Genomic imprint details

1. PRESENTER: DR. SWARUPA MALLA,
1ST YEAR POSTGRADUATE.
MODERATOR: DR.G.VAHINI,
PROFESSOR,
DEPARTMENT OF PATHOLOGY.
PRESENTER: DR. SWARUPA MALLA,
1ST YEAR POSTGRADUATE.
MODERATOR: DR.G.VAHINI,
PROFESSOR,
DEPARTMENT OF PATHOLOGY.

2. GENES
CONCLUSION
GENOMIC
IMPRINTING IN
TUMORIGENESIS
WHAT IS GENOMIC
IMPRINTING?

3. LEVELS OF ORGANIZATION

6.  The human genome contains some 3.2 billion DNA base
pairs.
 Yet, within the genome there are only about 20,000
protein-encoding genes.
 This constitutes just 1.5% of the genome.

7.  This 1.5% genes are the blueprints that instruct the
assembly of the enzymes, structural elements, and
signaling molecules within the 50 trillion cells that make
up the human body.
 However, over 85% of the human genome is ultimately
transcribed; nearly 80% is devoted to regulation of gene
expression.

8.  Proteins provide the building blocks and machinery
required for assembling cells, tissues, and organisms.
 It is the noncoding regions of the genome that provide
the critical “architectural planning.”

9.  There are five major classes of functional non–
protein coding sequences in the human genome:
1. Promoter and enhancer regions
2. Chromatin structures.
3. Noncoding regulatory RNAs.
4. Mobile genetic elements (e.g., transposons)
5. Telomeres and centromeres

10.  Promoter and enhancer regions that provide
binding sites for transcription factors.

15.  Over 60% of the genome is transcribed into RNAs that are
never translated but regulate gene expression through a
variety of mechanisms.
 The two best-studied varieties—micro-RNAs (miRNAs) and
long noncoding RNAs (lncRNAs).

16.  Mobile genetic elements (e.g., transposons)- make up
more than a third of the human genome.
 These “jumping genes” can move around the genome during
evolution, resulting in variable copy number and positioning
even among closely related species (e.g., humans and other
primates).

17.  A major component of centromeres is so-called satellite
DNA, consisting of large arrays—up to megabases in
length—of repeating sequences (from 5 bp up to 5 kb).
 Although classically associated with spindle apparatus
attachment, satellite DNA is also important in maintaining the
dense, tightly packed organization of heterochromatin.

18.  Many genetic variations (polymorphisms) associated with
diseases are located in non–protein-coding regions of the
genome.
 Thus variation in gene regulation may prove to be more
important in disease causation than structural changes in
specific proteins.
 The two most common forms of DNA variation in the human
genome are single nucleotide polymorphisms (SNPs) and
copy number variations (CNVs).

19. Nucleosomes consist of DNA segments 147 bp long that are
wrapped around a central core structure of low molecular weight
proteins called histones.

22.  Actively transcribed genes in euchromatin are
associated with histone marks/modifications that make
the DNA accessible to RNA polymerases.
 In contrast, inactive genes have histone
marks/modifications that enable DNA compaction into
heterochromatin.
 Histone marks are reversible through the activity of
“chromatin erasers.”

23.  VARIOUS HISTONE MODIFICATIONS ARE:
1. Histone methylation
2. Histone acetylation
3. Histone phosphorylation
4. DNA methylation
5. Chromatin organizing factors

24.  Histone methylation :
 Both lysines and arginines can be methylated by
specific writer enzymes.
 Methylation of histone lysine residues can lead to
transcriptional activation or repression, depending on
which histone residue is marked.
.

25.  DNA methylation:
 High levels of DNA methylation in gene regulatory
elements typically result in transcriptional silencing.
 Like histone modifications, DNA methylation is tightly
regulated by methyltransferases, demethylating
enzymes, and methylated-DNA-binding proteins.

27.  Histone phosphorylation- Serine residues can be
modified by phosphorylation; depending on the specific
residue, the DNA may be opened for transcription or
condensed and inactive.
 Chromatin organizing factors- They are believed to bind to
noncoding regions and control long-range looping of DNA.
 Thus regulating the spatial relationships between enhancers
and promoters that control gene expression.

29.  An allele is one of two or more versions of DNA
sequence (a single base or a segment of bases) at a
given genomic location.
 Alleles are a pair of genes that occupy a specific location
on a particular chromosome and control the same trait.

31.  Mendelian Disorders
 Complex Multigenic Disorders
 Chromosomal Disorders
 Single-Gene Disorders With nonclassic Inheritance

32. MENDELIAN DISORDERS :
 Transmission Patterns of Single-Gene Disorders:
 Autosomal Dominant Disorders
 Autosomal Recessive Disorders
 X-Linked Disorders
 Biochemical and Molecular Basis of Single-Gene
(Mendelian) Disorders:
 Enzyme Defects and Their Consequences
 Defects in Receptors and Transport Systems
 Alterations in Structure, Function, or Quantity of nonenzyme
Proteins
 Genetically Determined Adverse Reactions to Drugs

33.  Disorders Associated With Defects in Structural Proteins:
 Marfan Syndrome
 Ehlers-Danlos Syndromes (EDSs)
 Disorders Associated With Defects in Receptor Proteins:
 Familial Hypercholesterolemia
 Disorders Associated With Enzyme Defects:
 Lysosomal Storage Diseases
 Glycogen Storage Diseases (Glycogenoses)
 Disorders Associated With Defects in Proteins That
regulate Cell Growth

34. 2. COMPLEX MULTIGENIC DISORDERS
3. CHROMOSOMAL DISORDERS:
 Cytogenetic Disorders Involving Autosomes:
 Trisomy 21 (Down Syndrome)
 Other Trisomies
 Chromosome 22q11.2 Deletion Syndrome
 Cytogenetic Disorders Involving Sex Chromosomes:
 Klinefelter Syndrome
 Turner Syndrome
 Hermaphroditism and Pseudohermaphroditism

35. 4. SINGLE-GENE DISORDERS WITH NONCLASSIC
INHERITANCE:
 Diseases Caused by Trinucleotide-Repeat Mutations:
 Fragile X Syndrome (FXS)
 Fragile X–Associated Tremor/Ataxia Syndrome and
Fragile X–Associated Primary Ovarian Failure
 Mutations in Mitochondrial Genes—
 Leber Hereditary Optic Neuropathy
 Genomic Imprinting
 Prader-Willi Syndrome and Angelman Syndrome
 Gonadal Mosaicism

37.  We all inherit two copies of each autosomal gene, carried on
homologous maternal and paternal chromosomes.
 In the past, it had been assumed that there is no functional
difference between the alleles derived from the mother or the
father.
 Studies have now provided definite evidence that, at least
with respect to some genes, important functional differences
exist between the paternal allele and the maternal allele.

38.  These differences result from an epigenetic process called
imprinting.
 In most cases, imprinting selectively inactivates either the
maternal or the paternal allele.
 Thus, maternal imprinting refers to transcriptional silencing of
the maternal allele.
 Paternal imprinting implies that the paternal allele is
inactivated.

39.  Imprinting occurs in the ovum or the sperm, before
fertilization, and then is stably transmitted to all somatic cells
through mitosis.
 As with other instances of epigenetic regulation, imprinting is
associated with differential patterns of DNA methylation at CG
nucleotides.
 Other mechanisms include histone H4 deacetylation and
methylation.

40.  The exact number of imprinted genes is not known; estimates
range from 200 to 600.
 Although imprinted genes may occur in isolation, more
commonly they are found in groups that are regulated by
common cisacting elements called imprinting control
regions.
 Genomic imprinting is best illustrated by two uncommon
genetic disorders: Prader-Willi syndrome and Angelman
syndrome.

41. PRADER-WILLI SYNDROME
 Intellectual disability
 short stature
 Hypotonia
 profound hyperphagia,
Obesity
 small hands and feet
 hypogonadism
 del(15)(q11.2q13)

42. ANGELMAN SYNDROME
 intellectual disability
 microcephaly,
 ataxic gait
 Seizures
 inappropriate
laughter(HAPPY
PUPPET)
 del(15)(q11.2q13)

43. 1. First, the modification must be made before
fertilization.
2. It must be able to confer transcriptional silencing.
3. It must be stably transmitted through mitosis in somatic
cells.
4. It must be reversible on passage through the opposite
parental germline.

44. 1. Deletions
2. Uniparental disomy
3. Defective imprinting

46.  It is known that a gene or set of genes on maternal
chromosome 15q12 is imprinted (and hence silenced),
and thus the only functional alleles are provided by the
paternal chromosome.
 When these are lost as a result of a deletion, the person
develops Prader-Willi syndrome.

47.  Conversely, a distinct gene that also maps to the same region
of chromosome 15 is imprinted on the paternal chromosome.
 Only the maternally derived allele of this gene is normally
active.
 Deletion of this maternal gene on chromosome 15 gives rise
to the Angelman syndrome.
 Deletions account for about 70% cases.

48.  Molecular studies of cytogenetically normal individuals
with Prader-Willi syndrome (i.e., those without the
deletion) have revealed that they have two maternal
copies of chromosome 15.
 Inheritance of both chromosomes of a pair from one
parent is called uniparental disomy.

49.  The net effect is the same (i.e., the person does not
have a functional set of genes from the [nonimprinted]
paternal chromosomes 15).
 Angelman syndrome, as might be expected, can also
result from uniparental disomy of paternal chromosome
15.
 This is the second most common mechanism,
responsible for 20% to 25% cases.

50.  In a small minority of patients (1% to 4%), there is an
imprinting defect.
 In some patients with Prader-Willi syndrome, the paternal
chromosome carries the maternal imprint.
 Conversely in Angelman syndrome, the maternal
chromosome carries the paternal imprint (hence there are no
functional alleles).

51.  In Angelman syndrome, the affected gene is a ubiquitin
ligase that is involved in catalyzing the transfer of
activated ubiquitin to target protein substrates.
 The gene, called UBE3A, maps within the 15q12 region,
is imprinted on the paternal chromosome, and is
expressed from the maternal allele primarily in specific
regions of the brain.

52.  Absence of UBE3A inhibits synapse formation and
synaptic plasticity.
 The imprinting is tissue-specific in that UBE3A is
expressed from both alleles in most tissues.

53.  In contrast to Angelman syndrome, no single gene has
been implicated in Prader-Willi syndrome.
 Instead, a series of genes located in the 15q11.2-q13
interval (which are imprinted on the maternal
chromosome and expressed from the paternal
chromosome) are believed to be involved.

54.  These include the SNORP family of genes that
encode small nucleolar RNAs.
 These RNAs are noncoding molecules that are involved in
post transcriptional modifications of ribosomal RNAs and
other small nuclear RNAs.
 Loss of SNORP functions is believed to contribute to Prader-
Willi syndrome, but the precise mechanisms are unclear.

55.  Amplification of a large segment of DNA containing the N-myc
protooncogene is a frequent finding in neuroblastomas, where
the presence of amplification confers a poor prognosis.
 In these tumors there is a strong bias in the parental origin of
RB allele losses. In one study, 90% of cases showed loss of
the maternal RB allele, presumably with mutation at the
retained paternal allele.

56.  In some families, the trait is
associated with constitutional
chromosomal inversions or
translocations at 1 1 p15.4 or
1 1 p15.5.
 But the phenotype is only
expressed after passage of the
structurally abnormal
chromosome through the
maternal germline.

57.  To understand the biological rationale and consequences of
imprinting, it will first be necessary to define the identities and
functions of what must be a fairly large number of as yet
uncharacterized imprinted genes.
 While some of these, such as the PWS and AS genes, will no
doubt be identified in the near future, innovative strategies will
be required to carry out a more general search.

58.  In terms of the mechanism of imprinting, new insights may
come from the study of the control of CpG methylation and
demethylation in early development and from the cloning and
characterization of imprinting modifier genes.
 Finally, a more complete understanding of the role of
imprinting in neoplasia can be expected to emerge rapidly
from the current intense scrutiny of the molecular pathology of
human embryonal tumors.