In onic Signaling Pa hway Sys em (ISPS)
Ex ended Scien i ic Documen a ion
In oduc ion The In onic Signaling Pa hway Sys em (ISPS) is a no el heo e ical amewo k p oposing
ha excised in ons, a he han being ine by-p oduc s o RNA splicing, e ain egula o y unc ions
h ough ansien in e ac ions wi h ansc ip ion ac o s (TFs). This mechanism may modula e gene
exp ession dynamics by seques e ing TFs in he nucleoplasm h ough s uc u ed RNA la ia s,
con ibu ing o nega i e eedback loops independen o classical DNA→TF egula ion.
Me hods We analyzed in onic sequences om p o-in lamma o y genes including TNF, IL6, and IL1B.
Fo each in on, we pe o med:
1. Ex ac ion o genomic sequences om UCSC Genome B owse (hg38), p ese ing co ec s and
o ien a ion.
2. B anch Poin (BP) iden i ica ion using he YNYURAY consensus mo i and imming 3′ in onic ails.
3. Mo i scanning using FIMO (MEME Sui e) wi h a pe missi e h eshold (p- alue = 0.1) app op ia e o
in onic TFBS.
4. S uc u al olding using RNA old (ViennaRNA package).
5. Visualiza ion o seconda y s uc u es using Fo na.
6. Mapping o TFBS coo dina es on o RNA s uc u al domains o de e mine accessibili y (loops, bulges,
mul iloops, s ems).
P elimina y Resul s We iden i ied ex ensi e clus e ing o NFκB1 and STAT-binding mo i s wi hin in ons
o IL1B and IL6. TFBS clus e s we e consis en ly en iched wi hin accessible s uc u al egions such as
loops and mul iloops. These indings suppo he ISPS hypo hesis ha in ons ac as dynamic TF
seques a ion pla o ms.
Clus e Region (n ) TFBS Coun Accessibili y
1 5–82 6 Highly accessible loops
2 158–201 8 La ge loop egion
3 206–260 5 Semi- lexible a m
4 280–343 10 Megaclus e – mul iloop
5 350–423 17 Megaclus e – la ges egion
6 429–498 4 Dis al loops
Rep esen a i e RNA S uc u es and TFBS Mapping Below a e included key s uc u al isualiza ions
om Fo na o IL1B in ons 1 and 2, highligh ing he spa ial o ganiza ion o TFBS clus e s ela i e o
RNA loops and s ems.
Ex ended Hypo hesis We p opose ha in onic RNA la ia s ac as ansien egula o y hubs capable o
modula ing he a ailabili y o ansc ip ion ac o s (TFs), pa icula ly unde in lamma o y condi ions. This
mechanism may explain:
• Rapid a enua ion o NFκB1-d i en ansc ip ion.
• Oscilla o y ac i a ion pa e ns obse ed in cy okine genes.
• Di e ences in eedback egula ion be ween in on- ich and in on-poo genes.
We hypo hesize ha ISPS cons i u es an e olu iona ily conse ed egula o y laye in eg a ing RNA
s uc u e, ansc ip ion ac o dynamics, and in lamma o y gene exp ession.
Re e ences 1. MEME Sui e: Mul iple EM o Mo i Elici a ion. 2. ViennaRNA Package: RNA Seconda y
S uc u e P edic ion. 3. UCSC Genome B owse : Ken e al. 4. NFκB Signaling Pa hway Re iews
(Na u e Re iews Immunology). 5. Splicing and RNA La ia Dynamics (RNA Jou nal).
