Chromatin-based mechanisms to coordinate convergent overlapping transcription

Abstract

In eukaryotic genomes, transcription units of genes often overlap with other proteincoding and/or noncoding transcription units 1,2 . In such intertwined genomes, coordinated transcription of nearby or overlapping genes would be important to ensure integrity of genome function; however, the mechanisms underlying this coordination are largely unknown [3][4][5][6] . Here, we show in Arabidopsis thaliana that genes with convergent orientation of transcription are major sources of overlapping bidirectional transcripts and that these bidirectionally transcribed genes are regulated by a putative LSD1 family histone demethylase, FLD 7,8 . Our genome-wide chromatin profiling revealed that FLD downregulated histone H3K4me1 in regions with convergent overlapping transcription. FLD localizes to actively transcribed genes where it colocalizes with elongating RNA polymerase II phosphorylated at Ser-2 or Ser-5 sites. Genome-wide transcription analyses suggest that FLD-mediated H3K4me1 removal negatively regulates bidirectional transcription by retaining the elongating transcription machinery. Furthermore, this effect of FLD on transcription dynamics is mediated by DNA topoisomerase I. Our study has revealed chromatinbased mechanisms to cope with overlapping bidirectional transcription, likely by modulating DNA topology. This global mechanism to cope with bidirectional transcription could be co-opted for specific epigenetic processes, such as cellular memory of responses to environment 9 . Main text:Methylation of histone H3 lysine-4 (H3K4me) is associated with active gene transcription. While H3K4 trimethylation (H3K4me3) occurs around transcription start sites (TSSs), H3K4 dimethylation (H3K4me2) and monomethylation (H3K4me1) occur in downstream regions (bodies), where transcription elongation occurs. The role of H3K4me1 in enhancers has been well studied in metazoans 10 , but H3K4me1 more generally occurs in gene bodies among eukaryotes, including yeasts and plants. Our previous genetic studies in a model plant Arabidopsis thaliana (hereafter Arabidopsis) showed the importance of H3K4me1 in the gene body in regulating active and inactive chromatin states 11 . In this report, by using genetic and genomic approaches, we uncover a novel mechanism underlying the global regulation of bidirectional transcription by controlling H3K4me1 in the gene body. FLD decreases H3K4me1 around TTS of convergently transcribed genes FLOWERING LOCUS D (FLD) is one of the four Arabidopsis orthologs of human LSD1 (Lysine-Specific Demethylase 1), a demethylase of H3K4me2 and H3K4me1 12 .FLD has been shown to regulate flowering, the transition from vegetative growth to reproductive development 7 . Although it has been proposed that FLD silences the key flowering-controlling gene, FLOWERING LOCUS C (FLC), through removal of H3K4me2 there 8,13 , the genome-wide function of FLD remains unexplored. In contrast to the results of previous reports, our chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) results showed that H3K4m...

Transcription-coupled and epigenome-encoded mechanisms direct H3K4 methylation

“…The results of previous studies might reflect indirect effects triggered by altered transcription and/or minor locus-specific effects. Our conclusion is also supported by the results showing that ATX1/2/R7 redundantly repress flowering via FLC activation and that ATXR7 and FLD counteract each other in FLC regulation, probably by modulating H3K4me1 14, 25, 45 .…”

“…ATXR7 seems to cooperate with the transcriptional machinery, while ATX1 and ATX2 seem to target genes in a manner that is informed by chromatin modifications, regardless of the abundance of the transcriptional machinery. Interestingly, many genes occupied by ATXR7 are also bound by the H3K4me1 demethylase FLD ( 14 , Supplementary Fig. 7a, b).…”

“…In Arabidopsis , the histone demethylase LDL2 removes H3K4me1 marks from the gene bodies that accumulate H3K9me2 and silences gene expression 13 . Another histone demethylase, FLD, removes H3K4me1 from sites where convergent overlapping transcription takes place 14 . Although the biological function of H3K4me remains unclarified, these diverse mechanisms converging on H3K4me1 suggest that the roles of H3K4me require the coordination and integration of a wide range of information.…”

“…Generally, H3K4me3 and H3K4me2 are found on the first several nucleosomes of genes, while H3K4me1 is found in downstream regions within the gene bodies [10][11][12] . Our previous genetic and genomic studies in Arabidopsis thaliana (hereafter Arabidopsis) have demonstrated key roles of gene body H3K4me1 in the control of transcription; a putative H3K4me1 demethylase, LYSINE-SPECIFIC DEMETHYLASE1-LIKE2 (LDL2), mediates transcriptional silencing induced by gene body H3K9me2 13 , while a related demethylase, FLOWERING LOCUS D (FLD), coordinates convergent overlapping transcription by removing H3K4me1 14 . Although these findings regarding the H3K4 demethylases of Arabidopsis suggest a link of H3K4me1 with other chromatin modifications and transcription, the mechanisms of H3K4me1 control remain elusive, mainly because methylase(s) for H3K4me1 has not been identified in plants.…”

“…For example, they were shown to redundantly inhibit flowering by activating the transcription of the flowering repressor FLOWERING LOCUS C (FLC) by increasing H3K4me1/2/3 levels within the FLC locus 22,25 . In the control of FLC, ATXR7 was shown to counteract FLD 25 , which demethylates H3K4me1 14 . However, the genome-wide impacts of these putative H3K4 methylases have not been elucidated.…”