The document summarizes transcriptional regulation in eukaryotes. It discusses the basic transcriptional machinery including RNA polymerase and general transcription factors. It describes various cis-regulatory elements like promoters, enhancers, silencers, insulators, and locus control regions. Promoters have core and proximal regions while distal elements regulate from farther distances. Transcription factors like activators and coactivators stimulate transcription while repressors and corepressors inhibit it. Precise transcriptional control is important for cell differentiation and proper gene expression.

1. Cell Biology Presentation

2. How does the exact same genome makes so
many different types of cells and products?

4. Basics of Transcriptional Regulation

5. INTRODUCTION
 One of the mechanism through which proteins levels
in the cell is controlled 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.

6. Basic transcriptional machinery
DNA-Dependent RNA Polymerase (RNAP) which
synthesizes various types of RNA
Core promoters on the DNA are used to position in
the RNAP.
Other nearby regions will regulate the transcription
proximal promoter regions, enhancers, silencers, and
insulators .

7. Transcriptional Machinery
Factors involved in the accurate transcription of
eukaryotic protein-coding genes by RNA polymerase II
can be classified into three groups.
 General or basic transcription factors (GTFs)
 Promoter specific active proteins (activators)
 Coactivators / Mediators

8. GTFs
 GTFs are multisubunit protein complexes
 Involved in:
 core promoter recognition,
 fundamental nucleation of the RNAPII transcriptional
PIC.
 the initiation of transcription.
 GTFs (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH) are
conserved in all eukaryotes including plants.

9. Source: Lauberth
A model of how TFIID subunits
interact with CPEs to facilitate PIC
formation.
TBP, TAF1, and TAF6 interact with
TATA, INR, and DPE of CPEs,
respectively. TAF1 and TAF3 also
interact with acetylated histone
H3 (yellow marks) and
trimethylated histone H3
(H3K4me3, red asterisks) as well
as enhancing recruitment of TFIID
and RNAPII.

10. 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

11. Activators

12. 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.

13. 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

14. 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.

15. Transcriptional regulatory elements
 Promoter:
 Core Promoter
 Proximal Promoter Elements
 Distal regulatory elements:
 Enhancers
 Silencers
 Insulators
 Locus Control Regions (LCR)

16. Transcription Regulatory Elements

17. 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

18. Core Promoter
 The core promoter is the region at the start of basic
transcriptional machinery and PIC assembly, and
defines the position of the TSS.
 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.
 Is a region around the TSS of a gene, which
contains several DNA elements that facilitate the
binding of regulatory proteins.

19. Pre Initiation
Complex:
Binding of
regulatory proteins
is required for the
formation of the
PIC.

20. Composition of 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. 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.

22. Proximal Promoter Elements
 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.

23. Distal regulatory
elements
Includes:
• enhancers
• silencers
• Insulators
• locus control
regions (LCR)

24. Enhancers and Silencers
 The first that was described was an enhancer sequence.
 Enhancers have the ability to greatly increase the expression
of genes in their vicinity.
 More recently, elements have been identified that decrease
transcription of neighboring genes, and these elements have
been called silencers.
 Extensive analysis of enhancers have detected several
features.
 First, these elements are functional over a large distance.
 For example, an enhancer has been placed 3000 nt from the
gene, and it can still increase expression.
 Second, these elements are orientation independent. This means
that the element can been be inverted, and it will still affect gene
expression.

25. Enhancers examples
 Enhancers are often associated with a gene that is
abundantly expressed.
 Examples:
 immunoglobulin genes
 genes that encode antibodies
Burkitt's lymphoma results from a translocation that puts the
oncogene c-myc in the vicinity of the enhancer. This possibly leads to
the over expression of the gene and causes the resulting cancer.

26. 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 Drosophila or
100,000 bp in human and mouse away from the gene
boundaries).

27. Silencer
 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.

28. Silencer 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.

29. 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.

30. Repressor
 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.

31. 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.

32. Types of insulators
 Two distinct types of insulators have been
discovered:
 I. barrier insulators
 II. enhancer-blocking

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

34. 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.

36. Locus Control Regions
 Locus control regions (LCRs) are operationally defined
by their ability to enhance the expression of linked genes
to physiological levels in a tissue-specific and copy
number–dependent manner at ectopic chromatin sites.
 The components of an LCR commonly co-localize to
sites of DNAse I hypersensitivity (HS) in the chromatin of
expressing cells.
 The core determinants at individual HSs are composed of
arrays of multiple ubiquitous and lineage-specific
transcription factor–binding sites.

37. LCRs
 The LCR was first identified in the human β-globin locus.
 The most prominent property of the LCRs is their
 strong,
 transcription-enhancing activity.
 The β-globin LCR is located 6 to 22 kb 5′ to the first (embryonic) globin gene in the
locus.
 It consists of 5 DNAse I–hypersensitive sites, 5′HSs 1 to 5. HSs 1 to 4 are formed
only in erythroid cells, while 5′HS5 is found in multiple lineages of cells, but it is not
constitutive.
 When the LCR is absent, transcription of the human β-globin gene is usually less than
1% of the endogenous murine β-globin mRNA in transgenic mice, if it is expressed at
all.
 Inclusion of the LCR increases β-globin gene expression to a level comparable to that
of the mouse β-globin genes in all transgenic animals, indicating that the LCR has
strong enhancer activity. LCR enhancer activity is also significant at its endogenous
location.
 These deletions in the native chromosomes of mouse or human cell lines severely
reduce the expression of globin genes.

38. Regulation
of beta globin gene
expression.

39. LCRs
 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.
 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.

40. LCRs 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

41. Recent findings related
to Transcription
Regulation
Source :
THE ROYAL SOCIETY
PUBLISHING
https://royalsocietypublishing.org/
doi/10.1098/rsob.190183#d3e1161
 Differences in the gut microbiota composition can affect energy
metabolism.
 E. coli may be beneficial to the human body and can also be
harmful. This depends mainly on the role of E. coli and its
transcription products in the human body.
 Transcriptional expression products of cells and organelles can
affect the growth, development, maturation and senescence of an
organism.
 For example, Msn2/4 protein produced by mitochondria can
affect ageing of the body;
 Kepulu transcription factor can maintain the autophagy ability of
cells. The Beat-1 enzyme and H3K4me3 enzyme can affect certain
metabolic processes in the body.
 Signalling pathways can also regulate the physical activity of
certain model organisms, such as ERK and JNK signalling
pathways.
 There are some transcription factors that can even affect the
function of the immune system.
 For example, the transcription factors Blimp and Hobit can
affect the development of T cells, which in turn affects the
body's ability to resist infection.
 Thus, transcriptional regulation plays a very important role in life
activities.

42. References
 Science Direct
(https://www.sciencedirect.com/topics/medicine-
and-dentistry/transcription-factor)
 NCBI/NIH(https://www.ncbi.nlm.nih.gov/pmc/article
s/PMC2811695/ )
 https://www.ndsu.edu/pubweb/~mcclean/plsc431/gen
eexpress/eukaryex4.html

43. Submitted To,
Dr. Kannan
Dr. Gopal
SBT
Madurai Kamraj University
Submitted By
Amreen Khan
MSc sem 1