No abstract

Mono-, di-, and trimethylation of histone H3 lysine 4 (H3K4me1/2/3) are associated with transcription, yet it remains controversial whether H3K4me1/2/3 promote or result from transcription. Our previous characterizations of Arabidopsis H3K4 demethylases suggest roles for H3K4me1 in transcription. However, the control of H3K4me1 remains unexplored in Arabidopsis, in which no methyltransferase for H3K4me1 has been identified. Here, we identify three Arabidopsis methyltransferases that direct H3K4me1. Analyses of their genome-wide localization using ChIP-seq and machine learning reveal that one of the enzymes cooperates with the transcription machinery, while the other two are associated with specific histone modifications and DNA sequences. Importantly, these two types of localization patterns are also found for the other H3K4 methyltransferases in Arabidopsis and mice. These results suggest that H3K4me1/2/3 are established and maintained via interplay with transcription as well as inputs from other chromatin features, presumably enabling elaborate gene control.

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...

Mushroom bodies (MBs), a higher-order center in the honeybee brain, comprise some subtypes/populations of interneurons termed as Kenyon cells (KCs), which are distinguished by their cell body size and location in the MBs, as well as their gene expression profiles. Although the role of MBs in learning ability has been studied extensively in the honeybee, the roles of each KC subtype and their evolution in hymenopteran insects remain mostly unknown. This mini-review describes recent progress in the analysis of gene/protein expression profiles and possible functions of KC subtypes/populations in the honeybee. Especially, the discovery of novel KC subtypes/populations, the “middle-type KCs” and “KC population expressing FoxP,” necessitated a redefinition of the KC subtype/population. Analysis of the effects of inhibiting gene function in a KC subtype-preferential manner revealed the function of the gene product as well as of the KC subtype where it is expressed. Genes expressed in a KC subtype/population-preferential manner can be used to trace the differentiation of KC subtypes during the honeybee ontogeny and the possible evolution of KC subtypes in hymenopteran insects. Current findings suggest that the three KC subtypes are unique characteristics to the aculeate hymenopteran insects. Finally, prospects regarding future application of genome editing for the study of KC subtype functions in the honeybee are described. Genes expressed in a KC subtype-preferential manner can be good candidate target genes for genome editing, because they are likely related to highly advanced brain functions and some of them are dispensable for normal development and sexual maturation in honeybees.

In insect brains, the mushroom bodies (MBs) are a higher-order center for sensory integration and memory. Honeybee (Apis mellifera L.) MBs comprise four Kenyon cell (KC) subtypes: class I large-, middle-, and small-type, and class II KCs, which are distinguished by the size and location of somata, and gene expression profiles. Although these subtypes have only been reported in the honeybee, the time of their acquisition during evolution remains unknown. Here we performed in situ hybridization of tachykinin-related peptide, which is differentially expressed among KC subtypes in the honeybee MBs, in four hymenopteran species to analyze whether the complexity of KC subtypes is associated with their behavioral traits. Three class I KC subtypes were detected in the MBs of the eusocial hornet Vespa mandarinia and the nidificating scoliid wasp Campsomeris prismatica, like in A. mellifera, whereas only two class I KC subtypes were detected in the parasitic wasp Ascogaster reticulata. In contrast, we were unable to detect class I KC subtype in the primitive and phytophagous sawfly Arge similis. Our findings suggest that the number of class I KC subtypes increased at least twice – first with the evolution of the parasitic lifestyle and then with the evolution of nidification.