title: Dynamic Changes in the Transcriptome and Methylome of Chlamydomonas reinhardtii throughout Its Life Cycle.
abstract: The green alga Chlamydomonas reinhardtii undergoes gametogenesis and mating upon nitrogen starvation. While the steps involved in its sexual reproductive cycle have been extensively characterized, the genome-wide transcriptional and epigenetic changes underlying different life cycle stages have yet to be fully described. Here, we performed transcriptome and methylome sequencing to quantify expression and DNA methylation from vegetative and gametic cells of each mating type and from zygotes. We identified 361 gametic genes with mating type-specific expression patterns and 627 genes that are specifically induced in zygotes; furthermore, these sex-related gene sets were enriched for secretory pathway and alga-specific genes. We also examined the C. reinhardtii nuclear methylation map with base-level resolution at different life cycle stages. Despite having low global levels of nuclear methylation, we detected 23 hypermethylated loci in gene-poor, repeat-rich regions. We observed mating type-specific differences in chloroplast DNA methylation levels in plus versus minus mating type gametes followed by chloroplast DNA hypermethylation in zygotes. Lastly, we examined the expression of candidate DNA methyltransferases and found three, DMT1a, DMT1b, and DMT4, that are differentially expressed during the life cycle and are candidate DNA methylases. The expression and methylation data we present provide insight into cell type-specific transcriptional and epigenetic programs during key stages of the C. reinhardtii life cycle.
authors.affiliation: Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.).
authors.forename: David
authors.identifier: http://orcid.org/0000-0001-9363-9329
authors.initials: D
authors.lastname: Lopez
authors.affiliation: Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.).
authors.forename: Takashi
authors.identifier: http://orcid.org/0000-0002-2801-2148
authors.initials: T
authors.lastname: Hamaji
authors.affiliation: Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.).
authors.forename: Janette
authors.identifier: http://orcid.org/0000-0001-8952-3286
authors.initials: J
authors.lastname: Kropat
authors.affiliation: Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.).
authors.forename: Peter
authors.identifier: http://orcid.org/0000-0002-0163-7535
authors.initials: P
authors.lastname: De Hoff
authors.affiliation: Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.).
authors.forename: Marco
authors.identifier: http://orcid.org/0000-0003-3351-5791
authors.initials: M
authors.lastname: Morselli
authors.affiliation: Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.).
authors.forename: Liudmilla
authors.identifier: http://orcid.org/0000-0002-9236-202X
authors.initials: L
authors.lastname: Rubbi
authors.affiliation: Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.).
authors.forename: Sorel
authors.identifier: http://orcid.org/0000-0001-7090-5719
authors.initials: S
authors.lastname: Fitz-Gibbon
authors.affiliation: Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.).
authors.forename: Sean D
authors.identifier: http://orcid.org/0000-0002-9773-6051
authors.initials: SD
authors.lastname: Gallaher
authors.affiliation: Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.).
authors.forename: Sabeeha S
authors.identifier: http://orcid.org/0000-0002-2594-509X
authors.initials: SS
authors.lastname: Merchant
authors.affiliation: Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.).
authors.forename: James
authors.identifier: http://orcid.org/0000-0003-4094-9045
authors.initials: J
authors.lastname: Umen
authors.affiliation: Molecular Biology Institute (D.L.), Department of Molecular, Cell, and Developmental Biology (D.L., M.M., L.R., S.F.-G., M.P.), Department of Chemistry and Biochemistry (J.K., S.F.-G., S.D.G., S.S.M.), and Institute for Genomics and Proteomics (S.S.M., M.P.), University of California, Los Angeles, California 90095;Donald Danforth Plant Science Center, St. Louis, Missouri 63132 (T.H., J.U.); andSalk Institute for Biological Studies, La Jolla, California 92037 (P.D.H.) matteop@mcdb.ucla.edu.
authors.forename: Matteo
authors.identifier: http://orcid.org/0000-0001-9355-9564
authors.initials: M
authors.lastname: Pellegrini
mesh_terms: D020418:Algal Proteins / Q000235:genetics / Q000378:metabolism; D016825:Chlamydomonas reinhardtii / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000235:genetics / Q000378:metabolism; D019175:DNA Methylation; D048028:DNA, Algal / Q000737:chemistry / Q000235:genetics; D018742:DNA, Chloroplast / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods; D008018:Life Cycle Stages / Q000235:genetics*; D008957:Models, Genetic; D012098:Reproduction / Q000235:genetics; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA / Q000379:methods; D013170:Spores / Q000235:genetics; D059467:Transcriptome
chemical_list: D020418:Algal Proteins; D048028:DNA, Algal; D018742:DNA, Chloroplast; D004248:DNA (Cytosine-5-)-Methyltransferases