lncRNA AND THEIR CLINICAL PERSPECTIVE

PRESENTED BY

MOHIT

REG.NO.- mslsmm01

M.Sc 2ND Sem. (CREDIT SEMINAR)

CENTER OF HUMAN GENETICS AND MOLECULAR MEDICINE

SCHOOL OF HEALTH SCIENCES

CENTRAL UNIVERSITY OF PUNJAB, BATHINDA

Central Dogma of Molecular Biology

“The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred back from protein to either protein or nucleic acid.”

-Francis Crick, 1958

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… in other words

Protein information cannot flow back to nucleic acids

Fundamental framework to understanding the transfer of sequence information between biopolymers

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.

FACTS:

• Less than 2% of the human genome encodes

proteins

•The bulk of transcriptional products consists of small

and long RNAs with very reduced coding potential

most eukaryotic transcribed DNA is non-coding

• C-value paradox

genome size does

not correlate with

organismal

complexity

• Gene-value

paradox;

relationship between

morphological

complexity and the

number of protein-

coding genes within

a genome

• simplistic

expectation +

contradictory data

= “paradox”

• The number of human genes is about the same as the

number required to specify a C. elegans

• The secret of evolution lies in gene regulation

complexity?

Prevasive Genome Transcription

• Main observations:

• Intronic transcripts

• Intergenic RNAs

• Antisense and overlapping transcription

• Concept of “transcribed dark matter”, i.e. transcripts with

unknown function and meaning

• Tests of function that depend on gene knockout or overexpression

only work for a fraction even of known protein-coding genes. Need to

establish non coding transcripts function

Prevasive Genome Transcription

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• RNA molecules both encode sequence information and possess great structural

plasticity

• RNA can directly interact with DNA and with other RNAs by base pairing

• Highly structured RNA can also provide docking sites for binding proteins

• RNA has a compact size and significant sequence specificity

• non-coding RNA known from long time:

• rRNA and tRNA in translation

• snRNA and snoRNA in mRNA processing

• ribozymes

Non-coding RNA

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• Genome-wide surveys have revealed that eukaryotic genomes are extensively

transcribed into thousands of long and short ncRNAs

• Important small ncRNA with regulatory roles:

• miRNAs

• siRNAs

• piRNAs (Piwi-interacting RNA, transposon silencing in spermatogenesis)

• Long ncRNAs, lncRNAs >200 nt

• Many lncRNAs show spatial and specific patterns of expression, indicating that

lncRNA expression is strongly regulated

• lncRNAs have specific biological functions

SMALL AND LONG NON-CODING RNA

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Characteristic's Of lncRNAs

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lncRNAs are

3' polyadenylated,

5' capped,

multi-exonic

transcriptional activation

Splicing activity.

mostly transcribed RNA polymerase II

They do not undergo, the standard mRNA processing .

lncRNA promoters are bound and regulated by transcriptional factors, including

Oct3/4, Sp1, Sox2, and p53.

No obvious ORF

80% of the transcription in mammalian genomes is exclusively associated with

long non-coding RNAs (lncRNAs)

lncRNA

Intergenic

lncRNA

Intronic

lncRNA

Sense

lncRNA

Antisense

lncRNA

According to their genomic context and location LncRNA are mainly classified into four types:-

Classification Of lncRNA

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Intergenic lncRNA

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Source :- (Ma et al., 2013)

long non-coding RNA saretranscribed from introns of the protein-coding region in different GENOMIC location in Human genome

Intronic lncRNA

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Source :- (Ma et al., 2013)

Anti Sense lncRNA

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Source :- (Ma et al., 2013)

These are transcribed

from sense strand of

protein-coding genes,

containing exon from

the mRNA that

containing protein

coding gene. It may

cover or overlap the

whole protein coding region

Sense lncRNAs

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Source :- (Ma et al., 2013)

The busy

lifetimes of

certain

lncRNAs

vary from

those of

mRNAs

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Source - (Quinn and Chang, 2015)

lncRNA Mechanisms can be described according to four, not mutually exclusive, archetypes:

• As signals

• As decoys

• As guides

• As scaffolds

lncRNAs Molecular Mechanisms

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lncRNAs can serve as molecular signals, because

transcription of individual lncRNAs occurs at a very specific

time and place to integrate developmental cues, interpret

cellular context, or respond to diverse stimuli.

the lncRNAs in this archetype can act as markers of functionally significant biological events.

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Source :- (Wang and Chang, 2011)

e.g. Pluripotency and Reprogramming: ROR lncRNA Pluripotency incorporated lincRNA was initially discovered in ESCs of a mouse. Somatic cell reprogramming to iPSCs is accompanied by enriched expression of

lincRNAs lincRNA-RoR, was shown to be directly targeted by the key pluripotency factors

Oct4, Sox2, and Nanog through co-localization of the three factors close its promoter region

RoR was downregulated upon Oct4 depletion, as well as during differentiation of iPSCs, implicating co-regulation of specific lincRNAs by key pluripotency factors

lncRNAs As Signals

as decoys, The archetype of lncRNAs is

transcribed and then binds and titrates

away a protein target, but does not exert

any additional functions.

probably act by effector negatively

regulating

as decoys, lncRNAs can compete

with mRNAs for miRNA target sites

lncRNAs As Decoys

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Source :- (Wang and Chang, 2011)

Glucocorticoid Resistance:-

GAS5 lncRNA make a hairpin loop like structure which make a motif which

similar to DNA motif of that promoter region so it can compete for hormone

to bind as they can act as molecular decoy.

• lncRNA is the guide—RNA binds protein(s), then directs the

localization of ribonucleoprotein complex to specific targets.

• lncRNAs can guide changes in gene expression either in

cis (on neighboring genes) or in trans (distantly located

genes) in a manner that is not easily predicted based on

lncRNA sequence.

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Source :- (Wang and Chang, 2011)

The gene regulatory components brought on by the lncRNAs include both

repressive (e.g., polycomb) and activating (MLL) complexes, as well as

transcription factors (TFIIB). However, no matter the distance or mechanism

(either cis or trans), the principle remains the same: to convey regulatory

information across an intervening stretch of DNA to control target gene expression, bringing about changes in the epigenome.

lncRNAs As Guides

lncRNAs As Scaffolds

•They act as scaffolds, lncRNAs can

bring together multiple proteins to form

ribonucleoprotein complexes.

• The lncRNA-RNP may act on

chromatin as to affect histone

modifications.

•LncRNAs can serve as central platforms

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Source :- (Wang and Chang, 2011)

•Telomerase catalytic activity requires the association of two universal telomerase

subunits: an integral RNA subunit, the telomerase RNA (TERC) that provides the

template for repeat synthesis, and a catalytic protein subunit, the TERT, as well as

several species-specific accessory proteins. The TERC in particular also possesses

structures that contribute to TERT binding and catalytic activity, in addition to those that

play major roles in stability of the complex.

• Thus, the primary functional role for TERC is to be a scaffold

LncRNA Function

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Source :- (Mercer et al., 2009)

The Roles Of lncRNAs In Complex Human Diseases

7/1/2016 6:38 AM 24Source :- (Li et al., 2014)

Role of lncRNA in Alzheimer’s

7/1/2016 6:38 AM 25Source:- ( Faghihi et al., 2008 )

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lncRNAs In Cancer

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lncRNAs In CANCER

lncRNAs in Cardiovascular Diseases

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Source:-(Jiang and Ning, 2015)

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lncRNAs In Diabetes

GWAS studies of type – 2 diabetes and related diseases has revealed >50 susceptibility

loci, most of which are not known to carry variations that alter protein coding sequence.

Such variants affect lncRNAs

There are >1100 intergenic and antisense islet cell lncRNAs found in human islet and beta

cell .

lncRNAs are an integral component of dynamic beta cell-specific differentiation.

HI-LNC25(beta cell specific lncRNA) positively regulates GLIS3 mRNA(encodes an islet

transcription factor)

Mutation in HI-LNC25 cause diabetes.

lncRNAs KCNQ1T1 and HI-LN45 significantly increase or decreased in type -2 diabetes.

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lncRNA are >200nt non-coding RNA, which play important role in gene expression and its regulation.

lncRNA are classified into 4 types lncRNA can function as either of the 4 types: as guides, as scaffold, as

signals, as decoys.These non-coding RNA play significant role in pathogenesis of several

complex diseases. LncRNA can thus serve as an important biomarker for early detection of

disease, or also can serve as a therapeutic target.

Conclusion

Future Prospective:

There is a need for large-scale LOF or gain-of-function studies to

causally demonstrate lncRNA functions..

There is a clear need to develop genetic model systems to understand

lncRNAs’ function in vivo

Use of ASOs, siRNA have been used to target diseases-associated

lncRNAs for therapeutic purpose.

They can act as novel epigenetic intervention tools for specific sites

within the genome

lncRNAs will provide new answer to old questions of evolution and

development

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References

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