Functional genomic profiling of O-GlcNAc reveals its context-specific interplay with RNA polymerase II
Abstract Background How reversible glycosylation of DNA-bound proteins acts on transcription remains scarcely understood. O-linked β-N-acetylglucosamine (O-GlcNAc) is the only known form of glycosylation modifying nuclear proteins, including RNA polymerase II (RNA Pol II) and many transcription fact...
Saved in:
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-03-01
|
| Series: | Genome Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13059-025-03537-2 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850063722813325312 |
|---|---|
| author | Sofia Rucli Nicolas Descostes Yulia Ermakova Urvashi Chitnavis Jeanne Couturier Ana Boskovic Matthieu Boulard |
| author_facet | Sofia Rucli Nicolas Descostes Yulia Ermakova Urvashi Chitnavis Jeanne Couturier Ana Boskovic Matthieu Boulard |
| author_sort | Sofia Rucli |
| collection | DOAJ |
| description | Abstract Background How reversible glycosylation of DNA-bound proteins acts on transcription remains scarcely understood. O-linked β-N-acetylglucosamine (O-GlcNAc) is the only known form of glycosylation modifying nuclear proteins, including RNA polymerase II (RNA Pol II) and many transcription factors. Yet, the regulatory function of the O-GlcNAc modification in mammalian chromatin remains unclear. Results Here, we combine genome-wide profiling of O-GlcNAc-modified proteins with perturbations of intracellular glycosylation, RNA Pol II-degron, and super-resolution microscopy. Genomic profiling of O-GlcNAc-modified proteins shows a non-random distribution across the genome, with high densities in heterochromatin regions as well as on actively transcribed gene promoters. Large-scale intersection of the O-GlcNAc signal at promoters with public ChIP-seq datasets identifies a high overlap with RNA Pol II and specific cofactors. Knockdown of O-GlcNAc Transferase (Ogt) shows that most direct target genes are downregulated, supporting a global positive role of O-GlcNAc on the transcription of cellular genes. Rapid degradation of RNA Pol II results in the decrease of the O-GlcNAc levels at promoters encoding transcription factors and DNA modifying enzymes. RNA Pol II depletion also unexpectedly causes an increase of O-GlcNAc levels at a set of promoters encoding for the transcription machinery. Conclusions This study provides a deconvoluted genomic profiling of O-GlcNAc-modified proteins in murine and human cells. Perturbations of O-GlcNAc or RNA Pol II uncover a context-specific reciprocal functional interplay between the transcription machinery and the O-GlcNAc modification. |
| format | Article |
| id | doaj-art-5e08b7d90dfc453a9ea0692cdf37396a |
| institution | DOAJ |
| issn | 1474-760X |
| language | English |
| publishDate | 2025-03-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj-art-5e08b7d90dfc453a9ea0692cdf37396a2025-08-20T02:49:30ZengBMCGenome Biology1474-760X2025-03-0126112510.1186/s13059-025-03537-2Functional genomic profiling of O-GlcNAc reveals its context-specific interplay with RNA polymerase IISofia Rucli0Nicolas Descostes1Yulia Ermakova2Urvashi Chitnavis3Jeanne Couturier4Ana Boskovic5Matthieu Boulard6Epigenetics & Neurobiology Unit, European Molecular Biology Laboratory, EMBL RomeEpigenetics & Neurobiology Unit, European Molecular Biology Laboratory, EMBL RomeEpigenetics & Neurobiology Unit, European Molecular Biology Laboratory, EMBL RomeEpigenetics & Neurobiology Unit, European Molecular Biology Laboratory, EMBL RomeEpigenetics & Neurobiology Unit, European Molecular Biology Laboratory, EMBL RomeEpigenetics & Neurobiology Unit, European Molecular Biology Laboratory, EMBL RomeEpigenetics & Neurobiology Unit, European Molecular Biology Laboratory, EMBL RomeAbstract Background How reversible glycosylation of DNA-bound proteins acts on transcription remains scarcely understood. O-linked β-N-acetylglucosamine (O-GlcNAc) is the only known form of glycosylation modifying nuclear proteins, including RNA polymerase II (RNA Pol II) and many transcription factors. Yet, the regulatory function of the O-GlcNAc modification in mammalian chromatin remains unclear. Results Here, we combine genome-wide profiling of O-GlcNAc-modified proteins with perturbations of intracellular glycosylation, RNA Pol II-degron, and super-resolution microscopy. Genomic profiling of O-GlcNAc-modified proteins shows a non-random distribution across the genome, with high densities in heterochromatin regions as well as on actively transcribed gene promoters. Large-scale intersection of the O-GlcNAc signal at promoters with public ChIP-seq datasets identifies a high overlap with RNA Pol II and specific cofactors. Knockdown of O-GlcNAc Transferase (Ogt) shows that most direct target genes are downregulated, supporting a global positive role of O-GlcNAc on the transcription of cellular genes. Rapid degradation of RNA Pol II results in the decrease of the O-GlcNAc levels at promoters encoding transcription factors and DNA modifying enzymes. RNA Pol II depletion also unexpectedly causes an increase of O-GlcNAc levels at a set of promoters encoding for the transcription machinery. Conclusions This study provides a deconvoluted genomic profiling of O-GlcNAc-modified proteins in murine and human cells. Perturbations of O-GlcNAc or RNA Pol II uncover a context-specific reciprocal functional interplay between the transcription machinery and the O-GlcNAc modification.https://doi.org/10.1186/s13059-025-03537-2O-linked β-N-acetylglucosamineO-GlcNAcOGTGlycosylationTranscriptionPromoter |
| spellingShingle | Sofia Rucli Nicolas Descostes Yulia Ermakova Urvashi Chitnavis Jeanne Couturier Ana Boskovic Matthieu Boulard Functional genomic profiling of O-GlcNAc reveals its context-specific interplay with RNA polymerase II Genome Biology O-linked β-N-acetylglucosamine O-GlcNAc OGT Glycosylation Transcription Promoter |
| title | Functional genomic profiling of O-GlcNAc reveals its context-specific interplay with RNA polymerase II |
| title_full | Functional genomic profiling of O-GlcNAc reveals its context-specific interplay with RNA polymerase II |
| title_fullStr | Functional genomic profiling of O-GlcNAc reveals its context-specific interplay with RNA polymerase II |
| title_full_unstemmed | Functional genomic profiling of O-GlcNAc reveals its context-specific interplay with RNA polymerase II |
| title_short | Functional genomic profiling of O-GlcNAc reveals its context-specific interplay with RNA polymerase II |
| title_sort | functional genomic profiling of o glcnac reveals its context specific interplay with rna polymerase ii |
| topic | O-linked β-N-acetylglucosamine O-GlcNAc OGT Glycosylation Transcription Promoter |
| url | https://doi.org/10.1186/s13059-025-03537-2 |
| work_keys_str_mv | AT sofiarucli functionalgenomicprofilingofoglcnacrevealsitscontextspecificinterplaywithrnapolymeraseii AT nicolasdescostes functionalgenomicprofilingofoglcnacrevealsitscontextspecificinterplaywithrnapolymeraseii AT yuliaermakova functionalgenomicprofilingofoglcnacrevealsitscontextspecificinterplaywithrnapolymeraseii AT urvashichitnavis functionalgenomicprofilingofoglcnacrevealsitscontextspecificinterplaywithrnapolymeraseii AT jeannecouturier functionalgenomicprofilingofoglcnacrevealsitscontextspecificinterplaywithrnapolymeraseii AT anaboskovic functionalgenomicprofilingofoglcnacrevealsitscontextspecificinterplaywithrnapolymeraseii AT matthieuboulard functionalgenomicprofilingofoglcnacrevealsitscontextspecificinterplaywithrnapolymeraseii |