INVESTIGATION Opposing Activities of DRM and MES-4 Tune Gene Expression and X-Chromosome Repression in Caenorhabditis elegans Germ Cells Tomoko M. Tabuchi,* ,† Andreas Rechtsteiner, † Susan Strome, † and Kirsten A. Hagstrom* ,1 *Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, and † Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064 ABSTRACT During animal development, gene transcription is tuned to tissue-appropriate levels. Here we uncover antagonistic regulation of transcript levels in the germline of Caenorhabditis elegans hermaphro- dites. The histone methyltransferase MES-4 (Maternal Effect Sterile-4) marks genes expressed in the germ- line with methylated lysine on histone H3 (H3K36me) and promotes their transcription; MES-4 also represses genes normally expressed in somatic cells and genes on the X chromosome. The DRM transcrip- tion factor complex, named for its Dp/E2F, Retinoblastoma-like, and MuvB subunits, affects germline gene expression and prevents excessive repression of X-chromosome genes. Using genome-scale analyses of germline tissue, we show that common germline-expressed genes are activated by MES-4 and repressed by DRM, and that MES-4 and DRM co-bind many germline-expressed genes. Reciprocally, MES-4 represses and DRM activates a set of autosomal soma-expressed genes and overall X-chromosome gene expression. Mutations in mes-4 and the DRM subunit lin-54 oppositely skew the transcript levels of their common targets and cause sterility. A double mutant restores target gene transcript levels closer to wild type, and the concomitant loss of lin-54 suppresses the severe germline proliferation defect observed in mes-4 single mutants. Together, “yin-yang” regulation by MES-4 and DRM ensures transcript levels appropriate for germ-cell function, elicits robust but not excessive dampening of X-chromosome-wide transcription, and may poise genes for future expression changes. Our study reveals that conserved transcriptional regulators implicated in development and cancer counteract each other to fine-tune transcript dosage. KEYWORDS gene regulation development chromatin germ cells X chromosome Proper development requires that genes be expressed at appropriate levels in appropriate tissues. Developmental gene regulation often is viewed as a series of all-or-none switches that turn genes on or off to promote cell identity and function. However, a gene that is “on” may only be expressed at moderate levels. Similarly, a gene that is “off” may not be completely or irreversibly inactivated but may instead be expressed at very low levels and poised for reactivation. Such fine- tuning is particularly important for genes for which a relatively small degree of transcriptional variability may have a profound influence on cell identity or function. For example, transcription of Oct3/4, which is critical for self-renewal, is precisely regulated in embryonic stem cells; either too much or too little Oct3/4 expression leads to differ- entiation (Niwa et al. 2000). How the transcriptional regulatory ma- chinery precisely controls and maintains proper transcript levels is not well understood. In some cases, tuning is achieved through the com- bined action of factors that activate and factors that repress transcrip- tion (Reynolds et al. 2013). In this study, we investigated gene expression regulation in the germ cells of Caenorhabditis elegans and uncovered a system of transcriptional fine-tuning by antagonistic transcriptional regulators. This transcriptional fine-tuning system acts Copyright © 2014 Tabuchi et al. doi: 10.1534/g3.113.007849 Manuscript received June 22, 2013; accepted for publication November 15, 2013; published Early Online November 26, 2013. This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License (http://creativecommons.org/licenses/ by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Supporting information is available online at http://www.g3journal.org/lookup/ suppl/doi:10.1534/g3.113.007849/-/DC1 Microarray data have been deposited in the National Center for Biotechnology Information’s Gene Expression Omnibus and are accessible through Gene Expression Omnibus series accession no. GSE52064. 1 Corresponding author: Program in Molecular Medicine, University of Massachusetts Medical School, Biotech Four, Suite 334, 377 Plantation St., Worcester, MA 01605. E-mail: hagstromkirsten@gmail.com Volume 4 | January 2014 | 143