Activators bind to enhancer sites, controlled by hormones or other

Activators bind to enhancer sites, controlled by hormones or other signals. They increase transcription of the regulated gene. Repressors bind to silencer sites, controlled by hormones or other signals.
They decrease transcription of the regulated gene, possibly by interfering with activators. Coactivators
bind to activators and/or repressors (at one end) and to basal factors (at the other end). The
coactivators somehow communicate the signal from activators and/or repressors to the RNA
polymerase. Basal factors act similar-ly to bacterial sigma factors. They enable RNA polymerase to
initiate transcription. However, they require interaction with coactivators.
Comparison of a simple eukaryotic promoter and extensively diversified metazoan regulatory
modules. a, Simple eukaryotic transcriptional unit. A simple core promoter (TATA), upstream
activator sequence (UAS) and silencer element spaced within 100–200 bp of the TATA box that
is typically found in unicellular eukaryotes. b, Complex metazoan transcriptional control
modules. A complex arrangement of multiple clustered enhancer modules interspersed with
silencer and insulator elements which can be located 10–50 kb either upstream or
downstream of a composite core promoter containing TATA box (TATA), Initiator sequences
(INR), and downstream promoter elements (DPE).
Possible mechanisms for the regulation of genome expression by non-coding
transcription. (A) Bidirectional PARs and mRNAs might originate from different preinitiation complexes (PICs) and compete for the same pool of transcription factors to
initiate transcription. Binding of TBP or other factors might be responsible for
directing the balance towards mRNA synthesis. (B) The transcriptional interference
mechanism, in which transcription factors (TFs) are displaced from the mRNA
promoter by the upstream cryptic transcription, is shown. The SRG1 cryptic noncoding RNA (ncRNA) interferes with the promoter of the downstream SER3 gene
through this mechanism. (C) Model for start site selection. The CUT and the mRNA
have the same promoter but originate from different transcription start sites and
compete for the same pool of PIC factors. An example of this type of regulation
occurs at the IMD2 locus. (D) Transcription-induced chromatin modifications, in
which cryptic transcription modifies promoter proximal chromatin to attenuate gene
expression. The GAL10–GAL1 locus is regulated through this mechanism; cryptic
transcription that originates upstream from the GAL10–GAL1 promoter induces the
methylation of H3K4 and/or H3K36 by the HMTs Set1 and Set2, respectively, and
tethers the Rpd3S histone deacetylase complex to attenuate gene expression of the
GAL locus. CUT, cryptic unstable transcript; H3, histone H3; HMT, histone methyl
transferase; IMD2, inosine monophosphate dehydrogenase 2; K, lysine; PAR,
promoter-associated non-coding RNA; Rpd3S, reduced potassium dependency 3
small; SER3, serine requiring 3; Set1/2, SET-domain-containing 1/2; SRG1, SER3
regulatory gene; TBP, TATA binding protein.
Models for cis- or trans-mediated RNA-dependent regulation of gene expression. (A) Regulation in cis:
when Rrp6 is delocalized or absent, the antisense CUT is stabilized and recruits HDACs, which are
responsible for promoter regulation and silencing. This occurs, for example, at the PHO84 locus. (B)
Regulation in trans: the CUT, which is transcribed from a distant locus and stabilized, induces the
recruitment of the HMT Set1, thereby inhibiting gene transcription. The RTL non-coding RNA regulates
the TY1 locus in this manner. CUT, cryptic unstable transcript; HDAC, histone deacetylase complex;
HMT, histone methyl transferase; PHO84, phosphate metabolism 84; Rrp6, ribosomal RNA processing
6; RTL, antisense of LTR; Set1, SET-domain-containing 1; TY1, transposon in yeast 1.
A well-known example for Transcription termination is the in the tryptophan gene. The trp
leader region can exist in alternative base-paired conformations:
In the figure on the left the form created (two hairpins) is a transcription terminating. On
the right the form created (one hairpin) is not terminating so the gene can be transcript.
Slow intermediate mechanism. RNAP is depicted as in Fig. 1. At most
template positions, fast translocation from the pretranslocated state to the
active state allows tight NTP binding (assisted by a properly positioned
3′OH) and rapid transcription (top horizontal pathway)]. When RNAP
encounters a pause, arrest, or termination site, it isomerizes to a slow
intermediate in which the RNA 3′ end frays away from the DNA. A slight
conformational opening of RNAP may precede and accelerate this change
or may accompany it. Further rearrangement of the slow intermediate
produces the different classes of paused, arrested, or terminating
complexes. Escape of the slow intermediate back to the elongation
pathway occurs by weak NTP binding and recapture of the 3′ OH in the
active site. Amino acid substitutions in RNAP favor or disfavor the slow
intermediate, whereas elongation factors NusA and NusG stabilize hairpinRNAP interaction or inhibit backtracking, respectively, at later steps in the
pathway. Whether termination sometimes involves hairpin-RNAP
interaction (dotted line) and whether it occurs via hairpin-induced bubble
collapse or RNA pull-out (18, 36) remains to be determined.
Обща схема на репликация на ДНК
Отрязване на интрони по механизма на “примката” (lariat)
Структура на репликационната вилка
Репликация на човешката ДНК
Figure 4.20 Dideoxy DNA sequencing.
Four separate reactions are performed,
using the target sequence as a template.
Each reaction contains a proportion of
one nucleotide represented as a
The dideoxynucleotide or the normal
nucleotide can be incorporated into the
growing strand, but incorporation of the
dideoxynucleotide results in termination
of DNA synthesis. Thus, each reaction
results in a population of differently
sized fragments that can be separated
on a polyacrylamide gel and visualized
by autoradiography. The sequence
homologous to the template is read
from bottom to top, 5‘ to 3‘, by noting
the lane in which a band appears.
Организация на генетичния материал в еукариотите
All tRNAs possess a common secondary
structure, the cloverleaf structure.
The base sequence in the flattened
model is for tRNA-Ala.
Figure 11: Wobble may exist in the pairing of a codon on mRNA with an anticodon on tRNA.
The mRNA and tRNA pair in an antiparallel fashion. Pairing at the first and second codon positions is in
accord with the Watson and Crick pairing rules (A with U, G with C); however, pairing rules are relaxed at the
third position of the codon, and G on the anticodon can pair with either U or C on the codon in this example.
Алтернативен сплайсинг
Alternative splicing results in different mature mRNAs and proteins.
In mammals, the protein tropomyosin is encoded by a gene that has 11 exons.
Tropomyosin pre-mRNA is spliced differently in different tissues, resulting in five
different forms of the protein.
Extensive variation in genome size within
and among the main groups of life.
Ever since the first general surveys of
nuclear DNA content were carried out in
the early 1950s, it has been apparent that
eukaryotic genome sizes vary enormously
and that this is unrelated to intuitive
ideas of morphological complexity. This
discrepancy between genome size and
complexity remains clear more than half a
century later, with genome sizes now
available for nearly 9,000 species of
animals and plants. In prokaryotes,
genome size and gene number are
strongly correlated, but in eukaryotes the
vast majority of nuclear DNA is noncoding. Nevertheless, there is some
overlap in genome size between the
largest bacteria and the smallest parasitic
protists. The figure illustrates the means
and overall ranges of genome size that
have been observed so far in the main
groups of living organisms, and are
loosely arranged according to common
ideas of complexity to further emphasize
the disparity between this parameter and
genome size. Some commonly cited
extreme values for amoebae (700,000
Mb) have been omitted, as there is
considerable uncertainty about the
accuracy of these measurements and the
ploidy level of the species involved.
Southern blotting and hybridization with probes can be used to locate a few specific fragments in a large pool of DNA.
The current model for the
biogenesis and post-transcriptional
suppression of microRNAs and
small interfering RNAs.
The nascent pri-microRNA (primiRNA) transcripts are first
processed into approximately 70nucleotide pre-miRNAs by Drosha
inside the nucleus. Pre-miRNAs are
transported to the cytoplasm by
Exportin 5 and are processed into
miRNA:miRNA* duplexes by Dicer.
Dicer also processes long dsRNA
molecules into small interfering RNA
(siRNA) duplexes. Only one strand of
the miRNA:miRNA* duplex or the
siRNA duplex is preferentially
assembled into the RNA-induced
silencing complex (RISC) , which
subsequently acts on its target by
translational repression or mRNA
cleavage, depending, at least in part,
on the level of complementarity
between the small RNA and its
target. ORF, open reading frame.
Gene regulation by RNA switches.
RNA regions that are involved in gene expression switching are shown in the same
color. a) Translation activation of virulence genes in the pathogen Listeria
monocytogenes. An increase in temperature melts the secondary structure around
the ribosome binding site (RBS) and start codon, allowing ribosome binding and
translation initiation. b) Upregulation of an Escherichia coli gene by the DsrA
antisense short RNA (sRNA). DsrA RNA pairs with the translational operator of the
rpoS gene using two sequences (colored blue and light blue) located within helices
1 and 2. This base pairing exposes translation initiation signals for ribosome
binding and increases mRNA stability.
Eukaryotic cells have alternative pathways for processing pre-mRNA.
(a) With alternative splicing; pre-mRNA can be spliced in different ways to produce different mRNAs. (b)
With multiple 3 cleavage sites, there are two or more potential sites for cleavage and polyadenylation; use
of the different sites produces mRNAs of different lengths.
A transcription unit includes a promoter, an RNA-coding region, and a terminator.
Transcription is initiated at RNA polymerase II promoters when the TFIID transcription factor binds to the
TATA box, followed by the binding of a preassembled holoenzyme containing general transcription factors,
RNA polymerase II, and the mediator. Steps 4 and 5 illustrate the binding of transcription activator
proteins to the enhancer region, followed by the looping of DNA in order to allow the newly-formed
structure to interact with the transcription apparatus.
Аденовирус и вирус на грипа
A transcription unit includes a promoter, an RNA-coding region, and a terminator.
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