Quiz 5

ENCODE project. The highest priority set (Tier 1) includes two widely studied immortalized cell lines:

1) H1ESC The H1 human embryonic stem cell line 2) GM12878 a-lymphoblastoid line (also being studied by the 1,000 Genomes Project) 3) K562 erythroleukemia cells

5 main classes of repetitive DNA:

1. Interspersed repeats 2. Processed pseudogenes 3. Simple sequence repeats 4. Segmental duplications 5. Blocks of tandem repeats

Sequenced the whole genomes from a total of 1092 individuals from a pool of 14 different populations selected by their ancient migratory history and genetic relationship to each other.

1000 Genomes Project

The first complete genome to be sequenced was:

A bacteriophage.

Centromere, which is located close to a telomere called..

Acrocentric centromere

Method of separating biochemical mixtures based on a highly specific interaction such as that between antigen and antibody, enzyme and substrate, or receptor and ligand called:

Affinity chromatography

De Novo Seq Template Includes:

Ancient DNA seq. Metagenomics

Applications of resequencing:

Assessment of genomic changes in disease-associated regions; Sequencing of all human exons in multiple individuals; Sequencing of large sets of genes associated with cancer

First viral genome sequence

Bacteriophage MS2 (3,569 bp)

Alignment programs:

Bowtie BWA

... is measured in base pairs or in picograms (pg) of DNA.

C-Value

One picogram of DNA corresponds to approximately 1 Gb.

C-Value

The haploid genome size of eukaryotes, called the C value, varies enormously.

C-Value paradox

The range in C values does not correlate well with the complexity of the organism called:

C-Value paradox

NGS is used to find transcription factor binding sites to the DNA

CHip-Seq

Type of NGS used to find Histone modification (it's locations) H3K4me monomethylation

CHip-Seq

Regulatory elements which predict the presence of genomic DNA features such as promoters, enhancers, silencers, Insulators called:

CRM cis-regulatory modules

The first multi-cell eukaryote genome sequenced.

Caenorhabditis elegans (Worm)

a region that remains unstained with many dyes, appears as a constriction

Centromere

Chromatin Immunoprecipitation abrv.

ChiP

NGS application to find TF binding sites:

ChiP seq

What is ChIP-sequencing?

Chip-Seq is a method used to analyze protein interactions with DNA

First human chromosome in 1999

Chromosome 22 (49 Mb)

Potein-protein interaction works by selecting an antibody that targets a known protein that is believed to be a member of a larger complex of proteins. By targeting this known member with an antibody it may become possible to pull the entire protein complex out of solution and thereby identify unknown members of the complex.

Co-immunoprecipitation (Co-IP)

This concept of pulling protein complexes out of solution. Also referred to as a "pull-down".

Co-immunoprecipitation (Co-IP)

The interactions of two purified proteins can be measured with techniques:

Co-immunoprecipitation (Co-IP). Affinity chromatography. Yeast two-hybrid system.

An example of a regulatory element: the dinucleotide cytosine followed by guanosine (CpG)

CpG islands

Transcript Assembly programs:

Cufflinks/Cuffmerge/Cuffcompare/Cuffdiff

NGS is used to study DNA methylation

DNA methylation, RRBS seq, RRB bisulfate

NGS is used to capture open chromatin

DNAse fair-seq

Method of sequencing involved in determining the DNA sequence of an organism as completely as possible is called:

De novo sequencing

Examples of Transcriptome:

Defining regulated mRNA transcripts; Identifying and quantifying mRNA in samples

One of the challenges of Protein networks::

Different categories of network or pathway maps.

Examples of Model organisms

E.coli (prokaryote), Saccharomyces cerevisiae (eukaryote)

ENCyclopedia of DNA Elements

ENCODE

Goal of this organization to discover and define the functional elements encoded in the human genome:

ENCODE - ENCyclopedia of DNA Elements

The aim of this project is to build a catalogue of functional elements of the human genome. Functional elements: genes, transcripts, transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns.

ENCODE - ENCyclopedia of DNA Elements

A short (50-1500 bp) region of DNA that can be bound with proteins to activate transcription of a gene or genes

Enhancer

High throughput sequencing can be used to assess the methylation status of a genome called:

Epigenomics

The modification of DNA or chromatin through DNA methylation and/or through the posttranslational modification of histones called:

Epigenomics

The study of the complete set of epigenetic modifications on the genetic material of a cell known as..

Epigenomics (epigenome)

Heritable changes other than those involving the 4DNA sequence per se.

Epigenomics or epigenetics

Single-celled or multicellular organisms that are distinguished from prokaryotes by the presence of a membrane-bound nucleus, and a cytoskeleton.

Euakaryotes

NGS application to seq Personalized genomes:

Exome-seq

Which of the following NGS technologies is used for personalized genome sequencing?

Exome-seq

Type of NGS used to sequence all exxons and not the whole genome

Exxon-seq

Epigenomics is sampling the genomes of many organisms from a particular environmental site- such as the human gut (organismal) or an ocean region (environmental).

False

Forward genetics asks "What is the phenotype of this mutant?"

False

Reverse genetics asks "What mutants have this particular phenotype?"

False

"What mutants have this particular phenotype?"

Forward genetics

"phenotype-driven" approach, altered phenotype first, then identify genes responsible is called

Forward genetics

Transcriptome Template Includes:

Full-length transcripts; SAGE - Serial Analysis of Gene Expression; Non-Coding RNA

The genome-wide study of the function of DNA.

Functional Genomics

Organism's full hereditary information.

Genotype

Difference between the genotype and the phenotype.

Genotype is an organism's full hereditary information. Phenotype is an organism's observable characteristics.

One of the challenges of Protein networks

Great variation in protein composition and behavior of different protein pathways.

First genome of a free-living organism, the bacterium

Haemophilus influenzae

NGS application to measure Chromosomal interactions:

Hi-C

Which of the following NGS technologies is used to study inter- and intra- chromosomal interactions?

Hi-C

NGS is used to capture chromosomal interactions

Hi-C (3C, 4C, 5C)

One of the challenges of Protein networks :

How to assess the accuracy of a protein network?

30x human genome sequenced by

Illumina

Dominant technology in high-throughput sequencing:

Illumina

Technique of precipitating a protein antigen out of solution using an antibody that specifically binds to that particular protein.

Immunoprecipitation

Examples of ReSequencing:

Individual human; Assessment of genomic arrangements of disease associated regions; Seq mutations in cancer

Collection of manually drawn maps in six areas: metabolism, genetic information processing, environmental information processing, cellular processes, human diseases, drug development.

KEGG Kyoto Encyclopedia of Genes and Genomes

The database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies

KEGG Kyoto Encyclopedia of Genes and Genomes

Imaging the chromosomes during metaphase, when each chromosome is a pair of sister chromatids

Karyotype

Which of the following is not a DNA sequencing technology?

Mass spectrometry

Examples of Epigenetics:

Measuring methylation in cancer

Centromeres located near the middle of the chromosome:

Metacentric centromere

Sampling the genomes of many organisms from a particular environmental site such as the human gut (organismal), or an ocean region (environmental)

Metagenomics

Epigenetics Template Includes:

Methylation changes

Simple sequence repeats (1-6 bp long)

Microsatellites

Simple sequence repeats (12-500 bp long)

Minisatellites

Organisms that are studied intensively.

Model organisms

Shares almost all genes with humans. Close functional and structural relationship with human genome

Mus Musculus

Three principal genome browsers for eukaryotes:

NCBI offers Map Viewer. Ensembl offers browsers for dozens of genomes. UCSC offers genome and table browsers for dozens of organisms.

Organism's observable characteristics.

Phenotype

A region of DNA that initiates transcription of a particular gene.

Promoter

One of the challenges: There are no accepted benchmark data sets comparable to those available for fields such as sequence alignment and structural biology.

Protein networks

Genes that are not actively transcribed or translated:

Pseudogenes

These genes have a stop codon or frameshift mutation that interrupts an open reading frame => they do not encode a functional protein.

Pseudogenes

They commonly arise from retrotransposition, or following gene duplication and subsequent gene loss.

Pseudogenes

NGS application to find Gene expression:

RNA-Seq

What NGS method is used to measure gene expression or transcript expression?

RNA-seq

Which NGS technology is used to measure gene expression?

RNA-seq

NGS application to Measuring methylation:

RRBS-seq

Which of the following NGS technologies is used to measure DNA methylation?

RRBS-seq

Application when Genome permits the variation between individuals to be assessed.

Resequencing

This application can guide medical decisions, personalized medicine

Resequencing

Which of the following is not true for resequencing of a genome?

Resequencing cannot guide medical decisions.

"What is the phenotype of this mutant?" This question is raised by what type of genetics?

Reverse genetics

"gene-driven" approach, targeted deletion or disruption of gene

Reverse genetics

Programs for gene/protein network visualization

STRING db, GENEMANIA

The first single-cell eukaryote genome sequenced

Saccharomyces cerevisiae (Eukaryote)

The first single-cell eukaryote whose genome was sequenced is:

Saccharomyces cerevisiae (yeast).

Examples of De Novo seq:

Seq > 1000 influenza genomes; Extinct Neanderthal Genomes; Human gut

A contiguous length of nucleotide bases that is generated using a sequencing machine called..

Sequencing read

..structures characterized by tandem arrays of repetitive sequences found at the chromosome ends.

Telomeres

They provide stability to chromosomes by preventing the degradation of the chromosome end and by blocking the fusion of chromosome ends.

Telomeres

Ancient DNA projects allow the sequencing of historical samples. A special challenge is:

The DNA is often fragmented.

Consortium applied and compared several experimental and computational methods to annotate functional elements in a defined 1% (30Mb) of the human genome.

The Pilot phase of the ENCODE project

One of the challenges of Protein networks :

The choice of experimental organism is important.

Why is genome sequencing important?

To obtain a 'blueprint' - DNA directs all the instructions needed for cell development and function, and underlies almost every aspect of human health, both, in function and disfunction. To study gene expression in a specific tissue, organ or tumor. To study human variation. To study how humans relate to other organisms. To find correlations how genome information relates to development of cancer, susceptibility to certain diseases and drug metabolism (pharmacogenomics). Personalized Genomics/Medicine.

Splice junction mapper program:

TopHat

Microarray-based gene expression profiling to study RNA expression levels.

Transcriptome

Transposable elements, or retro-transposon "jumping genes"

Transposon

A knockout mouse is a genetically engineered mouse in which researchers have inactivated or "knocked out" an existing gene by replacing it or disrupting it with an artificial piece of DNA.

True

At least 30x coverage is required for human genome sequencing meaning that each nucleotide has been sequenced at least 30 times.

True

Co-IP is a powerful technique for analyzing protein-protein interactions.

True

Genome sequencing is important to study gene expression in a specific tissue/organ/tumor and human variation as well as to discover how genome information relates to development of cancer.T/F

True

Illumina is the dominant technology in high-throughput sequencing.

True

In Illumina multiplexing technology the following steps are followed: attach barcode- mix samples- sequence- identify and remove barcode.

True

Pseudogenes can be captured using RNA-seq.

True

The 1000 genomes project sequenced the whole genomes from a total of 1092 individuals from a pool of 14 different populations selected by their ancient migratory history and genetic relationship to each other.

True

The concept of pulling protein complexes out of solution is referred to as a "pull-down".

True

The draft sequence of the human genome was published in 2001 by 2 separate groups the International Human Genome Sequencing Consortium and Celera Genomics. T/F

True

CpG islands are regions commonly found in... (direction) regulatory regions near the transcription start sites of genes

Upstream

One of the challenges of Protein networks:

What data to use?

ReSequencing Template Includes:

Whole Genomes Genomic Regions Somatic Mutations

NGS is used to seq everything (whole genome)

Whole genome-seq

Aim of 1000 genomes project:

to identify the SNPs that are present at 1% or greater frequency