Lecture 13 Guide

Lecture 13 Guide -...

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Genomics
 I.
Structural
genomics
 
 
A.
Construction
of
genomic
libraries 
 
B.
Physical
mapping
 
 
C.
Bioinformatics
 
 

 II.
Functional
genomics
 
 
 
 

 
 
 
 
 
 
 
 A.
Characterize
proteome
 B.
Define
transcriptome
 
1.
Microarrays
 C.
Interactome
 
1.
Yeast
two‐hybrid
 
2.
Chromatin
immunoprecipitation
assay
(ChIP)
 D.
Mutational
analysis
 
1.
Targeted
mutagenesis
 
2.
RNA
interference
 III.
Comparative
genomics
 
 A.
Power
of
conservation
 
 

 
 
 
Genomics

 Objectives:
 
 Be
able
to
describe
the
basic
process
of
going
from
a
genomic
library
to
the

 sequence
of
a
genome
 
 Know
the
different
forms
of
evidence
that
are
used
to
make

 gene
predictions
(see
Fig
13‐12)
 
 Know
the
definitions
and
purposes
of
the
techniques
used
in
functional
genomics
 
 Understand
the
utility
of
genomics
for
understanding
the
genomes

 of
individual
people;
the
conservation
of
genes
across
species;

 and
the
roles
of
genes
that
are
different,
both
within
and
between
species
 Vocabulary:
 annotation
 bioinformatics
 contig
 structural
genomics
 functional
genomics
 comparative
genomics
 consensus
sequence
 microarray
 open
reading
frame
 sequence
assembly
 transcriptome
 proteome
 interactome
 RNA
interference
 pseudogene
 homolog
 chromatin
immunoprecipitation
assay
(ChIP)
 yeast
two
hybrid
assay
 in
situ
hybridizaton,
FISH
 The human nuclear genome viewed as a set of labeled DNA Chapter
13
Opener
 
 FISH
is
used
to
identify
where
a
particular
gene
falls
within
an
individual's
 chromosomes.
The
first
step
is
to
prepare
short
sequences
of
single‐stranded
DNA
 that
match
a
portion
of
the
gene
the
researcher
is
looking
for.
These
probes
are
 labeled
by
attaching
one
of
a
number
of
colors
of
fluorescent
dye.
 
 FISH
was
used
to
localize
DNA
sequences
to
specific
chromosomes,
as
part
of
 the
human
genome
project.
The
previous
slide
shows
that
now
multiple
unique
 sequences
for
every
chromosome
have
been
identified,
and
are
visualized
as
a
 different
color
for
each
chromosome.
 The logic of creating a sequence map of the genome Figure
13‐2
 Strategy for ordered-clone sequencing Figure
13‐8
 Strategy for whole-genome shotgun sequencing assembly Analysis of DNA sequence: Gene hunting and annotation A protein encoding gene can be viewed/identified in accordance with binding sites related to regulating transcription, producing a mRNA transcript, and encoding a protein Many forms of evidence are integrated to make gene predictions Figure
13‐12
 The sequence map of human chromosome 20 The transcriptome is studied with the use of DNA microarrays DNA microarrays reveal profiles of gene expression Studying protein interactions with the use of the yeast two-hybrid system Figure
13‐20
 Steps in a chromatin immunoprecipitation assay (ChIP) Figure
13‐21
 Producing cells containing a targeted gene knockout Figure
20‐31a
 Producing a mouse containing the targeted gene knockout Disrupting gene function with the use of targeted mutagenesis Figure
13‐22
 Disrupting gene function with the use of RNA interference The mouse and human genome have large syntenic blocks of genes in common Testing the role of a conserved element in gene regulation Figure
13‐16
 Assignment

 Achieve
Objectives
List
(slide
2)
through
study
 and
practice.
 Solve
problems
from
textbook.

 Chapter
13:
 2,
6,
9,
12,
13,
16,
21,
22,
23
 ...
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