Chromatin enrichment for proteomics in plants (ChEP-P) implicates the histone reader ALFIN-LIKE 6 in jasmonate signalling

Abstract Background Covalent modifications of core histones govern downstream DNA-templated processes such as transcription by altering chromatin structure and function. Previously, we reported that the plant homeodomain protein ALFIN-LIKE 6 (AL6), a bona fide histone reader that preferentially bind...

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Autores principales:	Isabel Cristina Vélez-Bermúdez, Wolfgang Schmidt
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Chromatin Histone reader Jasmonate Jasmonate signalling Proteomics Skotomorphogenesis Biotechnology TP248.13-248.65 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/0a8e585d3005420a8aa5b60aa9001a49
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spelling	oai:doaj.org-article:0a8e585d3005420a8aa5b60aa9001a492021-11-28T12:23:11ZChromatin enrichment for proteomics in plants (ChEP-P) implicates the histone reader ALFIN-LIKE 6 in jasmonate signalling10.1186/s12864-021-08160-61471-2164https://doaj.org/article/0a8e585d3005420a8aa5b60aa9001a492021-11-01T00:00:00Zhttps://doi.org/10.1186/s12864-021-08160-6https://doaj.org/toc/1471-2164Abstract Background Covalent modifications of core histones govern downstream DNA-templated processes such as transcription by altering chromatin structure and function. Previously, we reported that the plant homeodomain protein ALFIN-LIKE 6 (AL6), a bona fide histone reader that preferentially binds trimethylated lysin 4 on histone 3 (H3K4me3), is critical for recalibration of cellular phosphate (Pi) homeostasis and root hair elongation under Pi-deficient conditions. Results Here, we demonstrate that AL6 is also involved in the response of Arabidopsis seedlings to jasmonic acid (JA) during skotomorphogenesis, possibly by modulating chromatin dynamics that affect the transcriptional regulation of JA-responsive genes. Dark-grown al6 seedlings showed a compromised reduction in hypocotyl elongation upon exogenously supplied JA, a response that was calibrated by the availability of Pi in the growth medium. A comparison of protein profiles between wild-type and al6 mutant seedlings using a quantitative Chromatin Enrichment for Proteomics (ChEP) approach, that we modified for plant tissue and designated ChEP-P (ChEP in Plants), yielded a comprehensive suite of chromatin-associated proteins and candidates that may be causative for the mutant phenotype. Conclusions Altered abundance of proteins involved in chromatin organization in al6 seedlings suggests a role of AL6 in coordinating the deposition of histone variants upon perception of internal or environmental stimuli. Our study shows that ChEP-P is well suited to gain holistic insights into chromatin-related processes in plants. Data are available via ProteomeXchange with identifier PXD026541.Isabel Cristina Vélez-BermúdezWolfgang SchmidtBMCarticleChromatinHistone readerJasmonateJasmonate signallingProteomicsSkotomorphogenesisBiotechnologyTP248.13-248.65GeneticsQH426-470ENBMC Genomics, Vol 22, Iss 1, Pp 1-21 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Chromatin Histone reader Jasmonate Jasmonate signalling Proteomics Skotomorphogenesis Biotechnology TP248.13-248.65 Genetics QH426-470
spellingShingle	Chromatin Histone reader Jasmonate Jasmonate signalling Proteomics Skotomorphogenesis Biotechnology TP248.13-248.65 Genetics QH426-470 Isabel Cristina Vélez-Bermúdez Wolfgang Schmidt Chromatin enrichment for proteomics in plants (ChEP-P) implicates the histone reader ALFIN-LIKE 6 in jasmonate signalling
description	Abstract Background Covalent modifications of core histones govern downstream DNA-templated processes such as transcription by altering chromatin structure and function. Previously, we reported that the plant homeodomain protein ALFIN-LIKE 6 (AL6), a bona fide histone reader that preferentially binds trimethylated lysin 4 on histone 3 (H3K4me3), is critical for recalibration of cellular phosphate (Pi) homeostasis and root hair elongation under Pi-deficient conditions. Results Here, we demonstrate that AL6 is also involved in the response of Arabidopsis seedlings to jasmonic acid (JA) during skotomorphogenesis, possibly by modulating chromatin dynamics that affect the transcriptional regulation of JA-responsive genes. Dark-grown al6 seedlings showed a compromised reduction in hypocotyl elongation upon exogenously supplied JA, a response that was calibrated by the availability of Pi in the growth medium. A comparison of protein profiles between wild-type and al6 mutant seedlings using a quantitative Chromatin Enrichment for Proteomics (ChEP) approach, that we modified for plant tissue and designated ChEP-P (ChEP in Plants), yielded a comprehensive suite of chromatin-associated proteins and candidates that may be causative for the mutant phenotype. Conclusions Altered abundance of proteins involved in chromatin organization in al6 seedlings suggests a role of AL6 in coordinating the deposition of histone variants upon perception of internal or environmental stimuli. Our study shows that ChEP-P is well suited to gain holistic insights into chromatin-related processes in plants. Data are available via ProteomeXchange with identifier PXD026541.
format	article
author	Isabel Cristina Vélez-Bermúdez Wolfgang Schmidt
author_facet	Isabel Cristina Vélez-Bermúdez Wolfgang Schmidt
author_sort	Isabel Cristina Vélez-Bermúdez
title	Chromatin enrichment for proteomics in plants (ChEP-P) implicates the histone reader ALFIN-LIKE 6 in jasmonate signalling
title_short	Chromatin enrichment for proteomics in plants (ChEP-P) implicates the histone reader ALFIN-LIKE 6 in jasmonate signalling
title_full	Chromatin enrichment for proteomics in plants (ChEP-P) implicates the histone reader ALFIN-LIKE 6 in jasmonate signalling
title_fullStr	Chromatin enrichment for proteomics in plants (ChEP-P) implicates the histone reader ALFIN-LIKE 6 in jasmonate signalling
title_full_unstemmed	Chromatin enrichment for proteomics in plants (ChEP-P) implicates the histone reader ALFIN-LIKE 6 in jasmonate signalling
title_sort	chromatin enrichment for proteomics in plants (chep-p) implicates the histone reader alfin-like 6 in jasmonate signalling
publisher	BMC
publishDate	2021
url	https://doaj.org/article/0a8e585d3005420a8aa5b60aa9001a49
work_keys_str_mv	AT isabelcristinavelezbermudez chromatinenrichmentforproteomicsinplantscheppimplicatesthehistonereaderalfinlike6injasmonatesignalling AT wolfgangschmidt chromatinenrichmentforproteomicsinplantscheppimplicatesthehistonereaderalfinlike6injasmonatesignalling
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Chromatin enrichment for proteomics in plants (ChEP-P) implicates the histone reader ALFIN-LIKE 6 in jasmonate signalling

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