Chapter 10: RNA Processing Flashcards
RNAs are synthesized from DNA templates that are not functional -> need to be modified to make mature, functional RNA
precursor RNAs (pre-RNAs)
alterations of pre-RNAs are known as ()
RNA processing
benefits of RNA processing: RNA processing provides:
- regulation of gene activity
- diversity
- quality control
tRNA and rRNA transcripts are made as () that must be processed
long precursors
an () precursor encodes 3 rRNAs and several tRNAs
E. coli
the () precursor encodes 3 rRNAs
S. cerevisiae
encoding several RNAs in one precursor ensures that ()
similar amounts of each RNA are made
() cleave RNAs into smaller parts
ribonucleases
successively remove nucleotides from the end of a transcript; most often in 3’ to 5’, but sometimes in 5’ to 3’
exonucleases
exonucleases are not usually (1), and generally act on (2)
- sequence-specific
- single-stranded ends
cleave the DNA within the strand; some are specific for double-stranded RNA, some for single-stranded
endonucleases
examples of endonucleases
RNase III and RNase P
excision of bacterial rRNAs from longer precursors is performed by (); as well as trimming if some RNAs and tRNAs
RNase III
RNase III binds () in the pre-RNAs and cleaves the dsRNAs
stem structures (dsRNA)
endonucleases similar to RNase III are involved in many processes, e.g. in eukaryotes, they generate (1) and (2) that inhibit the expression of detrimental genes
- microRNA (miRNA)
- small interfering RNAs (siRNAs)
5’ trimming of tRNAs is done by the endonuclease ()
ribonuclease P, RNase P
unlike RNase III, RNase P enzymes have (1) component and (2) components
- bacterial RNA
- protein
in RNase P, the bacterial RNA component alone can cut RNA, thus acting as a ()
ribozyme
the () RNase P RNA component cannot cut RNA alone, but is essential for function
eukaryotic, archaeal, and mitochondrial
() are present in some tRNAs and rRNAs
introns
tRNA splicing is catalyzed by ()
protein factors
some rRNAs introns can catalyze their own removal -> they are ()
self-splicing
the 3’ ends of mature tRNAs have a conserved () -> attachment site for the amino acid
CCA sequence
CCA sequence is mostly added by ()
polymerization without template
CCA-adding enzyme takes () in a nucleotide-binding pocket that sequentially changes in size and shape depending on the 3’ end sequence of the bound tRNA
CTP or ATP
the presence of CTP or ATP in the nucleotide-binding pocket of the CCA-adding enzyme determines where () is added
C or A
additional role of CCA-adding enzyme
targeting unstable tRNAs for degradation
CCA-adding enzymes target unstable tRNAs for degradation through the addition of longer ()
CCACCA or CCACC tails
tRNA and rRNA nucleotides are often () modified after transcription
chemically
t/rRNA modification can be on the (1) or (2)
- nucleotide base
- ribose sugar ring
examples of relatively small t/rRNA modifications
- addition of H atom
- methylation of nitrogen or oxygen
- addition of selenium
examples of relatively large t/rRNA modifications
- incorporation of threonine
- multiple independent modifications
modifications in tRNAs:
- contribute overall to (1)
- give tRNAs the ability to (2)
- increase the () of tRNA molecules
- structural stability
- interact with other molecules
- repertoire of shapes, structures, and stability
the most common rRNA modifications
- ribose 2’-O-methylation
- pseudouridylation
in eukaryotes and archaea, () guide methylation and pseudouridylation of rRNAs and tRNAs; these molecules guide enzymes to the correct site
small nucleolar RNAs (snoRNAs)
snoRNAs associate with a complex of proteins to make ()
snoRNP
most vertebrate snoRNAs are made from the introns of ()
precursor mRNAs
snoRNAs that direct ribose methylation
boc C/D snoRNAs
snoRNAs that direct pseudouridylation
H/ACA snoRNAs
5’ ends of eukaryotic mRNAs are capped with (1) via a (2)
- 7-methylguanine nucleotide
- 5’-5’ triphosphate linkage
in the mRNA 5’ cap, the guanine is methylated at ()
N7
in more complex eukaryotes, in addition to the 5’ cap, the () of the second and sometimes third base are methylated
2’ oxygen
there are () steps in 5’ capping
3
proteins in action during 5’ capping in yeast
done by different enzymes
proteins in action during 5’ capping in C. elegans and mammals
first 2 reactions are done by a single enzyme
the 3’ end of most eukaryotic mRNAs has about 200 adenosines added
polyadenosine or polyA tail
mRNAs have () where pre-mRNAs are cleaved and the poly(A) tail is added
polyadenylation sites
mRNAs encoding () are exceptions and do not have poly(A) tails
metazoan histones
functions of poly(A) tail
- protects mRNA from degradation by exonucleases
- involved in initiation of protein synthesis
multiple polyadenylation sites are found in some mRNAs, and these can participate in regulation
alternative polyadenylation sites (APA)
polyadenylation at the distal site of cyclin D mRNA () regulatory sequences
retains multiple
polyadenylation at the proximal site of cyclin D mRNA () regulatory sequences
eliminates
functions of alternative polyadenylation sites
- regulate protein synthesis
- expand range of proteins products from a single mRNA
mRNA stability and translation are often regulated by ()
3’ untranslated regions (3’ UTR)
the variable 3’ UTR lengths specified by () can determine what regulatory sequences will be included
different polyadenylation site selections
polyadenylation at the 3’ end of eukaryotic mRNAs starts with an ()
intial cleavage
the initial cleavage in polyadenylation usually occurs after a (1) that lies between a (2) and a (3)
- CA
- conserved AAUAAA hexamer
- U or GU-rich region
after the initial cleavage in polyadenylation, ~200 adenosines are added by ()
poly(A) polymerase
a (smaller/larger) protein complex is required for polyadenylation that for 5’ capping
larger -> more complex to recognize different polyadenylation sites in different mRNAs
metazoan histones carry highly conserved () that recruit proteins of similar functions to those that bind poly(A) tails
stem-loop structures
5’ capping and 3’ polyadenylation are linked with each other and with other RNA polymerization processes via ()
RNA pol II
() is needed to allow RNA pol II to continue elongation
5’ capping
() is needed for efficient transcription termination
polyadenylation
the () is the largest subunit of RNA pol II
C-terminal domain (CTD)
at the CTD of RNA Pol II, () is responsible for mediating mRNA processing
RPB1
CTD becomes () on transcription initiation and recruits capping enzyme
partially phosphorylated
elongation leads to more phosphorylation of CTD, which recruits ()
splicing machinery
recruitment of splicing machinery leads to recruitment of ()
cleavage and polyadenylation complex
transcription and processing of eukaryotic mRNA occurs in the ()
nucleus
protein factors needed for mRNA transport to cytoplasm are loaded onto the mRNA during transcription, but () is needed before the RNA-protein complex can be released from the transcription complex
polyadenylation
Some mRNAs are located in specific regions of the cytoplasm –> this requires “()”, usually found at the 3′ end. They also regulate translation.
localization elements
most introns do not themselves contain genes and are excised and degraded; but there are exceptions:
snoRNAs and miRNAs
mechanism of intron removal
transesterification reactions
introns are far more prevalent in (1) than in (2)
- eukaryotes
- bacteria
introns allow for (), where exons are exchanged and reordered via recombination, allowing evolution of different genes
exon shuffling
() of introns gives different transcripts from the same gene
differential removal
2 steps of transesterifications
- intron is detached from exon 1
- exon 1 reacts with exon 2
most eukaryotic introns are removed by a complex called the (1), but some (including some introns in bacteria) are (2)
- spliceosome
- self-splicing
a reaction wherein a single phosphodiester bond is broken, and replaced by another phosphodiester bond of similar energy
transesterification reactions
similar energy of the 2 bonds involved in transesterification reactions means that ()
- reaction is ATP-independent
- reaction is easily reversible
insertion of introns into DNA; may have played a role in intron dispersal and genome evolution
reverse splicing of introns
Group () introns are found in bacteria, viruses, lower eukaryotes, and plants -> these introns excise themselves (i.e. ribozymes) from primary transcript and are ~120-145 nucleotides long
I (one)
in the 1st transesterification reaction of group I introns, a () attacks and detaches the 5’ end from exon 1
free guanosine
() are defined by the 3D structure of the intron by recognition of a conserved G-U wobble pair (for both group I and II introns)
splice sites
group () introns are in bacteria and in genes in the organelles of plants and fungi; ~400-1000 nucleotides long
II (two)
in the first transesterification reaction of group II introns, () within the intron attacks the exon1-intron junction
2’ OH of a specific A within the intron
in the second transesterification reaction of group II introns, the () of the newly released exon attacks the intron-exon2 junction
terminal 3’ OH
once released, a group II intron forms a branched ()
lariat intermediate
group II introns can also act as () by reverse splicing; they often have open reading frames within the introns that assist splicing
mobile genetic elements
most eukaryotic splicing is mediated by the spliceosome, which is made of several ()
small nuclear riboproteins (snRNPs)
a spliceosome catalyzed splicing is similar to that of group (I/II) introns
II
splice sites in mRNA are recognized by spliceosomes are defined by short sequence motifs:
- 5’ and 3’ splice sites
- branch-point nucleotide w/in intron
- polypyrimidine tract before 3’ splice site
usually, introns have (1) and (2) at their ends
- GU
- AG
the spliceosome has 5 snRNPs:
U1, U2, U4, U5, U6
each snRNP has a () of about 100-300 nucleotides, plus proteins
small nuclear RNA (snRNA)
the snRNAs in snRNPs work as the () of the snRNPs by forming base pairs
recognition part
a protein involved in splicing; found near the active site of the assembled spliceosome and thought to be important in catalysis
PRP8
proteins involved in splicing; probably help with structural rearrangements and promote lariat and mRNA release after processing
ATPases
the () is a component of the human spliceosome that marks the transcript as processed -> allows transcript to eventually be recognized by translational machinery for export and translation
exon-junction complex
() provide insights into the mechanistic details of splicing by the spliceosome
high-resolution cryoEM structures
majority of pre-mRNA introns have GU and AG dinucleotides at their termini and are recognized by () spliceosome
major
some introns in multicellular organisms are processed by ()
minor, or U12-dependent spliceosome
the minor/U12-dependent spliceosome includes the same U5 component but 4 different snRNPs
U11, U12, U4atac, U6atac
certain introns spliced by the minor spliceosome have () splice sequences
unusual (e.g. AU and AC at the intron termini)
() splicing is where exons in the same molecule are joined together
Cis
() splicing is unusual, and joins exons from different RNA molecules
Trans
in trans splicing, a short RNA (1), is joined to different mRNAs
spliced leader RNA, SL RNA
in trans splicing, SL RNA replaces the (), and interacts with other snRNPs at the 3’ splice site
U1 snRNP
majority of genes in eukaryotes undergo () where different combinations of exons are used
alternative splicing
possible outcomes of alternative splicing: use of (4)
- different combinations of exons
- alternative splice sites
- alternative transcriptional starts
- different termination sites
alternative splicing is important for (), such as in the Drosophila dscam gene
genetic diversity
The sequences defining intron-exon junctions are simple, so they can occur elsewhere by chance–these are ()
cryptic splice sites
2 broad conceptual models for how the spliceosome recognizes only true splice sites
- exon definition
- intron definition
() definition is thought to occur in mammals; 5’ and 3’ ends of an exon are brought together by interactions between U1 and U2 complex
exon
the exon is typically marked with (1), and the introns are bound with (2), which masks cryptic splice sites
- SR proteins
- hnRNPs
in () definition, introns are defined by interactions between 5’ and 3’ bound factors
intron
mutations at a 5’ splice site cause:
- in exon definition: (1)
- in intron definition (2)
- exon exclusion
- intron inclusion
in both intron and exon definition, the 5’ and 3’ splice sites are marked as they are (), facilitated by RNA pol and splicing components
transcribed (i.e. co-transcriptionally)
in both exon and intron definition, the final splicing complex must be one in which the ()
5’ and 3’ complexes interact with each other acroos the intron
needed in exon definition, but not in intron definition
reorganization of splicing intermediates
non-splice site regulatory sequences that strongly affect spliceosomal function
- splicing enhancers - positively affect splicing
- silencer sequences - mask splice sites or block spliceosome activity
splicing enhancers can be (2)
- intronic splicing enhancer sequences (ISE)
- exonic splicing enhancer sequences (ESE)
silencer sequences can be (2)
(intronic, exonic) splicing silencer sequences - ISS, ESS
() proteins appear to bind ESE sequences and can be important for exon definition
SR
an example of a silencer protein is (), which binds to intron elements and silences neighboring weak introns -> works in c-src mRNA
polypyrimidine tract binding protein (PTB)
alternative splicing is found in the (1), which encodes SRC tyrosine kinase -> positive and negative inputs regulates inclusion of (2) in the final mRNA product
- c-src mRNA
- neural-specific N1 exon
in neuronal cells, () binds to either side of the N1 exon in c-src mRNA and doesn’t repress its inclusion
PTBP2
additional modifications of mRNA () further enhances the range of molecules that can be produced
RNA editing
in RNA editing, specific nucleotides can be ()
modified, inserted, or deleted
nucleotide insertions can be (1) or (2)
- 1-2 nucleotides
- more extensive
example of a gene that undergoes extensive editing
Trypanosoma brucei NADH dehydrogenase 7 gene
3 main common RNA edits
- deamination of adenosine -> inosine
- deamination of cytidine -> uridine
- methylation of adenosine
most common RNA edit in more complex eukaryotes
deamination of adenosine to inosine
inosine is interpreted as (), thus changing the coding region and can change the final protein sequence
guanosine
() catalyze the deamination of adenosine to inosine by targeting double-stranded RNA regions
adenosine deaminases that act on RNA (ADARs)
RNA edit that has been found mainly but not exclusively in plant mitochondrial and chloroplast mRNAs
deamination of cytidine to uridine
RNA edit that was revealed by deep sequencing
methylation of adenosine
cytidine to uridine deamination is also observed in the mRNA that makes human (), which is involved in the binding and transport of lipids throughout the human body
apolipoprotein B
reversible methylation of adenosine is mediated by () proteins in the nucleus
writer and eraser
methylated adenosines are read by () proteins in the cytoplasm
reader
binding proteins of ‘reader’ proteins to methylated adenosines in () may be involved in regulation of translations
5’ untranslated regions (UTRs)
in uridine addition, 20-50 nucleotide () bind to mRNAs and define insertion and deletion locations
guide RNAs
uridine addition is catalyzed by (1), while uridine deletion is mediated by (2)
- 3’ terminal uridylyl transferase
- 3’ tp 5’ exonuclease
RNAs need to be (), removing RNAs that are no longer needed and recycling the nucleotides
degraded
RNA stability is described as (), the time in which the amount of RNA is reduced by half
RNA half-life
RNA stability is affected by several factors
- structures at the 5’ and 3’ ends (5’ cap, 3’ poly(A) tail)
- stem-loop structures
- other RNA processes (splicing, transport, translation, etc)
the 5’ cap in eukaryotic mRNAs protects against ()
exonuclease digestion
in bacterial, a 3’ poly(A) tail (1) stability, while it (2) stability in eukaryotic mRNA
- decreases
- increases
elements like () that remove poly(A) tails in eukaryotes decrease stability
AU-rich elements (ARE)
3’ stem-loop in bacteria (incl. those formed in Rho-independent termination) protect against ()
3’ to 5’ exonuclease activity
() in vertebrates encodes an ARE-containing short-lived transcription factor that promotes cellular growth
c-fos
some tumor causing viruses in vertebrates express (), which does not have ARE -> transcript is not degraded properly, leading to excessive cell growth
v-fos
in bacterial mRNAs, degradation is often initiated by an (1), often (2)
- endonuclease
- RNase E
products of the first digestion of bacterial mRNAs are then degraded by ()
3; to 5’ exonucleases
RNase E is part of the (), which also has an RNA helicase and a 3’ to 5’ exonuclease
degradosome complex
species lacking RNase E use (), which has 5’ to 3’ exonuclease as well as endonuclease activity
RNase J
a 5’ triphosphate inhibits RNase E activity -> this is converted to a monophosphate by ()
RppH
3’ poly(A) tails hinder rather than aid in degradation in eukaryotes -> first step in degradation is often tail shortening by a ()
deadenylase
mammalian cells respond to (1) levels -> partially regulated by the (2)
- iron
- transferrin receptors (allow import of transferrin-bound iron)
when cellular iron is low, transferring receptor mRNA is protected from degradation by (1) that bind to stem-loop (2)
- iron regulatory proteins (IRP1, IRP2)
- iron response elements (IRE)
Foreign nucleic acids are removed by (1) in eukaryotes and (2) in bacteria.
- RNA interference (RNAi)
- CRISPR interference
recognition and degradation of foreign (double-stranded) RNAs was termed (1) in C. elegans and (2) in plants
- RNA interference (RNAi)
- post-transcriptional gene silencing (PTGS)
in RNAi/PTGS, double-stranded RNA is first cleaved into small fragments by ()
Dicer
in RNAi/PTGS, double-stranded fragments are loaded onto the () and one strand is released
RNA-induced silencing complex (RISC)
in RNAi/PTGS, the remaining guide strand directs RISC to complementary full-length RNAs, which are cleaved by the () within RISC
Argonaute protein
In bacteria and archaea, () are involved in degradation of foreign DNA; foreign DNA is integrated into the () loci
clustered regularly interspaced palindromic repeats (CRISPR)
in eukaryotic cells, defective mRNAs are removed by (3)
- nonsense-mediated decay (NMD)
- non-stop decay (NSD)
- no-go decay (NGD)
defective () are removed by specific decay mechanisms
endogenous RNAs
in eukaryotes, ribosomes on defective RNAs are marked by interaction with proteins such as the (), which recruit RNases to degrade the RNA
EJC
in bacteria, stalled ribosomes are recognized by a complex containing (), an RNA that acts both as a tRNA and as an mRNA
tmRNA
to mediate precise RNA-protein interactions, proteins have specific ()
RNA-binfing motifs
examples of RNA-binding motifs
- RRM
- KH
- PAZ
most common RNA-binding motif is the (), which has alpha helices and 4 beta sheets in a sandwich -> adaptable and can bind RNAs with different structures
RNA-recognition motif (RRM)
the RRM is also known as ()
RNA-binding domain (RBD) or ribonucleoprotein (RNP) domain
() domains also bind single-stranded RNA
KH and PAZ
() domains have an RNA-binding groove formed by 2 alpha helices and 1 beta strand
KH
() domains have a pocket formed from beta strands and an alpha helix; this pocket interacts with the single-stranded overhangs of siRNA
PAZ
PAZ domains are found in many (1) proteins, like (2)
- RNAi
- Dicer
RNase III family enzymes have (); these proteins have an alpha helix and 2 loop regions that interact with 3 grooves on dsDNA
double-stranded RNA-binding domains (dsRBDs)
interacting grooves in RNase III family enzymes
1 major, 2 minor grooves
RNA-binding proteins often have (1/ >1) binding motif
> 1
