BIOL 349 Exam 3

supervised learning variable(s)

x and y

supervised learning

given an observation x, what is the best label y?

supervised learning example(s)

classification, regression

unsupervised learning variable(s)

x

unsupervised learning

given a set of x’s, output their hidden structure

unsupervised learning example(s)

clustering

idea behind K-means clustering

a good clustering is one for which the within-cluster variation is as small as possible

within-cluster variation

measure of the amount by which the observations within a cluster differ from each other

pre-specify the number of clusters K

requirement of K-means clustering that can be a disadvantage

hierarchical clustering

alternate approach which does NOT require that we commit to a particular choice of K

most common type of hierarchical clustering

bottom-up/agglomerative clustering

bottom-up/agglomerative clustering refers to…

the fact that a dendrogram is built starting from the leaves and combining clusters up to the trunk

what do these images show?

hierarchical clustering algorithm

hierarchical clustering algorithm: step 1

start with each point in its own cluster

hierarchical clustering algorithm: step 2

identify the two closest clusters and merge them

hierarchical clustering algorithm: step 3

repeat steps 1 (identifying clusters as one point) and 2 (merging two closest clusters)

hierarchical clustering algorithm: step 4

ends when all points are in a single cluster

What does this image show?

Visualizing differential expression results using hierarchical clustering

what are the columns above?

groups of sample type separated into control vs overexpression

what are the labels at the bottom?

individual sample types

what are the rows representative of?

a specific differentially expressed gene

what does the colors and scale represent?

darker red/color indicates higher gene expression while lighter red/color indicates lower gene expression

TRUE OR FALSE: one transcription factor can regulate many different genes

TRUE

TRUE OR FALSE: multiple different transcription factors can be required to initiate or regulate a gene or multiple genes

true

TF binding motif

term describing the sequence recognized by a transcription factor

single regulator

gene has one regulator (TF)

repetitive motifs

gene needs multiple of one regulator (TF)

multiple regulators

multiple different regulators (TF) can bind to multiple different genes at the same time to control expression

co-occurring regulators

two or more different regulators (TF) overlap/bind to the same gene to control expression

what does the presence of co-occurring regulators suggest?

physical interaction between the regulators

ChIP-seq

Chromatin Immunoprecipitation Sequencing

step 1 of ChIP-seq

cross-linking

cross-linking

introduces stable covalent bond between TF and DNA

step 2 of ChIP-seq

sonication

sonication

breaks apart chromatin into smaller fragments

step 3 of ChIP-seq

IP (immunoprecipitation)

immunoprecipitation

antibody binds to TF to selectively isolate protein-DNA complex

step 4 of ChIP-seq

sequencing isolated DNA using next-generation sequencing (NGS) to map reads back to reference genome and identify binding peaks

where are the genes recognized by the TF?

the two peaks where reads pile up

where is the sequence correlated to the TF?

the middle between the two peaks where it’s protected

DNA methylation is also known as…

5th base pair

DNA methylation process

cytosine is undergoes methylation to form 5-methyl cytosine

DNA methylation can only happen to…

cytosine

methylation impact on gene expression

gene expression repressed by TF competitors

unmethylated impact on gene expression

no impact; gene expression is not repressed

bisulfite sequencing

gold standard for genome-wide profiling of DNA methylation

bisulfite treatment changes…

unmethylated cytosine to uracil

bisulfite treatment does not change…

methylated C, which is protected by the methyl group

what step is after bisulfite treatment?

PCR to make DNA copies from the bisulfite-treated strands

Host defense is…

silence endogenous parasitic sequence caused by DNA methylation

Imprinting is due to…

gene expression silenced by DNA methylation

X-chromosome inactivation is due to…

DNA methylation silencing one of the two double X chromosomes

genomic related functions of DNA methylation in mammalian system

heterochromatin maintenance, chromosome stability, telomere length

TRUE OR FALSE: A function of DNA methylation in mammalian system is gene expression control.

True

histone code

epigenetic beacons for gene expression regulation

what three letters/numbers do histones start with?

H3K

histone modifications

used to mark different function of different region in genome

types of histone codes/modifications

enhancers, promoters, repressed genes, transcribed gene bodies

two types of ChIP-seq

1. TF

2. histone

TF ChIP-seq

tells where TF is bound to DNA

Histone ChIP-seq

where in DNA the histone interacts with DNA

lower methylation is correlated with…

is higher expression

DNA

naked, double helix

chromatin

DNA in its compaction structure in the cells

nucleosome

basic unit of chromatin, 146bp DNA wrapped around 8 histones proteins

regular TF ChIP-seq

sonication, antibody against TF

histone mark ChIP-seq

sonication or MNase, antibody against the histone modification

super enhancers from ChIP-seq

clusters of multiple, closely located enhancers that bind high concentrations of transcription factors and co-activators

The width of ChIP-seq signals from super enhancers are…

broad

how many TF ChIP-seq in this image?

four

how many histone ChIP-seq in this image?

two

which side has the regular enhancer?

left

which side has the super-enhancer?

right

what does this image show?

separate fluorescence channels of different chromosomes present in the human cell nucleus with one image overlapping all channels

what does this image show?

a color map identifying where each labelled chromosome is located within the nucleus

What is Hi-C used for?

to investigate chromatin interactions genome-wide

Hi-C step 1

crosslink DNA

Hi-C step 2

cut with restriction enzyme

Hi-C step 3

fill ends and mark with biotin

Hi-C step 4

ligate

Hi-C step 5

purify and shear DNA; pull down biotin

Hi-C step 6

sequence using paired-ends

Hi-C is used to sequence…

DNA that is in touch with each other to observe their interactions

where does Hi-C take place?

in cell nucleus

This image is a…

Hi-C data matrix

What are the axes?

the location in the chromosome per kilobase (kb, so per 1000 bp)

What are the values in each square?

the interaction value between each position in the chromosome

What do the more red/pigmented data squares represent?

higher/more interaction between the corresponding positions in the chromosome

This image is…

TADs graphed

TADs

Topologically Associating Domains

Most TADs are…

stable in different cell types

TADs are conserved across…

species

Disruption of domain (TADs) structure is associated with…

limb malformation

conserved

high function

which potential function of TADs does this image represent?

gene co-regulation

which potential function of TADs does this image represent?

enhancer blocking

which potential function of TADs does this image represent?

boundary function

which potential function of TADs does this image represent?

blocking spread of transcription

Compartment A vs B: A tends to interact with…

A

Compartment A vs B: B tends to interact with…

B