Abstract
Numerous cytogenetic observations have shown that homologous chromosomes (or individual chromosomal loci) can engage in specific pairing interactions in the apparent absence of DNA breakage and recombination, suggesting that canonical recombination-mediated mechanisms may not be the only option for sensing DNA/DNA homology. One proposed mechanism for such recombination-independent homology recognition involves direct contacts between intact double-stranded DNA molecules. The strongest in vivo evidence for the existence of such a mechanism is provided by the phenomena of homology-directed DNA modifications in fungi, known as repeat-induced point mutation (RIP, discovered in Neurospora crassa) and methylation-induced premeiotically (MIP, discovered in Ascobolus immersus). In principle, Neurospora RIP can detect the presence of gene-sized DNA duplications irrespectively of their origin, underlying nucleotide sequence, coding capacity or relative, as well as absolute positions in the genome. Once detected, both sequence copies are altered by numerous cytosine-to-thymine (C-to-T) mutations that extend specifically over the duplicated region. We have recently shown that Neurospora RIP does not require MEI-3, the only RecA/Rad51 protein in this organism, consistent with a recombination-independent mechanism. Using an ultra-sensitive assay for RIP mutation, we have defined additional features of this process. We have shown that RIP can detect short islands of homology of only three base-pairs as long as many such islands are arrayed with a periodicity of 11 or 12 base-pairs along a pair of DNA molecules. While the presence of perfect homology is advantageous, it is not required: chromosomal segments with overall sequence identity of only 35–36 % can still be recognized by RIP. Importantly, in order for this process to work efficiently, participating DNA molecules must be able to co-align along their lengths. Based on these findings, we have proposed a model, in which sequence homology is detected by direct interactions between slightly-extended double-stranded DNAs. As a next step, it will be important to determine if the uncovered principles also apply to other processes that involve recombination-independent interactions between homologous chromosomal loci in vivo as well as to protein-free DNA/DNA interactions that were recently observed under biologically relevant conditions in vitro.
Similar content being viewed by others
References
Amselem J, Lebrun MH, Quesneville H (2015) Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes. BMC Genom 16:141. doi:10.1186/s12864-015-1347-1
Apte MS, Meller VH (2012) Homologue pairing in flies and mammals: gene regulation when two are involved. Genet Res Int. ID 430587. doi:10.1155/2012/430587
Baldwin GS, Brooks NJ, Robson RE, Wynveen A, Goldar A, Leikin S, Seddon JM, Kornyshev AA (2008) DNA double helices recognize mutual sequence homology in a protein free environment. J Phys Chem B 112:1060–1064. doi:10.1021/jp7112297
Baranello L, Levens D, Gupta A, Kouzine F (2012) The importance of being supercoiled: how DNA mechanics regulate dynamic processes. Biochim Biophys Acta 1819:632–638. doi:10.1016/j.bbagrm.2011.12.007
Barzel A, Kupiec M (2008) Finding a match: how do homologous sequences get together for recombination? Nat Rev Genet 9:27–37. doi:10.1038/nrg2224
Boateng KA, Bellani MA, Gregoretti IV, Pratto F, Camerini-Otero RD (2013) Homologous pairing preceding SPO11-mediated double-strand breaks in mice. Dev Cell 24:196–205. doi:10.1016/j.devcel.2012.12.002
Borkovich KA, Alex LA, Yarden O, Freitag M, Turner GE, Read ND, Seiler S, Bell-Pedersen D, Paietta J, Plesofsky N, Plamann M, Goodrich-Tanrikulu M, Schulte U, Mannhaupt G, Nargang FE, Radford A, Selitrennikoff C, Galagan JE, Dunlap JC, Loros JJ, Catcheside D, Inoue H, Aramayo R, Polymenis M, Selker EU, Sachs MS, Marzluf GA, Paulsen I, Davis R, Ebbole DJ, Zelter A, Kalkman ER, O’Rourke R, Bowring F, Yeadon J, Ishii C, Suzuki K, Sakai W, Pratt R (2004) Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism. Microbiol Mol Biol Rev 68:1–108
Bowring FJ, Yeadon PJ, Stainer RG, Catcheside DE (2006) Chromosome pairing and meiotic recombination in Neurospora crassa spo11 mutants. Curr Genet 50:115–123. doi:10.1007/s00294-006-0066-1
Burgess SM, Kleckner N (1999) Collisions between yeast chromosomal loci in vivo are governed by three layers of organization. Genes Dev 13:1871–1883
Burgess SM, Kleckner N, Weiner BM (1999) Somatic pairing of homologs in budding yeast: existence and modulation. Genes Dev 13:1627–1641
Butler DK, Metzenberg RL (1993) Amplification of the nucleolus organizer region during the sexual phase of Neurospora crassa. Chromosoma 102:519–525
Cambareri EB, Jensen BC, Schabtach E, Selker EU (1989) Repeat-induced G-C to A-T mutations in Neurospora. Science 244:1571–1575
Cha RS, Weiner BM, Keeney S, Dekker J, Kleckner N (2000) Progression of meiotic DNA replication is modulated by interchromosomal interaction proteins, negatively by Spo11p and positively by Rec8p. Genes Dev 14:493–503
Cheng R, Baker TI, Cords CE, Radloff RJ (1993) Mei-3, a recombination and repair gene of Neurospora crassa, encodes a RecA-like protein. Mutat Res 294:223–234
Clutterbuck AJ (2011) Genomic evidence of repeat-induced point mutation (RIP) in filamentous ascomycetes. Fungal Genet Biol 48:306–326. doi:10.1016/j.fgb.2010.09.002
Colot HV, Park G, Turner GE, Ringelberg C, Crew CM, Litvinkova L, Weiss RL, Borkovich KA, Dunlap JC (2006) A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors. PNAS 103:10352–10357. doi:10.1073/pnas.0601456103
Cook PR (1997) The transcriptional basis of chromosome pairing. J Cell Sci 110:1033–1040
Danilowicz C, Lee CH, Kim K, Hatch K, Coljee VW, Kleckner N, Prentiss M (2009) Single molecule detection of direct, homologous, DNA/DNA pairing. PNAS 106:19824–19829. doi:10.1073/pnas.0911214106
Dekker J, Rippe K, Dekker M, Kleckner N (2002) Capturing chromosome conformation. Science 295:1306–1311. doi:10.1126/science.1067799
Ding DQ, Okamasa K, Yamane M, Tsutsumi C, Haraguchi T, Yamamoto M, Hiraoka Y (2012) Meiosis-specific noncoding RNA mediates robust pairing of homologous chromosomes in meiosis. Science 336:732–736. doi:10.1126/science.1219518
Duncan IW (2002) Transvection effects in Drosophila. Annu Rev Genet 36:521–556. doi:10.1146/annurev.genet.36.060402.100441
Foss HM, Selker EU (1991) Efficient DNA pairing in a Neurospora mutant defective in chromosome pairing. Mol Gen Genet 231:49–52
Foss EJ, Garrett PW, Kinsey JA, Selker EU (1991) Specificity of repeat-induced point mutation (RIP) in Neurospora: sensitivity of non-Neurospora sequences, a natural diverged tandem duplication, and unique DNA adjacent to a duplicated region. Genetics 127:711–717
Freitag M, Williams RL, Kothe GO, Selker EU (2002) A cytosine methyltransferase homologue is essential for repeat-induced point mutation in Neurospora crassa. PNAS 99:8802–8807. doi:10.1073/pnas.132212899
Freitag M, Hickey PC, Raju NB, Selker EU, Read ND (2004) GFP as a tool to analyze the organization, dynamics and function of nuclei and microtubules in Neurospora crassa. Fungal Genet Biol 41:897–910. doi:10.1016/j.fgb.2004.06.008
Galagan JE, Selker EU (2004) RIP: the evolutionary cost of genome defense. Trends Genet 20:417–423. doi:10.1016/j.tig.2004.07.007
Gladyshev E, Kleckner N (2014) Direct recognition of homology between double helices of DNA in Neurospora crassa. Nat Commun 5:3509. doi:10.1038/ncomms4509
Gladyshev E, Kleckner N (2016) Recombination-independent recognition of DNA homology for repeat-induced point mutation (RIP) is modulated by the underlying nucleotide sequence. PLoS Genet 12:e1006015. doi:10.1371/journal.pgen.1006015
Goll MG, Bestor TH (2005) Eukaryotic cytosine methyltransferases. Annu Rev Biochem 74:481–514. doi:10.1146/annurev.biochem.74.010904.153721
Goyon C, Barry C, Grégoire A, Faugeron G, Rossignol JL (1996) Methylation of DNA repeats of decreasing sizes in Ascobolus immersus. Mol Cell Biol 16:3054–3065
Hane J, Williams A, Taranto A, Solomon P, Oliver R, Vandenberg M, Maruthachalam K (2015) Repeat-induced point mutation: a fungal-specific, endogenous mutagenesis process. Genet Transform Syst Fungi 2:55–68. doi:10.1007/978-3-319-10503-1_4
Irelan JT, Hagemann AT, Selker EU (1994) High frequency repeat-induced point mutation (RIP) is not associated with efficient recombination in Neurospora. Genetics 138:1093–1103
Ishiguro K, Kim J, Shibuya H, Hernández-Hernández A, Suzuki A, Fukagawa T, Shioi G, Kiyonari H, Li XC, Schimenti J, Höög C, Watanabe Y (2014) Meiosis-specific cohesin mediates homolog recognition in mouse spermatocytes. Genes Dev 28:594–607. doi:10.1101/gad.237313.113
Keeney S, Kleckner N (1996) Communication between homologous chromosomes: genetic alterations at a nuclease-hypersensitive site can alter mitotic chromatin structure at that site both in cis and in trans. Genes Cells 1:475–489
Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ (2015) The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc 10:845–858. doi:10.1038/nprot.2015.053
Kleckner N, Weiner BM (1993) Potential advantages of unstable interactions for pairing of chromosomes in meiotic, somatic, and premeiotic cells. Cold Spring Harb Symp Quant Biol 58:553–565
Klutstein M, Cooper JP (2014) The chromosomal courtship dance-homolog pairing in early meiosis. Curr Opin Cell Biol 26:123–131. doi:10.1016/j.ceb.2013.12.004
Kornyshev AA, Leikin S (2001) Sequence recognition in the pairing of DNA duplexes. Phys Rev Lett 86:3666–3669
Kouzminova E, Selker EU (2001) dim-2 Encodes a DNA methyltransferase responsible for all known cytosine methylation in Neurospora. EMBO J 20:4309–4323. doi:10.1093/emboj/20.15.4309
Kubitschek HE, Henderson TR (1966) DNA replication. PNAS 55:512–519
Lake CM, Hawley RS (2012) The molecular control of meiotic chromosomal behavior: events in early meiotic prophase in Drosophila oocytes. Annu Rev Physiol 74:425–451. doi:10.1146/annurev-physiol-020911-153342
Malagnac F, Wendel B, Goyon C, Faugeron G, Zickler D, Rossignol JL, Noyer-Weidner M, Vollmayr P, Trautner TA, Walter J (1997) A gene essential for de novo methylation and development in Ascobolus reveals a novel type of eukaryotic DNA methyltransferase structure. Cell 91:281–290
Mazur AK (2016) Homologous pairing between long DNA double helices. Phys Rev Lett 116:158101. doi:10.1103/PhysRevLett.116.158101
McGavin S (1977) A model for the specific pairing of homologous double-stranded nucleic acid molecules during genetic recombination. Heredity (Edinb) 39:15–25
McKee BD, Yan R, Tsai JH (2012) Meiosis in male Drosophila. Spermatogenesis 2:167–184. doi:10.4161/spmg.21800
Molnar M, Kleckner N (2008) Examination of interchromosomal interactions in vegetatively growing diploid Schizosaccharomyces pombe cells by Cre/loxP site-specific recombination. Genetics 178:99–112. doi:10.1534/genetics.107.082826
O’ Lee DJ, Wynveen A, Albrecht T, Kornyshev AA (2015) Which way up? Recognition of homologous DNA segments in parallel and antiparallel alignments. J Chem Phys 142:045101. doi:10.1063/1.4905291
O’ Lee DJ, Danilowicz C, Rochester C, Kornyshev AA, Prentiss M (2016) Evidence of protein-free homology recognition in magnetic bead force-extension experiments. Proc Math Phys Eng Sci 472:20160186. doi:10.1098/rspa.2016.0186
Prentiss M, Prévost C, Danilowicz C (2015) Structure/function relationships in RecA protein-mediated homology recognition and strand exchange. Crit Rev Biochem Mol Biol 50:453–476. doi:10.3109/10409238.2015.1092943
Rog O, Dernburg AF (2013) Chromosome pairing and synapsis during Caenorhabditis elegans meiosis. Curr Opin Cell Biol 25:349–356. doi:10.1016/j.ceb.2013.03.003
Rossignol JL, Faugeron G (1994) Gene inactivation triggered by recognition between DNA repeats. Experientia 50:307–317
Sakamoto N, Chastain PD, Parniewski P, Ohshima K, Pandolfo M, Griffith JD, Wells RD (1999) Sticky DNA: self-association properties of long GAA.TTC repeats in R.R.Y triplex structures from Friedreich’s ataxia. Mol Cell 3:465–475
Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. PNAS 74:5463–5467
Scherthan H, Bähler J, Kohli J (1994) Dynamics of chromosome organization and pairing during meiotic prophase in fission yeast. J Cell Biol 127:273–285
Schroeder AL (1986) Chromosome instability in mutagen sensitive mutants of Neurospora. Curr Genet 10:381–387
Schroeder AL, Raju NB (1991) Mei-2, a mutagen-sensitive mutant of Neurospora defective in chromosome pairing and meiotic recombination. Mol Gen Genet 231:41–48
Selker EU (1990) Premeiotic instability of repeated sequences in Neurospora crassa. Annu Rev Genet 24:579–613. doi:10.1146/annurev.ge.24.120190.003051
Selker EU, Garrett PW (1988) DNA sequence duplications trigger gene inactivation in Neurospora crassa. PNAS 85:6870–6874
Selker EU, Cambareri EB, Jensen BC, Haack KR (1987) Rearrangement of duplicated DNA in specialized cells of Neurospora. Cell 51:741–752
Sen D, Gilbert W (1988) Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis. Nature 334:364–366. doi:10.1038/334364a0
Song J, Rechkoblit O, Bestor TH, Patel DJ (2011) Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation. Science 331:1036–1040. doi:10.1126/science.1195380
Song J, Teplova M, Ishibe-Murakami S, Patel DJ (2012) Structure-based mechanistic insights into DNMT1-mediated maintenance DNA methylation. Science 335:709–712. doi:10.1126/science.1214453
Stewart MN, Dawson DS (2008) Changing partners: moving from non-homologous to homologous centromere pairing in meiosis. Trends Genet 24:564–573. doi:10.1016/j.tig.2008.08.006
Testa AC, Oliver RP, Hane JK (2016) OcculterCut: a comprehensive survey of AT-rich regions in fungal genomes. Genome Biol Evol 8:2044–2064. doi:10.1093/gbe/evw121
Tsai JH, McKee BD (2011) Homologous pairing and the role of pairing centers in meiosis. J Cell Sci 124:1955–1963. doi:10.1242/jcs.006387
Watters MK, Randall TA, Margolin BS, Selker EU, Stadler DR (1999) Action of repeat-induced point mutation on both strands of a duplex and on tandem duplications of various sizes in Neurospora. Genetics 153:705–714
Weiner BM, Kleckner N (1994) Chromosome pairing via multiple interstitial interactions before and during meiosis in yeast. Cell 77:977–991
Yang J, Li F (2016) Are all repeats created equal? Understanding DNA repeats at an individual level. Curr Genet. doi:10.1007/s00294-016-0619-x
Yang N, Xu RM (2013) Structure and function of the BAH domain in chromatin biology. Crit Rev Biochem Mol Biol 48:211–221. doi:10.3109/10409238.2012.742035
Acknowledgments
This work was supported by the Grants GM044794 and GM025326 from the National Institutes of Health to N. K. and The Helen Hay Whitney Foundation, The Howard Hughes Medical Institute, and Charles A. King Trust to E.G.
Author information
Authors and Affiliations
Corresponding authors
Additional information
Communicated by M. Kupiec.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Gladyshev, E., Kleckner, N. Recombination-independent recognition of DNA homology for repeat-induced point mutation. Curr Genet 63, 389–400 (2017). https://doi.org/10.1007/s00294-016-0649-4
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00294-016-0649-4