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Stable Caenorhabditis Elegans Chromatin Domains Separate Broadly Expressed and Developmentally Regulated Genes

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Stable Caenorhabditis Elegans Chromatin Domains Separate Broadly Expressed and Developmentally Regulated Genes Stable Caenorhabditis elegans chromatin domains separate broadly expressed and developmentally regulated genes Kenneth J. Evansa, Ni Huanga, Przemyslaw Stempora, Michael A. Chesneya, Thomas A. Downa, and Julie Ahringera,1 aDepartment of Genetics, The Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom Edited by Paul W. Sternberg, California Institute of Technology, Pasadena, CA, and approved September 20, 2016 (received for review May 24, 2016) Eukaryotic genomes are organized into domains of differing three organisms (10). However, because chromatin differences structure and activity. There is evidence that the domain organiza- also exist, the jointly derived chromatin states are not ideal for tion of the genome regulates its activity, yet our understanding of C. elegans-specific analyses, and no other C. elegans chromatin domain properties and the factors that influence their formation is state maps have been published. poor. Here, we use chromatin state analyses in early embryos and Previous studies have described broad properties of C. elegans third-larval stage (L3) animals to investigate genome domain orga- genome organization. The distal “arms” and central regions of nization and its regulation in Caenorhabditis elegans.Atbothstages the autosomal chromosomes show differences in transcriptional we find that the genome is organized into extended chromatin activity, chromatin composition, and recombination rate (6, 7, domains of high or low gene activity defined by different subsets 11, 13, 14). Central regions have higher average gene expression, of states, and enriched for H3K36me3 or H3K27me3, respectively. moderate enrichment of histone modifications associated with The border regions between domains contain large intergenic re- active transcription, and lower meiotic recombination than distal gions and a high density of transcription factor binding, suggesting arm regions. In contrast, most features associated with hetero- a role for transcription regulation in separating chromatin domains. chromatin, such as H3K9 methylation and nuclear envelope Despite the differences in cell types, overall domain organization is association, are found on the chromosome arms (7, 15). How- remarkably similar in early embryos and L3 larvae, with conserva- ever, the chromosome arms are not purely heterochromatic. tion of 85% of domain border positions. Most genes in high- Actively transcribed genes reside on the chromosome arms and activity domains are expressed in the germ line and broadly across these genes are marked by histone modifications associated with cell types, whereas low-activity domains are enriched for genes gene activity, as in the central regions (7). In addition, the X that are developmentally regulated. We find that domains are chromosome shows extensive chromatin differences compared regulated by the germ-line H3K36 methyltransferase MES-4 with autosomes because of dosage compensation (16). These and that border regions show striking remodeling of H3K27me1, previous studies have provided a large-scale picture of C. elegans supporting roles for H3K36 and H3K27 methylation in regulating chromosome organization. domain structure. Our analyses of C. elegans chromatin domain Here, we investigate C. elegans chromatin and genome organi- structure show that genes are organized by type into domains zation and its regulation through the generation and analyses of that have differing modes of regulation. C. elegans-specific chromatin state maps for early embryos (EE) and third larval (L3) stages. As in other organisms, chromatin chromatin states | chromatin domains | C. elegans | boundary states correlate with many biological features, including enhancers, promoters, transcription elongation, gene ends, repeat regions, he complete genome sequence, which provides the information and inactive genes. Analyzing patterns of states revealed that Tnecessary for constructing an organism, is interpreted in the chromatin domains of differing activity separate germ-line and context of chromatin. Covalent modifications of histone tails and broadly expressed genes from developmentally regulated genes. histone variants can regulate or reflect genome function, and so are The properties of domains and the border regions between them markers of chromatin state and genomic activity (1). For example, H3K4me3 often marks active promoters, H3K36me3 transcription Significance elongation, and H3K27me3 Polycomb-silenced regions. Previous studies have shown that genomic regions of similar activity harbor Genomes are organized into domains of different structure and shared combinations of modifications, termed chromatin states, activity, yet our understanding of their formation and regulation and that subdividing the genome according to these combinations is poor. We show that Caenorhabditis elegans chromatin domain is a powerful method for annotation and uncovering novel func- – organization in early embryos and third-larval stage animals is tional regions (2 5). Here, we apply chromatin state mapping to remarkably similar despite the two developmental stages con- two developmental stages of the model organism Caenorhabditis taining very different cell types. Chromatin domains separate elegans and use the resulting maps to investigate genome domain genes into those with stable versus developmentally regulated organization and its regulation. expression. Analyses of chromatin domain structure suggest C. elegans is highly amenable for global studies of chromatin that transcription regulation and germ-line chromatin regulation structure and function because it has a small, well-annotated ge- × play roles in separating chromatin domains. Our results further nome (30 smaller than human), and work of the modENCODE our understanding of genome domain organization. consortium has provided a large number of datasets mapping the locations of chromatin-associated factors, such as histone modi- Author contributions: K.J.E., T.A.D., and J.A. designed research; K.J.E. and N.H. performed fications and transcription factors (TFs) (6–10). C. elegans chro- research; K.J.E., N.H., P.S., M.A.C., and J.A. analyzed data; and K.J.E. and J.A. wrote matin shows features in common with those of other organisms, the paper. such as the type of marking at regulatory regions and at active or The authors declare no conflict of interest. inactive genes (7, 10–12). Additionally, the derivation of a single This article is a PNAS Direct Submission. set of chromatin states for C. elegans, Drosophila, and human using 1To whom correspondence should be addressed. Email: [email protected]. a single joint genome analysis and data from eight histone modi- This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. fications highlighted the common properties of chromatin in the 1073/pnas.1608162113/-/DCSupplemental. E7020–E7029 | PNAS | Published online October 25, 2016 www.pnas.org/cgi/doi/10.1073/pnas.1608162113 Downloaded by guest on October 2, 2021 point to roles for transcription regulatory regions and germ-line for each stage we generated a separate map for autosomes and the PNAS PLUS chromatin marking in domain separation. Our results provide a X chromosome (Fig. 1A, Fig. S1,andDataset S1). The EE and L3 framework for future studies of chromatin structure and function autosomal chromatin states show much greater similarity to each in C. elegans. other than do the EE and L3 chromosome X states (Figs. S1 and S2), consistent with alterations in chromatin structure and marking Results induced by dosage compensation after the EE stage (16). The Twenty State Models of C. elegans Chromatin. To investigate features chromatin states were annotated by analyzing the associations of and domain organization of C. elegans chromatin, we derived 20 states with a range of different genomic features (Fig. 1 and Figs. state EE and L3 chromatin state maps, using hidden Markov S1, S3,andS4). As well as differences in enrichment levels for models (HMM) and ChIP data for 17 histones or modifications histone modifications, the states show differences in median length (Materials and Methods). Patterns and levels of enrichment of many (250–1,250 bp), genomic coverage (2.2–9%), and GC content (25– histone modifications differ on C. elegans autosomes compared with 44%) (Fig. S1). Below, we briefly describe chromatin state anno- the X chromosome, reflecting dosage compensation (7, 16–18), tation and properties using L3 autosomes as an example. We then which caused whole-genome chromatin state maps to subdivide into use the states to investigate autosomal chromatin domain organi- separate autosomal and X-chromosome–specific states. Therefore, zation and its regulation. A Annotation 1 2 3 4 Txn elongation II: exon and intron 5 Txn elongtion III: exon and gene end 6 Txn elongation IV low expression and repeats 7 Txn elongation V: introns and repeats 8 9 Enhancer II: intergenic GENETICS 10 Enhancer III: weak 11 12 13 Retrotransposons, pseudogenes, H3K9me3, H3K27me3 14 15 Repeats, RNA pseudogenes, H3K9me2 16 17 Pc/H3K27me3 I:low expr/silent and pseudogenes 18 Pc/H3K27me3 II: low expr/silent 19 20 H3 HTZ1 H4K8ac H3K27ac H3K4me2 H3K4me1 H3K9me3 H3K9me2 H3K4me3 H4K20me1 H3K36me2 H3K79me3 H3K36me3 H3K36me1 H3K79me2 H3K27me3 H3K27me1 -2 -1 0 1 2 B Chr I: 7,996,451- 8,337,598 genes EE domains L3 domains EE states 1-5 EE states 6-15 EE states 16-20 L3 states 1-5 L3 states 6-15 L3 states 16-20 EE H3K36me3 EE H3K27me3 L3 H3K36me3 L3 H3K27me3 Fig. 1. Chromatin states and
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