PowerPoint Presentation

NON CODING RNABy: KOMAL K SAPARA CSIR-CSMCRI

CONTENTSIntroductionTypes of non coding RNA (ncRNA)Long non coding RNA (lncRNA)Small non coding RNA (sncRNA)Micro RNA (miRNA)piRNASmall interfering RNA (siRNA)General functions of non coding RNAs.

IntroductionCentral 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 9798% 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 RNANcRNAs 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?- chromatin modulation, transcriptional regulation, and 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 123 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 (2431 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.

siRNAsSmall 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 2030 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., Leito, 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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