W6L1

Question 1

what are cell really?

Answer 1

A cell is a collection of molecules that cannot avoid interacting with one another
* Competing for resources
* Dependency on each other
* Physical proximity
* Somehow this process works.

Question 2

complexity of cell example: ecoli

Answer 2

-E.coli have 4400 genes, % of them are transcribed by RNApol at anypoint in time
-replication 40 base persecond, mistake 1/100000
-ribosome transcribe in 24 second
-average cell contain 3x10^6 protein

Question 3

How do we define fuction (not examable)

Answer 3

-a discrete genome segment that encodes a defined product or displays a reproducible biochemical signature (dna binding, protein binding or a specific chromatin structure)

Question 4

Genome-wide characterization of TF activity in ENCODE

Answer 4

• Original ENCODE paper generated 1640 genome- wide datasets across 147 cell types, primarily TF ChIP-seq
• Find that groups of TFs colocalise to particular genetic regions
• Some of this is purposeful e.g. the transcription initiation machinery has many moving parts that need to come together

Question 5

How do we know the sequences TFs bind and how is this motif found

Answer 5

• Most TFs have a preferred DNA sequence (a “motif”) they bind best, determined by their DNA binding domain
• Motif discovery in ChIP-seq peaks is one way to discover this sequence

Question 6

TF specificity

Answer 6

-specificity are rare, like to bind to the same thing
- no real distinct binding site
-TF can also bind to secondary motif (not picky)

Question 7

Exploring histone mark redundancy

Answer 7

• Profiled multiple histone modifications across 127 human cell types, alongside whole genome sequences, RNA-seq, DNA-methylation and other
• ChromHMM identifies 15 distinct chromatin states in the Roadmap Epigenomics data (these are robust across samples and studies and species)
  -chromatin state can define cell-type specificity better than other

Question 8

DNA and the nucleus 3D structure

Answer 8

• there are specific area for each chromosome in the nucleus
  -exist chromosome territory
• the chromosome state are reproducible

Question 9

Topologically Active Domains

Answer 9

• Chromosomes are further segmented into Topologically Active Domains (TADs), nuclear lamina prevent expression
• 1MB on average, contain multiple genes and their regulatory environment
• High correlation of transcriptional state within a TAD

Question 10

What’s happening inside TADs

Answer 10

• Chromatin-chromatin interactions are structured in a fractal fashion
• And the transcription factor CTCF seems to be involved in most of them
  -between TADs, there are CTCF loops that prevent transcription between TADs

Question 11

The regulatory landscape of a single gene

Answer 11

Successful regulation entails interactions between multiple regulatory mechanisms that operate at different scales.
* Ultimately all of these mechanisms depend on small chemical molecules interacting with each other at the right time in the right place
* This stochasticity creates a need for redundancy in gene regulation
* No single gene regulatory mechanism is both robust enough and flexible enough to account for constraint and mutation at the same time
* Complexity in regulation emerges from the need for interaction between multiple mechanisms