Classes of Transcription Factors and Functional Genomics

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Classes of Transcription Factors and Functional Genomics

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1.      Tfs are categorised based on their role in chromatin context

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genertal tf

general tf topics

Ex

Mechanism

Location

Function

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lineage specific factors

lineage specific facrtors topics

Function

Mechanism

Problem

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pioneer tfs

pioneer tfs topics

Example

Function

Mechanism

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1.      Identify regulatory regions

1.      Identify regulatory regions

topics

Use

Examples

Function

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1.      Histone modifications

1.      Histone modifications

topics

Function

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2.      Active enhancers

2.      Active enhancers

topics

Marked by

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3.      Poised enhancers

3.      Poised enhancers

topics

Def

Contain

General transcription factorsexample

(e.g., TFIID)

general tf

mech

form the pre-initiation complex

general tf location

at the TATA box

general tf func

global transcription.

Lineage-specific factors func

coordinate tissue-specific programs

lineage specific factors mech

by binding accessible chromatin.

lineage specific factors problem

much of the genome is initially inaccessible;

pioneer transcription factors example

(e.g., SOX2, PAX7)

pioneer tfs

func

have the unique ability to bind nucleosome-occupied DNA,

pioneer tfs

mech

recruiting remodelers to open chromatin for other factors.

To identify these regulatory regions, researchers use

functional genomics tools

identify reg regions

examples of tools

DNase I hypersensitive sites (DHSs) and ATAC-seq,

identify reg regions

func

map open, accessible regions of the genome.

specific histone modifications

function

mark the state of an enhancer:

Active enhancers are marked by

H3K27ac and H3K4me1,

Poised enhancers def

(ready for future activation)

poised enhancers contain

H3K27me3 and H3K4me1.