Introduction to gene silencing Levels of Gene silencing DNA methylation RNA interference CRISPR-cas System

1. Gene Silencing
Hajra
The Women University Multan

2. TABLE OF CONTENTS
• Introduction to gene silencing
• Levels of Gene silencing
• DNA methylation
• RNA interference
• CRISPR-cas System

3. INTRODUCTION
• Interruption or suppression of transcription or translation of the
mRNA of the target gene by mechanisms other than genetic
modification
• Generally used to describe the "switching off" of a gene
• Knock down process

4. Levels of Gene silencing
Silencing of Genes regulation at either the transcriptional or post-
transcriptional level
Transcriptional gene silencing (TGS)
• It Causes gene silencing by:
• DNA methylation.
• Heterochromatin formation.

5. Post transcriptional gene silencing
(PTGS)
• It is known commonly as RNA interference
(RNAi). It causes silencing by destruction of the
mRNA of the gene to which the siRNA shows
perfect complementarity.

6. Transcriptional gene silencing
• Makes DNA inaccessible to transcriptional machinery (RNA
polymerase, transcription factors , etc.)
• TGS Involved in the regulation of many cellular processes,
including X chromosome inactivation, chromosome stability, chromatin
structure and embryonic development
•

7. DNA methylation
• DNA methylation ---a major source of transcriptional gene
silencing (TGS)
• DNA methylation---addition of methyl group from a cofactor S-
adenosylmethionine are transferred to purine ring to the 5
position of the cytosine pyrimidine ring or the number 6
nitrogen of The adenine

8. • DNA methylation comes under phenomenon of epigenetics
• The term ‘Epigenetics’ describes heritable genetic modifications that are
not attributable to changes in the primary DNA sequence.
• CpG islands (Cytocine-phospho-Guanine) are 300-3000 bp stretches of
DNA rich in CpG

9. Location of CpG Islands
• CpG island often located in the promoter regions of genes in
the normal cell are typically unmethylated, allowing transcription
• CpGs found outside promoter regions are commonly methylated
involved in silencing of transcription of repetitive sequences
and parasitic sequence elements, such as viral DNA

12. • The addition of methyl groups is carried out by a family of enzymes,
DNA methyltransferases (DNMTs)
• DNMT1 is the proposed maintenance methyltransferase that is
responsible for copying DNA methylation patterns to the daughter
strands during DNA replication
• DNMT3a and DNMT3b are the de novo methyltransferases that set
up DNA methylation patterns in naked DNA early in development

14. • DNMT3L is a protein that is homologous to the other DNMT3s but
no catalytic activity
• DNMT3L assists the de novo methyltransferases by increasing
ability to bind to DNA and stimulating their activity
• DNMT2 (TRDMT1) does not methylate DNA but instead methylates
cytosine-38 in the anticodon loop of aspartic acid transfer RNA

15. • DNA methylation works with histone modifications and microRNA
(miRNA) to regulate transcription
• Chemical modifications that include methylation, acetylation,
ubiquitination, and phosphorylation added to three specific amino
acids on the N-terminal histone tails
• Dnmts directly interact with enzymes that regulate histone
modifications typically involved in gene repression
• Dnmt1 and Dnmt3b can both bind to histone deacetylases that remove
acetylation from histones to make DNA pack more tightly and restrict
access for transcription

16. • Methylation may affect the transcription of genes in two ways
• 1) impede physical access of TFs and, therefore, suppress gene
regulation.
• 2) methylated DNA may be bound by proteins known as methyl-CpG-
binding domain proteins (MBDs)
• Recruit additional proteins to the locus, such as histone deacetylases
and other chromatin remodeling proteins that can modify histones,
thereby forming compact, inactive chromatin, termed
heterochromatin

17. DNA demethylation is either passive or active
• Passive DNA demethylation occurs in dividing cells. As
Dnmt1 actively maintains DNA methylation during cell
replication, its inhibition or dysfunction allows newly
incorporated cytosine to remain unmethylated and conse-
quently reduces the overall methylation level following
each cell division

18. • Active DNA demethylation can occur in both
dividing and non-dividing cells but the process
requires enzymatic reactions to process the 5mC
in order to revert it back to a naked cytosine

19. Post transcriptional gene silencing (PTGS)
• RNA interference
• A molecular mechanism in which fragments of double stranded nucleic acid
(dsRNA) interfere with the expression of a particular gene that shares a
homologous sequence with the dsRNA
• Cellular components of Gene Silencing
• MicroRNAs (miRNAs)
• Small interference RNAs (siRNAs)
• Dicer
• RISC

20. • MicroRNAs (miRNAs) constitute a novel, phylogenetically
extensive family of small RNAs (~22 nucleotides)
• produced by Dicer from the precursors of ~70 nucleotides (pre-
miRNAs)
• Small interfering RNAs (siRNAs)
• These are double stranded RNA from exogenous sources like
viruses, transgenes or transposons, i.e; originate from double
stranded RNAs

21. PAZ: proteins Piwi, Argonaut and Zwille.

23. • dsRNA is sliced by an ATP dependent ribonuclease (DICER)
into short interfering RNAs
• Duplexes of 21-24 nucleotides with 2 nucleotides 3'overhang
,5'phosphate termini and 3' hydroxyl group
• siRNA or miRNA molecules associate with an enzyme complex
called the RNA-induced silencing complex (RISC)
• Within the RISC, the short double-stranded RNA is denatured
and the sense strand is degraded

24. • The RNA/RISC complex becomes a functional and highly specific
agent of RNAi
• RNAi can take one of two different pathways
• Anti-sense RNA in the RISC is perfectly complementary to the
mRNA, the RISC will cleave the mRNA.
• The antisense RNA within the RISC is not exactly complementary to
the mRNA, the RISC complex stays bound to the mRNA, interfering
with the ability of ribosomes to translate the mRNA--- cleaved mRNA
is then degraded by ribonucleases

25. • Repress the transcription of specific genes and larger regions of the
genome by RNA-induced initiation of transcription silencing complex
(RITS)
• RITS then recruits chromatin remodeling enzymes to these regions
• These enzymes methylate histones and DNA, resulting in
heterochromatin formation and subsequent transcriptional silencing

27. CRISPR-cas System

28. • An array of short repeated sequences separated by spacers in a region of
DNA called Clustered Regularly Interspaced Short Palindromic Repeats
(CRISPR)
• The spacers derived from nucleic acid of viruses and plasmids and act as
recognition elements to find matching virus genomes
• Antiviral defense system
• Targets DNA or RNA protecting against viruses and other mobile genetic
elements

29. • The CRISPR locus, first observed in Escherichia coli
• Found on both chromosomal and plasmid DNA
• CRISPR activity requires the presence of a set of CRISPR-
associated (cas) genes
• Code for proteins essential to the immune response
• Offspring inherit the protection due to genome modification by
spacer acquisition

30. Stages of CRISPR-cas
mediated defense

31. • The key steps of CRISPR-cas immunity.
• 1) Adaptation: insertion of new spacers into the CRISPR locus.
• 2) Expression: transcription of the CRISPR locus into long
precursor CRISPR RNA and processing of pre-CRISPR RNA
into mature crRNA by cas proteins and accessory factors
• 3) Interference: detection and degradation of mobile genetic
elements by CRISPR RNA and cas protein

32. Stages of CRISPR-cas mediated defense

33. Types of CRISPR-cas
systems

34. Type I CRISPR-cas system
• Signature protein Cas3, a protein with both helicase and DNase domains
responsible for degrading the target
• Cascade binds crRNA and locates the target, and most variants are also
responsible for processing the crRNA
• Complex of different Cas proteins---Cascade (CRISPR-associated
complex for antiviral defense)

35. • The first 6–12 nt of the crRNA spacer are most important for target
binding and are termed the seed sequence
• Production of R-loop by base pairing of the crRNA with the
complementary DNA strand and additional displacement of the non-
complementary strand
• Cascade recruits Cas3 to degrade the targeted viral DNA molecule
• Dissociation of Cascade and ready for action again
• No base pairing of 5' terminal tag of the crRNA and the PAM sequence to
avoid host genomic encoded CRISPR cluster degradation

37. Type II CRISPR-cas system
• Require only the Cas9 protein for adaptation, crRNA expression
and interference
• in addition tracrRNA and the crRNA
• trans-activating crRNA (tracrRNA) contains a 25 nt long stretch
that is complementary to the crRNA repeat sequence
• Two separate lobes for target recognition and nuclease activity

38. • Recognition lobe is important for binding crRNA and target DNA
• The nuclease lobe cleave the complementary and non-complementary
strands of the target
• Cas9 ---RNA duplex formation by base pairing of tracrRNA and pre-
crRNA
• Cleavage of duplex by RNase III generates mature crRNAs
• In the interference Cas9 cleaves the DNA strand complementary to the
crRNA and non complementary strand

40. Type III CRISPR-cas system
• pre-crRNA maturation by sequence-specific processing step mediated by Cas6
• Yield mature crRNAs with a defined 5' end and variable 3' end
• Interference by complex of Csm or Cmr proteins
• Csm complexes target DNA and Cmr complexes targets RNA
• No PAMs are detected for Type III systems
• Extension of crRNA base pairing into the repeat region of host DNA---self-
nonself descrimination

42. • Only the type II CRISPR/Cas systems are established for genome editing
or gene silencing
• Difference between the three major CRISPR/Cas types
• The interference reaction of both, type I and III systems, relies on multi-
protein complexes
• Protein-engineering of a single Cas9 protein is more straightforward than
optimization of Cascade or Cmr/Csm complexes
• No need of PAM sequences for interference should be advantageous for
more versatile editing events

43. Applications of
CRISPR-cas system

44. • In genotyping method is known as spacer oligonucleotide typing
(spoligotyping) to identify closely related bacterial strains e.g. M.
tuberculosis
• In dairy industry, production of Danisco----marketing starter cultures
for improved cheese production and other applications. The cultures
contain bacteria that have CRISPRs with improved resistance to
phages
• Cas9 produces a single double-stranded break in the DNA, an
important feature of a gene-editing tool

45. • Cas9 has been developed as an antimicrobial agent that can be used
to specifically target antibiotic-resistant and/or highly virulent
strains of bacteria
• Gene therapy applications have also been demonstrated by repairing
the cftr gene in cultured cells from human cystic fibrosis patients
• Cas9 also holds potential for treatment of viral infections, as
demonstrated for HIV and hepatitis B

46. • CRISPR-Cas systems used for gene silencing by interfering
with RNA polymerase binding or elongation
• A short version of Cas9 to be deliverable by Adeno-associated
virus, greatly facilitating its use in somatic gene therapy

47. Biological role of gene silencing
• Protection against pathogens including viruses
• Production of resistant plants
• Protection against endogenous transposable elements
• Protection against foreign or duplicated genes

48. Applications of Gene silencing
• In biotechnology for production of virus resistant plants and
engineering of food plants that produce lower levels of natural
plant toxins
• In animals, parasite treatment in mammals
• In scientific research, knock out genes with known sequence to
study their functions under functional genomics
• In medicine: AIDS: It has been shown that siRNAs can inhibit
HIV replication effectively in culture either by inhibiting viral
genes or human genes