Lecture 16 and 17: TRANSCRIPTOMICS 1 AND 2

Question 1

DEFINE TRANSCRIPTOME:

Answer 1

1. The ‘transcriptome’ is the SEQUENCE and EXPRESSION PATTERN OF ALL TRANSCRIPTS IN A CELL (where, when, how much).
2. • This means the COMPLETE SET OF ALL ‘RNA’ MOLECULES, or “transcripts”, PRODUCED IN ONE OR A POPULATION OF CELLS.

Question 2

The term transcriptome can be applied to the: 2

Answer 2

1. total set of transcripts in a GIVEN ORGANISM or
2. – the specific SUBSET of TRANSCRIPTS present in a PARTICULAR CELL OR TISSUE TYPE

Question 3

The transcriptome: 3

• does it vary?
• what does it do in particular?
• what does it reflect?

Answer 3

1. • Unlike the genome, the ‘transcriptome’ VARIES WITH CHANGING ENVIRONMENTAL CONDITIONS
2. • Nearly every cell in the body CONTAINS THE SAME GENES/GENOME, ‘BUT DIFFERENT CELLS SHOW DIFFERENT PATTERNS OF GENE EXPRESSION.’ (‘which
     makes them the cell they are’).
3. • Since all transcripts are CONTAINED IN THE CELL, the transcriptome REFLECTS THE ‘GENES’ THAT ARE BEING ‘ACTIVELY EXPRESSED’ AT A GIVEN TIME.

Question 4

Transcriptomics measures more than just mRNA…4

Answer 4

1. • Transcriptomics includes IDENTIFYING and MEASURING EXPRESSION of:
2. • NONCODING RNAs
3. • ALTERNATIVELY SPLICED ISOFORMS
4. • ALTERNATIVE 3’
     ENDS, polyA, 3’UTRs etc

Question 5

Transcriptomics questions: 3

‘Now that more and more genome sequences are being completed, new questions arise:’

Answer 5

1. – What are the functional roles of different genes and in what cellular processes do they participate?
2. – How are genes regulated and how do genes and gene
   products interact?
3. – How do gene expression levels differ in various cell
   types and cell states and how is gene expression changed by various diseases or treatments?

Question 6

‘Differential gene expression’ – HOW ARE = Genes are EXPRESSED when they are TRANSCRIBED…4

Answer 6

1. • copied into mRNA
2. then to — protein,
3. OR non- coding genes/functional RNAs like tRNA
4. OR small nuclear RNA
   (snRNA) .

Question 7

UNDERSTANDING Differential gene expression: 3

Answer 7

1. • which genes are EXPRESSED IN WHICH CELLS or TISSUES AT A GIVEN POINT IN TIME OR IN LIFE OF THE ORGANISM.
2. • Total RNA can be ISOLATED FROM CELLS OR TISSUES UNDER DIFFERENT EXPERIMENTAL CONDITIONS AND THE RELATIVE AMOUNTS OF TRANSCRIBED ‘RNA’ CAN BE MEASURED.
3. • The CHANGE IN EXPRESSION PATTERN IN RESPONSE to an
     EXPERIMENTAL CONDITION, ENVIRONMENTAL CHANGE, DRUG TREATMENT, ETC , etc ‘SHEDS LIGHT INTO THE DYNAMIC FUNCTIONING OF A CELL’

Question 8

What can we learn from transcriptomics? = 4

Answer 8

1. An understanding of genes and pathways involved in biological processes

2.Elucidate the function of unknown genes based on their spatial and temporal expression

3.* Identify marker genes for diagnosis of diseases à “expression signature”.

4. • May be a proxy for changes in the proteome and metabolome (but not always!)

Question 9

What can we learn from transcriptomics?

EXPLAIN - An understanding of genes and pathways involved in biological
processes:

Answer 9

“guilt by association”: genes with similar expression may be functionally related and under the same genetic control mechanism.

Question 10

What can we learn from transcriptomics?

EXPLAIN -Elucidate the function of unknown genes based on their spatial
and temporal expression. = 2

Answer 10

1. • E.g. if an unknown gene’s expression levels are dramatically higher in cancer cells than in healthy cells, the unknown gene may play a
     role in cell growth.
2. • E.g. if an unknown gene is expressed in fat tissue but not in bone or muscle tissue, the unknown gene may be involved in fat storage or metabolism

Question 11

transcriptomics: applications

MEDICINE:

Answer 11

1. – Disease-associated expression patterns (diagnosis, including primary source of cancer).
2. – Cell-cycle monitoring (cancer research).
3. – Treatment-induced expression pattern (drug development and response).

Question 12

transcriptomics: applications : BIOLOGY = 5

Answer 12

1. – Development and morphology (juveniles vs adults, male vs female,
   tissue A vs tissue B).
2. – Interactions between organisms and their environments (temperature,
   radiation, draught, nutrient levels, toxins and heavy metals).
3. – Evolution (within- and between species variation, hybrids vs parents,
   diploids vs polyploids).
4. – Functional analyses (wild type vs mutant).
5. – Time series.

Question 13

Transcriptomics databases: 5

Answer 13

1. • We already know the transcriptome of many BASAL STATES
2. • THE MAMMALIAN GENE COLLECTION
     – free, public library of human, mouse and rat mRNA sequences.
3. • THE MOUSE TRANSCRIPTOME PROJECT
     – free, public database of gene transcripts for many
     mouse tissues.
4. • GENOTYPE-TISSUE EXPRESSION PROJECT (GTEx)
     – catalogue of human gene expression in a variety of
     different tissues.
5. • ENCYCLOPEDIA OF ‘DNA’ ELEMENTS (ENCODE)
     – aim is for researchers to characterize and understand the working parts of the genome, including the transcriptome