non coding RNA

NON CODING RNA
By: KOMAL K SAPARA
CSIR-CSMCRI

CONTENTS
• Introduction
• Types of non coding RNA (ncRNA)
• Long non coding RNA (lncRNA)
• Small non coding RNA (sncRNA)
• Micro RNA (miRNA)
• piRNA
• Small interfering RNA (siRNA)
• General functions of non coding RNAs.

Introduction
• Central dogma?
• Coding or non- coding?
• The term non-coding RNA (ncRNA) is commonly employed for RNA
that does not encode a protein, (Costa et al.,2012)
• In human 97–98% of the transcriptional output = non coding RNA.
• Basic identification and processing?
http://hyperphysics.phy-astr.gsu.edu/hbase/organic/dogma.html

Types of non coding RNA
• NcRNAs divided on the
basis of their size into
small and long classes:
• long ncRNAs(lncRNA)
• small ncRNAs (sncRNA)
Figure 1 Non-coding RNAs (ncRNAs) are arbitrarily grouped
basing on size, (Fenoglio et al.,2013)

Long ncRNAs
• Long non coding RNA?
• In genome organisation, long ncRNAs often overlapping with, or
interspersed between multiple coding and non-coding transcripts.
(Mercer et al.,2009)
• Involved in what type of cellular function?-
1. chromatin modulation,
2. transcriptional regulation, and
3. post transcriptional regulation.

Figure 2 Functions of long non-coding RNAs (ncRNAs), (Mercer et al., 2009.)

Small non-coding RNA
• What is it?
• The small ncRNAs (sncRNA) being less than 200 nucleotides, (Mercer et
al.,2009)
• These families are different in their origin, but they share specific
steps in their biosynthetic pathways and regulatory mechanisms.
• For regulation process these small ncRNA requires two main proiens
called Processors and Effectors. (Costa et al.,2012)
• Processor?
• Effector?

Micro-RNAs (miRNAs)
• Among non-coding RNAs, the best known family is constituted by
miRNAs.
• These RNA molecules are firstly discovered in Caenorhabditis elegans
which are short 1–23 nucleotide generated by some typical cellular
pathway which initiate from specific genomic loci and processed in
direction from nucleus to cytoplasm. (Costa et al.,2012)
• Biogenesis of miRNA occur by two main pathways:
1. Canonical pathway
2. Non canonical pathway.

• In Canonical pathways,
the pre miRNA would
be convert into mature
miRNA by activity of
specialised nucleases
that cleave RNA
transcript.
• Drosha and Dicer
enzyme
• Non canonical
pathway: spliceosome
dependent mechanism.
• Regulation of
biogenesis of miRNAs
Figure 3 (a) Canonical and non-canonical miRNA biogenesis
pathways (Li, Z., & Rana, T. M. (2014).

• The diverse mechanisms of
microRNA (miRNA) activity are
presented together with the related
miRNA targeting strategies.
• Two strategies: one which increase
miRNAs activity, another one which
reduce the miRNAs activity. (Ling et
al.2013)
• miRNA is initially transcribed as
primary miRNA (pri-miRNA), then
processed into precursor miRNA
(pre-miRNA) by a microprocessor
complex composed of Drosha and
DiGeorge syndrome critical region 8
(DGCR8), and then transported to
nucleus to cytoplasm.
Figure 3 (b) Mechanisms of action of miRNAs, (Ling et al.2013)

• Further it processed in mature form by Dicer.
• Recruited to RNA-induced silencing complex (RISC) and regulates the
output of protein-coding genes through diverse mechanisms.
By interacting with different region it regulate gene expression.

Low nutrient in soil upregulates signalling
molecules which can act as an activator of
nutrient stress responsive miRNA
biosynthesis following interaction with mir –
promoter. Activation of miRNA attenuates
the transporter gene expression. Reduction
of miRNA biosynthesis further stabilizes
transporter gene expression and more
nutrients are transported. Signal molecules
can induce phloem specific small or miRNA
biosynthesis which in turn regulates the
mobility of nutrients through phloem by
activating the transporters. Elevated or
ambient condition of nutrients can induce
other signal molecules which act as an
effector and facilitate the biosynthesis of
other groups of miRNA or smallRNAs that
interact with low nutrient stress responsive-
miRNA in a opposite way stimulating the
specific group of transporters. The effector
molecules may act as suppressor against the
low nutrient stress responsive-activator or
inducer to mitigate the activity of low
nutrient stress responsive-activator. Effect
or molecules can also reduce the
biosynthesis of phloem specific miRNA or
smallRNA families and the phloem mediated
transport is regulated.
Figure 4 Proposed model of miRNA-mediated signaling network for regulation of nutrient
homeostasis, (Paul et al.,2015)

piRNAs
• piRNAs are slightly longer than miRNAs (24–31 nt in length).
• piRNAs derive from long single-stranded RNAs transcribed from
specific regions within the genome.
• In fact, piRNAs are generated from regions harboring transposons,
and they were firstly described as a mechanism to protect the cells
against the internal attacks of transposon. (Costa et al.,2012)
• piRNAs are able to interact with a specialized family of argonaute
proteins called PIWI that will guide them to their targets and silence
the transposon transcripts by their slicing activity.

siRNAs
• Small interfering RNA (siRNA), sometimes known as short interfering
RNA or silencing RNA, is a class of double-stranded RNA molecules,
20-25 base pairs in length.
• siRNA plays many roles, but it is most notable in the RNA interference
(RNAi) pathway, where it interferes with the expression of specific
genes with complementary nucleotide sequences. (Costa et al.,2012)
• These siRNAs are generated from long double strand RNAs through
various biological processes .

1. An siRNA pathway prevents transgenerational retrotransposition in
plants subjected to stress, (Ito et al., 2011)
• Eukaryotic genomes consist to a significant extent of retrotransposons
that are suppressed by host epigenetic mechanisms, preventing their
uncontrolled propagation.
• Here it is showed that in Arabidopsis seedlings subjected to heat
stress, a copia-type retrotransposon named ONSEN (Japanese ‘hot
spring’) not only became transcriptionally active but also synthesized
extrachromosomal DNA copies.
• In summary of experimental results illustrating the role of the siRNA
pathway in transgenerational control of ONSEN mobility

• Upper part of the figure represents
wild-type control of ONSEN activity
and lower part illustrates
uncontrolled accumulation of ONSEN
copy number in siRNA-biogenesis
deficient plants.
• The graphs under the arrows
illustrate the kinetics of ONSEN DNA
accumulation on heat treatment.
• The open triangles on five
Arabidopsis chromosomes represent
eight endogenous ONSEN copies.
• The black triangles illustrate new
ONSEN insertions found in the
second generation. White circles on
the chromosomes specify the
location of the centromeres
Figure 5 summary of experiments shown the role of siRNA in preventing transgenerational
retrotransposition in plants subjected to stress, (Ito et al., 2011)

• After stress, both ONSEN transcripts and extrachromosomal
DNAgradually decayed and were no longer detected after 20–30 days.
• Surprisingly, a high frequency of new ONSEN insertions was observed
in the progeny of stressed plants deficient in siRNAs. Insertion
patterns revealed that this transgenerational retrotransposition
occurred during flower development and before gametogenesis.
• Therefore in plants with compromised siRNA biogenesis, memory of
stress was maintained throughout development, priming ONSEN to
transpose during differentiation of generative organs.
• Retrotransposition was not observed in the progeny of wild-type
plants subjected to stress or in non-stressed mutant controls, pointing
to a crucial role of the siRNApathway in restricting retrotransposition
triggered by environmental stress.

• General
function of
all non-
coding RNA
Figure 6 major functions of various non-coding RNAs (Basak, J., & Nithin, C.
2015).

References
Basak, J., & Nithin, C. (2015). Targeting non-coding RNAs in Plants with the CRISPR-Cas
technology is a challenge yet worth accepting. Frontiers in plant science, 6.
Costa, M. C., Leitão, A. L., & Enguita, F. J. (2012). Biogenesis and mechanism of action of
small non-coding RNAs: insights from the point of view of structural biology.
International journal of molecular sciences, 13(8), 10268-10295
Fenoglio, C., Ridolfi, E., Galimberti, D., & Scarpini, E. (2013). An emerging role for long
non-coding RNA dysregulation in neurological disorders. International journal of
molecular sciences, 14(10), 20427-20442.
Ito, H., Gaubert, H., Bucher, E., Mirouze, M., Vaillant, I., & Paszkowski, J. (2011). An siRNA
pathway prevents transgenerational retrotransposition in plants subjected to stress.
Nature, 472(7341), 115-119.

Li, Z., & Rana, T. M. (2014). Therapeutic targeting of microRNAs: current status
and future challenges. Nature reviews Drug discovery, 13(8), 622-638.
Ling, H., Fabbri, M., & Calin, G. A. (2013). MicroRNAs and other non-coding RNAs
as targets for anticancer drug development. Nature reviews Drug discovery,
12(11), 847-865.
Mercer, T. R., Dinger, M. E., & Mattick, J. S. (2009). Long non-coding RNAs: insights
into functions. Nature Reviews Genetics, 10(3), 155-159.
Paul, S., Datta, S. K., & Datta, K. (2015). miRNA regulation of nutrient homeostasis
in plants. Frontiers in plant science, 6.

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