The expanding world of RNAs

Question 1

What is the central dogma?

Answer 1

The flow of information: DNA → RNA → PROTEIN/FUNCTION

Question 2

Does the number of protein-coding genes correlate with genome complexity, and what proves it?

Answer 2

NO! Only ~2% of the genomic DNA encodes protein vs. at least 80% of the human genome is transcribed

Question 3

What does increase with developmental complexity in the genome?

Answer 3

The more complex the organism, the HIGHER THE % OF NON-PROTEIN-CODING DNA

Question 4

What does constitute the vast majority of the genomic output of complex organisms?

Answer 4

In human cells, ~97-98% of transcription results in non-protein-coding RNAs.
Often expressed in a cell and developmental stage specific manner

Question 5

What is the “corrected” central dogma?

Answer 5

Gene: a sequence of DNA that codes for (not a protein, but…) a molecule that has a function

Question 6

Long non-coding RNAs (lncRNAs):
Transcribed by (enzyme)?
ORF presence? 
Cellular localization?
Abundance?
Specific expression?

Answer 6

Long non-coding RNAs (lncRNAs):
Transcribed by RNA polymerase II
Little or no Open Reading Frame (ORF)
Nuclear or cytoplasmic (or both) localization
Low abundance compared with mRNAs
Highly tissue cell or developmental stage specific expression

Question 7

Classification of lncRNAs according to genomic organization (position types on the DNA, 4 in total)?

Answer 7

Antisense lncRNAs: overlap with a coding transcript on the opposite DNA strand (>70% of genes have anti-sense transcripts)
Intronic lncRNAs: derived from the intron of a coding transcript
Divergent lncRNAs: bidirectional => away from a coding transcript
Intergenic lncRNAs (llncRNAs): between two genes

Question 8

Long non-coding RNAs (lncRNAs) modes of function in cytoplasm (4 in total)?

Answer 8

1. mRNA stability
2. mRNA translation
3. microRNA competitors
4. Small peptides

Question 9

Long non-coding RNAs (lncRNAs) modes of function in nucleus (5 in total)?

Answer 9

1. regulation of gene-specific transcription
2. regulation of epigenetic changes (chromatin modifying complexes)
3. transcriptional regulator
4. chromosome to chromosome interaction
5. post-transcriptional regulation (splicing)

Question 10

Are microRNAs conserved among species?

Answer 10

Yes highly! The more complex the being the more microRNAs it has (nearly every branching point in the evolutionary tree is characterized by the addition of at least one new miRNA gene)
Complex animals cannot live without microRNAs

Question 11

MicroRNAs function?

Answer 11

Suppress protein production:
Regulate the majority of protein-coding genes
Their expression is often altered in diseases
Virtually all biological processes are regulated by miRNAs (apoptosis, cell proliferation, cell-cell communication, cell motility)

Question 12

The biogenesis and mode of action of microRNAs?

Answer 12

• Transcribed as long ncRNAs - “pri-miRNA”
• Hairpin-structures are cleaved - “pre-miRNA”
• Exported to the cytoplasm
• Processed into the single-stranded “mature miRNA”
• The mature microRNA forms a complex with RISC (RNA-Induced Silencing Complex) and binds to target mRNA
• Suppress their translation/induce their degradation

Question 13

Does microRNA profiles correlate with cell identity?

Answer 13

Yes! MicroRNAs are expressed in a tissue, developmental stage, or differentiation-specific manner
Each tissue and cell-type has a characteristic miRNA signature
In general, the top 10-15 microRNAs constitute ~80% of all microRNAs

Question 14

Are microRNAs expressed at a high level?

Answer 14

Yes, much more than mRNAs!
MicroRNA has dozens-hundreds of targets
MicroRNAs are relatively easily detectable

Question 15

Can microRNAs regulate cell differentiation?

Answer 15

Yes!
Differentiation: stem cell to terminally differentiated cell
De-differentiation: reprogram terminally differentiated somatic cells to pluripotent stem cells
Trans-differentiation: direct conversion of one terminally differentiated cell to another