In-cell NMR suggests that DNA i-motif levels are strongly depleted in living human cells

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F24%3A00585257" target="_blank" >RIV/68081707:_____/24:00585257 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00216224:14740/24:00136213

Výsledek na webu

<a href="https://www.nature.com/articles/s41467-024-46221-y" target="_blank" >https://www.nature.com/articles/s41467-024-46221-y</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1038/s41467-024-46221-y" target="_blank" >10.1038/s41467-024-46221-y</a>

Jazyk výsledku

angličtina

Název v původním jazyce

In-cell NMR suggests that DNA i-motif levels are strongly depleted in living human cells

Popis výsledku v původním jazyce

I-Motifs (iM) are non-canonical DNA structures potentially forming in the accessible, single-stranded, cytosine-rich genomic regions with regulatory roles. Chromatin, protein interactions, and intracellular properties seem to govern iM formation at sites with i-motif formation propensity (iMFPS) in human cells, yet their specific contributions remain unclear. Using in-cell NMR with oligonucleotide iMFPS models, we monitor iM-associated structural equilibria in asynchronous and cell cycle-synchronized HeLa cells at 37 degrees C. Our findings show that iMFPS displaying pH(T) < 7 under reference in vitro conditions occur predominantly in unfolded states in cells, while those with pH(T) > 7 appear as a mix of folded and unfolded states depending on the cell cycle phase. Comparing these results with previous data obtained using an iM-specific antibody (iMab) reveals that cell cycle-dependent iM formation has a dual origin, and iM formation concerns only a tiny fraction (possibly 1%) of genomic sites with iM formation propensity. We propose a comprehensive model aligning observations from iMab and in-cell NMR and enabling the identification of iMFPS capable of adopting iM structures under physiological conditions in living human cells. Our results suggest that many iMFPS may have biological roles linked to their unfolded states.

Název v anglickém jazyce

In-cell NMR suggests that DNA i-motif levels are strongly depleted in living human cells

Popis výsledku anglicky

I-Motifs (iM) are non-canonical DNA structures potentially forming in the accessible, single-stranded, cytosine-rich genomic regions with regulatory roles. Chromatin, protein interactions, and intracellular properties seem to govern iM formation at sites with i-motif formation propensity (iMFPS) in human cells, yet their specific contributions remain unclear. Using in-cell NMR with oligonucleotide iMFPS models, we monitor iM-associated structural equilibria in asynchronous and cell cycle-synchronized HeLa cells at 37 degrees C. Our findings show that iMFPS displaying pH(T) < 7 under reference in vitro conditions occur predominantly in unfolded states in cells, while those with pH(T) > 7 appear as a mix of folded and unfolded states depending on the cell cycle phase. Comparing these results with previous data obtained using an iM-specific antibody (iMab) reveals that cell cycle-dependent iM formation has a dual origin, and iM formation concerns only a tiny fraction (possibly 1%) of genomic sites with iM formation propensity. We propose a comprehensive model aligning observations from iMab and in-cell NMR and enabling the identification of iMFPS capable of adopting iM structures under physiological conditions in living human cells. Our results suggest that many iMFPS may have biological roles linked to their unfolded states.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10608 - Biochemistry and molecular biology

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2024

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Nature Communications

ISSN

2041-1723

e-ISSN

2041-1723

Svazek periodika

15

Číslo periodika v rámci svazku

1

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

12

Strana od-do

1992

Kód UT WoS článku

001180394600033

EID výsledku v databázi Scopus

2-s2.0-85186873110