definition of human transcriptional regultory element

1. Transcriptional Regulatory Elements
by: amirhossein heydarian

2. Introduction
The completion of the human genome sequence led to the
cataloging of∼20,000–25,000 protein-coding genes
And key question is how these genes and their products
function??

3. introduction
To understand the molecular mechanisms that govern
specific expression patterns it is important to identify the
transcriptional regulatory elements
Here we review the various classes of transcriptional
regulatory elements and the current understanding of how
they function.

4. Transcriptional regulation
One of the mechanisms through which protein levels in the
cell are controlled is through transcriptional regulation.
Certain regions, called cis-regulatory elements, on the
DNA are footprints for the transacting proteins involved in
transcription, either for the positioning of the basic
transcriptional machinery or for the regulation

5. Basic transcriptional machinery
DNA-dependent RNA polymerase (RNAP) which
synthesizes various types of RNA
core promoters on the DNA are used to position the RNAP
other nearby regions will regulate the transcription:
proximal promoter regions, enhancers, silencers, and
insulators

6. Transcriptional Machinery
Factors involved in the accurate transcription of eukaryotic
protein-coding genes by RNA polymerase II can be classified into
three groups:
I. general (or basic) transcription factors (GTFs)
II. promoter-specific activator proteins (activators)
III. coactivators

7. GTFs
GTFs assemble on the core promoter in order to form a
transcription preinitiation complex (PIC) ,which directs RNA
polymerase II to the transcription start site (TSS).

8. Activators
In general, activators are sequence-specific DNA-binding
proteins whose recognition sites are usually present in
sequences upstream of the core promoter
Examples of activator families:
 Cysteine rich zinc finger
 helix-loop-helix (HLH)
 basic leucine zipper (bZIP)
 DNA binding domain
The activity of an activator may be modulated by coactivators

9. Activators

10. Coactivators
coactivators stimulating PIC assembly or modifying
chromatin.
in a cell can play a major role in determining the
regulatory response, as they can modify an activator’s
ability to positively or negatively regulate transcription

11. Eukaryotic transcription regulation
The expression of eukaryotic protein-coding genes (also
called class II or structural genes) can be regulated at several
steps, including:
 transcription initiation most regulation
 Elongation
 mRNA processing
 Transport
 translation,

12. Cis-acting transcriptional regulatory
elements
Genes transcribed by RNA polymerase II typically contain two
distinct families of cis-acting transcriptional regulatory elements:
 promoter
 distal regulatory element
These cis-acting transcriptional regulatory elements contain
recognition sites For trans-acting DNA-binding transcription
factors, which function either to enhance or repress transcription

13. Transcriptional regulatory elements
 promoter:
 Core Promoter
 Proximal Promoter Elements
 distal regulatory elements:
 Enhancers
 Silencers
 Insulators
 Locus Control Regions (LCR)

14. Transcriptional regulatory elements

15. Transcriptional regulatory elements

16. Promoter
promoter is a region of DNA that initiates transcription of
a particular gene
Promoters are located near the transcription start sites of
genes.
Promoters can be about 100–1000 base pairs long.

17. promoter
a promoter, which is composed of a core promoter and nearby
(proximal) regulatory elements

18. The core promoter is the region at the start of basic transcriptional
machinery and PIC assembly, and defines the position of the TSS.
The core promoter usually refers to the region from the transcription
start site including the TATA box, which resides approximately 30 bp
upstream of the transcriptionn initiation site.
The core promoter is a region around the TSS (+1) of a gene, which
contains several DNA elements that facilitate the binding of regulatory
proteins.
Core promoter definition

19. PIC :
Binding of
regulatory proteins is
required formation of
the PIC
(pre-initiation
complex).

20. Core Promoter
Metazoan core promoters are composed of:
TATA box The first described core promoter element
Initiator element (Inr) the most common element
Downstream Promoter Element (DPE)
Downstream Core Element (DCE)
TFIIB-Recognition Element (BRE)
Motif Ten Element (MTE).

21. Core Promoter

22. Core promoter
core promoters are diverse in their content and
organization.
it is clear that PIC assembly does not depend on a single
nucleation point, such as a TATA box; rather, many of the
core promoter elements interact with TFIID and stabilize
PIC assembly

23. Core Promoter

24. Proximal Promoter Elements
In Metazon, several other promoter elements exist which
are located upstream of the core promoter:
the proximal promoter elements
The proximal promoter is defined as the region
immediately upstream (up to a few hundred base pairs) from
the core promoter, and typically contains multiple binding
sites for activators.

25. Proximal Promoter Elements function
An interesting feature of∼60% of human genes is that their
promoter falls near a CpG island
DNA methylation is associated with transcriptional silencing.
Methylation at CpG dinucleotides is believed to repress
transcription by blocking the ability of transcription factors to
bind their recognition sequences
The refractory nature of CpG islands to methylation suggests
that a role for proximal promoter elements may be to block the
local region from being methylated, and therefore inappropriately
silenced.

26. Distal regulatory elements
Including:
 enhancers
 silencers
 Insulators
 locus control regions (LCR)

27. Distal regulatory elements

28. Enhancers
enhancer is a short (50-1500 bp) region of DNA that can be
bound with proteins (activators) to activate transcription of a
gene or genes.
These proteins are usually referred to as transcription factors

29. Enhancers
Enhancers were characterised almost 20 years ago.
Enhancers are typically composed of a cluster of TFBSs
that work cooperatively to enhance transcription and The
transcription factors that bind to enhancers are called
transcriptional activators

30. Enhancers location
These enhancer regions can be found:
 up- and downstream of the TSS
 within exons or introns
 in the 5 and 3 untranslated (UTR) regions of genes
and even as far as 10,000 bp in Drosophilaor 100,000 bp in
human and mouse away from the gene boundaries

31. Enhancers
enhancer activation often needs the binding of several
transcription factors to cis-regulatory motifs to the enhancer.
Looping in chromatin plays a role in bringing enhancers
physically close to the proximal or core promoter region of a
target gene.
Once active, the enhancer can bind to the PIC or to
tethering elements in the proximal region of the promoter
and influence (the rate of) transcription by itself.

32. Enhancers

33. Silencers
Silencer is a DNA sequence capable of binding
transcription regulation factors, called repressors.
Silencers are sequence-specific elements that confer a
negative effect on the transcription of a target gene
Typically, they function independently of orientation and
distance from the promoter, although some position-
dependent silencers have been encountered.

34. Silencers location
They can be situated as as part of a proximal promoter, as
part of a distal enhancer and they can be located far from
their target gene, in its intron, or in its 3-untranslated region.

35. Silencers
Two distinct classes of silencers exist:
position-independent motifs that via their bound TF
(repressors) proteins actively interfere with the PIC assembly
are called silencer elements and are normally found upstream
of the TSS
position-dependent silencers or negative regulatory
elements (NREs) that passively prevent the binding of TFs to
their respective cis-regulatory motifs and can be found both
up- and downstream of the TSS and within introns and exons

36. Silencers
silencers may cooperate in binding to DNA, and they can
act synergistically.
Silencers are binding sites for negative transcription factors
called repressors.
Repressor function can require the recruitment of negative
cofactors, also called corepressors, and in some cases, an
activator can switch to a repressor by differential cofactor
Recruitment.

37. Models for repressor function:
 Blocking the binding of a nearby activator, or by directly
competing for the same site.
 prevent activators and/or GTFs from accessing a promoter
by establishing a repressive chromatin structure through
the recruitment of histone-modifying activities or
chromatin-stabilizing factors.
 block transcription activation by inhibiting PIC assembly

38. Insulators
Insulators function to block genes from being affected by
the transcriptional activity of neighboring genes.
They can block such interactions such as block enhancer-
promoter
It is thought that an insulator must reside between the
enhancer and promoter to inhibit their subsequent
interactions.

39. Insulators
Two distinct types of insulators have been discovered:
I. barrier insulators
II. enhancer-blocking insulators

40. Barrier insulators
Barrier insulators safeguard against the spread of
heterochromatin, and thus of chromatin-mediated
silencing, and lie on the border of heterochromatin
domains.

41. enhancer-blocking insulators
The enhancer-blocking insulators protect against gene
activation by enhancers and interfere with the enhancer–
promoter interaction only if the insulator is located
between the enhancer and the promoter.

42. Insulators

43. Insulators

44. Locus Control Regions
The LCR was identified over 20 years ago in studies of
transgenic mice.
These studies determined that the LCR was required for
normal regulation of beta-globin gene expression

45. regulation of beta-globin gene
expression

46. Locus Control Regions
Locus control regions (LCRs) are groups of regulatory
elements involved in regulating an entire locus or gene
cluster.
LCRs are typically composed of multiple cis-acting
elements, including enhancers, silencers, insulators, and
nuclear-matrix or chromosome scaffoldattachment regions.

47. Locus Control Regions
These elements are bound by transcription factors
coactivators, repressors, and/or chromatin modifiers.
Each of the components differentially affects gene
expression, and it is their collective activity that functionally
defines an LCR and confers proper spatial/temporal gene
expression.

48. Locus Control Regions
LCRs are often marked by a cluster of nearby DNase I
hypersensitive sites and are thought to provide an open-
chromatin domain for genes to which they are linked.

49. Locus Control Regions location
Although LCRs are typically located upstream of their
target gene(s), they can also be found within:
 intron of the gene they regulate, exemplified by the
human adenosine deaminase LCR
 downstream of the gene, as in the case of
the CD2 or Th2 LCR
 in the intron of a neighboring gene, as occurs
with the CD4 LCR

50. Transcriptional regulatory elements
involved in human diseases

51. Transcriptional regulatory elements
involved in human diseases

52. Transcriptional machinery components
involved in human diseases