlled activation or repression of a target gene
Q.69 Which of the following best describes 'RNA editing'?
The removal of introns from pre-mRNA
The post-transcriptional modification of RNA nucleotides
The addition of a poly-A tail to mRNA
The splicing of mRNA into multiple isoforms
Explanation - RNA editing changes the nucleotide sequence of an RNA transcript without altering the underlying DNA.
Correct answer is: The post-transcriptional modification of RNA nucleotides
Q.70 What does 'qPCR' stand for in the context of gene expression validation?
Quantitative PCR
Qualitative PCR
Quasi PCR
Quenching PCR
Explanation - qPCR quantifies DNA amplification in real-time, allowing precise measurement of transcript abundance.
Correct answer is: Quantitative PCR
Q.71 In a genome-wide association study (GWAS), what is a 'linkage disequilibrium (LD) block'?
A region where genetic variants are inherited together more often than expected by chance
A region of the genome that is not transcribed
A group of genes that encode proteins of similar function
A segment of DNA that contains no variation
Explanation - LD blocks indicate correlated SNPs, useful for mapping disease-associated loci.
Correct answer is: A region where genetic variants are inherited together more often than expected by chance
Q.72 Which of the following is NOT a common read alignment tool for RNA-seq data?
TopHat
Bowtie
STAR
HISAT2
Explanation - Bowtie is designed for DNA alignment; specialized spliced aligners like TopHat, STAR, and HISAT2 handle RNA-seq splicing.
Correct answer is: Bowtie
Q.73 Which of the following best characterizes a 'translational regulator'?
A protein that binds mRNA to inhibit translation
A DNA element upstream of a promoter
A transcription factor that enhances RNA polymerase recruitment
A histone modification that changes chromatin structure
Explanation - Translational regulators, such as microRNAs or RNA-binding proteins, modulate translation efficiency post-transcriptionally.
Correct answer is: A protein that binds mRNA to inhibit translation
Q.74 What is the role of 'RNA-binding proteins (RBPs)' in mRNA metabolism?
They serve as transcription factors
They modulate splicing, transport, stability, and translation of mRNAs
They degrade DNA during replication
They act as enzymes for DNA methylation
Explanation - RBPs interact with RNA to control its processing, localization, and lifespan.
Correct answer is: They modulate splicing, transport, stability, and translation of mRNAs
Q.75 In the context of functional genomics, what does 'saturation mutagenesis' aim to achieve?
To create a complete library of all possible mutations in a gene
To increase the expression of a gene
To identify non-coding RNAs
To remove all mutations from a genome
Explanation - Saturation mutagenesis systematically introduces mutations across a target region to study structure‑function relationships.
Correct answer is: To create a complete library of all possible mutations in a gene
Q.76 Which of the following best describes a 'promoter capture Hi-C' experiment?
A technique to enrich for promoter–promoter interactions in Hi-C libraries
A method to capture mRNA molecules in the nucleus
A sequencing approach for promoter sequences only
A computational algorithm for predicting promoter activity
Explanation - Promoter capture Hi-C uses capture probes to focus on promoter-containing chromatin contacts.
Correct answer is: A technique to enrich for promoter–promoter interactions in Hi-C libraries
Q.77 What is the primary output of a 'mass spectrometry-based proteomics' experiment?
DNA sequence data
Protein fragment mass spectra and identified peptides
Chromatin accessibility maps
Gene expression heatmaps
Explanation - Mass spectrometry detects mass-to-charge ratios of peptides, allowing protein identification and quantification.
Correct answer is: Protein fragment mass spectra and identified peptides
Q.78 In gene regulatory network inference, what does 'mutual information' measure?
The correlation between two gene expression profiles
The amount of shared information between two variables, capturing non-linear dependencies
The difference in expression levels between two genes
The physical interaction between two proteins
Explanation - Mutual information quantifies the degree of statistical dependence, useful for detecting regulatory relationships.
Correct answer is: The amount of shared information between two variables, capturing non-linear dependencies
Q.79 Which of the following best describes 'differential exon usage' analysis?
Comparing the number of exons per gene across species
Detecting changes in exon inclusion levels between conditions
Assessing the total expression of a gene
Identifying intron retention events
Explanation - Differential exon usage studies how alternative splicing patterns vary across samples or treatments.
Correct answer is: Detecting changes in exon inclusion levels between conditions
Q.80 What does the 'TATA box' represent in eukaryotic promoters?
A DNA sequence that recruits RNA polymerase II for transcription initiation
A histone modification site
An enhancer element located downstream of the gene
A splice site sequence
Explanation - The TATA box is a core promoter element recognized by the transcription initiation complex.
Correct answer is: A DNA sequence that recruits RNA polymerase II for transcription initiation
Q.81 Which of these is a commonly used metric for evaluating clustering quality in gene expression data?
Silhouette score
RPKM
GC content
P-value
Explanation - The silhouette score measures how similar an object is to its own cluster compared to other clusters.
Correct answer is: Silhouette score
Q.82 In the context of CRISPR screening, what is a 'guide RNA (gRNA)'?
A DNA sequence that directs Cas9 to a target site
A small RNA that pairs with the target DNA sequence to guide Cas9 cleavage
A protein that activates transcription
A fluorescent marker used to track cells
Explanation - gRNA forms a ribonucleoprotein complex with Cas9, enabling site-specific DNA cleavage.
Correct answer is: A small RNA that pairs with the target DNA sequence to guide Cas9 cleavage
Q.83 Which of the following best describes the 'epigenome-wide association study (EWAS)'?
A study correlating DNA methylation patterns with phenotypes
A genome sequencing project of multiple individuals
A transcriptomic profiling of cancer tissues
An analysis of protein–protein interaction networks
Explanation - EWAS investigates associations between epigenetic marks and traits or diseases across the genome.
Correct answer is: A study correlating DNA methylation patterns with phenotypes
Q.84 Which of the following is a key feature of 'polygenic trait' inheritance?
Inheritance is determined by a single gene
Multiple genes contribute small effects to the phenotype
The trait is caused by environmental factors only
The trait follows Mendelian inheritance exclusively
Explanation - Polygenic traits result from the combined action of many genes, each contributing a modest effect.
Correct answer is: Multiple genes contribute small effects to the phenotype
Q.85 In functional genomics, what is the purpose of 'synthetic biology' approaches?
To replicate natural biological processes exactly
To design and construct novel biological parts, devices, and systems
To sequence genomes of synthetic organisms
To analyze gene expression in natural ecosystems
Explanation - Synthetic biology applies engineering principles to create new biological functions or improve existing ones.
Correct answer is: To design and construct novel biological parts, devices, and systems
Q.86 Which of the following best describes the 'poly(A) tail' added to mRNA?
A stretch of poly-adenine residues that stabilizes and facilitates export of mRNA
A sequence that signals termination of transcription
A DNA sequence found in promoters
An RNA modification that changes adenosine to inosine
Explanation - Polyadenylation adds a poly(A) tail, improving mRNA stability and transport from nucleus to cytoplasm.
Correct answer is: A stretch of poly-adenine residues that stabilizes and facilitates export of mRNA
Q.87 Which of the following is a limitation of bulk RNA-seq compared to single-cell RNA-seq?
It cannot detect gene expression levels
It averages gene expression across heterogeneous cell populations, masking cell-specific patterns
It requires more sequencing depth per cell
It cannot identify alternative splicing events
Explanation - Bulk RNA-seq provides a composite signal, hiding differences between individual cells.
Correct answer is: It averages gene expression across heterogeneous cell populations, masking cell-specific patterns
Q.88 Which of the following best describes a 'mRNA cap'?
A methylated guanine at the 5' end of eukaryotic mRNA
A poly(A) tail at the 3' end of mRNA
A protein-binding motif on mRNA
A sequence that marks the start of translation
Explanation - The 5' cap protects mRNA from degradation and assists in ribosome recruitment.
Correct answer is: A methylated guanine at the 5' end of eukaryotic mRNA
Q.89 Which of the following best describes 'transcriptome-wide association study (TWAS)'?
A method that correlates gene expression levels with phenotypic traits across populations
A study focusing on protein-protein interactions
An analysis of chromatin accessibility across tissues
A technique to measure DNA methylation patterns
Explanation - TWAS integrates GWAS and eQTL data to identify genes whose expression is associated with traits.
Correct answer is: A method that correlates gene expression levels with phenotypic traits across populations
Q.90 Which of the following best captures the concept of 'epigenetic memory'?
The inheritance of DNA sequence variants across generations
The persistence of gene expression patterns across cell divisions due to epigenetic marks
The ability of a cell to remember environmental stimuli via protein folding
The storage of genetic information in RNA molecules
Explanation - Epigenetic memory refers to stable changes in gene expression maintained through DNA methylation or histone modifications.
Correct answer is: The persistence of gene expression patterns across cell divisions due to epigenetic marks
Q.91 Which of the following best characterizes a 'transcriptional enhancer'?
A DNA element that increases transcription of a gene by binding activator proteins
A region that encodes a protein domain
An RNA sequence that modulates translation efficiency
A protein that degrades mRNA
Explanation - Enhancers enhance transcription from a promoter, often located far upstream or downstream of the gene.
Correct answer is: A DNA element that increases transcription of a gene by binding activator proteins
Q.92 What is the primary advantage of using CRISPR-Cas13 for gene regulation?
It introduces permanent mutations into the DNA
It targets RNA molecules for knockdown without altering DNA
It increases the rate of DNA replication
It enhances protein translation directly
Explanation - Cas13 is an RNA-guided RNA-targeting nuclease, enabling transient knockdown at the transcript level.
Correct answer is: It targets RNA molecules for knockdown without altering DNA
Q.93 In functional genomics, what does a 'gene set enrichment analysis (GSEA)' test for?
The presence of mutations within a gene
Whether predefined sets of genes show statistically significant, concordant differences between two biological states
The binding affinity of a protein to DNA
The total number of exons in a transcript
Explanation - GSEA identifies coordinated changes in biological pathways rather than individual genes.
Correct answer is: Whether predefined sets of genes show statistically significant, concordant differences between two biological states
Q.94 What does a 'k-mer' represent in the context of genomic data analysis?
A segment of a protein with a specific function
A substring of DNA or RNA of length k
A computational algorithm for sequence alignment
A type of RNA polymerase subunit
Explanation - K-mers are short sequences used in genome assembly and analysis to find overlaps between reads.
Correct answer is: A substring of DNA or RNA of length k
Q.95 Which of the following best describes 'transcriptional elongation rate'?
The speed at which RNA polymerase transcribes DNA into RNA
The amount of mRNA produced per hour
The rate of protein synthesis
The frequency of mRNA splicing events
Explanation - Elongation rate refers to how quickly the polymerase moves along the DNA template during transcription.
Correct answer is: The speed at which RNA polymerase transcribes DNA into RNA
Q.96 In a CRISPR knockout screen, a guide RNAs' depletion from the pool indicates:
The guide is ineffective
The targeted gene is essential for cell survival or proliferation
The guide causes off-target effects
The cell line is resistant to CRISPR
Explanation - Depletion suggests loss of cell fitness upon knockout, implying gene essentiality.
Correct answer is: The targeted gene is essential for cell survival or proliferation
Q.97 Which of the following best describes a 'CRISPR interference (CRISPRi) system'?
A method that permanently deletes target genes
A system using dCas9 fused to a repressor to inhibit transcription without cutting DNA
A technique that edits the genome at high efficiency
A way to overexpress a gene by activating transcription
Explanation - CRISPRi blocks transcription initiation or elongation by steric hindrance or recruitment of repressive complexes.
Correct answer is: A system using dCas9 fused to a repressor to inhibit transcription without cutting DNA
Q.98 What is the key difference between 'RNA-seq' and 'qPCR' in measuring gene expression?
RNA-seq can identify novel transcripts, while qPCR measures known sequences
qPCR provides higher throughput than RNA-seq
RNA-seq does not require reverse transcription
qPCR cannot be quantitative
Explanation - RNA-seq is an unbiased, genome-wide approach; qPCR is targeted and quantitative for specific transcripts.
Correct answer is: RNA-seq can identify novel transcripts, while qPCR measures known sequences
Q.99 Which of the following best describes 'DNA methylation' at the CpG context?
The addition of a methyl group to cytosine residues followed by guanine
The removal of a methyl group from adenine
The insertion of a phosphate group into DNA
The substitution of guanine with uracil
Explanation - CpG methylation is a common epigenetic modification influencing gene expression.
Correct answer is: The addition of a methyl group to cytosine residues followed by guanine
Q.100 What does a 'high-throughput screening (HTS)' platform typically involve?
Testing a small number of compounds in a single experiment
Analyzing large libraries of genetic perturbations or chemical compounds in parallel
Sequencing a single gene in depth
Using low-resolution imaging techniques
Explanation - HTS allows rapid assessment of thousands of candidates for phenotypic effects.
Correct answer is: Analyzing large libraries of genetic perturbations or chemical compounds in parallel
Q.101 Which of the following is an example of a 'translational regulator' in mRNA processing?
Splicing factor
miRNA
DNA polymerase
Histone acetyltransferase
Explanation - miRNAs bind target mRNAs to inhibit translation or promote degradation.
Correct answer is: miRNA
Q.102 Which of the following best characterizes a 'gene knockout model' in mice?
A mouse where a specific gene has been inserted artificially
A mouse with a targeted deletion or inactivation of a specific gene
A mouse with increased expression of a gene
A mouse with a natural variation in a gene
Explanation - Knockout models allow study of gene function by observing phenotypic changes when the gene is absent.
Correct answer is: A mouse with a targeted deletion or inactivation of a specific gene
Q.103 Which of the following best describes a 'functional assay'?
An experiment that measures the biochemical activity or biological effect of a gene product
A method for sequencing DNA fragments
An approach to align RNA-seq reads to a reference genome
A statistical test for differential expression
Explanation - Functional assays assess how a gene or protein functions in a biological context.
Correct answer is: An experiment that measures the biochemical activity or biological effect of a gene product
Q.104 Which of the following best captures the term 'spatiotemporal gene expression'?
Gene expression measured only in a single cell type
Gene expression measured at a single time point across tissues
Gene expression variation across different locations and times in an organism
Gene expression that is constant throughout development
Explanation - Spatiotemporal expression refers to spatial (tissue-specific) and temporal (developmental stage) patterns.
Correct answer is: Gene expression variation across different locations and times in an organism
Q.105 What is the role of 'polycomb group (PcG) proteins' in functional genomics?
They promote transcription by acetylating histones
They mediate transcriptional repression by modifying histones to create a compact chromatin structure
They splice mRNA transcripts
They bind DNA methyltransferases
Explanation - PcG proteins form complexes (PRC1/PRC2) that catalyze histone modifications leading to gene silencing.
Correct answer is: They mediate transcriptional repression by modifying histones to create a compact chromatin structure
Q.106 Which of the following best describes a 'DNA repair enzyme' in functional genomics?
An enzyme that synthesizes RNA from DNA
An enzyme that identifies and corrects DNA lesions to maintain genome integrity
An enzyme that methylates histones
An enzyme that degrades RNA in the cytoplasm
Explanation - DNA repair enzymes recognize damage and catalyze repair pathways to preserve DNA fidelity.
Correct answer is: An enzyme that identifies and corrects DNA lesions to maintain genome integrity
Q.107 What is the main advantage of using a 'dual-luciferase' reporter assay over a single-luciferase assay?
It is less expensive
It allows simultaneous measurement of experimental and reference luciferase activities for normalization
It requires fewer plasmids
It eliminates the need for a promoter
Explanation - The second luciferase serves as an internal control to correct for transfection efficiency and other variables.
Correct answer is: It allows simultaneous measurement of experimental and reference luciferase activities for normalization
Q.108 Which of the following best describes a 'gene cluster' in a genome?
A set of genes located on a plasmid
A group of genes that are co-regulated and often physically close on a chromosome
A group of unrelated genes scattered throughout the genome
A collection of genes with no functional relationship
Explanation - Gene clusters are physically adjacent genes that are often transcribed together or share regulatory elements.
Correct answer is: A group of genes that are co-regulated and often physically close on a chromosome
Q.109 In a 'transposon mutagenesis screen', what is the primary outcome?
The introduction of a foreign DNA element that disrupts genes randomly to identify essential genes or pathways
The measurement of mRNA levels by sequencing
The identification of epigenetic marks across the genome
The analysis of protein–protein interactions
Explanation - Transposons insert randomly, disrupting gene function and revealing phenotypes related to gene disruption.
Correct answer is: The introduction of a foreign DNA element that disrupts genes randomly to identify essential genes or pathways
Q.110 What does the term 'genome-wide CRISPR activation (CRISPRa)' refer to?
Using Cas9 to induce double-strand breaks across the genome
Using dCas9 fused to transcriptional activators to upregulate target genes genome-wide
Deleting large chromosomal regions
Introducing point mutations throughout the genome
Explanation - CRISPRa harnesses dCas9-activator fusions to increase transcription of specific genes.
Correct answer is: Using dCas9 fused to transcriptional activators to upregulate target genes genome-wide
Q.111 Which of the following best describes a 'promoter'?
A regulatory DNA sequence where transcription starts
A protein that degrades mRNA
An enhancer that sits downstream of the gene
A non-coding RNA
Explanation - Promoters are upstream DNA elements essential for initiation of transcription.
Correct answer is: A regulatory DNA sequence where transcription starts
Q.112 In the context of gene editing, what is a 'base editor'?
An enzyme that changes one DNA base to another without causing double-stranded breaks
A tool that inserts large DNA fragments into the genome
A system that deletes entire genes
An enzyme that introduces random mutations across the genome
Explanation - Base editors enable precise single-nucleotide edits by deaminating cytosine or adenine residues.
Correct answer is: An enzyme that changes one DNA base to another without causing double-stranded breaks
Q.113 Which of the following best explains 'RNA interference (RNAi)'?
A mechanism that enhances gene transcription
A biological process where small RNA molecules guide the degradation of target mRNAs
The addition of a poly-A tail to mRNA
The initiation of DNA replication
Explanation - RNAi employs siRNAs or shRNAs to silence gene expression post-transcriptionally.
Correct answer is: A biological process where small RNA molecules guide the degradation of target mRNAs
Q.114 What does an 'enrichment plot' typically show in a Gene Set Enrichment Analysis (GSEA) output?
The distribution of sequencing reads across the genome
The running sum statistic indicating enrichment of a gene set along a ranked list of genes
The number of transcripts per gene
The fold change of individual genes
Explanation - The enrichment plot visualizes the cumulative enrichment score across the ranked gene list.
Correct answer is: The running sum statistic indicating enrichment of a gene set along a ranked list of genes
Q.115 Which of the following best describes a 'DNA barcode' in functional genomics experiments?
A short DNA sequence used to uniquely identify individual samples or cells
A marker for gene expression in single-cell sequencing
A sequence that enhances transcription factor binding
A part of the ribosomal RNA
Explanation - Barcodes enable multiplexing of samples or cells within a single sequencing run.
Correct answer is: A short DNA sequence used to uniquely identify individual samples or cells
Q.116 Which of the following is a typical challenge when analyzing ATAC-seq data?
The short read lengths limit mapping accuracy
High levels of sequence bias and variable fragment size distributions
Inability to detect open chromatin regions
The requirement for large input amounts of DNA
Explanation - ATAC-seq data can be biased by transposase preferences, requiring careful normalization.
Correct answer is: High levels of sequence bias and variable fragment size distributions
Q.117 Which of the following best describes 'chromatin immunoprecipitation followed by sequencing (ChIP-seq)'?
A method for measuring DNA methylation across the genome
A technique to identify protein–DNA interactions by sequencing DNA fragments bound to a specific protein
A high-throughput method for RNA quantification
A protocol for detecting protein–protein interactions
Explanation - ChIP-seq isolates DNA bound by a target protein and sequences it to map binding sites.
Correct answer is: A technique to identify protein–DNA interactions by sequencing DNA fragments bound to a specific protein
Q.118 Which of the following best describes a 'knockdown' experiment?
Complete deletion of a gene
Partial suppression of gene expression using RNAi or CRISPRi
Overexpression of a gene
Insertion of a transgene
Explanation - Knockdown reduces but does not eliminate gene expression, enabling study of partial loss-of-function.
Correct answer is: Partial suppression of gene expression using RNAi or CRISPRi
Q.119 Which of the following best characterizes a 'transcript isoform' generated by alternative promoter usage?
A transcript that arises from splicing variants only
A transcript that uses a different start site and therefore has a different N-terminal sequence
A transcript with a longer poly-A tail
A transcript that is exclusively expressed in the brain
Explanation - Alternative promoters produce transcripts with distinct 5' ends and potentially different protein isoforms.
Correct answer is: A transcript that uses a different start site and therefore has a different N-terminal sequence
Q.120 What is the purpose of a 'spike-in control' in RNA-seq experiments?
To calibrate sequencing depth and account for technical variation
To increase read length
To measure DNA methylation levels
To identify protein–protein interactions
Explanation - Spike-ins are known RNA molecules added in a fixed amount to enable normalization across samples.
Correct answer is: To calibrate sequencing depth and account for technical variation
Q.121 Which of the following best describes 'cis-acting regulatory SNPs (cSNPs)'?
SNPs that alter protein coding sequence
SNPs located in enhancer or promoter regions that influence the expression of nearby genes
SNPs that affect distant gene expression through trans interactions
SNPs found only in mitochondrial DNA
Explanation - cSNPs directly affect regulatory elements, modulating gene expression of adjacent genes.
Correct answer is: SNPs located in enhancer or promoter regions that influence the expression of nearby genes
Q.122 Which of the following best describes a 'gene knockout' in a plant model?
The insertion of a fluorescent marker gene
The complete deletion of a target gene
The overexpression of a regulatory gene
The introduction of a silent mutation
Explanation - Gene knockouts remove gene function to study its role in plant development or physiology.
Correct answer is: The complete deletion of a target gene
Q.123 In the context of functional genomics, what does 'translatome' refer to?
The entire set of proteins in a cell
The set of RNA molecules actively being translated into proteins
The collection of all mRNA transcripts
The genome of a particular organism
Explanation - Translatome profiling captures ribosome-protected fragments, revealing which transcripts are being translated.
Correct answer is: The set of RNA molecules actively being translated into proteins
Q.124 Which of the following best defines a 'gene ontology (GO) term' for biological processes?
A unique protein structure
A standardized description of a biological process that a gene product participates in
A sequence of nucleotides in a promoter
A measure of gene expression level
Explanation - GO terms classify gene functions into categories such as biological processes, cellular components, and molecular functions.
Correct answer is: A standardized description of a biological process that a gene product participates in
Q.125 Which of the following is an example of a 'chromatin remodeler'?
DNA polymerase
SWI/SNF complex
RNA polymerase I
Transcription factor p53
Explanation - Chromatin remodelers reposition nucleosomes to modulate access of transcription machinery to DNA.
Correct answer is: SWI/SNF complex
Q.126 What does a 'phospho-proteomics' experiment aim to identify?
Phosphorylated sites on proteins across the proteome
Gene expression levels
DNA methylation patterns
RNA splicing variants
Explanation - Phospho-proteomics enriches and identifies phosphorylated peptides to study signaling networks.
Correct answer is: Phosphorylated sites on proteins across the proteome
Q.127 Which of the following best explains the term 'transcriptional pausing'?
When RNA polymerase permanently stops transcribing
Temporary halting of RNA polymerase during transcription elongation
The process of mRNA splicing
The addition of the poly-A tail
Explanation - Pausing controls gene expression kinetics and allows for co-transcriptional processing events.
Correct answer is: Temporary halting of RNA polymerase during transcription elongation