10/1/2018 Primary transcript - Wikipedia

Primary transcript
A prim ary transcript is the single-stranded ribonucleic acid (RNA)
product sy nthesized by transcription of DNA, and processed to y ield
v arious mature RNA products such as mRNAs, tRNAs, and rRNAs. The
primary transcripts designated to be mRNAs are modified in preparation
for translation. For example, a precursor m RNA (pre-m RNA) is a ty pe
of primary transcript that becomes a messenger RNA (mRNA) after
processing.

Pre-mRNA is the first form of RNA

Pre-mRNA is sy nthesized from a DNA template in the cell nucleus by created through transcription in
transcription. Pre-mRNA comprises the bulk of heterogeneous nuclear protein synthesis. The pre-mRNA
RNA (hnRNA). Once pre-mRNA has been completely processed, it is lacks structures that the messenger
termed "mature messenger RNA", or simply "messenger RNA". The term RNA (mRNA) requires. First all
introns have to be removed from the
hnRNA is often used as a sy nony m for pre-mRNA, although, in the strict
transcribed RNA through a process
sense, hnRNA may include nuclear RNA transcripts that do not end up as
known as splicing. Before the RNA is
cy toplasmic mRNA. ready for export, a Poly(A)tail is
added to the 3' end of the RNA and a
There are sev eral steps contributing to the production of primary 5' cap is added to the 5' end.
transcripts. All these steps inv olv e a series of interactions to initiate and
complete the transcription of DNA in the nucleus of eukary otes. Certain
factors play key roles in the activ ation and inhibition of transcription,
where they regulate primary transcript production. Transcription
produces primary transcripts that are further modified by sev eral
processes. These processes include the 5' cap, 3'-poly adeny lation, and
alternativ e splicing. In particular, alternativ e splicing directly contributes
to the div ersity of mRNA found in cells. The modifications of primary
transcripts hav e been further studied in research seeking greater
knowledge of the role and significance of these transcripts. Experimental
studies based on molecular changes to primary transcripts the processes
before and after transcription hav e led to greater understanding of diseases
inv olv ing primary transcripts.

Micrograph of gene transcription of

Contents ribosomal RNA illustrating the
growing primary transcripts
Production
Regulation
R-loops
RNA processing
Processing
5' capping
Polyadenylation
Alternative splicing
https://en.wikipedia.org/wiki/Primary_transcript 1/7
10/1/2018 Primary transcript - Wikipedia

Experiments
Related diseases
See also
References
External links

Production
The steps contributing to the production of primary transcripts inv olv e a series of molecular interactions that
initiate transcription of DNA within a cell's nucleus. Based on the needs of a giv en cell, certain DNA sequences are
transcribed to produce a v ariety of RNA products to be translated into functional proteins for cellular use. To
initiate the transcription process in a cell's nucleus, DNA double helices are unwound and hy drogen bonds
connecting compatible nucleic acids of DNA are broken to produce two unconnected single DNA strands. [1] One
strand of the DNA template is used for transcription of the single-stranded primary transcript mRNA. This DNA
strand is bound by an RNA poly merase at the promoter region of the DNA. [2]

In eukary otes, three kinds of RNA—rRNA, tRNA, and mRNA—are produced

based on the activ ity of three distinct RNA poly merases, whereas, in
prokary otes, only one RNA poly merase exists to create all kinds of RNA
molecules. [3] RNA poly merase II of eukary otes transcribes the primary
transcript, a transcript destined to be processed into mRNA, from the
antisense DNA template in the 5' to 3' direction, and this newly sy nthesized
primary transcript is complementary to the antisense strand of DNA. [1]
RNA poly merase II constructs the primary transcript using a set of four
specific ribonucleoside monophosphate residues (Adenosine
monophosphate (AMP), Cy tidine monophosphate (CMP), Guanosine
monophosphate (GMP), and Uridine monophosphate (UMP)) that are
added continuously to the 3' hy droxy l group on the 3' end of the growing Transcription of DNA by RNA
mRNA. [1] polymerase to produce primary
transcript
Studies of primary transcripts produced by RNA poly merase II rev eal that
an av erage primary transcript is 7 ,000 nucleotides in length, with some
growing as long as 20,000 nucleotides in length. [2] The inclusion of both exon and intron sequences within primary
transcripts explains the size difference between larger primary transcripts and smaller, mature mRNA ready for
translation into protein.

Regulation
A number of factors contribute to the activ ation and inhibition of transcription and therefore regulate the
production of primary transcripts from a giv en DNA template.

Activ ation of RNA poly merase activ ity to produce primary transcripts is often controlled by sequences of DNA
called enhancers. Transcription factors, proteins that bind to DNA elements to either activ ate or repress
transcription, bind to enhancers and recruit enzy mes that alter nucleosome components, causing DNA to be either
more or less accessible to RNA poly merase. The unique combinations of either activ ating or inhibiting transcription
factors that bind to enhancer DNA regions determine whether or not the gene that enhancer interacts with is

https://en.wikipedia.org/wiki/Primary_transcript 2/7
10/1/2018 Primary transcript - Wikipedia

activ ated for transcription or not. [4] Activ ation of transcription depends on whether or not the transcription
elongation complex, itself consisting of a v ariety of transcription factors, can induce RNA poly merase to dissociate
from the Mediator complex that connects an enhancer region to the promoter. [4]

Inhibition of RNA poly merase activ ity can also be regulated by DNA
sequences called silencers. Like enhancers, silencers may be located at
locations farther up or downstream from the genes they regulate. These
DNA sequences bind to factors that contribute to the destabilization of the
initiation complex required to activ ate RNA poly merase, and therefore
inhibit transcription. [5] Role of transcription factors and
enhancers in gene expression
Histone modification by transcription factors is another key regulatory regulation
factor for transcription by RNA poly merase. In general, factors that lead to
histone acety lation activ ate transcription while factors that lead to histone
deacety lation inhibit transcription. [6] Acety lation of histones induces repulsion between negativ e components
within nucleosomes, allowing for RNA poly merase access. Deacety lation of histones stabilizes tightly coiled
nucleosomes, inhibiting RNA poly merase access. In addition to acety lation patterns of histones, methy lation
patterns at promoter regions of DNA can regulate RNA poly merase access to a giv en template. RNA poly merase is
often incapable of sy nthesizing a primary transcript if the targeted gene's promoter region contains specific
methy lated cy tosines— residues that hinder binding of transcription-activ ating factors and recruit other enzy mes to
stabilize a tightly bound nucleosome structure, excluding access to RNA poly merase and prev enting the production
of primary transcripts. [4]

R-loops
R-loops are formed during transcription. An R-loop is a three-stranded nucleic acid structure containing a DNA-RNA
hy brid region and an associated non-template single-stranded DNA. Activ ely transcribed regions of DNA often form
R-loops that are v ulnerable to DNA damage. Introns reduce R-loop formation and DNA damage in highly expressed
y east genes. [7]

RNA processing
Transcription, a highly regulated phase in gene expression, produces primary transcripts. Howev er, transcription is
only the first step which should be followed by many modifications that y ield functional forms of RNAs. [8] Otherwise
stated, the newly sy nthesized primary transcripts are modified in sev eral way s to be conv erted to their mature,
functional forms to produce different proteins and RNAs such as mRNA, tRNA, and rRNA.

Processing
The basic primary transcript modification process is similar for tRNA and rRNA in both eukary otic and prokary otic
cells. On the other hand, primary transcript processing v aries in mRNAs of prokary otic and eukary otic cells. [8] For
example, some prokary otic bacterial mRNAs serv e as templates for sy nthesis of proteins at the same time they are
being produced v ia transcription. Alternativ ely , pre-mRNA of eukary otic cells undergo a wide range of
modifications prior to their transport from the nucleus to cy toplasm where their mature forms are translated. [8]
These modifications are responsible for the different ty pes of encoded messages that lead to translation of v arious

https://en.wikipedia.org/wiki/Primary_transcript 3/7
10/1/2018 Primary transcript - Wikipedia

ty pes of products. Furthermore, primary transcript processing prov ides a control for gene expression as well as a
regulatory mechanism for the degradation rates of mRNAs. The processing of pre-mRNA in eukary otic cells includes
5' capping, 3' Poly adeny lation, and alternativ e splicing.

5' capping
Shortly after transcription is initiated in eukary otes, a pre-mRNA's 5' end is modified by the addition of a 7 -
methy lguanosine cap, also known as a 5' cap. [8] The 5' capping modification is initiated by the addition of a GTP to
the 5' terminal nucleotide of the pre-mRNA in rev erse orientation followed by the addition of methy l groups to the G
residue. [8] 5' capping is essential for the production of functional mRNAs since the 5' cap is responsible for aligning
the mRNA with the ribosome during translation. [8]

Polyadenylation
In eukary otes, poly adeny lation further modifies pre-mRNAs during which a structure called the poly -A tail is
added. [8] Signals for poly adeny lation, which include sev eral RNA sequence elements, are detected by a group of
proteins which signal the addition of the poly -A tail (approximately 200 nucleotides in length). The poly adeny lation
reaction prov ides a signal for the end of transcription and this reaction ends approximately a few hundred
nucleotides downstream from the poly -A tail location. [8]

Alternative splicing
Eukary otic pre-mRNAs hav e their introns spliced out by spliceosomes made up of small nuclear
ribonucleoproteins. [9][10]

In complex eukary otic cells, one primary transcript is able to prepare large amounts of mature mRNAs due to
alternativ e splicing. Alternate splicing is regulated so that each mature mRNA may encode a multiplicity of proteins.

The effect of alternativ e splicing in gene expression can be seen in complex

eukary otes which hav e a fixed number of genes in their genome y et
produce much larger numbers of different gene products. [8] Most
eukary otic pre-mRNA transcripts contain multiple introns and exons. The
v arious possible combinations of 5' and 3' splice sites in a pre-mRNA can
lead to different excision and combination of exons while the introns are
eliminated from the mature mRNA. Thus, v arious kinds of mature mRNAs Alternative splicing of the primary
are generated. [8] Alternativ e splicing takes place in a large protein transcript
complex called the spliceosome. Alternativ e splicing is crucial for tissue-
specific and dev elopmental regulation in gene expression. [8] Alternativ e
splicing can be affected by v arious factors, including mutations such as chromosomal translocation.

In prokary otes, splicing is done by autocataly tic cleav age or by endoly tic cleav age. Autocataly tic cleav ages, in
which no proteins are inv olv ed, are usually reserv ed for sections that code for rRNA, whereas endoly tic cleav age
corresponds to tRNA precursors.

Experiments

https://en.wikipedia.org/wiki/Primary_transcript 4/7
10/1/2018 Primary transcript - Wikipedia

A study by Cindy L. Wills and Bruce J. Dolnick from the Department of Experimental Therapeutics at the Roswell
Park Memorial Institute in Buffalo, New Y ork and from the Cell and Molecular Biology Program at Univ ersity of
Wisconsin in Madison, Wisconsin was made to understand cellular processes inv olv ing primary transcripts.
Researchers wanted to understand whether 5-Fluorouracil (FUra), a drug known for use in cancer treatment, inhibits
or shuts down dihy drofolate reductase (DHFR) pre-mRNA processing and/or nuclear mRNA stability in
methotrexate-resistant KB cells. Long-term exposure to FUra had no effect on the lev el of DHFR pre-mRNA
containing certain introns, which are sections of pre-mRNA that are usually cut out of the sequence as a part of
processing. Howev er, lev els of total DHFR mRNA decreased two-fold in cells exposed to 1.0 μM FUra. There was no
significant change in the half-life, which refers to the time it takes 50% of the mRNA to decay , of total DHFR mRNA or
pre-mRNA observ ed in cells exposed to FUra. And nuclear/cy toplasmic RNA labeling experiments demonstrated
that the rate of nuclear DHFR RNA changing to cy toplasmic DHFR mRNA decreased in cells treated with FUra. These
results prov ide further ev idence that FUra may help in the processing of mRNA precursors and/or affect the
stability of nuclear DHFR mRNA. [11]

Judith Lengy el and Sheldon Penman from the department of Biology at the Massachusetts Institute of Technology
(MIT) in Cambridge, Massachusetts wrote an article about one ty pe of primary transcript inv olv ed in the genes of
two dipterans, or insects that hav e two wings: Drosophila and Aedes. The article describes how researchers looked at
hnRNA, or basically pre-mRNA, primary transcripts in the two kinds of insects. The size of hnRNA transcripts and
the fraction of hnRNA that is conv erted to mRNA in cell lines, or groups of cells deriv ed from a single cell of
whatev er one is study ing, of Drosophila melanogaster and Aedes albopictus were compared. Both insects are
dipterans, but Aedes has a larger genome than Drosophila. This means that Aedes has more DNA, which means more
genes. The Aedes line make larger hnRNA than did the Drosophila line ev en though the two cell lines grew under
similar conditions and produced mature or processed mRNA of the same size and sequence complexity . These data
suggest that the size of hnRNA increases with increasing genome size, which is obv iously shown by Aedes. [12]

Iv o Melcak, Stepanka Melcakov a, Vojtech Kopsky , Jaromıra Vecerov a and Iv an Raska from the department of Cell
Biology at the Institute of Experimental Medicine, at the Academy of Sciences of Czech Republic in Prague studied
the influences of nuclear speckles on pre-mRNA. Nuclear speckles (speckles) are a part of the nuclei of cells and are
enriched with splicing factors known for inv olv ement in mRNA processing. Nuclear speckles hav e shown to serv e
neighboring activ e genes as storage places of these splicing factors. In this study , researchers showed that, in HeLa
cells which deriv ed from cells of a person who had cerv ical cancer and hav e prov en useful for experiments, the first
group of spliceosomes on pre-mRNA come from these speckles. Researchers used microinjections of spliceosome-
accepting and mutant adenov irus pre-mRNAs with differential splicing factor binding to make different groups and
then followed the sites in which they were heav ily present. Spliceosome-accepting pre-mRNAs were rapidly targeted
into the speckles, but the targeting was found to be temperature-dependent. The poly py rimidine tract sequences in
mRNA promote the construction of spliceosome groups and is required for targeting, but, by itself, was not
sufficient. The downstream flanking sequences were particularly important for the targeting of the mutant pre-
mRNAs in the speckles. In supportiv e experiments, the behav ior of the speckles was followed after the
microinjection of antisense deoxy oligoribonucleotides (complementary sequences of DNA and or RNA to a specific
sequence) and, in this case, specific sequences of snRNAs. snRNAs are known for helping in the processing of pre-
mRNA as well. Under these conditions, spliceosome groups formed on endogenous pre-mRNAs. Researchers
concluded that the spliceosome groups on microinjected pre-mRNA form inside the speckles. Pre-mRNA targeting
and buildup in the speckles is a result of the loading of splicing factors to the pre-mRNA, and the spliceosome groups
gav e rise to the speckled pattern observ ed. [13]

Related diseases
https://en.wikipedia.org/wiki/Primary_transcript 5/7
10/1/2018 Primary transcript - Wikipedia

Research has also led to greater knowledge about certain diseases related to changes within primary transcripts. One
study inv olv ed estrogen receptors and differential splicing. The article entitled, "Alternativ e splicing of the human
estrogen receptor alpha primary transcript: mechanisms of exon skipping" by Paola Ferro, Alessandra Forlani,
Marco Muselli and Ulrich Pfeffer from the laboratory of Molecular Oncology at National Cancer Research Institute in
Genoa, Italy , explains that 17 85 nucleotides of the region in the DNA that codes for the estrogen receptor alpha (ER-
alpha) are spread ov er a region that holds more than 300,000 nucleotides in the primary transcript. Splicing of this
pre-mRNA frequently leads to v ariants or different kinds of the mRNA lacking one or more exons or regions
necessary for coding proteins. These v ariants hav e been associated with breast cancer progression. [14] In the life
cy cle of retrov iruses, prov iral DNA is incorporated in transcription of the DNA of the cell being infected. Since
retrov iruses need to change their pre-mRNA into DNA so that this DNA can be integrated within the DNA of the host
it is affecting, the formation of that DNA template is a v ital step for retrov irus replication. Cell ty pe, the
differentiation or changed state of the cell, and the phy siological state of the cell, result in a significant change in the
av ailability and activ ity of certain factors necessary for transcription. These v ariables create a wide range of v iral
gene expression. For example, tissue culture cells activ ely producing infectious v irions of av ian or murine leukemia
v iruses (ASLV or MLV) contain such high lev els of v iral RNA that 5–10% of the mRNA in a cell can be of v iral origin.
This shows that the primary transcripts produced by these retrov iruses do not alway s follow the normal path to
protein production and conv ert back into DNA in order to multiply and expand. [15]

See also
Transcription (biology)
Transcriptome

References
1. T. Strachan; Andrew P. Read (January 2004). Human Molecular Genetics 3 (https://books.google.com/books?id=g4hC6
3UrPbUC). Garland Science. pp. 16–17. ISBN 978-0-8153-4184-0.
2. Alberts, B. "Molecular Biology of the Cell 3rd Edition" (https://www.ncbi.nlm.nih.gov/books/NBK28319/). NCBI. New
York: Garland Science.
3. Griffiths, AJF. "An Introduction to Genetic Analysis" (https://www.ncbi.nlm.nih.gov/books/NBK21853/). NCBI. New York:
W.H. Freeman.
4. Scott F. Gilbert (15 July 2013). Developmental Biology (https://books.google.com/books?id=-e_bmgEACAAJ). Sinauer
Associates, Incorporated. pp. 38–39, 50. ISBN 978-1-60535-173-5.
5. Brown, T.A. "Genomes 2nd Edition" (https://www.ncbi.nlm.nih.gov/books/NBK21115/). NCBI. Oxford: Wiley-Liss.
6. Harvey Lodish (2008). Molecular Cell Biology (https://books.google.com/books?id=K3JbjG1JiUMC). W. H. Freeman.
pp. 303–306. ISBN 978-0-7167-7601-7.
7. Bonnet A, Grosso AR, Elkaoutari A, Coleno E, Presle A, Sridhara SC, Janbon G, Géli V, de Almeida SF, Palancade B
(2017). "Introns Protect Eukaryotic Genomes from Transcription-Associated Genetic Instability". Mol. Cell. 67 (4): 608–
621.e6. doi:10.1016/j.molcel.2017.07.002 (https://doi.org/10.1016%2Fj.molcel.2017.07.002). PMID 28757210 (https://w
ww.ncbi.nlm.nih.gov/pubmed/28757210).
8. Cooper, GM. "The Cell: A Molecular Approach. 2nd edition" (https://www.ncbi.nlm.nih.gov/books/NBK9864/). NCBI.
Sunderland (MA): Sinauer Associates; 2000.
9. Weaver, Robert F. (2005). Molecular Biology, p.432-448. McGraw-Hill, New York, NY. ISBN 0-07-284611-9.
10. Wahl, M. C.; Will, C. L.; Lührmann, R. (2009). "The Spliceosome: Design Principles of a Dynamic RNP Machine". Cell.
136 (4): 701–718. doi:10.1016/j.cell.2009.02.009 (https://doi.org/10.1016%2Fj.cell.2009.02.009). PMID 19239890 (http
s://www.ncbi.nlm.nih.gov/pubmed/19239890).

https://en.wikipedia.org/wiki/Primary_transcript 6/7
10/1/2018 Primary transcript - Wikipedia

11. Will, CL; Dolnick, BJ (Dec 1989). "5-Fluorouracil inhibits dihydrofolate reductase precursor mRNA processing and/or
nuclear mRNA stability in methotrexate-resistant KB cells". J Biol Chem. 264 (35): 21413–21. PMID 2592384 (https://w
ww.ncbi.nlm.nih.gov/pubmed/2592384).
12. Lengyel, J; Penman, S (Jul 1975). "hnRNA size and processing as related to different DNA content in two dipterans:
Drosophila and Aedes". Cell. 5 (3): 281–90. doi:10.1016/0092-8674(75)90103-8 (https://doi.org/10.1016%2F0092-8674%
2875%2990103-8). PMID 807333 (https://www.ncbi.nlm.nih.gov/pubmed/807333).
13. Melčák, Ivo; Melčáková, Štěpánka; Kopsky, Vojtěch; Večeřová, Jaromíra; Raška, Ivan (February 2001).
"Prespliceosomal Assembly on Microinjected Precursor mRNA Takes Place in Nuclear Speckles" (https://www.ncbi.nl
m.nih.gov/pmc/articles/PMC30951). Mol Biol Cell. 12 (2): 393–406. CiteSeerX 10.1.1.324.8865 (https://citeseerx.ist.psu.
edu/viewdoc/summary?doi=10.1.1.324.8865). doi:10.1091/mbc.12.2.393 (https://doi.org/10.1091%2Fmbc.12.2.393).
PMC 30951 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC30951). PMID 11179423 (https://www.ncbi.nlm.nih.gov/pub
med/11179423).
14. Ferro, P; Forlani, A; Muselli, M; Pfeffer, U (Sep 2003). "Alternative splicing of the human estrogen receptor alpha
primary transcript: mechanisms of exon skipping". Int J Mol Med. 12 (3): 355–63. PMID 12883652 (https://www.ncbi.nl
m.nih.gov/pubmed/12883652).
15. Coffin JM, Hughes SH, Varmus HE, editors. Retroviruses. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory
Press; 1997. Available from: https://www.ncbi.nlm.nih.gov/books/NBK19441/

External links
Scienceden.com RNA Article (https://web.archive.org/web/20060813113552/http://www.scienceden.com/mbiology/conc
epts/rna)

Retrieved from "https://en.wikipedia.org/w/index.php?title=Primary_transcript&oldid=848417660"

This page was last edited on 1 July 2018, at 19:43 (UTC).

Text is available under the Creative Commons Attribution-ShareAlike License; additional terms may apply. By using this site,
you agree to the Terms of Use and Privacy Policy. Wikipedia® is a registered trademark of the Wikimedia Foundation, Inc.,
a non-profit organization.

https://en.wikipedia.org/wiki/Primary_transcript 7/7