Profiling spatial enrichment of chromatin marks suggests an additional epigenomic dimension in gene regulation

Chica, Claudia; Szarzyńska, Bogna; Chen-Min-Tao, Romy; Duvernois-Berthet, Evelyne; Kassam, Mohamed; Colot, Vincent; Roudier, François

doi:10.1080/21553769.2013.844734

Cited by 10 publications

(6 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The enrichment profile of a given HM (i.e. the genomic span and shape of a ChIP-seq peak, which reflect the number of successive nucleosomes at a locus and the proportion of nucleosomes at a given nucleosome position that are modified by a HM in a cell population, respectively) is related to the expression and biological functions of the associated genes 39 , 40 . To investigate the relationship between biological functions and the span of HMs observed in xylem, we analysed the representation and distribution of biological functions among genes occupied by HMs of differing length (as determined by the length in basepairs of significant peaks) (Fig.…”

Section: Resultsmentioning

confidence: 99%

Integrated analysis and transcript abundance modelling of H3K4me3 and H3K27me3 in developing secondary xylem

Hussey

Loots

Merwe

et al. 2017

Sci Rep

View full text Add to dashboard Cite

Despite the considerable contribution of xylem development (xylogenesis) to plant biomass accumulation, its epigenetic regulation is poorly understood. Furthermore, the relative contributions of histone modifications to transcriptional regulation is not well studied in plants. We investigated the biological relevance of H3K4me3 and H3K27me3 in secondary xylem development using ChIP-seq and their association with transcript levels among other histone modifications in woody and herbaceous models. In developing secondary xylem of the woody model Eucalyptus grandis, H3K4me3 and H3K27me3 genomic spans were distinctly associated with xylogenesis-related processes, with (late) lignification pathways enriched for putative bivalent domains, but not early secondary cell wall polysaccharide deposition. H3K27me3-occupied genes, of which 753 (~31%) are novel targets, were enriched for transcriptional regulation and flower development and had significant preferential expression in roots. Linear regression models of the ChIP-seq profiles predicted ~50% of transcript abundance measured with strand-specific RNA-seq, confirmed in a parallel analysis in Arabidopsis where integration of seven additional histone modifications each contributed smaller proportions of unique information to the predictive models. This study uncovers the biological importance of histone modification antagonism and genomic span in xylogenesis and quantifies for the first time the relative correlations of histone modifications with transcript abundance in plants.

show abstract

Section: Resultsmentioning

confidence: 99%

Integrated analysis and transcript abundance modelling of H3K4me3 and H3K27me3 in developing secondary xylem

Hussey

Loots

Merwe

et al. 2017

Sci Rep

View full text Add to dashboard Cite

show abstract

“…Other mRNA-seq data for G. arboreum and G. hirsutum were downloaded from the Sequence Read Archive (SRA; Table S1 ). Aradibopsis ChIP-seq data (GSE50636) was downloaded from the NCBI Gene Expression Omnibus (GEO) 40 . The first published genome of G. arboreum was used as a reference genome 19 , the G. hirsutum genome referred to the Nanjing Agricultural University version 21 , and the Arabidopsis genome referred to the release 10 (TAIR10) version 41 .…”

Section: Methodsmentioning

confidence: 99%

Genome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation

You

Zhang

et al. 2017

Sci Rep

View full text Add to dashboard Cite

Polyploidy is a common evolutionary occurrence in plants. Recently, published genomes of allotetraploid G. hirsutum and its donors G. arboreum and G. raimondii make cotton an accessible polyploid model. This study used chromatin immunoprecipitation with high-throughput sequencing (ChIP-Seq) to investigate the genome-wide distribution of H3K4me3 in G. arboreum and G. hirsutum, and explore the conservation and variation of genome structures between diploid and allotetraploid cotton. Our results showed that H3K4me3 modifications were associated with active transcription in both cottons. The H3K4me3 histone markers appeared mainly in genic regions and were enriched around the transcription start sites (TSSs) of genes. We integrated the ChIP-seq data of H3K4me3 with RNA-seq and ESTs data to refine the genic structure annotation. There were 6,773 and 12,773 new transcripts discovered in G. arboreum and G. hirsutum, respectively. Furthermore, co-expression networks were linked with histone modification and modularized in an attempt to explain differential H3K4me3 enrichment correlated with changes in gene transcription during cotton development and evolution. Taken together, we have combined epigenomic and transcriptomic datasets to systematically discover functional genes and compare them between G. arboreum and G. hirsutum, which may be beneficial for studying diploid and allotetraploid plants with large genomes and complicated evolution.

show abstract

“…We next focused on the distribution of different histone modifications by (i) using publicly available ChIP‐seq datasets on WT and (b) using the ChIP–dot blot approach on the WT and two low‐copy lines (L6, L9). We started with the dataset from young rosette leaves (PRJNA218138; Chica et al ., 2013) to determine the distribution of H3K4me3 and H3K27me3 histone marks. The levels of both marks were very low in the rDNA locus, as confirmed by both dot blot (Figure S6(a,b)) and ChIP‐seq, when compared to other genomic regions (Figure S7).…”

Section: Resultsmentioning

confidence: 99%

Nucleolar rDNA folds into condensed foci with a specific combination of epigenetic marks

et al. 2021

View full text Add to dashboard Cite

Arabidopsis thaliana 45S ribosomal genes (rDNA) are located in tandem arrays called nucleolus organizing regions on the termini of chromosomes 2 and 4 (NOR2 and NOR4) and encode rRNA, a crucial structural element of the ribosome. The current model of rDNA organization suggests that inactive rRNA genes accumulate in the condensed chromocenters in the nucleus and at the nucleolar periphery, while the nucleolus delineates active genes. We challenge the perspective that all intranucleolar rDNA is active by showing that a subset of nucleolar rDNA assembles into condensed foci marked by H3.1 and H3.3 histones that also contain the repressive H3K9me2 histone mark. By using plant lines containing a low number of rDNA copies, we further found that the condensed foci relate to the folding of rDNA, which appears to be a common mechanism of rDNA regulation inside the nucleolus. The H3K9me2 histone mark found in condensed foci represents a typical modification of bulk inactive rDNA, as we show by genome-wide approaches, similar to the H2A.W histone variant. The euchromatin histone marks H3K27me3 and H3K4me3, in contrast, do not colocalize with nucleolar foci and their overall levels in the nucleolus are very low. We further demonstrate that the rDNA promoter is an important regulatory region of the rDNA, where the distribution of histone variants and histone modifications are modulated in response to rDNA activity.

show abstract

Profiling spatial enrichment of chromatin marks suggests an additional epigenomic dimension in gene regulation

Cited by 10 publications

References 41 publications

Integrated analysis and transcript abundance modelling of H3K4me3 and H3K27me3 in developing secondary xylem

Integrated analysis and transcript abundance modelling of H3K4me3 and H3K27me3 in developing secondary xylem

Genome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation

Nucleolar rDNA folds into condensed foci with a specific combination of epigenetic marks

Contact Info

Product

Resources

About