Epigenome and interactome profiling uncovers principles of distal regulation in the barley genome

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60077344%3A_____%2F26%3A00646273" target="_blank" >RIV/60077344:_____/26:00646273 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/61389030:_____/26:00646273

Výsledek na webu

<a href="https://doi.org/10.1016/j.xgen.2025.101037" target="_blank" >https://doi.org/10.1016/j.xgen.2025.101037</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.xgen.2025.101037" target="_blank" >10.1016/j.xgen.2025.101037</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Epigenome and interactome profiling uncovers principles of distal regulation in the barley genome

Popis výsledku v původním jazyce

Regulation of transcription initiation is the ground level of modulating gene expression during plant development. This process relies on interactions between transcription factors and cis-regulatory elements (CREs), which become promising targets for crop bioengineering. To annotate CREs in the barley genome and understand mechanisms of distal regulation, we profiled several epigenetic features across three stages of barley embryo and leaves and performed HiChIP to identify activating and repressive genomic interactions. Using machine learning, we integrated the data into seven chromatin states, predicting similar to 77,000 CRE candidates, collectively representing 1.43% of the barley genome. Identified genomic interactions, often spanning multiple genes, linked thousands of predicted CREs with their putative targets and revealed notably frequent promoter-promoter contacts. Using the LEA gene family as an example, we discuss possible roles of these interactions in transcription regulation. On the Vrn3 gene, we demonstrate the potential of our datasets to predict CREs for other developmental stages.

Název v anglickém jazyce

Epigenome and interactome profiling uncovers principles of distal regulation in the barley genome

Popis výsledku anglicky

Regulation of transcription initiation is the ground level of modulating gene expression during plant development. This process relies on interactions between transcription factors and cis-regulatory elements (CREs), which become promising targets for crop bioengineering. To annotate CREs in the barley genome and understand mechanisms of distal regulation, we profiled several epigenetic features across three stages of barley embryo and leaves and performed HiChIP to identify activating and repressive genomic interactions. Using machine learning, we integrated the data into seven chromatin states, predicting similar to 77,000 CRE candidates, collectively representing 1.43% of the barley genome. Identified genomic interactions, often spanning multiple genes, linked thousands of predicted CREs with their putative targets and revealed notably frequent promoter-promoter contacts. Using the LEA gene family as an example, we discuss possible roles of these interactions in transcription regulation. On the Vrn3 gene, we demonstrate the potential of our datasets to predict CREs for other developmental stages.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10603 - Genetics and heredity (medical genetics to be 3)

Projekt

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

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2026

Kód důvěrnosti údajů

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

Název periodika

Cell Genomics

ISSN

2666-979X

e-ISSN

2666-979X

Svazek periodika

6

Číslo periodika v rámci svazku

1

Stát vydavatele periodika

NL - Nizozemsko

Počet stran výsledku

16

Strana od-do

101037

Kód UT WoS článku

001669935900001

EID výsledku v databázi Scopus

2-s2.0-105025046111