Fascinating world of Non-coding RNAs

1. Fascinating world ofNon-coding RNAs

2. Fascinating world ofNon-coding RNAs Non-coding RNA (ncRNA) is a RNA molecule that functions w/o being translated into a protein

3. How big is ncRNA’s world

4. Fascinating world of Non-coding RNAs • tRNA & rRNA • 4.5S & 7S RNA (Signal Recognition Particles) • snRNA – Pre-mRNA splicing • snoRNA – rRNA modification • siRNA – small interfering RNA • gRNA – guide RNA in RNA editing • Telomerase RNA – primer for telomeric DNA synthesis • tmRNA is a hybrid molecule, half tRNA, half mRNA • Xist: The X chromosome silencing is mediated by Xist – a 16,000 nt long ncRNA • shRNA (small heterochromatic RNAs ): expresses only one allele while other is silenced • LNA Locked Nucleic Acid • piRNAPiwi-interacting RNA

5. Regulatory ncRNAs • Transcriptional regulators • Translational regulators • anti-sense mechanism • RNA interference • Modulators of protein function (altering their structure, enzymatic activities) • Regulators of RNA and protein distribution

6. House keeping ncRNAs 4.5S & 7S RNA

7. 4.5S RNA (E. coli) and 7S RNA (human)signal recognition particle (SRP)(RNP) Signal sequence • SRP recognizes signalling amino acid sequence in the N-terminus of growing polypeptide chain • Upon signal recognition, ribosome is attached to endoplasmatic reticlum so that the protein, made by ribosome, enters the secretory pathway ribosome SRP mRNA SRP receptor SRP translocon Endoplasmatic reticlum membrane

8. Structure of SRP RNA holds together the protein subunits of SRP as well as helps to bind to ribosome

9. snRNP (spliceosome)

10. Small nucleolar RNA (snoRNA) Class of small RNA molecules that primarily guide chemical modifications of other RNAs, mainly ribosomal RNAs, transfer RNAs and small nuclear RNAs.

11. Small nucleolar RNA (snoRNA) • There are two main classes of snoRNA, • C/D box which are associated with methylation, and • H/ACA box which are associated with pseudouridylation.

12. siRNA short interfering RNA or silencing RNA, is a class of double-stranded RNA molecules, 20-25 nucleotides in length, that play in the RNA interference siRNA RNA interference Disrupts Hepatitis B Virus

13. Classes of siRNAs • Trans-acting short interfering RNAs (tasiRNA): • Repeat-associated short interfering RNAs (rasi-RNAs): • Scan RNA (scn RNA): • Long siRNAs (lsiRNAs):

14. Repeat associated small interfering RNA (rasiRNA) • These are involved in: • establishing and maintaining heterochromatin structure, • controlling transcripts that emerge from repeat sequences, and • silencing transposons and retrotransposons

15. Trans-acting short interfering RNAs (tasiRNA) They convert RNA viral transcripts to dsRNA by the action of RNA dependent RNA polymerase (RdRP) and prevent their transcription (post- transcriptional gene silencing )

16. Scan RNA (scn RNA):  They are involved in scanning DNA sequences in order to induce genome rearrangement. scn RNAs from the micro-nucleus (in cilliates like Paramecium) are derived and they eliminate corresponding loci from its own genome while giving rise to macro-nucleus.

17. Long siRNAs (lsiRNAs): These are about 30-40 nucleotides in length. Their formation is induced in response to bacterial infection or growth conditions. One of the lsiRNAs targets a protein that gives resistance against bacterial infection(PTGS).

18. Guide RNA (gRNA): the editor of RNA

19. Guide RNA The Editosome Complex

20. Guide RNA C to U & A to I Insertion & deletion

21. tmRNA and trans-translation • tmRNA is a hybrid molecule, half tRNA, half mRNA • tmRNA helps to rescue ribosomes, bound to mRNA which lacks the termination codon • In addition, tmRNA adds a degradation signal to nascent protein

22. Ala tmRNA The tagged protein is degraded due to the signal sequence in C-terminus

23. Xist RNA & Silencing of one female X chromosome in mammals • The X chromosome silencing is mediated by Xist – a 16,000 nt long ncRNA • Xist recruit a specific histone isoform – H2A1.2 which maintains the chromosome in inactive state • Additionally, Xist containing complexes recruit histone deacetylases and methylases

24. Xist RNA & Silencing of one female X chromosome in mammals

25. Piwi interacting RNA (piRNA) piRNAs (26-31 nt) (interact with piwi protein) are thought to be involved in gene silencing of transposons (during spermatogenesis to maintain fertility. PIWI = P-element induced wimpy (weak and ineffectual) testis in Drosophila

26. LNA: Locked Nucleic Acid Third-generation antisense nucleotides are Single-stranded LNA oligonucleotides & siRNA LNA have high binding capacity

27. miRNA miRNAs are post-transcriptional regulators that bind to complementary sequences on target messenger RNA transcripts (miRNAs), usually resulting in translational repression or target degradation and gene silencing

28. shRNAs and Genetic imprinting • Genetic imprinting = expression of only one allele of gene. • The differences of expression from both alleles Activity of small heterochromatic RNAs (shRNAs) appear to be essential for establishing and maintaining the imprinted status of genes

29. shRNAs and Genetic imprinting recognition of DNA or nascent RNA transcripts by a RISC-like targeting complex. RNA-mediated clustering of heterochromatic domains

30. shRNA