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15.3: Eukaryotic Transcription - Biology

15.3: Eukaryotic Transcription - Biology


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15.3: Eukaryotic Transcription

External Links - read chapters online (internet connection required)

PDFs: for viewing content offline and printing.

Attribution:

The Genetic Code. OpenStax CNX. Feb 25, 2016 http://cnx.org/contents/[email protected]

Prokaryotic Transcription. OpenStax CNX. Feb 25, 2016 http://cnx.org/contents/[email protected]

Eukaryotic Transcription. OpenStax CNX. Apr 10, 2013 http://cnx.org/contents/[email protected]

RNA Processing in Eukaryotes. OpenStax CNX. Apr 10, 2013 http://cnx.org/contents/[email protected]

Ribosomes and Protein Synthesis. OpenStax CNX. Jun 26, 2013 http://cnx.org/contents/[email protected]


The Central Dogma: DNA Encodes RNA RNA Encodes Protein

The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma (Figure 9.14), which states that genes specify the sequences of mRNAs, which in turn specify the sequences of proteins.

Figure 9.14 The central dogma states that DNA encodes RNA, which in turn encodes protein.

The copying of DNA to mRNA is relatively straightforward, with one nucleotide being added to the mRNA strand for every complementary nucleotide read in the DNA strand. The translation to protein is more complex because groups of three mRNA nucleotides correspond to one amino acid of the protein sequence. However, as we shall see in the next module, the translation to protein is still systematic, such that nucleotides 1 to 3 correspond to amino acid 1, nucleotides 4 to 6 correspond to amino acid 2, and so on.


Elongation control

Regulation of elongation focused on identification of new players. Heeyoun Bunch (Harvard Medical School, USA) used an immobilized template with a paused gene, human HSPA1B, to pull down TRIM28, a factor with previously identified roles in chromatin remodeling. Knockdown of the factor affected the expression of several paused genes, and redistributed Pol II to the gene body genome-wide, pointing to a pausing stabilization role. Building on previous work, Qiang Zhou (UC Berkeley, USA) found that AFF1, a central scaffolding protein for the super elongation complex (SEC), promotes HIV transcriptional elongation, at least in part, by enhancing P-TEFb extraction from the 7SK snRNP by the viral encoded Tat protein.

Consistent with multiple functions of the AFF family (AFF1–4), Ali Shilatifard (Stowers Institute for Medical Research, USA) described work showing that P-TEFb-containing complexes demonstrated higher levels of activity than P-TEFb alone towards the Pol II carboxy-terminal domain, identifying SECs as the most active versions of P-TEFb. In addition to these factors, Monsef Benkirane (Institut Genetique Humaine, France) was able to show that the Integrator complex, which is better known for processing snRNA 3′ ends, regulates NELF-mediated Pol II pausing at protein coding genes. ChIP analyses show that Integrator associates with the transcriptional start site (TSS) of its target genes together with NELF, DSIF and Pol II. Knockdown of the Integrator catalytic subunit results in pause release and enhanced elongation by Pol II. However, Integrator also appears to be required for proper termination by Pol II. Thus, pause release and elongation are control points regulated by a number of factors.

Underscoring unexpected roles and mechanisms for known factors, work from David Price (University of Iowa, USA) and David Levens (National Cancer Institute, USA) examined the role of the oncogenic transcription factor Myc. David Levens demonstrated that Myc caused a global amplification of transcription in activated B cells with only a modest bonus at genes containing its cognate E-box binding site. David Price asserted that the genomic distribution of Myc suggested that the transcription machinery, rather than specific sequences, are the driving force for Myc occupancy. It remains to be seen how dispensable sequence-specific DNA binding is for Myc, and whether such promiscuity is widespread among other transcription factor families.


15.3: Eukaryotic Transcription - Biology

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In eukaryotic cells, transcription factors are proteins that can bind to DNA and regulate the expression of genes. In order to initiate transcription, each RNA polymerase requires several different proteins, called general transcription factors, to bind to promoter regions. For example, the first and largest of these proteins, called TFIID, will bind to the TATA Box region found in most promoters. Along with other proteins, they recruit the polymerase to the promoter region and form the pre-initiation complex.

Specific transcription factors, on the other hand, can bind to distal regulatory regions called enhancer sites away from the transcription start site, sometimes thousands of base pairs upstream or downstream of a gene, and induce higher rates of transcription. In a process called looping, the DNA strand will bend in a way that allows transcription factors bound to enhancer sites to establish protein-protein interactions with mediator proteins and the pre-initiation complex.

Specific transcription factors that bind to enhancer sites to promote transcription are known as activators, while those that block or reduce transcription are called repressors. The presence of specific transcription factors and distal regulatory elements allows for differential gene expression, such as the turning on or off of different genes during early development to determine whether the cell will become a skin cell or a neuron, as well as the coordinated transcription of related functional genes.

Over 1,500 different transcription factors have been identified in humans that regulate a wide range of critical genes, from the determination of cell types early in development to the cellular response to different environmental conditions.

14.3: Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of certain tissues or body parts without affecting the entire organism.

An additional layer of complexity is added by transcription factors in eukaryotes exerting combinatorial control. That means input provided by several transcription factors synchronously regulate the expression of a single gene. The combination of several transcriptional activators and repressors enables a gene to be differentially regulated and adapt to a variety of environmental changes without the need for additional genes.

Lee, Tong Ihn, and Richard A. Young. &ldquoTranscriptional Regulation and Its Misregulation in Disease.&rdquo Cell 152, no. 6 (March 14, 2013): 1237&ndash51. [Source]

Inukai, Sachi, Kian Hong Kock, and Martha L. Bulyk. &ldquoTranscription Factor&ndashDNA Binding: Beyond Binding Site Motifs.&rdquo Current Opinion in Genetics & Development 43 (April 2017): 110&ndash19. [Source]


Development, Differentiation and Disease of the Para-Alimentary Tract

G Histone Modifications Modulate MPC Fate

Transcriptional activation and repression involves characteristic changes in the chromatin structure of regulated genes. Because key developmental regulators often bind to thousands of genes (e.g., Refs. 76,77 ), broad changes in chromatin structure might be expected. Histone deacetylases (HDAC) are central players in the control of chromatin structure through their regulated activity that removes covalent acetyl-modifications from histones and other chromosomal proteins including DNA-binding TFs. Chemical inhibitors of HDACs, for example, can induce widespread gene activation. Surprisingly, in some developmental contexts, nonspecific inhibition of HDAC activity can favor one developmental lineage over another. In particular, treatment of embryonic pancreatic explants in long-term culture with HDAC inhibitors suppresses acinar development. 78 In explants treated with the inhibitors, the number of cells that express the proendocrine TF Ngn3 increases several-fold and persists many days longer than normal. This observation suggests that HDAC activity normally biases the cell-fate options toward the acinar program by suppressing the opportunity to enter the bipotent intermediate toward islet or ductal fates ( Fig. 3 ). A thorough analysis of histone marks and DNA methylation in acinar and nonacinar cells will provide a road map for the pancreatic epigenome.


15.3: Eukaryotic Transcription - Biology

DNA Replication & Transcription

In principle : DNA replication is semi-conservative
H - bonds 'unzip', strands unwind,
complementary nucleotides added to existing strands [ iGen3 03-02 ]
After replication, each double-helix has one "old" & one "new" strand
[note alternative conservative & dispersive models: Homework #4 ] [ iGen3 03-01 ]

DNA is not the "Genetic Code" for proteins
information in DNA must first be transcribed into RNA
messenger RNA transcript is base-complementary to template strand of DNA
& therefore co-linear with sense strand of DNA

DNA & RNA syntheses occur only in the 5' 3' direction

DNA synthesis in prokaryotes:
Nucleotides are added simultaneously to both strands, but
DNA grows in the 5' 3' direction ONLY [ iGen3 03-03 ] [iG1 10.10]

Distinguish:
Replication: duplication of a double-stranded DNA ( dsDNA ) molecule
an exact 'copy' of the existing molecule (cf. xerox copy)
Synthesis: biochemical creation of a new single-stranded DNA ( ssdNA ) molecule
a base-complementary 'copy' of an existing strand (cf. silly putty copy)
occurs only in the 5' 3' direction

DNA Synthesis in prokaryotes [ iGen3 03-04 , -05, -06 ]
(1) Formation of replication fork at Origin of Replication [iG1 10.16, 19]
provides two single-stranded DNA template ( ssDNA )
multiple replications forks ( replicons ) [ iGen3 03-09 ]
(2) Synthesis of RNA primer [iG1 10.15]
(3) Addition of dNTPs by DNAPol III at 3' end only
continuous synthesis on leading strand [ iG1 10.13 ]
(4) discontinuous synthesis on lagging strand [ iG1 10.20 ]
Okazaki fragments
proof-reading by 3' 5' exonuclease activity [ iG1 10.12]
leading & lagging strand synthesis simultaneously [ iGen3 03-08 ] [iG1 10.21 ]
A single, dimeric DNAPol IIIreplicates both strands
(5) Excision of RNA primer by DNAPol I
ligation
(connection) of fragment ends at gaps by DNA ligase [ [iG1 10.22 ]

DNA synthesis in eukaryotes

Eukaryotic genomes are much larger [the " C-value Paradox "]
eukaryotic DNA synthesis is more efficient:
More DNAPol molecules, slower rate of synthesis, more replicons,
E. coli: 15 DNAPol add 100,000 bases/min over 3,500 replicons
4.2 x 10 6 bp genome replicated in 20

40 min
Drosophila: 50,000 DNAPol add 500

5,000 bases/min over 25,000 replicons
330 x 10 6 bp diploid genome replicated in < 3 min : net 600x faster

Transcription : synthesis of messenger RNA (mRNA) (online MGA2 animation)

' gene ' [iG1 4.18 ]
Promoters - short DNA sequences that regulate transcription
typically 'upstream' = ' leftward' from 5' end of sense strand [iG1 4.12 ]
(2) Initiation & Elongation [ iGen3 05-04ab , -04cd ] [iG1 4.22, 23, 24 ]
mRNA synthesized 5'3' from DNA template strand
mRNA sequence therefore homologous to DNA sense strand

Colinear : mRNA and DNA sense strand "line up"

(in prokaryotes, but not eukaryotes: see below)
Process similar to DNA replication [iG1 4.25 ], except
No primer
is required
Transcription may occur from either strand
Most DNA is not transcribed into RNA
(3) Termination [ iGen3 05-05 ] [iG1 4.27, 28, 29 ]

Regulation of transcription
In prokaryotes, transcription & translation may occur simultaneously
In eukaryotes, transcription occurs in nucleus [ex.: Lampbrush chromosomes]
translation occurs in cytoplasm (see next section):
RNA must cross nuclear membrane [ iGen3 05-09 ]
transcription & translation are physically separated
primary RNA transcript is extensively processed
heterogeneous nuclear RNA ( hnRNA ) mRNA

Post-transcriptional processing of eukaryotic RNA is complex [iG1 4.9]
promoters [iG1 4.19] & enhancers [iG1 ] determine initiation & control rate
'cap' ( 7-methyl guanosine , 7mG) added to 5' end [ iGen3 05-10 ] [iG1 4.26 ]
'tail' of poly-A (5'-

AAAAAAAAAA-3') added to 3' end [ iGen3 05-11 ] [iG1 4.33 ]
'splicing' of hnRNA : eukaryotic genes are "split" [ iGen3 05-12 ]
intron DNA sequence equivalents removed from hnRNA : "intervening" [ iGen3 05-14 ]
exon DNA sequence equivalents represented in mRNA: "expressed" in protein
1

12's of exons / 'gene'
>90% of transcript may be ' spliced ou t'
[An important note on terminology ]
Splicing mechanism uses donor and acceptor sites [iG1 5.18, 19, 20]

Eukaryotic genes & mRNA are not colinear!
DNA / RNA hybridization produces heteroduplexes
DNA introns 'loop out'
DNA exons pair with mRNA
Eukaryotic exons may be widely separated

Alternative splicing of the same transcript produces different products [iG1 4.16 ]
Different exon regions are combined as different mRNAs [iG1 5.01]
Alternative exon combinations differ functionally [iG1 5.22]

Summaries of transcription [& translation] in prokaryotes & eukaryotes

Homework #5: Suggested problems from

MGA2 (2002), Chapter 2, pp. 52-54
Solved problems 1 & 2
problem ## 7, 8, 9, 11, 14, 15 , 18, 19, 21, 26, 27

iGen3 (2010), Chapter 5, pp. 98-101
Problems ## 2, 4, 6, 7, 12, 13, 15, 16, 21

Ongoing Homework problem :
What is a ' gene ' ? How do the discoveries of (1) introns and exons amd (2) alternative splicing in eukaryotic genomes modify the concept?



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Prokaryotic transcription takes place in the cytoplasm. On the other hand, eukaryotic transcription takes place in the nucleus. This is the key difference between prokaryotic and eukaryotic transcription. Furthermore, prokaryotic transcription produces polycistronic mRNA while eukaryotic transcription produces monocistronic mRNA. Thus, it is also a difference between prokaryotic and eukaryotic transcription. Also, one more difference between prokaryotic and eukaryotic transcription is that the prokaryotic transcription involves one type of RNA polymerase while eukaryotic transcription involves three types of RNA polymerases.

Moreover, another difference between prokaryotic and eukaryotic transcription is that the transcription and translation are coupled in prokaryotes while they are not coupled in eukaryotes. Furthermore, in prokaryotes, post-transcriptional modifications are not taking place while in eukaryotes, post-transcriptional modification occurs. Thus, it is also a difference between prokaryotic and eukaryotic transcription.

Below infographic on the difference between prokaryotic and eukaryotic transcription provides more information on the differences.


To start transcription, general transcription factors, such as TFIID, TFIIH, and others, must first bind to the TATA box and recruit RNA polymerase to that location. The binding of additional regulatory transcription factors to cis-acting elements will either increase or prevent transcription. In addition to promoter sequences, enhancer regions help augment transcription. Enhancers can be upstream, downstream, within a gene itself, or on other chromosomes. Transcription factors bind to enhancer regions to increase or prevent transcription.

The binding of ________ is required for transcription to start.

What will result from the binding of a transcription factor to an enhancer region?

  1. decreased transcription of an adjacent gene
  2. increased transcription of a distant gene
  3. alteration of the translation of an adjacent gene
  4. initiation of the recruitment of RNA polymerase


Watch the video: Transcription (September 2022).


Comments:

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