Genetics; Germ Cells; Stem Cells; Developmental Biology; Caenorhabditis elegans; Genomics; Epigenomics
Public Health Interests
Genetics; Reproductive Biology
Stem Cell Center, Yale: Stem Cell Self-Renewal and Cell Symmetry
Germ cells are highly specialized cells with the unique responsibility of producing healthy offspring, thus ensuring the continuity of a species across generations. These cells guard their DNA very carefully to allow the production of sperm and eggs with the right number of chromosomes and no mutations. We wish to understand how germ cells protect their DNA, while turning different genes on and off at the right times to make functional sperm and eggs. To grasp the most important trends, we use global genomic technologies to investigate many genes simultaneously. We are studying germ cell regulation primarily using the model organism C. elegans, a nematode, because of the large number of germ cells it contains, and because of the many experimental advantages it offers. Because the genes in C. elegans are related to those in higher organisms, the results from our studies should help us to understand how germ cells function in humans as well.
Extensive Research Description
The genome carries all the information necessary for the development and function of an organism. This information is embedded at multiple levels - in the regulatory information of individual genes, in the partitioning of that sequence into chromatin domains, and in the spatial segregation of these domains into functionally distinct regions of the nucleus. This linear and spatial organization is essential for effective and precise deployment of genetic information, yet the underlying mechanisms that govern the three-dimensional architecture of the genome are just now being addressed, and fundamental questions remain unanswered: How does genome organization influence epigenetic information, and vice versa? How extensively does genome organization contribute to coordinated expression of functionally related genes? How does genome organization stabilize and instruct tissue-specific gene expression?
We address these questions in vivo with unprecedented cell specificity and comprehensiveness, utilizing innovative methods to investigate how genome structure and organization influences gene expression specifically in the C. elegans germ line. Specific projects are focused on:
Germline-specific expression of piRNA clusters. The C. elegans genome contains a remarkable genomic domain subject to tissue-specific expression. In C. elegans, thousands of individually transcribed loci encoding the piRNA class of small noncoding RNAs are clustered into two sharply demarcated regions on a single chromosome. Amazingly, these piRNAs exhibit synchronized expression in the germ line, despite being interspersed among hundreds of coding genes with diverse expression patterns. piRNA clustering is evolutionarily conserved, indicating that physical proximity is a key feature for coordinated expression, yet how germline-specific expression is implemented is a mystery. We have found that SNAP190 preferentially binds across both piRNA clusters only in the germ line and promotes piRNA expression. SNAP190 is a transcription factor known to stimulate the activity of both RNA polymerase II and III, and we have found that RNA polymerase III (pol III) also exhibits increased occupancy in piRNA clusters. Recently, pol III and core components of the pol III complex such as TFIIIC have been demonstrated to establish boundaries between genomic domains, and regulate gene expression within those domains. We are now determining the mechanisms by which SNAP190 and the core RNA polymerase III machinery coordinately regulate this piRNA-rich genomic domain in a tissue-specific manner, within the native developmental context.
Regulation and function of germline transcription factors. In C. elegans, the germ line maintains a specific gene expression profile largely through the interaction between chromatin state and post-transcriptional RNA regulation. However, certain key transcription factors play a vital role in establishing and maintaining germline identity and separating the germline programs from the soma. In particular, the C. elegans version of the tumor suppressor complex Rb/E2F is vital to distinguishing germline and somatic identities. Gene expression and DNA binding profiles indicate that the complex acts as a repressor in the soma, and an activator in the germ line on completely separate gene targets. How this complex differentially regulates distinct target genes in specific tissues is poorly understood. We are now determining the tissue-specfici chromatin mechanisms by which this complex interacts with target genes. This analysis will have implications not only for germline development but also for human development and tumorigenesis. More broadly, we have defined additional novel regulatory factors that also appear to be expressed specifically in the germline and that have important roles in germline development. We are investigating how these factors are regulated as well as how they function, using a variety of genomic, genetic and biochemical assays.
The C. elegans SNAPc component SNPC-4 coats piRNA domains and is globally required for piRNA abundance.
Kasper DM, Wang G, Gardner KE, Johnstone TG, Reinke V. Dev Cell. 2014 Oct 27;31(2):145-58
Homeland security in the C. elegans germ line: insights into the biogenesis and function of piRNAs.
Kasper DM, Gardner KE, Reinke V. Epigenetics. 2014 Jan;9(1):62-74.
Regulatory analysis of the C. elegans genome with spatiotemporal resolution
Araya CL, Kawli T, Kundaje A, Jiang L, Wu B, Vafeados D, Terrell R, Weissdepp P, Gevirtzman L, Mace D, Niu W, Boyle AP, Xie D, Ma L, Murray JI, Reinke V, Waterston RH, Snyder M. Nature. 2014 Aug 28;512(7515):400-5
Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs.
Kudron M, Niu W, Lu Z, Wang G, Gerstein M, Snyder M, Reinke V. Genome Biol. 2013 Jan 23;14(1):R5
C. elegans meg-1 and meg-2 differentially interact with nanos family members to either promote or inhibit germ cell proliferation and survival.
Kapelle WS, Reinke V. Genesis. 2011 May;49(5):380-91.
The kinase VRK1 is required for normal meiotic progression in mammalian oogenesis.
Schober CS, Aydiner F, Booth CJ, Seli E, Reinke V. Mech Dev. 2011 Mar-Apr;128(3-4):178-90.
A spatial and temporal map of C. elegans gene expression.
Spencer WC, Zeller G, Watson JD, Henz SR, Watkins KL, McWhirter RD, Petersen S, Sreedharan VT, Widmer C, Jo J, Reinke V, Petrella L, Strome S, Von Stetina SE, Katz M, Shaham S, Rätsch G, Miller DM 3rd. Genome Res. 2011 Feb;21(2):325-41.
Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans.
Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, Brdlik CM, Janette J, Chen C, Alves P, Preston E, Slightham C, Jiang L, Hyman AA, Kim SK, Waterston RH, Gerstein M, Snyder M, Reinke V. Genome Res. 2011 Feb;21(2):245-54.
Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response.
Zhong M, Niu W, Lu ZJ, Sarov M, Murray JI, Janette J, Raha D, Sheaffer KL, Lam HY, Preston E, Slightham C, Hillier LW, Brock T, Agarwal A, Auerbach R, Hyman AA, Gerstein M, Mango SE, Kim SK, Waterston RH, Reinke V, Snyder M. Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. PLoS Genet. 2010 Feb 19;6(2):e1000848
Genome-wide analysis of germ cell proliferation in C.elegans identifies VRK-1 as a key regulator of CEP-1/p53.
Waters K, Yang AZ, Reinke V. Dev Biol. 2010 Aug 15;344(2):1011-25.
DPL-1 (DP) acts in the germ line to coordinate ovulation and fertilization in C. elegans.
Chi W, Reinke V. Mech Dev. 2009 May-Jun;126(5-6):406-16
Massively parallel sequencing of the polyadenylated transcriptome of C. elegans.
Hillier LW, Reinke V, Green P, Hirst M, Marra MA, Waterston RH. Genome Res. 2009 Apr;19(4):657-66.
A C. elegans Piwi, PRG-1, regulates 21U-RNAs during spermatogenesis.
Wang G, Reinke V. Curr Biol. 2008 Jun 24;18(12):861-7
Full List of PubMed Publications
- Sin O, de Jong T, Mata-Cabana A, Kudron M, Zaini MA, Aprile FA, Seinstra RI, Stroo E, Prins RW, Martineau CN, Wang HH, Hogewerf W, Steinhof A, Wanker EE, Vendruscolo M, Calkhoven CF, Reinke V, Guryev V, Nollen EA: Identification of an RNA Polymerase III Regulator Linked to Disease-Associated Protein Aggregation. Mol Cell. 2017 Mar 16. PMID: 28306505
- Weicksel SE, Mahadav A, Moyle M, Cipriani PG, Kudron M, Pincus Z, Bahmanyar S, Abriola L, Merkel J, Gutwein M, Fernandez AG, Piano F, Gunsalus KC, Reinke V: A novel small molecule that disrupts a key event during the oocyte-to-embryo transition in C. elegans. Development. 2016 Oct 1; 2016 Aug 10. PMID: 27510972
- Boeck ME, Huynh C, Gevirtzman L, Thompson OA, Wang G, Kasper DM, Reinke V, Hillier LW, Waterston RH: The time-resolved transcriptome of C. elegans. Genome Res. 2016 Oct; 2016 Aug 16. PMID: 27531719
- Reinke V: Single cell analysis in C. elegans. Genesis. 2016 Apr. PMID: 27099198
- Kasper DM, Wang G, Gardner KE, Johnstone TG, Reinke V: The C. elegans SNAPc component SNPC-4 coats piRNA domains and is globally required for piRNA abundance. Dev Cell. 2014 Oct 27. PMID: 25373775
- Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, Ma L, Niu W, Rehm EJ, Rozowsky J, Slattery M, Spokony R, Terrell R, Vafeados D, Wang D, Weisdepp P, Wu YC, Xie D, Yan KK, Feingold EA, Good PJ, Pazin MJ, Huang H, Bickel PJ, Brenner SE, Reinke V, Waterston RH, Gerstein M, White KP, Kellis M, Snyder M: Comparative analysis of regulatory information and circuits across distant species. Nature. 2014 Aug 28. PMID: 25164757
- Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R: Comparative analysis of the transcriptome across distant species. Nature. 2014 Aug 28. PMID: 25164755
- Araya CL, Kawli T, Kundaje A, Jiang L, Wu B, Vafeados D, Terrell R, Weissdepp P, Gevirtzman L, Mace D, Niu W, Boyle AP, Xie D, Ma L, Murray JI, Reinke V, Waterston RH, Snyder M: Regulatory analysis of the C. elegans genome with spatiotemporal resolution. Nature. 2014 Aug 28. PMID: 25164749
- Byrne AB, Walradt T, Gardner KE, Hubbert A, Reinke V, Hammarlund M: Insulin/IGF1 signaling inhibits age-dependent axon regeneration. Neuron. 2014 Feb 5; 2014 Jan 16. PMID: 24440228
- Kasper DM, Gardner KE, Reinke V: Homeland security in the C. elegans germ line: insights into the biogenesis and function of piRNAs. Epigenetics. 2014 Jan; 2013 Oct 22. PMID: 24149573
- Doh JH, Jung Y, Reinke V, Lee MH: C. elegans RNA-binding protein GLD-1 recognizes its multiple targets using sequence, context, and structural information to repress translation. Worm. 2013 Oct 1. PMID: 24744981
- Reinke V, Krause M, Okkema P: Transcriptional regulation of gene expression in C. elegans. WormBook. 2013 Jun 4; 2013 Jun 4. PMID: 23801596
- Kapelle WS, Reinke V: C. elegans meg-1 and meg-2 differentially interact with nanos family members to either promote or inhibit germ cell proliferation and survival. Genesis. 2011 May. PMID: 21305687
- Schober CS, Aydiner F, Booth CJ, Seli E, Reinke V: The kinase VRK1 is required for normal meiotic progression in mammalian oogenesis. Mech Dev. 2011 Mar-Apr; 2011 Jan 26. PMID: 21277975
- Waters KA, Reinke V: Extrinsic and intrinsic control of germ cell proliferation in Caenorhabditis elegans. Mol Reprod Dev. 2011 Mar; 2011 Feb 17. PMID: 21337453
- Lu ZJ, Yip KY, Wang G, Shou C, Hillier LW, Khurana E, Agarwal A, Auerbach R, Rozowsky J, Cheng C, Kato M, Miller DM, Slack F, Snyder M, Waterston RH, Reinke V, Gerstein MB: Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data. Genome Res. 2011 Feb; 2010 Dec 22. PMID: 21177971
- Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, Brdlik CM, Janette J, Chen C, Alves P, Preston E, Slightham C, Jiang L, Hyman AA, Kim SK, Waterston RH, Gerstein M, Snyder M, Reinke V: Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. Genome Res. 2011 Feb; 2010 Dec 22. PMID: 21177963
- Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM 3rd, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X, modENCODE Consortium., Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH: Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science. 2010 Dec 24; 2010 Dec 22. PMID: 21177976
- Waters K, Yang AZ, Reinke V: Genome-wide analysis of germ cell proliferation in C.elegans identifies VRK-1 as a key regulator of CEP-1/p53. Dev Biol. 2010 Aug 15; 2010 Jun 23. PMID: 20599896
- Agarwal A, Koppstein D, Rozowsky J, Sboner A, Habegger L, Hillier LW, Sasidharan R, Reinke V, Waterston RH, Gerstein M: Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays. BMC Genomics. 2010 Jun 17; 2010 Jun 17. PMID: 20565764
- Zhong M, Niu W, Lu ZJ, Sarov M, Murray JI, Janette J, Raha D, Sheaffer KL, Lam HY, Preston E, Slightham C, Hillier LW, Brock T, Agarwal A, Auerbach R, Hyman AA, Gerstein M, Mango SE, Kim SK, Waterston RH, Reinke V, Snyder M: Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. PLoS Genet. 2010 Feb 19; 2010 Feb 19. PMID: 20174564
- Chi W, Reinke V: DPL-1 (DP) acts in the germ line to coordinate ovulation and fertilization in C. elegans. Mech Dev. 2009 May-Jun; 2009 Feb 6. PMID: 19368797
- Reinke V, Cutter AD: Germline expression influences operon organization in the Caenorhabditis elegans genome. Genetics. 2009 Apr; 2009 Feb 9. PMID: 19204375
- Reinke V: Gene regulation: a tale of germline mRNA tails. Curr Biol. 2008 Oct 14. PMID: 18957237
- Kudron MM, Reinke V: C. elegans nucleostemin is required for larval growth and germline stem cell division. PLoS Genet. 2008 Aug 22; 2008 Aug 22. PMID: 18725931
- Wang G, Reinke V: A C. elegans Piwi, PRG-1, regulates 21U-RNAs during spermatogenesis. Curr Biol. 2008 Jun 24; 2008 May 22. PMID: 18501605
- Lin B, Reinke V: The candidate MAP kinase phosphorylation substrate DPL-1 (DP) promotes expression of the MAP kinase phosphatase LIP-1 in C. elegans germ cells. Dev Biol. 2008 Apr 1; 2008 Jan 8. PMID: 18304523
- Leacock SW, Reinke V: MEG-1 and MEG-2 are embryo-specific P-granule components required for germline development in Caenorhabditis elegans. Genetics. 2008 Jan. PMID: 18202375
- Leacock SW, Reinke V: Expression profiling of MAP kinase-mediated meiotic progression in Caenorhabditis elegans. PLoS Genet. 2006 Nov 10. PMID: 17096596
- Chi W, Reinke V: Promotion of oogenesis and embryogenesis in the C. elegans gonad by EFL-1/DPL-1 (E2F) does not require LIN-35 (pRB). Development. 2006 Aug; 2006 Jul 19. PMID: 16854972
- Reinke V: Germline genomics. WormBook. 2006 Jan 20; 2006 Jan 20. PMID: 18050476
- Reinke V, Gil IS, Ward S, Kazmer K: Genome-wide germline-enriched and sex-biased expression profiles in Caenorhabditis elegans. Development. 2004 Jan; 2003 Dec 10. PMID: 14668411
- Reinke V: Functional exploration of the C. elegans genome using DNA microarrays. Nat Genet. 2002 Dec. PMID: 12454651
- Reinke V, White KP: Developmental genomic approaches in model organisms. Annu Rev Genomics Hum Genet. 2002; 2002 Apr 15. PMID: 12142361
- Cheung KH, White K, Hager J, Gerstein M, Reinke V, Nelson K, Masiar P, Srivastava R, Li Y, Li J, Zhao H, Li J, Allison DB, Snyder M, Miller P, Williams K: YMD: a microarray database for large-scale gene expression analysis. Proc AMIA Symp. 2002. PMID: 12463803