1) The document discusses the promoters, regulatory sequences, and transcription factors that control gene expression in eukaryotes. It describes the basic components of promoters like the TATA box and initiator elements.
2) It explains how the pre-initiation complex of RNA polymerase II and general transcription factors assembles at promoters. This includes the sequential binding of TBP, TFIIB, the Pol II-TFIIF complex, TFIIE, and TFIIH.
3) It covers different types of transcription factors that bind DNA, including zinc finger proteins, helix-turn-helix proteins, leucine zipper proteins, and discusses how they interact with DNA and each other to regulate transcription.
Transcription in eukaryotes: A brief view
Transcription is the process by which single stranded RNA is synthesized by double stranded DNA. Transcription in eukaryotes and prokaryotes has many similarities while at the same time both showing their individual characteristics due to the differences in organization. RNA Polymerase (RNAP or RNA Pol) is different in prokaryotes and eukaryotes. Coupled transcription is seen in prokaryotes but not in Eukaryotes. In eukaryotes the pre-RNA should be spliced first to be translated.
In Eukaryotic transcription, synthesis of RNA occurs in the 3’→5’ direction. The 3’ end is more reactive due to the hydroxide group. 5’ end containing phosphate groups meanwhile, is not very reactive when it comes to adding new nucleotides. In Eukaryotes, the whole genome is not transcribed at once. Only a part of the genome is transcribed which also acts as the first, principle stage of genetic regulation.
Eukaryotes have five nuclear polymerases:
• RNA Polymerase I: This produces rRNA (23S, 5.8S, and 18S) which are the major components in a ribosome. This also produces pre-rRNA in yeasts.
• RNA Polymerase II: Helps in the production of mRNA (messenger RNA), snRNA (small, nuclear RNA), miRNA. This is the most studied type and requires several transcription factors for its binding
• RNA Polymerase III: This synthesizes tRNA (transfer RNA), 5S rRNA and other small RNAs required in the cytosol and nucleus.
• RNA Polymerase IV: Synthesizes siRNA (small interfering RNA) in plants.
• RNA Polymerase V: This is the least studied polymerase and synthesizes siRNA-directed heterochromatin in plants.
Eukaryotic transcription can be broadly divided into 4 stages:
• Pre-Initiation
• Initiation
• Elongation
• Termination
Transcription is an elaborate process which cells use to copy the genetic information stored in DNA into RNA. This pre-RNA is modified into mRNA before being transcribed to proteins. Transcription is the first step to utilizing the genetic information in a cell. Both Eukaryotes and Prokaryotes employ this process with the basic phases remaining the same. However eukaryotic transcription is more complex indicating the changes transcription has undergone towards perfection during evolution.
Alternative splicing is a deviation from the conventional splicing as it removes introns in a different manner. It has a lot of significance in the development of diseases like cancers and in plants adapting to various stress conditions.
Eukaryotic transcription is the elaborate process that eukaryotic cells use to copy genetic information stored in DNA into units of transportable complementary RNA replica.
Transcription in eukaryotes: A brief view
Transcription is the process by which single stranded RNA is synthesized by double stranded DNA. Transcription in eukaryotes and prokaryotes has many similarities while at the same time both showing their individual characteristics due to the differences in organization. RNA Polymerase (RNAP or RNA Pol) is different in prokaryotes and eukaryotes. Coupled transcription is seen in prokaryotes but not in Eukaryotes. In eukaryotes the pre-RNA should be spliced first to be translated.
In Eukaryotic transcription, synthesis of RNA occurs in the 3’→5’ direction. The 3’ end is more reactive due to the hydroxide group. 5’ end containing phosphate groups meanwhile, is not very reactive when it comes to adding new nucleotides. In Eukaryotes, the whole genome is not transcribed at once. Only a part of the genome is transcribed which also acts as the first, principle stage of genetic regulation.
Eukaryotes have five nuclear polymerases:
• RNA Polymerase I: This produces rRNA (23S, 5.8S, and 18S) which are the major components in a ribosome. This also produces pre-rRNA in yeasts.
• RNA Polymerase II: Helps in the production of mRNA (messenger RNA), snRNA (small, nuclear RNA), miRNA. This is the most studied type and requires several transcription factors for its binding
• RNA Polymerase III: This synthesizes tRNA (transfer RNA), 5S rRNA and other small RNAs required in the cytosol and nucleus.
• RNA Polymerase IV: Synthesizes siRNA (small interfering RNA) in plants.
• RNA Polymerase V: This is the least studied polymerase and synthesizes siRNA-directed heterochromatin in plants.
Eukaryotic transcription can be broadly divided into 4 stages:
• Pre-Initiation
• Initiation
• Elongation
• Termination
Transcription is an elaborate process which cells use to copy the genetic information stored in DNA into RNA. This pre-RNA is modified into mRNA before being transcribed to proteins. Transcription is the first step to utilizing the genetic information in a cell. Both Eukaryotes and Prokaryotes employ this process with the basic phases remaining the same. However eukaryotic transcription is more complex indicating the changes transcription has undergone towards perfection during evolution.
Alternative splicing is a deviation from the conventional splicing as it removes introns in a different manner. It has a lot of significance in the development of diseases like cancers and in plants adapting to various stress conditions.
Eukaryotic transcription is the elaborate process that eukaryotic cells use to copy genetic information stored in DNA into units of transportable complementary RNA replica.
This presentation provides an overview of What is a transposon,different types of transposons, their mechanism of action, examples for each type of transposons, changes caused due to insertion of transposon into the target gene and applications of Transposons. They are controlling factors in gene expression. Jumping genes is a special area of interest in Genetic research.
RNAi is a powerful, conserved biological process through which the small, double-stranded RNAs specifically silence the expression of homologous genes, largely through degradation of their cognate mRNA.
Khaled El Masry, is an assistant Lecturer of Human Anatomy & Embryology, Mansoura University, Egypt. Great thanks to Prof. Dr Salwa Gawish, professor of Cytology & Histology, Mansoura University, for her great effort in explaining Genetics course.
RNA interference (RNAi) is a mechanism that inhibits gene expression at the stage of translation or by hindering the transcription of specific genes.
RNAi targets include RNA from viruses and transposons.
Basics of Undergraduate/university fellows
Transcription is more complicated in eukaryotes than in prokaryotes because
eukaryotes possess three different classes of RNA polymerases and because of the
way in which transcripts are processed to their functional forms.
More proteins and transcription factors are involved in eukaryotic transcription.
This presentation provides an overview of What is a transposon,different types of transposons, their mechanism of action, examples for each type of transposons, changes caused due to insertion of transposon into the target gene and applications of Transposons. They are controlling factors in gene expression. Jumping genes is a special area of interest in Genetic research.
RNAi is a powerful, conserved biological process through which the small, double-stranded RNAs specifically silence the expression of homologous genes, largely through degradation of their cognate mRNA.
Khaled El Masry, is an assistant Lecturer of Human Anatomy & Embryology, Mansoura University, Egypt. Great thanks to Prof. Dr Salwa Gawish, professor of Cytology & Histology, Mansoura University, for her great effort in explaining Genetics course.
RNA interference (RNAi) is a mechanism that inhibits gene expression at the stage of translation or by hindering the transcription of specific genes.
RNAi targets include RNA from viruses and transposons.
Basics of Undergraduate/university fellows
Transcription is more complicated in eukaryotes than in prokaryotes because
eukaryotes possess three different classes of RNA polymerases and because of the
way in which transcripts are processed to their functional forms.
More proteins and transcription factors are involved in eukaryotic transcription.
Transcription factors and their role in plant disease resistanceSachin Bhor
The transcription of DNA to make messenger RNA is highly controlled by the cell. For higher organisms (plant or animal) to function, genes must be turned on and off in coordinated groups in response to a variety of situations. For a plant this may be “abiotic” (non-living) stress such as the rising or setting sun, drought, or heat, “biotic” (living) stress such as insects, viral or bacterial infection, or any of a limitless number of other events.
The job of coordinating the function of groups of genes falls to proteins called transcription factors (TF’s). TFs are proteins that binds to specific sequence of DNA in promoter region and regulate transcription.
All eukaryotes have at least three different RNA polymerase (Pol I, II,and III; and plants have a Pol IV & a Pol V). In addition, whereas bacteria require only one additional initiation factor (σ), several initiation factors are required for efficient and promoter-specific initiation in eukaryotes. These are called the general transcription factors (GTFs)
Eukaryotic TranscriptionOverall, the process of RNA synthesis in e.pdfmohammadirfan136964
Eukaryotic Transcription
Overall, the process of RNA synthesis in eukaryotes is similar to that of prokaryotes. There are
some real differences, however. For one thing, initial transcripts in eukaryotes contain introns,
which must be removed after transcription (this will be examined later). Eukaryotes also have
three RNA polymerases, instead of just one. Each of these polymerases transcribes a different
class of genes, as outlined in the table below:
Our consideration of eukaryotic transcription will focus on genes transcribed by RNA
polymerase II (known as class II genes). As with prokaryotes, the transcription process can be
broken down into the steps of initiation, elongation, and termination. In eukaryotes, there is also
the additional step of RNA processing, which occurs during and after transcription.
Initiation
Initiation in eukaryotes is much more complex than it is in prokaryotes. Eukaryotic genes must
be much more carefully regulated, because many genes are only expressed in specific cells or
tissues at specific times in the organism\'s life. To achieve this careful regulation, eukaryotes
have evolved a more complicated initiation scheme than prokaryotes. In addition to promoters,
eukaryotic genes also have regulatory regions called enhancers. Both elements (promoter and
enhancer) are required for full, correct expression of eukaryotic genes. As a result of this added
complexity, eukaryotic RNA polymerases do not have anything equivalent to the sigma subunit
found in prokaryotic RNA polymerases. Instead, eukaryotes have groups of transcription factors,
which are proteins, independent of the RNA polymerases, that recognize promoter and enhancer
sequences.
Eukaryotic promoters, like prokaryotic promoters, contain conserved sequences that are
important for initiation. (Eukaryotes, because of their added complexity, tend to have more
conserved sequences in their promoters than do prokaryotes.) One important sequence in most
eukaryotic promoters is found around -30, and has the sequence TATAAA (or something close
to it). This promoter element, known as the TATA Box, is analogous to the -10 element in
prokaryotes. Other promoter sequences vary from gene to gene, but a common one is
GGCCAATCT, otherwise known as the CCAAT Box (for the central bases in the sequence),
which tends to occur around -80.
A group of basal transcription factors helps to initiate transcription of class II genes. Each
member of this group is named \"TFII\" for Transcription Factor, class II genes. The individual
factors are assigned a separate letter designation. For example, TFIID, a factor made of multiple
polypeptides, recognizes and binds to the TATA box. This factor and the other factors (TFIIA,
TFIIB, TFIIE, TFIIF, TFIIH, and TFIIJ) forms a complex on the DNA that recruits RNA
polymerase II to the promoter, and promotes initiation of transcription. These transcription
factors are sufficient to get a basal (minimal) level of transcription. Other transcription .
Synthetic Fiber Construction in lab .pptxPavel ( NSTU)
Synthetic fiber production is a fascinating and complex field that blends chemistry, engineering, and environmental science. By understanding these aspects, students can gain a comprehensive view of synthetic fiber production, its impact on society and the environment, and the potential for future innovations. Synthetic fibers play a crucial role in modern society, impacting various aspects of daily life, industry, and the environment. ynthetic fibers are integral to modern life, offering a range of benefits from cost-effectiveness and versatility to innovative applications and performance characteristics. While they pose environmental challenges, ongoing research and development aim to create more sustainable and eco-friendly alternatives. Understanding the importance of synthetic fibers helps in appreciating their role in the economy, industry, and daily life, while also emphasizing the need for sustainable practices and innovation.
June 3, 2024 Anti-Semitism Letter Sent to MIT President Kornbluth and MIT Cor...Levi Shapiro
Letter from the Congress of the United States regarding Anti-Semitism sent June 3rd to MIT President Sally Kornbluth, MIT Corp Chair, Mark Gorenberg
Dear Dr. Kornbluth and Mr. Gorenberg,
The US House of Representatives is deeply concerned by ongoing and pervasive acts of antisemitic
harassment and intimidation at the Massachusetts Institute of Technology (MIT). Failing to act decisively to ensure a safe learning environment for all students would be a grave dereliction of your responsibilities as President of MIT and Chair of the MIT Corporation.
This Congress will not stand idly by and allow an environment hostile to Jewish students to persist. The House believes that your institution is in violation of Title VI of the Civil Rights Act, and the inability or
unwillingness to rectify this violation through action requires accountability.
Postsecondary education is a unique opportunity for students to learn and have their ideas and beliefs challenged. However, universities receiving hundreds of millions of federal funds annually have denied
students that opportunity and have been hijacked to become venues for the promotion of terrorism, antisemitic harassment and intimidation, unlawful encampments, and in some cases, assaults and riots.
The House of Representatives will not countenance the use of federal funds to indoctrinate students into hateful, antisemitic, anti-American supporters of terrorism. Investigations into campus antisemitism by the Committee on Education and the Workforce and the Committee on Ways and Means have been expanded into a Congress-wide probe across all relevant jurisdictions to address this national crisis. The undersigned Committees will conduct oversight into the use of federal funds at MIT and its learning environment under authorities granted to each Committee.
• The Committee on Education and the Workforce has been investigating your institution since December 7, 2023. The Committee has broad jurisdiction over postsecondary education, including its compliance with Title VI of the Civil Rights Act, campus safety concerns over disruptions to the learning environment, and the awarding of federal student aid under the Higher Education Act.
• The Committee on Oversight and Accountability is investigating the sources of funding and other support flowing to groups espousing pro-Hamas propaganda and engaged in antisemitic harassment and intimidation of students. The Committee on Oversight and Accountability is the principal oversight committee of the US House of Representatives and has broad authority to investigate “any matter” at “any time” under House Rule X.
• The Committee on Ways and Means has been investigating several universities since November 15, 2023, when the Committee held a hearing entitled From Ivory Towers to Dark Corners: Investigating the Nexus Between Antisemitism, Tax-Exempt Universities, and Terror Financing. The Committee followed the hearing with letters to those institutions on January 10, 202
How to Make a Field invisible in Odoo 17Celine George
It is possible to hide or invisible some fields in odoo. Commonly using “invisible” attribute in the field definition to invisible the fields. This slide will show how to make a field invisible in odoo 17.
Francesca Gottschalk - How can education support child empowerment.pptxEduSkills OECD
Francesca Gottschalk from the OECD’s Centre for Educational Research and Innovation presents at the Ask an Expert Webinar: How can education support child empowerment?
Introduction to AI for Nonprofits with Tapp NetworkTechSoup
Dive into the world of AI! Experts Jon Hill and Tareq Monaur will guide you through AI's role in enhancing nonprofit websites and basic marketing strategies, making it easy to understand and apply.
Biological screening of herbal drugs: Introduction and Need for
Phyto-Pharmacological Screening, New Strategies for evaluating
Natural Products, In vitro evaluation techniques for Antioxidants, Antimicrobial and Anticancer drugs. In vivo evaluation techniques
for Anti-inflammatory, Antiulcer, Anticancer, Wound healing, Antidiabetic, Hepatoprotective, Cardio protective, Diuretics and
Antifertility, Toxicity studies as per OECD guidelines
Read| The latest issue of The Challenger is here! We are thrilled to announce that our school paper has qualified for the NATIONAL SCHOOLS PRESS CONFERENCE (NSPC) 2024. Thank you for your unwavering support and trust. Dive into the stories that made us stand out!
The Roman Empire A Historical Colossus.pdfkaushalkr1407
The Roman Empire, a vast and enduring power, stands as one of history's most remarkable civilizations, leaving an indelible imprint on the world. It emerged from the Roman Republic, transitioning into an imperial powerhouse under the leadership of Augustus Caesar in 27 BCE. This transformation marked the beginning of an era defined by unprecedented territorial expansion, architectural marvels, and profound cultural influence.
The empire's roots lie in the city of Rome, founded, according to legend, by Romulus in 753 BCE. Over centuries, Rome evolved from a small settlement to a formidable republic, characterized by a complex political system with elected officials and checks on power. However, internal strife, class conflicts, and military ambitions paved the way for the end of the Republic. Julius Caesar’s dictatorship and subsequent assassination in 44 BCE created a power vacuum, leading to a civil war. Octavian, later Augustus, emerged victorious, heralding the Roman Empire’s birth.
Under Augustus, the empire experienced the Pax Romana, a 200-year period of relative peace and stability. Augustus reformed the military, established efficient administrative systems, and initiated grand construction projects. The empire's borders expanded, encompassing territories from Britain to Egypt and from Spain to the Euphrates. Roman legions, renowned for their discipline and engineering prowess, secured and maintained these vast territories, building roads, fortifications, and cities that facilitated control and integration.
The Roman Empire’s society was hierarchical, with a rigid class system. At the top were the patricians, wealthy elites who held significant political power. Below them were the plebeians, free citizens with limited political influence, and the vast numbers of slaves who formed the backbone of the economy. The family unit was central, governed by the paterfamilias, the male head who held absolute authority.
Culturally, the Romans were eclectic, absorbing and adapting elements from the civilizations they encountered, particularly the Greeks. Roman art, literature, and philosophy reflected this synthesis, creating a rich cultural tapestry. Latin, the Roman language, became the lingua franca of the Western world, influencing numerous modern languages.
Roman architecture and engineering achievements were monumental. They perfected the arch, vault, and dome, constructing enduring structures like the Colosseum, Pantheon, and aqueducts. These engineering marvels not only showcased Roman ingenuity but also served practical purposes, from public entertainment to water supply.
Operation “Blue Star” is the only event in the history of Independent India where the state went into war with its own people. Even after about 40 years it is not clear if it was culmination of states anger over people of the region, a political game of power or start of dictatorial chapter in the democratic setup.
The people of Punjab felt alienated from main stream due to denial of their just demands during a long democratic struggle since independence. As it happen all over the word, it led to militant struggle with great loss of lives of military, police and civilian personnel. Killing of Indira Gandhi and massacre of innocent Sikhs in Delhi and other India cities was also associated with this movement.
1. Chap. 7 Transcriptional Control of Gene
Expression (Part B)
Topics
• RNA Polymerase II Promoters and General Transcription
Factors
• Regulatory Sequences in Protein-coding Genes and the Proteins
Through Which They Function
Goals
• Learn about transcription
control elements and methods
of promoter analysis.
• Learn how the RNA
polymerase II pre-initiation
complex assembles at a
promoter.
• Learn about the structures of
eukaryotic transcription
factors.
Transcriptionally active polytene
chromosomes
2. Overview of Eukaryotic Promoters
The promoter of a eukaryotic gene can be defined as a sequence
that sets the transcription start site for RNA polymerase. Strong
RNA Pol II promoters contain an A/T rich sequence known as the
TATA box located 26-31 bp upstream of the start site (Fig.
7.14). Other genes have alternative sequence elements known as
initiators (Inr) which also serve as promoters that set the RNA Pol
II start site. Finally, CG-rich repeat sequences (CpG islands) are
used by RNA Pol II as promoters in 60-70% of genes. Most of
these genes are weakly expressed.
3. Transcription Initiation by RNA Pol II
RNA Pol II requires general TFs in addition to tissue-specific
transcription factors for transcription of most genes in vivo.
General TFs position RNA Pol II at start sites and assist the
enzyme in melting promoter DNA. General TFs are highly
conserved across species. The general TFs used at TATA box
promoters are TFIIA, B, D, etc. TFIIA is required for
transcription only in vivo. TFIID consists of TBP (TATA box
binding protein) and 13 TBP-associated factors (TAFs). While
the complete TFIID complex is required for transcription in
vivo, only TBP is required in vitro. Formation of the pre-
initiation complex in vitro is illustrated in the next two slides
(Fig. 7.17).
4. Pol II Pre-initiation Complex Formation (I)
The sequential steps leading to
the assembly of the RNA Pol
II pre-initiation complex in
vitro are shown in Fig. 7.17.
First, TBP binds to the TATA
box and bends DNA near the
promoter. Next, TFIIB binds,
and then a complex between
Pol II and TFIIF loads onto
the promoter. TFIIF positions
the Pol II active site at the
mRNA start site. TFIIF also
possesses histone acetylase
activity and helps maintain
chromatin at the promoter in
an uncondensed state. TFIIE
then binds creating a TFIIH
docking site (next slide).
5. Pol II Pre-initiation Complex Formation (II)
With the addition of TFIIH,
the assembly of the pre-
initiation complex is complete.
Subsequently, one subunit of
TFIIH melts DNA at the
promoter, obtaining energy by
ATP hydrolysis. Pol II then
begins transcribing the
mRNA. Another subunit of
TFIIH phosphorylates the Pol
II CTD, making Pol II highly
processive. In vitro, all
factors except TBP dissociate
from the promoter region
after Pol II moves
downstream. Tissue-specific
TFs bound to enhancers and
promoter-proximal elements
also play important roles in
transcription initiation in vivo.
6. Linker Scanning Mutagenesis Analysis of
Gene Regulatory Sites
A technique called linker
scanning mutagenesis
commonly is used to
identify transcription
control regions known as
promoter-proximal
elements that lie within
100-200 bp of a start
site Fig. 7.21. These
elements are required for
transcription but are not
directly involved in start
site selection. Large
changes in the locations of
these elements can
interfere with
transcription. Promoter-
proximal elements are
commonly important for
cell type-specific
transcription of genes.
7. Summary of Gene Control Elements
A spectrum of control elements regulate transcription by RNA Pol
II in eukaryotes. Their locations relative to the exons of a gene
are summarized in Fig. 7.22. Enhancers are transcription control
elements of 50-200 bp in length that can act from sites distant
from the regulated gene. They often are important for cell type-
specific regulation of transcription. Enhancers can be positioned
upstream, downstream, or even within introns while still being
functional. They further may be located 50 kb away from a
transcription start site. Enhancers are composed of ~6-10 bp
DNA modules that are bound by transcription factors. Promoter-
proximal elements typically need to be with ~200 bp of the
transcription start site to be functional. Yeast genes usually
contain only upstream activating sequences (UAS) and a TATA box
for control of transcription. UASs act similarly to enhancers and
promoter-proximal elements in higher eukaryotes.
8. DNase I Footprinting
The human genome encodes ~2,000 transcription factors (TFs). A
method (DNase I footprinting) for determining locations of TF
binding sites in DNA is shown in Fig. 7.23. First, DNA labeled on
one strand is incubated with the protein of interest. Then the
complex is treated with a small amount of DNase I, which cleaves
DNA where it is not masked by the TF (Fig. 7.23a). A control
DNA sample lacking the TF is treated under parallel conditions.
Finally, the banding patterns from the two samples are compared
by gel electrophoresis to locate the "footprint" region where the
TF has shielded the DNA from cleavage (Fig. 7.23b).
9. Analysis of TF Activity in vivo
TFs can be assayed for their
ability to bind to DNA control
elements and regulate gene
expression by in vivo
transfection assays (Fig.
7.25). In this method, a
plasmid encoding the putative
TF (protein X) is introduced
into an animal cell along with
a second vector encoding a
reporter gene and the
putative protein X binding
site. If protein X binds to
the site and is a transcription
activator, then the reporter
gene is switched on. Note
that the cells must not
express protein X per se.
10. Modular Structure of Activators I
Transcription
activators are modular
proteins composed of
distinct functional
domains. They typically
contain both DNA-
binding and activation
domains. A deletion
analysis performed
with the yeast GAL4
activator illustrating
that it contains these
two types of domains is
shown in Fig. 7.26.
The N-terminal amino
acids of GAL4
modulate DNA binding,
whereas its C-terminal
region contains an
activation domain.
11. Modular Structure of Activators II
Functional domains in activators are joined by flexible protein linker
sequences (Fig. 7.27). Due to the presence of linkers, the spacing
and location of DNA control elements often can be shifted without
interfering with DNA binding and regulation of promoters. The
evolution of gene control regions through shuffling of DNA binding
sequences between genes may have been favored due to the lack of
strong requirements for control element spacing and location. The
evolution of new activator protein genes through domain swapping
has probably also been facilitated by linker sequences.
Note, that transcription of some genes is controlled by repressors.
Repressors typically contain a DNA-binding domain and a repression
domain. The repression domain interacts with other TFs at a control
site, inhibiting their activity. The inactivation of a repressor can
lead to constitutive expression of the gene it controls.
12. Secondary Structure Motifs
Secondary structure motifs are evolutionarily conserved
collections of secondary structure elements which have a defined
conformation. They also have a consensus sequence because the
aa sequence ultimately determines structure. A given motif can
occur in a number of proteins where it carries out the same or
similar functions. Some well known examples such as the coiled-
coil, EF hand/helix-loop-helix, and zinc-finger motifs are
illustrated in Fig. 3.9. These motifs typically mediate protein-
protein association, calcium/DNA binding, and DNA or RNA
binding, respectively.
13. Helix-turn-helix TFs
DNA-binding proteins bind
specifically to DNA via non-
covalent interactions. a-
helices are one of the most
common types of DNA-
binding sequences (Fig.
7.28). The side-chains of
residues within the a-helix
often bind to the surfaces
of bases exposed in the
major groove of double-
helical DNA. Binding to
phosphates and bases in the
minor groove typically is less
important. One of the most
common DNA-binding
structure motifs is the
helix-turn-helix.The second
helix in this motif (the DNA
recognition helix) typically
binds to a specific sequence of bases in DNA. The recognition
helices in the dimeric bacteriophage 434 repressor are
indicated with asterisks in Fig. 7.28a. Helix-turn-helix TFs
are common in bacteria.
14. Zinc-finger TFs
The most common DNA-
binding motif in human and
multicellular animal TFs is the
zinc finger. Two types of zinc
finger TFs are discussed
here--C2H2 zinc finger TFs
(Fig. 7.29a) and C4 zinc
finger TFs (Fig. 7.29b). Most
TFs that contain C2H2 zinc
fingers are monomeric. Its 2
cysteine and 2 histidine
residues bind to zinc ions
(Zn2+) (Fig. 7.29a), and the
a-helix containing the 2
histidines binds to bases in
the major groove. Much less
common are TFs containing C4 zinc fingers. Most TFs containing
this motif are dimeric. Nuclear receptors, which bind steroid
hormones and other compounds, contain this motif. The
glucocorticoid receptor is shown in Fig. 7.29b. Zinc ions are
bound to the DNA recognition helix of this motif, which contacts
bases in the major groove.
15. Leucine-zipper TFs
Leucine-zipper TFs contain extended a-helices wherein every 7th
amino acid is leucine. This periodicity creates a nonpolar face on
one side of the helix that is ideal for dimerization with another
such protein via a coiled-coil motif (Fig. 7.29c). So-called basic
zipper (bZip) TFs have a similar structure except that some
leucines are replaced by other nonpolar amino acids. The N-
terminal ends of both leucine-zipper and bZip proteins contain
basic amino acids that interact with bases in the major groove
(Fig. 7.29c). Leucine zipper proteins are now considered to be a
subclass of bZip proteins.
Another class of TF, the
basic helix-loop-helix (bHLH)
proteins are similar to bZip
proteins, but contain a loop
between the DNA recognition
helix and the coiled-coil
region (Fig. 7.29d). bZip and
bHLH proteins commonly
form heterodimeric TFs.
Basic residues
16. Regulation of TF Activity
Many TFs bind ligands or co-activator/co-repressor proteins that
modulate their structure and activity. In the yeast GAL4 TF, its
"acidic activation domain" adopts an essentially random-coil
structure until it binds to a co-activator protein. This control
mechanism keeps the TF turned off until the appropriate cofactor
is present in the nucleus. Nuclear receptors such as the estrogen
receptor contain partially structured activation domains that
undergo conformational changes to the active structural state on
binding to hormone (e.g., estrogen) (Fig. 7.30b). In the active
conformation, the estrogen receptor can bind to co-activator
proteins required for transcription. The estrogen antagonist,
tamoxifen, that is used in breast cancer therapy, locks the
receptor in its inactive conformation that cannot bind co-activator
proteins (Fig. 7.30c).
17. Heterodimeric TFs
The formation of heterodimeric
TFs by bZip and bHLH TFs is
important in increasing the
complexity of transcriptional
regulation of genes. Sometimes
monomers within the
heterodimer recognize the same
DNA element, but have
different activation domains
(Fig. 7.31a). Different
regulatory responses result from
the different combinations of
activation domains bound to the
site. In other cases, monomers
within the heterodimer bind
different DNA elements (Fig.
7.31b). Each site then binds a
unique species of heterodimer.
Lastly, an inhibitory factor that
binds to only one type of
monomer will only affect sites
used by that monomer (Fig.
7.31c).
18. Cooperative Binding of TFs to DNA
In many cases, a TF will bind to a DNA element with high
affinity only when complexed with a second TF (Fig. 7.32a).
Such cooperative binding to DNA adds further complexity to
gene regulation. Namely, a certain TF will bind to its DNA
element only if its interacting partner also is expressed in that
cell type. In addition, expression levels of interacting TFs can
be varied between tissues to adjust gene transcription rates.
19. Multiprotein Complexes at Enhancers
Enhancers typically contain several DNA sequence elements that
are recognized by different DNA binding proteins (e.g., the ß-
interferon enhancer, Fig. 7.33). The resulting nucleoprotein
complex is called an enhanceosome. Enhancers often are involved
in tissue-specific control of transcription. Given the complex
structures of enhanceosomes, it is easy to see how the absence
of even one of the factors that bind to the enhancer in a certain
tissue could change the expression level of the gene.