Hydrogen bonding between aligned loops (“kissing loops”) leads to dimer initiation followed by stem isomerization and the formation of a longer interstrand duplex: i.e., the strands “zipper” together. In this example, bilateral transcription in cis has juxtaposed nascent sense and nascent antisense transripts (cis-NAT).

This mechanism of RNA duplex formation is reported for the homo-dimerization of telomerase and retroviral genomic RNAs, although, because telomerase and retroviral RNAs are of the same strand orientation, specific loop sequences are required to maintain a conformation that is competent for initial dimer contact^1,2,3

1. A role for a novel ‘trans-pseudoknot’ RNA–RNA interaction in the functional dimerization of human telomerase. Ly H, L Xu, MA Rivera, TG. Parslow, EH. Blackburn. Genes Dev. 2003. 17(9):1078-83.

2. Kissing-loop model of HIV-1 genome dimerization. HIV-1 RNAs can assume alternative dimeric forms, and all sequences upstream or downstream of hairpin 248-271 are dispensable for dimer formation. Laughrea M, Jetté L. Biochemistry. 1996. 35(5):1589-98.

3. HIV-1 DIS stem loop forms an obligatory bent kissing intermediate in the dimerization pathway. Mundigala H, Michaux JB, Feig AL, Ennifar 3, Rueda D. Nucleic Acids Res 2014. 42:11 7281-7289.

 

Overlapping sense/antisense RNAs are common in vertebrates¹. Endo-siRNA formation secondary to transcription from the same genomic locus or from pseudogenes participates in oocyte development². Hairpin formations, such as those formed by highly conserved sequences in Transposable Elements (TE), (eg, the stem loop structures within Alu Repeats), might seed kissing stem loops or otherwise signal the recruitment of a transcription silencing complex.

1. Genome-wide analysis of coordinate expression and evolution of human cis-encoded sense-antisense transcripts. Chen J, Sun M, Hurst LD, Carmichael GG, Rowley JD. Trends Genet. 2005. 21(6):326-9.

2. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Tam OH1, Aravin AA, Stein P, Girard A, Murchison EP, Cheloufi S, Hodges E, Anger M, Sachidanandam R, Schultz RM, Hannon GJ. Nature. 2008 May 22;453(7194):534-8.

 

In this model, bilateral transcription follows the activation of a cryptic promoter, such as those found in LTR-retrotransposons. Nascent sense RNA + nascent antisense transripts (NATs) form a kissing complex that triggers endo-siRNA synthesis.

If both sense and antisense endo-siRNA fragments prime Argonauts that silence downstream nucleosomes, a nexus of recycling RNAPIIs may form at a precise DNA loci. If cis-NAT formation proceeds into an exonic region, endo-siRNA to mRNA may be synthesized. Endo-siRNA to Odor Receptor 1 (odr-1) mRNA has been reported to increase during the development of scent adaptation in c.elegans.¹

Controlling the directionality of transcription by controlling the transciption of cryptic promoters would be a flexible and efficient way of modulating adaptive transcriptional responses.

1. Endogenous nuclear RNAi mediates behavioral adaptation to odor. Juang BT1, Gu C, Starnes L, Palladino F, Goga A, Kennedy S, L'Etoile ND.

• Importance of RNA in transcription regulation

• Importance of RNAPII elongation as rate limiting step

BUT: It is not possible to have unique Tat-like protein for all possible nascent RNAs...

In 1997, Fire and Mello discovered RNA-Induced Silenceing complexes, explaining how it might be possible to have a unique RNA (like TAR) targeting effector complex (like TAT/PTEFb) for ANY GENE (not just HIV).

Epigenetic Gene Silencing
• RNA guide = nascent RNA
• Effector complex = Argonaute + histone modifiers
= Reprogrammable with different nascent RNAs!

Note: Differences between HIV’sTAR/TAT system and the ancient primed-Argonaute system include 1)TAT protein recruits an RNAPII activator to nascent TAR transcripts (PTEFb) whereas Argonauts recruit histone modifiers that ultimately slow RNAPII down (usually).