L11 Cellular Genetics

Question 1

Cellular genetics

Answer 1

see onenote

study of how the global pattern of gene expression determines the cellular phenotype

going from a genomic profile to a cellular phenotype is a big challenge

Question 2

Gene regulation is complex

Answer 2

see onenote

genes can be regulated at many points

1. transcription
2. post-transcription
3. post-translational

Question 3

Molecular pathways/networks are complex

Answer 3

see onenote

Question 4

molecular interactions in a cell are stochastic

Answer 4

molecules involved move stochastically

there is an inherent degree of randomness to these interactions

Question 5

Measuring gene expression levels

Answer 5

quantitive PCR - good for 10-100s genes

microarray - good for thousands of genes

RNAseq - good for assaying the entire genome

Question 6

Measuring gene expression with microarrays

Answer 6

see onenote

Question 7

Measuring gene expression with RNAseq

Answer 7

see onenote

Question 8

qPCR at the blastocyst stage

Answer 8

see onenote

Take tissue samples and do RNA seq to look at gene expression differences

Question 9

The problem with tissue level analysis

Answer 9

fine if all cells are the same but any differential gene expression between cells is averaged out and lost

SOLUTION
single cell gene expression analysis

Question 10

What if we worked on individual cells?

Answer 10

see onenote

Question 11

qPCR of 137 cells ranging from E3.25 to E4.5

Answer 11

see onenote slides

Question 12

Interpreting gene expression arrays

Answer 12

see onenote

Question 13

Cell-type discovery by transcriptome profiling of single cells

Answer 13

see onenote

Question 14

Finding cell types using RNAseq

Answer 14

see onenote slides

Took cell from developing lung bud

BP - bipotential cells can differentiate into AT1 and AT2

Certain genes expressed in certain cell types

Question 15

RNAseq on 80 individual cells

Answer 15

see onenote slides

and identified new marker genes

Question 16

Validating new marker genes

Answer 16

see onenote

able to generate antibodies to some of the newly identified genes and confirmed that they were found in the same cells as the previously known markers

Question 17

Gene ontology

Answer 17

formal naming and definitions of the types, properties and interrelationships of the entities for a particular domain of discourse

Question 18

Gene ontology project

Answer 18

describe gene products in terms of their associated biological processes, cellular components, molecular functions

Question 19

hierarchical controlled vocabulary

Answer 19

see onenote

Describing things in increasingly general/specific terms

Question 20

Embryonic stem cells from the inner cell mass

Answer 20

ESC are able to self-renew

pluripotent since they can give rise to many differentiated cell types of the body

huge potential in human therapies but there are ethical issues

Question 21

induced pluripotent stem (iPS) cells

Answer 21

see onenote slides

encourage other cell types to express the same genes as epiblasts, could we turn them into pluripotent stem cells?

found four genes (oct4, kif4, sox2 and myc) which when expressed together in fibroblasts could turn them into pluripotent stem cells

Question 22

in vitro differentiation

Answer 22

see onenote

when iPS cells are allowed to form aggregates, they begin to specialise and differentiate

by supplying right sequence of signalling proteins and growth factors, one can guide them down the differentiation path to defined cell types

Question 23

induced stem cells, stem-cell therapies

Answer 23

see onenote

will be possible to take cells from patient, induce them to become iPS cells, repair disease-causing mutations and then create healthy differentiated cells to reintroduce into the body

Question 24

some cells can self-organise into tissues

Answer 24

see onenote

given the right conditions, some stem cells have the ability to give rise to complex tissues with multiple cell types