Polyadenylation

polyadenylatedpoly(A) tailpolyApoly-A taildeadenylationpolyadenine tailpoly(A)polyA tailpoly A tailpoly-A
Polyadenylation is the addition of a poly(A) tail to a messenger RNA.wikipedia
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Transcription (biology)

transcriptiontranscribedtranscriptional
The process of polyadenylation begins as the transcription of a gene terminates.
Transcription termination in eukaryotes is less well understood than in bacteria, but involves cleavage of the new transcript followed by template-independent addition of adenines at its new 3' end, in a process called polyadenylation.

Alternative splicing

alternatively splicedtranscript variantssplice variant
Therefore, polyadenylation can produce more than one transcript from a single gene (alternative polyadenylation), similar to alternative splicing.
In addition, the primary transcript contained multiple polyadenylation sites, giving different 3’ ends for the processed mRNAs.

MicroRNA

miRNAmicroRNAsmiRNAs
There are small RNAs where the poly(A) tail is seen only in intermediary forms and not in the mature RNA as the ends are removed during processing, the notable ones being microRNAs.
As a result, these mRNA molecules are silenced, by one or more of the following processes: (1) Cleavage of the mRNA strand into two pieces, (2) Destabilization of the mRNA through shortening of its poly(A) tail, and (3) Less efficient translation of the mRNA into proteins by ribosomes.

Long non-coding RNA

Long noncoding RNAlncRNAlncRNAs
But, for many long noncoding RNAs – a seemingly large group of regulatory RNAs that, for example, includes the RNA Xist, which mediates X chromosome inactivation – a poly(A) tail is part of the mature RNA.
While the abundance of long ncRNAs was unanticipated, this number represents a conservative lower estimate, since it omitted many singleton transcripts and non-polyadenylated transcripts (tiling array data shows more than 40% of transcripts are non-polyadenylated).

XIST

XIST geneXist RNAX-inactive specific transcript
But, for many long noncoding RNAs – a seemingly large group of regulatory RNAs that, for example, includes the RNA Xist, which mediates X chromosome inactivation – a poly(A) tail is part of the mature RNA.
It is processed in a similar way to mRNAs, through splicing and polyadenylation.

Primary transcript

pre-mRNAtranscriptprecursor mRNA
The processive polyadenylation complex in the nucleus of eukaryotes works on products of RNA polymerase II, such as precursor mRNA.
These processes include the 5' cap, 3'-polyadenylation, and alternative splicing.

Poly(A)-binding protein

PABPpoly (A)poly-A
The poly(A) tail acts as the binding site for poly(A)-binding protein.
Poly(A)-binding protein (PAB or PABP) is a RNA-binding protein which binds to the poly(A) tail of mRNA.

Histone 3' UTR stem-loop

stem-loop3' UTR stem-loophistone
These are the only mRNAs in eukaryotes that lack a poly(A) tail, ending instead in a stem-loop structure followed by a purine-rich sequence, termed histone downstream element, that directs where the RNA is cut so that the 3' end of the histone mRNA is formed.
The mRNAs of metazoan histone genes lack polyadenylation and a poly-A tail, instead 3' end processing occurs at a site between this highly conserved stem-loop and a purine rich region around 20 nucleotides downstream (the histone downstream element, or HDE).

Messenger RNA

mRNAmRNAstranscripts
Polyadenylation is the addition of a poly(A) tail to a messenger RNA.
The balance between translation and decay is reflected in the size and abundance of cytoplasmic structures known as P-bodies The poly(A) tail of the mRNA is shortened by specialized exonucleases that are targeted to specific messenger RNAs by a combination of cis-regulatory sequences on the RNA and trans-acting RNA-binding proteins.

Gene expression

expressionexpressedexpress
It, therefore, forms part of the larger process of gene expression.
In eukaryotes, RNA is stabilised by certain post-transcriptional modifications, particularly the 5' cap and poly-adenylated tail.

Cleavage and polyadenylation specificity factor

CPSFcleavage and polyadenylation specificity factor (CPSF)
The cleavage is catalysed by the enzyme CPSF and occurs 10–30 nucleotides downstream of its binding site. Cytoplasmic polyadenylation requires the RNA-binding proteins CPSF and CPEB, and can involve other RNA-binding proteins like Pumilio.
It is the first protein to bind to the signaling region near the cleavage site of the pre-mRNA, to which the poly(A) tail will be added by polynucleotide adenylyltransferase.

Cleavage factor

CFI
The cleavage is the first step in adding a polyadenine tail to the pre-mRNA, which is one of the necessary post-transcriptional modifications necessary for producing a mature mRNA molecule.

Three prime untranslated region

3' UTR3' untranslated region3'UTR
This deadenylation and degradation process can be accelerated by microRNAs complementary to the 3' untranslated region of an mRNA.
Several regions of the mRNA molecule are not translated into protein including the 5' cap, 5' untranslated region, 3' untranslated region, and the poly(A) tail.

Cleavage stimulation factor

cleavage stimulatory factorCSTFcleavage stimulation factor (CstF)
For example, the expression of CstF-64, a subunit of cleavage stimulatory factor (CstF), increases in macrophages in response to lipopolysaccharides (a group of bacterial compounds that trigger an immune response).
CstF is recruited by cleavage and polyadenylation specificity factor (CPSF) and assembles into a protein complex on the 3' end to promote the synthesis of a functional polyadenine tail, which results in a mature mRNA molecule ready to be exported from the cell nucleus to the cytosol for translation.

GLD-2

Depending on the cell type, the polymerase can be the same type of polyadenylate polymerase (PAP) that is used in the nuclear process, or the cytoplasmic polymerase GLD-2.
GLD-2 (which stands for Germ Line Development 2) is a cytoplasmic poly(A) polymerase (cytoPAPs) which adds successive AMP monomers to the 3’ end of specific RNAs, forming a poly(A) tail, which is a process known as polyadenylation.

Exosome complex

exosomeexosomes
mRNAs that are not exported are degraded by the exosome.
In the nucleus, the processing of rRNA and snoRNA by the exosome is mediated by the TRAMP complex, which contains both RNA helicase (Mtr4) and polyadenylation (Trf4) activity.

CPEB

CPE binding proteinCPEB3
Cytoplasmic polyadenylation requires the RNA-binding proteins CPSF and CPEB, and can involve other RNA-binding proteins like Pumilio.
CPEB, or cytoplasmic polyadenylation element binding protein, is a highly conserved RNA-binding protein that promotes the elongation of the polyadenine tail of messenger RNA.

Polynucleotide adenylyltransferase

Polyadenylate polymerasepoly(A) polymerasepolyadenine polymerase
Polyadenylate polymerase builds the poly(A) tail by adding adenosine monophosphate units from adenosine triphosphate to the RNA, cleaving off pyrophosphate.
This enzyme is responsible for the addition of the 3' polyadenine tail to a newly synthesized pre-messenger RNA (pre-mRNA) molecule during the process of gene transcription.

TRAMP complex

Trf4
This polyadenylation is done in the nucleus by the TRAMP complex, which maintains a tail that is around 4 nucleotides long to the 3' end.
TRAMP complex (Trf4/Air2/Mtr4p Polyadenylation complex) is a multiprotein, heterotrimeric complex having distributive polyadenylation activity and identifies wide varieties of RNAs produced by polymerases.It was originally discovered in Saccharomyces cerevisiae by LaCava et al., Vanacova et al. and Wyers et al. in 2005.

Poly(A)-specific ribonuclease

PARNDANDAN (protein)
In animals, poly(A) ribonuclease (PARN) can bind to the 5' cap and remove nucleotides from the poly(A) tail.
Exonucleolytic degradation of the poly(A) tail is often the first step in the decay of eukaryotic mRNAs.

RNA polymerase II

RNA pol IIIIpolymerase II
The processive polyadenylation complex in the nucleus of eukaryotes works on products of RNA polymerase II, such as precursor mRNA.
The newly phosphorylated Ser5 recruits enzymes to cap the 5' end of the newly synthesized RNA and the "3' processing factors to poly(A) sites".

Polynucleotide phosphorylase

PNPasepolyribonucleotide nucleotidyltransferasePNPT1
While many bacteria and mitochondria have polyadenylate polymerases, they also have another type of polyadenylation, performed by polynucleotide phosphorylase itself.
It accounts for all of the observed residual polyadenylation in strains of Escherichia coli missing the normal polyadenylation enzyme.

Eukaryotic initiation factor

eukaryotic initiation factorsinitiation factortranslation initiation factor
Poly(A)-binding protein also can bind to, and thus recruit, several proteins that affect translation, one of these is initiation factor-4G, which in turn recruits the 40S ribosomal subunit.
eIF4E recognizes and binds to the 5' cap structure of mRNA, while eIF4G binds PABP, which binds the poly(A) tail, potentially circularizing and activating the bound mRNA.

Five-prime cap

5' cap5′ capcap
In animals, poly(A) ribonuclease (PARN) can bind to the 5' cap and remove nucleotides from the poly(A) tail.
As soon as the 5′ end of the new transcript emerges from RNA polymerase II, the CEC carries out the capping process (this kind of mechanism ensures capping, as with polyadenylation).

Directionality (molecular biology)

533' end
The 3'-most segment of the newly made pre-mRNA is first cleaved off by a set of proteins; these proteins then synthesize the poly(A) tail at the RNA's 3' end.
The 3′-end of nascent messenger RNA is the site of post-transcriptional polyadenylation, which attaches a chain of 50 to 250 adenosine residues to produce mature messenger RNA.