DNA

1. Post Transcriptional
Modifications
RNA Splicing & Alternative Splicing
Submitted By:
 Haseeb Ahmed
 Umm-e-Aiman Sheikh
 Maheen Sarfraz Ahmed
 Muqadas
 Yusra Aslam
 Hajra Arshad
 Eiman Afroz

2. • Post-transcriptional modifications of pre-mRNA occurs in three
main steps
1. Capping
2. Polyadenylation
3. Splicing
• It takes place in the nucleus.
• After these modifications, the mature mRNA molecules have to
be translocated into the cytoplasm, where protein synthesis
occurs.
INTRODUCTION

4. Purpose
To be recognized by molecules that mediate RNA translation into
proteins.
To cut out that RNA sequence portions that are not supposed to be
translated into proteins.
To increase the translation process significantly.

5. 5′ End Capping
• As soon as RNA polymerase lI has produced about 25
nucleotides of RNA, the 5' end of the new RNA molecule is
modified by addition of a "cap" that consists of a modified
guanine nucleotide.
• The capping reaction is performed by three enzymes
acting in succession:
• one (a phosphatase) removes one phosphate from the 5
end of the nascent RNA, another (a guanyl transferase)
adds a GMP in a reverse linkage (5 to 5' instead of 5' to 3),
and a third (a methyl transferase) adds a methyl group to
the guanosine.
• Because all three enzymes bind to the phosphorylated
RNA polymerase tail, they will modify the 5 end of the
nascent transcript a soon as it emerges
from the polymerase.

6. Polyadenylation
• The poly-A tail is a long chain of adenine nucleotides that is
added to messenger RNA (mRNA) molecule during RNA
processing to increase the stability of the molecule.
• Immediately after a gene in a eukaryotic cell is transcribed, the
new RNA molecule undergoes several modifications known as
RNA processing.
• These modifications alter both ends of the primary RNA
transcript to produce a mature mRNA molecule. The processing
of the 3' end adds a poly-A tail to the RNA molecule.
• First, the 3' end of the transcript is cleaved to free a 3' hydroxyl.
Then an enzyme called poly-A polymerase adds a chain of
adenine nucleotides to the RNA.

7. • This process, called polyadenylation, adds a poly-A tail that is between100
and 250 residues long.
• The poly-A tail makes the RNA molecule more stable and prevents its
degradation.
• Additionally, the poly-A tail allows the mature messenger RNA molecule to
be exported from the nucleus and translated into a protein by ribosomes in
the cytoplasm.

8. RNA Splicing
• The protein coding sequences of eukaryotic genes
are typically interrupted by noncoding intervening
sequences(introns).
• An intron is a long stretch of noncoding DNA found
between exons (or coding regions) in a gene.
• Genes that contain introns are known as
discontinuous or split genes as the coding regions
are not continuous. Introns are found only in
eukaryotic organisms.
• It is considered as "junk DNA", introns likely play an
important role in regulation and gene expression

9. ● “A large RNA-protein
complex that catalyzes the
removal of introns from
nuclear pre m-RNA”
● Nuclear pre-mRNA splicing
is catalyzed by the
spliceosome, a multi-
megadalton ribonucleoprotein
(RNP) complex.
Spliceosome Complex

10. Types of Spliceosomes
Two unique spliceosomes coexist in most eukaryotes:
 the U2-dependent spliceosome
 less abundant U12-dependent spliceosome

11. Parts of pre m-RNA that take part
in splicing
• Information provided by a pre-mRNA
that contributes to defining an intron is
• limited to short, conserved sequences
at the 5′ splice site (ss),
• 3′ splice site (ss)
• branch site (BS).
• polypyrimidine tract (PPT)
• cis-acting pre-mRNA elements include
exonic and intronic splicing enhancers
(ESEs and ISEs)
• silencers (ESSs and ISSs)

12. snRNPs
“Small nuclear ribonucleoproteins; RNA protein complexes
combine with unmodified m-RNA and various other proteins to
form a spliceosome”.
Five snRNPs combine together to form complex spliceosome (a
large RNA protein molecule complex upon which splicing of
pre m-RNA occurs.
• U1
• U2
• U4
• U5
• U6 (U4 AND U6 are present in conjugation with each other)

13. snRNPs Structure

14. Procedure of Splicing of pre m-RNA
using spliceosomal complex

15. Simple Representation
STEP:01
STEP:02
STEP:03

16. STEP:04
STEP:05

17. Trans-Splicing
“Trans-splicing is another form of
RNA splicing where exons from
two different primary RNA
transcripts are joined end to end
and ligated. It is usually found in
eukaryotes and mediated by
spliceosome.”

18. Mechanism
 Trans-splicing is characterized by the joining of two separate exons
transcribed RNAs.
 The signal for this splicing is the INTRON at the 5′end of the mRNA, in
the absence of a functional 5′ splice site upstream.
 When the 5′ INTRON in spliced, the 5′ splice site of the spliced leader
RNA is branched to the intron and forms an intermediate.
 This step results in a free spliced leader exon. The exon is then spliced to
the first exon on the pre-mRNA and the intermediate is released.
 Trans-splicing differs from cis-splicing in that there is no 5' splice site on
the pre-mRNA. Instead the 5' splice site is provided by the SL sequences

19. Types of Trans-splicing
 5 trans-splicing
3 trans-splicing
Internal Trans-splicing

20. RNA Splicing
“Splicing is a post-
transcriptional process in
which introns are removed
and exons are joined into
a mature transcript.”

21. Alternative Splicing
• “Alternative splicing is a regulated process where
multiple protein isoforms are encoded by a single
gene via exons, parts of exons, or introns being
differentially joined or skipped.”
• In humans, more than 95% of multi-exonic genes are
alternatively sliced. This increases the diversity of
proteins encoded by the genome.

23. Explanation
 The diagram shows an mRNA transcript that needs to be
spliced.
 The introns get spliced out, some of them are degraded
while others act as regulatory processes.
 The exons are differentially joined or skipped resulting in
multiple protein isoforms.
 So in alternative splicing, multiple protein isoforms are formed
which are encoded by a single gene and this occurs because
exons are joined or skipped in different ways resulting in a lot
of different combinations.

24. Explanation
 Now these 3 isoforms are still mRNA transcripts which
are then encoded into proteins.
 Since the protein isoforms have different sequences, they
are translated at the ribosome into proteins with different
structures. These structures are related since they are
made from the same exon sequences but in different
combination orders.
 These different structures lead to different functions.
Thus all the protein isoforms are from the same gene but
because of alternative splicing they carry out different
functions in the cell.

25. A highly regulated
process!

26. Regulatory Elements
Exonic Splicing
Enhancers
(ESEs)
• Short nucleotide
sequences within
the exons that
promote exon
inclusion by
binding to
splicing
regulatory
proteins.
Exonic Splicing
Silencers (ESSs)
• Sequences
within exons that
inhibit exon
inclusion by
preventng the
binding of
splicing
regulatory
proteins.
Intronic Splicing
Enhancers (ISEs)
• Sequences
within introns
that promote
exon inclusion by
interacting with
splicing
regulatory
proteins.
Intronic Splicing
Silencers (ISSs)
• Sequences
within introns
that exhibit exon
inclusion by
preventing the
binding of
spicing
regulatory
proteins.
1. Specific Nucleotide Sequences

27. Regulatory Elements
2. Activator and Repressor Proteins
They control which places get cut, which places get skipped and which places
get joined.
3. RNA/Protein Complex: Spliceosome
It works together with the activator and repressor proteins to cut and join in the
right places.

28. • Alternative splicing of pre-mRNA is an essential
mechanism to enhance the complexity of gene
expression, and it also plays a vital role in cellular
differentiation and organism development.
• Alternative splicing has a role in almost every aspect of
protein function, including binding between proteins
and ligands, nucleic acids or membranes, localization,
and enzymatic properties.
• Alternative splicing is also essential for other functions
like the identification of novel diagnostic and
prognostic biomarkers, as well as new strategies for
therapy in cancer patients.

29. Modes of Alternative Splicing

30. • Exclusion of one or more exons
from the final mRNA transcript.
• Results in a mature mRNA
with a different exon
composition.
Results in a mature mRNA
with a different exon
• Inclusion of one or more introns
within the mature mRNA
transcript.
• Adds variability to the mRNA
and resulting protein.
1. Exon Skipping
(Cassette Exon)
2. Intron Retention

31. 3.Alternative 5′ Splice Site
• Recognition of different 5' splice
sites within an exon.
• Leads to the inclusion of
different portions of the exon in
the mature mRNA.
• Recognition of different 3' splice sites
within an exon.
• Results in the inclusion of different
portions of the exon in the mature
mRNA.
4.Alternative 3′ splice site

32. 5.Mutually Exclusive
Exons:
• Presence of two or more
exons, with only one
included in the mature
mRNA at a time.
• Gives rise to distinct
protein isoforms.
• Utilization of different
transcription start sites.
• Influences the inclusion of
different exons in mRNA
transcripts.
6.Alternative Promoter
Usage

33. • Selection of different
polyadenylation sites within a gene.
• Leads to different 3' untranslated
regions in mature mRNA transcripts.
• Splicing can occur in either direction for
a single exon flanked by two introns.
• Adds complexity by allowing the
production of mRNA isoforms with
different exon compositions.
7.Alternative polyadenylation 8.Bidirectional splicing

34. Significance of Alternative Splicing
• Enhances proteome diversity.
• Plays a role in tissue-specific
expression.
• Regulates protein function and
cellular processes.
• Implicated in diseases, including
cancer and neurodegenerative
disorders.

35. Mechanism
• Alternative splicing is a process in
eukaryotic gene expression by which
a single pre-messenger RNA (pre-
mRNA) can be spliced in different
ways to produce multiple mRNA
isoforms.
• The mechanism of alternative splicing
involves the selection of different
splice sites within a pre-mRNA
molecule, leading to the inclusion or
exclusion of specific exons or
portions of exons in the mature
mRNA.

36. • 1-Transcription:
• The first step is the transcription of DNA into a pre mRNA
molecule. pre-mRNA contains exons (coding regions) and
introns (non-coding regions).
• 2-Splicing Signals:
• Within the pre-mRNA, there are specific sequences called splice
sites. These include the 5' splice site (at the beginning of an
intron), the 3' splice site (at the end of an intron), and a branch
point sequence Additionally it contains regulatory elements in
exons

37. 3-Spliceosome Assembly: The spliceosome is a large and dynamic
molecular machine composed of small nuclear ribonucleoproteins
(snRNPs) and other proteins. The spliceosome assembles on the pre
mRNA at the splice sites, forming a complex.
4-Splicing Steps:
1. Recognition of Splice Sites: The spliceosome recognizes the 5' and
3' splice sites, aided by the branch point sequence.
2. Formation of Lariat Structure: The intron is excised, forming a
lariat structure with the 5' end of the intron attached to the branch
point.
3. Exon Ligation: The exons are ligated together, resulting in the
mature mRNA.

38. 5-Alternative Splicing:
 In alternative splicing, different splice sites can be utilized during this
process. This can lead to different combinations of exons being included in
the mature mRNA, resulting in multiple mRNA isoforms from a single gene.
 There are several types of alternative splicing patterns, including exon
skipping, intron retention, alternative 5' splice site usage, and alternative 3'
splice site usage. The specific combination of exons included in the mature
mRNA can result in different protein products, contributing to the diversity of
the proteome. The regulation of alternative splicing is complex and involves
various factors, including splicing factors and regulatory elements

39. Splicing and DNA Damage Response
• Detection of DNA Damage:
DNA repair pathways and cell cycle checkpoints, are activated to assess and repair the
damage.
• Activation of Checkpoints:
DNA damage activates cell cycle checkpoints that temporarily halt the cell cycle,
allowing time for repair processes to take place.
• Transcription-Coupled Repair:
Its mechanisms identify and repair damage during active transcription.

40.  Detection of DNA Damage
during Transcription
 Stalling of Transcription
Machinery
 Recruitment of Repair Factor
 DNA Repair
 Resumption of Transcription

41. Splicing and DNA Damage Response
 Alternative Splicing Regulation:
The cell may alter the splicing of certain pre-mRNAs to produce mRNA
variants with different exon compositions.
 Splicing Factors and DNA Repair Genes:
Changes in splicing factor activity may influence the inclusion or
exclusion of exons in mRNA transcripts related to DNA repair

42. Splicing factors and DNA repair

43. Splicing and DNA Damage Response
 ATM and DNA Damage Signaling:
The ATM (ataxia-telangiectasia mutated) protein, a key player in DNA
damage response, is involved in splicing regulation.
 Apoptosis Regulation:
where DNA damage is severe and irreparable, alternative splicing can
lead to the production of mRNA variants that promote apoptosis
(programmed cell death) as a protective measure.

44. Experimental Manipulation of Splicing
 Antisense Oligonucleotides (ASOs):
ASOs can be designed to target specific splice sites, modulating splicing
patterns by blocking or enhancing the recognition of splice junctions.
Antisense oligonucleotides are utilized in the manipulation of splicing as:
 Binding to Pre-mRNA: ASOs are designed to be complementary to
specific regions of pre-mRNA, which is the precursor to messenger RNA
(mRNA) and undergoes splicing to generate mature mRNA.

45.  Modulation of Splicing Patterns:
The binding of ASOs to pre-mRNA can lead to various effects on the splicing
process. One common strategy is to promote exon skipping or inclusion.
 Correction of Splicing Errors:
In some genetic disorders, mutations may lead to splicing errors, causing the
inclusion of incorrect exons or skipping of essential exons.

46. ASOs and SPLICING MANIPULATION

47.  RNA Interference (RNAi):
RNAi techniques involve introducing short RNA molecules to silence or
knockdown specific splicing factors, thereby impacting the splicing of target
genes.
 Exon Skipping or Inclusion:
Designing synthetic RNA molecules, such as modified mRNA or viral vectors,
to promote exon skipping or inclusion, leading to the production of desired
mRNA isoforms.
 Splice-Switching Oligonucleotides (SSOs):
SSOs are designed to redirect splicing by binding to specific target sequences,
modifying splice site recognition and influencing the splicing process.

48. Mutation and Diseases related to
RNA Splicing & Alternative
Splicing

49. Pre-mRNA splicing and Human
disease
● Disruption of pre-mRNA splicing results in a primary cause of disease
Classification of splicing mutations
● Cis effects: mutations that disrupt use of constitutive splice sites
● Cis effects: mutations that disrupt use of alternative splice sites
● Trans effects: mutations that affect the basal splicing machinery
● Trans effects: mutations that affect regulators of alternative splicing

50. Cis effects: Mutations that disrupt use of constitutive
splice sites
● Mutations that disrupt classical splicing signals of a constitutive exon are
often single nucleotide substitution.
● The result is expression of unnatural mRNAs, and most often loss of
function of the mutated allele due to nonsense-mediated decay (NMD) or
expression of proteins containing internal deletions, a shift in the reading
frame, or C-terminal truncations.

51. Cis effects: Mutations that disrupt use of Alternative
Splice Sites
● Mutations affecting alternative splice sites shift the ratio of natural protein
isoforms rather than causing aberrant splicing with a loss of function

52. Familial Isolated Growth Hormone Deficiency Type II
(IGHD II):
● IGHD II is a dominantly inherited disorder caused by mutations in the growth
hormone gene (GH-1).
● G → A mutation in the first nucleotide of intron 3 disrupts the 5′ splice site and
causes complete exon skipping and expression of the 17.5-kD isoform

53. Frasier Syndrome (FS):
● Mutations in the Wilms tumor suppressor gene (WT1),
impacting kidney and gonad development.
● Individuals with FS were found to have mutations that
inactivate the downstream 5′ splice site, resulting in a shift to
the −KTS isoform

54. Frontotemporal Dementia and Parkinsonism linked
to Chromosome 17 (FTDP-17):
● FTDP-17 is caused by mutations in the MAPT gene, leading to tau
protein aggregation.
● Mutations affecting splicing, particularly in and around exon 10,
alter the balance between 4R-tau and 3R-tau isoforms.

55. Trans effects: mutations that affect the basal
splicing machinery
Specifically mutations in components of the spliceosome and auxiliary factors
regulating alternative splicing
Spinal Muscular Atrophy (SMA)
 SMA is an autosomal recessive disorder primarily caused by a homozygous
loss of the telomeric copy of the SMN1 gene
 The deficiency of SMN causes defects in pre-mRNA splicing, leading to
weakness, atrophy, and paralysis of voluntary muscles.

56. Mutations in the splicing machinery and
associated diseases
 U1 snRNA Mutations and Medulloblastomas (Brain
Cancer)
U1 snRNA is involved in the earliest stages of
spliceosome assembly by binding to the 5'-splice site
(5'-SS)
A hotspot A > G/C transition mutation in U1 snRNA was
associated with the Sonic Hedgehog (SHH)
 U5 Prp8 Mutations and Retinitis Pigmentosa:
Autosomal dominant
Prp8 clustered in the Jab1/MPN domain,
impacting its interactions with the RNA helicase
Brr2

57. Trans effects: Mutations that affect regulators of
Alternative Splicing
Myotonic Dystrophy (DM):
• DM is an autosomal dominant disorder
• DM1 and DM2, caused by expansions in the CTG and CCTG repeats, respectively
Inactivation of a splicing regulator affects natural pre-mRNA targets

58. Conclusion
● Regulation of alternative splicing represents an important means to fine-tune
gene expression.
● Individual splicing regulators control much larger group of genes than specific
transcription factors.
● The combination of alternative splicing database, tandem mass spectrometry
may aid with identification, analysis and characterization of potential
alternative splicing isoforms.
● Combining alternative splice variants dramatically expands the proteomics of
genomes.-

59. Thank you!