Klemm SL, Shipony Z, Greenleaf WJ. Chromatin accessibility and the regulatory epigenome. Nat Rev Genet. 2019;20(4):207–20. https://doi.org/10.1038/s41576-018-0089-8.
Article
CAS
PubMed
Google Scholar
Liu CL, Kaplan T, Kim M, Buratowski S, Schreiber SL, Friedman N, et al. Single-nucleosome mapping of histone modifications in S. cerevisiae. PLoS Biol. 2005;3(10):e328.
Article
PubMed
PubMed Central
Google Scholar
Pokholok DK, Harbison CT, Levine S, Cole M, Hannett NM, Lee TI, et al. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell. 2005;122(4):517–27. https://doi.org/10.1016/j.cell.2005.06.026.
Article
CAS
PubMed
Google Scholar
Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature. 2007;448(7153):553–60. https://doi.org/10.1038/nature06008.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rando OJ, Winston F. Chromatin and transcription in yeast. Genetics. 2012;190(2):351–87. https://doi.org/10.1534/genetics.111.132266.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, et al. Comparative analysis of metazoan chromatin organization. Nature. 2014;512(7515):449–52. https://doi.org/10.1038/nature13415.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, McCombie WR, et al. Role of transposable elements in heterochromatin and epigenetic control. Nature. 2004;430(6998):471–6. https://doi.org/10.1038/nature02651.
Article
CAS
PubMed
Google Scholar
Cam HP, Sugiyama T, Chen ES, Chen X, FitzGerald PC, Grewal SI. Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome. Nat Genet. 2005;37(8):809–19. https://doi.org/10.1038/ng1602.
Article
CAS
PubMed
Google Scholar
Lewis ZA, Honda S, Khlafallah TK, Jeffress JK, Freitag M, Mohn F, et al. Relics of repeat-induced point mutation direct heterochromatin formation in Neurospora crassa. Genome Res. 2009;19(3):427–37. https://doi.org/10.1101/gr.086231.108.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sasaki T, Lynch KL, Mueller CV, Friedman S, Freitag M, Lewis ZA. Heterochromatin controls gammaH2A localization in Neurospora crassa. Eukaryot Cell. 2014;13(8):990–1000. https://doi.org/10.1128/EC.00117-14.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang X, Clarenz O, Cokus S, Bernatavichute YV, Pellegrini M, Goodrich J, et al. Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol. 2007;5(5):e129. https://doi.org/10.1371/journal.pbio.0050129.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jamieson K, Rountree MR, Lewis ZA, Stajich JE, Selker EU. Regional control of histone H3 lysine 27 methylation in Neurospora. Proc Natl Acad Sci U S A. 2013;110(15):6027–32. https://doi.org/10.1073/pnas.1303750110.
Article
CAS
PubMed
PubMed Central
Google Scholar
Connolly LR, Smith KM, Freitag M. The Fusarium graminearum histone H3 K27 methyltransferase KMT6 regulates development and expression of secondary metabolite gene clusters. PLoS Genet. 2013;9(10):e1003916. https://doi.org/10.1371/journal.pgen.1003916.
Article
CAS
PubMed
PubMed Central
Google Scholar
Basenko EY, Sasaki T, Ji L, Prybol CJ, Burckhardt RM, Schmitz RJ, et al. Genome-wide redistribution of H3K27me3 is linked to genotoxic stress and defective growth. Proc Natl Acad Sci U S A. 2015;112(46):E6339–48. https://doi.org/10.1073/pnas.1511377112.
Article
CAS
PubMed
PubMed Central
Google Scholar
Margueron R, Reinberg D. The Polycomb complex PRC2 and its mark in life. Nature. 2011;469(7330):343–9. https://doi.org/10.1038/nature09784.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lewis ZA. Polycomb Group Systems in Fungi: new models for understanding Polycomb repressive complex 2. Trends Genet. 2017;33(3):220–31. https://doi.org/10.1016/j.tig.2017.01.006.
Article
CAS
PubMed
Google Scholar
Guillemette B, Bataille AR, Gevry N, Adam M, Blanchette M, Robert F, et al. Variant histone H2A.Z is globally localized to the promoters of inactive yeast genes and regulates nucleosome positioning. PLoS Biol. 2005;3(12):e384.
Article
PubMed
PubMed Central
Google Scholar
Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, et al. High-resolution profiling of histone methylations in the human genome. Cell. 2007;129(4):823–37. https://doi.org/10.1016/j.cell.2007.05.009.
Article
CAS
PubMed
Google Scholar
Bargaje R, Alam MP, Patowary A, Sarkar M, Ali T, Gupta S, et al. Proximity of H2A.Z containing nucleosome to the transcription start site influences gene expression levels in the mammalian liver and brain. Nucleic Acids Res. 2012;40(18):8965–78. https://doi.org/10.1093/nar/gks665.
Article
CAS
PubMed
PubMed Central
Google Scholar
Weber CM, Ramachandran S, Henikoff S. Nucleosomes are context-specific, H2A.Z-modulated barriers to RNA polymerase. Mol Cell. 2014;53(5):819–30. https://doi.org/10.1016/j.molcel.2014.02.014.
Article
CAS
PubMed
Google Scholar
Dai X, Bai Y, Zhao L, Dou X, Liu Y, Wang L, et al. H2A.Z represses gene expression by modulating promoter nucleosome structure and enhancer histone modifications in Arabidopsis. Mol Plant. 2017;10(10):1274–92. https://doi.org/10.1016/j.molp.2017.09.007.
Article
CAS
PubMed
Google Scholar
Courtney AJ, Kamei M, Ferraro AR, Gai K, He Q, Honda S, et al. Normal patterns of histone H3K27 methylation require the histone variant H2A.Z in Neurospora crassa. Genetics. 2020;216(1):51–66. https://doi.org/10.1534/genetics.120.303442.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lu Z, Marand AP, Ricci WA, Ethridge CL, Zhang X, Schmitz RJ. The prevalence, evolution and chromatin signatures of plant regulatory elements. Nat Plants. 2019;5(12):1250–9. https://doi.org/10.1038/s41477-019-0548-z.
Article
CAS
PubMed
Google Scholar
Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods. 2013;10(12):1213–8. https://doi.org/10.1038/nmeth.2688.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lu Z, Hofmeister BT, Vollmers C, DuBois RM, Schmitz RJ. Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes. Nucleic Acids Res. 2017;45(6):e41. https://doi.org/10.1093/nar/gkw1179.
Article
CAS
PubMed
Google Scholar
Satpathy AT, Saligrama N, Buenrostro JD, Wei Y, Wu B, Rubin AJ, et al. Transcript-indexed ATAC-seq for precision immune profiling. Nat Med. 2018;24(5):580–90. https://doi.org/10.1038/s41591-018-0008-8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lin J, Zhao Y, Ferraro AR, Yang E, Lewis ZA, Lin X. Transcription factor Znf2 coordinates with the chromatin remodeling SWI/SNF complex to regulate cryptococcal cellular differentiation. Commun Biol. 2019;2(1):412. https://doi.org/10.1038/s42003-019-0665-2.
Article
CAS
PubMed
PubMed Central
Google Scholar
Segal E, Fondufe-Mittendorf Y, Chen L, Thastrom A, Field Y, Moore IK, et al. A genomic code for nucleosome positioning. Nature. 2006;442(7104):772–8. https://doi.org/10.1038/nature04979.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zaret KS, Carroll JS. Pioneer transcription factors: establishing competence for gene expression. Genes Dev. 2011;25(21):2227–41. https://doi.org/10.1101/gad.176826.111.
Article
CAS
PubMed
PubMed Central
Google Scholar
Magnani L, Eeckhoute J, Lupien M. Pioneer factors: directing transcriptional regulators within the chromatin environment. Trends Genet. 2011;27(11):465–74. https://doi.org/10.1016/j.tig.2011.07.002.
Article
CAS
PubMed
Google Scholar
Soufi A, Garcia MF, Jaroszewicz A, Osman N, Pellegrini M, Zaret KS. Pioneer transcription factors target partial DNA motifs on nucleosomes to initiate reprogramming. Cell. 2015;161(3):555–68. https://doi.org/10.1016/j.cell.2015.03.017.
Article
CAS
PubMed
PubMed Central
Google Scholar
Meers MP, Janssens DH, Henikoff S. Pioneer factor-nucleosome binding events during differentiation are motif encoded. Mol Cell. 2019;75(3):562–75 e565. https://doi.org/10.1016/j.molcel.2019.05.025.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sancar C, Ha N, Yilmaz R, Tesorero R, Fisher T, Brunner M, et al. Combinatorial control of light induced chromatin remodeling and gene activation in Neurospora. PLoS Genet. 2015;11(3):e1005105. https://doi.org/10.1371/journal.pgen.1005105.
Article
CAS
PubMed
PubMed Central
Google Scholar
Consortium EP, Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007;447(7146):799–816. https://doi.org/10.1038/nature05874.
Article
CAS
Google Scholar
Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science. 2007;316(5830):1484–8. https://doi.org/10.1126/science.1138341.
Article
CAS
PubMed
Google Scholar
Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, et al. Widespread transcription at neuronal activity-regulated enhancers. Nature. 2010;465(7295):182–7. https://doi.org/10.1038/nature09033.
Article
CAS
PubMed
PubMed Central
Google Scholar
Duttke SH, Chang MW, Heinz S, Benner C. Identification and dynamic quantification of regulatory elements using total RNA. Genome Res. 2019;29(11):1836–46. https://doi.org/10.1101/gr.253492.119.
Article
CAS
PubMed
PubMed Central
Google Scholar
Spracklin G, Pradhan S. Protect-seq: genome-wide profiling of nuclease inaccessible domains reveals physical properties of chromatin. Nucleic Acids Res. 2020;48(3):e16. https://doi.org/10.1093/nar/gkz1150.
Article
CAS
PubMed
Google Scholar
Krogan NJ, Kim M, Tong A, Golshani A, Cagney G, Canadien V, et al. Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol. 2003;23(12):4207–18. https://doi.org/10.1128/MCB.23.12.4207-4218.2003.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li B, Howe L, Anderson S, Yates JR 3rd, Workman JL. The Set2 histone methyltransferase functions through the phosphorylated carboxyl-terminal domain of RNA polymerase II. J Biol Chem. 2003;278(11):8897–903. https://doi.org/10.1074/jbc.M212134200.
Article
CAS
PubMed
Google Scholar
Li J, Moazed D, Gygi SP. Association of the histone methyltransferase Set2 with RNA polymerase II plays a role in transcription elongation. J Biol Chem. 2002;277(51):49383–8. https://doi.org/10.1074/jbc.M209294200.
Article
CAS
PubMed
Google Scholar
Schaft D, Roguev A, Kotovic KM, Shevchenko A, Sarov M, Shevchenko A, et al. The histone 3 lysine 36 methyltransferase, SET2, is involved in transcriptional elongation. Nucleic Acids Res. 2003;31(10):2475–82. https://doi.org/10.1093/nar/gkg372.
Article
CAS
PubMed
PubMed Central
Google Scholar
Smolle M, Venkatesh S, Gogol MM, Li H, Zhang Y, Florens L, et al. Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange. Nat Struct Mol Biol. 2012;19(9):884–92. https://doi.org/10.1038/nsmb.2312.
Article
CAS
PubMed
PubMed Central
Google Scholar
Maltby VE, Martin BJ, Schulze JM, Johnson I, Hentrich T, Sharma A, et al. Histone H3 lysine 36 methylation targets the Isw1b remodeling complex to chromatin. Mol Cell Biol. 2012;32(17):3479–85. https://doi.org/10.1128/MCB.00389-12.
Article
CAS
PubMed
PubMed Central
Google Scholar
Venkatesh S, Smolle M, Li H, Gogol MM, Saint M, Kumar S, et al. Set2 methylation of histone H3 lysine 36 suppresses histone exchange on transcribed genes. Nature. 2012;489(7416):452–5. https://doi.org/10.1038/nature11326.
Article
CAS
PubMed
Google Scholar
Keogh MC, Kurdistani SK, Morris SA, Ahn SH, Podolny V, Collins SR, et al. Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell. 2005;123(4):593–605. https://doi.org/10.1016/j.cell.2005.10.025.
Article
CAS
PubMed
Google Scholar
Carrozza MJ, Li B, Florens L, Suganuma T, Swanson SK, Lee KK, et al. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell. 2005;123(4):581–92. https://doi.org/10.1016/j.cell.2005.10.023.
Article
CAS
PubMed
Google Scholar
Adhvaryu KK, Morris SA, Strahl BD, Selker EU. Methylation of histone H3 lysine 36 is required for normal development in Neurospora crassa. Eukaryot Cell. 2005;4(8):1455–64. https://doi.org/10.1128/EC.4.8.1455-1464.2005.
Article
CAS
PubMed
PubMed Central
Google Scholar
Janevska S, Baumann L, Sieber CMK, Munsterkotter M, Ulrich J, Kamper J, et al. Elucidation of the two H3K36me3 histone methyltransferases Set2 and Ash1 in Fusarium fujikuroi unravels their different chromosomal targets and a major impact of Ash1 on genome stability. Genetics. 2018;208(1):153–71. https://doi.org/10.1534/genetics.117.1119.
Article
CAS
PubMed
Google Scholar
Bicocca VT, Ormsby T, Adhvaryu KK, Honda S, Selker EU. ASH1-catalyzed H3K36 methylation drives gene repression and marks H3K27me2/3-competent chromatin. Elife. 2018;7. https://doi.org/10.7554/eLife.41497.
Thorvaldsdottir H, Robinson JT, Mesirov JP. Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14(2):178–92. https://doi.org/10.1093/bib/bbs017.
Article
CAS
PubMed
Google Scholar
Sasaki T, Lynch KL, Mueller CV, Friedman S, Freitag M. Heterochromatin controls γH2A localization in Neurospora crassa. Eukaryot Cell. 2014;13(8):990–1000. https://doi.org/10.1128/EC.00117-14.
Article
CAS
PubMed
PubMed Central
Google Scholar
Borkovich KA, Alex LA, Yarden O, Freitag M, Turner GE, Read ND, et al. Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism. Microbiol Mol Biol Rev. 2004;68(1):1–108. https://doi.org/10.1128/MMBR.68.1.1-108.2004.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dion MF, Kaplan T, Kim M, Buratowski S, Friedman N, Rando OJ. Dynamics of replication-independent histone turnover in budding yeast. Science. 2007;315(5817):1405–8. https://doi.org/10.1126/science.1134053.
Article
CAS
PubMed
Google Scholar
Choi ES, Shin JA, Kim HS, Jang YK. Dynamic regulation of replication independent deposition of histone H3 in fission yeast. Nucleic Acids Res. 2005;33(22):7102–10. https://doi.org/10.1093/nar/gki1011.
Article
CAS
PubMed
PubMed Central
Google Scholar
Storck WK, Abdulla SZ, Rountree MR, Bicocca VT, Selker EU. A light-inducible strain for genome-wide histone turnover profiling in Neurospora crassa. Genetics. 2020;215(3):569–78. https://doi.org/10.1534/genetics.120.303217.
Article
CAS
PubMed
PubMed Central
Google Scholar
Smith KM, Sancar G, Dekhang R, Sullivan CM, Li S, Tag AG, et al. Transcription factors in light and circadian clock signaling networks revealed by genomewide mapping of direct targets for neurospora white collar complex. Eukaryot Cell. 2010;9(10):1549–56. https://doi.org/10.1128/EC.00154-10.
Article
CAS
PubMed
PubMed Central
Google Scholar
Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014;507(7493):455–61. https://doi.org/10.1038/nature12787.
Article
CAS
PubMed
PubMed Central
Google Scholar
Core LJ, Martins AL, Danko CG, Waters CT, Siepel A, Lis JT. Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat Genet. 2014;46(12):1311–20. https://doi.org/10.1038/ng.3142.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hu G, Cui K, Northrup D, Liu C, Wang C, Tang Q, et al. H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation. Cell Stem Cell. 2013;12(2):180–92. https://doi.org/10.1016/j.stem.2012.11.003.
Article
CAS
PubMed
Google Scholar
Kahn TG, Schwartz YB, Dellino GI, Pirrotta V. Polycomb complexes and the propagation of the methylation mark at the Drosophila ubx gene. J Biol Chem. 2006;281(39):29064–75. https://doi.org/10.1074/jbc.M605430200.
Article
CAS
PubMed
Google Scholar
Alhaj Abed J, Ghotbi E, Ye P, Frolov A, Benes J, Jones RS. De novo recruitment of Polycomb-group proteins in Drosophila embryos. Development. 2018;145(23):dev165027.
Jamieson K, McNaught KJ, Ormsby T, Leggett NA, Honda S, Selker EU. Telomere repeats induce domains of H3K27 methylation in Neurospora. Elife. 2018;7. https://doi.org/10.7554/eLife.31216.
Grau DJ, Chapman BA, Garlick JD, Borowsky M, Francis NJ, Kingston RE. Compaction of chromatin by diverse Polycomb group proteins requires localized regions of high charge. Genes Dev. 2011;25(20):2210–21. https://doi.org/10.1101/gad.17288211.
Article
CAS
PubMed
PubMed Central
Google Scholar
Plys AJ, Davis CP, Kim J, Rizki G, Keenen MM, Marr SK, et al. Phase separation of Polycomb-repressive complex 1 is governed by a charged disordered region of CBX2. Genes Dev. 2019;33(13–14):799–813. https://doi.org/10.1101/gad.326488.119.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schwaiger M, Schonauer A, Rendeiro AF, Pribitzer C, Schauer A, Gilles AF, et al. Evolutionary conservation of the eumetazoan gene regulatory landscape. Genome Res. 2014;24(4):639–50. https://doi.org/10.1101/gr.162529.113.
Article
CAS
PubMed
PubMed Central
Google Scholar
Andersson R, Sandelin A. Determinants of enhancer and promoter activities of regulatory elements. Nat Rev Genet. 2020;21(2):71–87. https://doi.org/10.1038/s41576-019-0173-8.
Article
CAS
PubMed
Google Scholar
McNaught KJ, Wiles ET, Selker EU. Identification of a PRC2 Accessory Subunit Required for Subtelomeric H3K27 Methylation in Neurospora crassa. Mol Cell Biol. 2020;40:e00003–20.
Sun G, Zhou Z, Liu X, Gai K, Liu Q, Cha J, et al. Suppression of WHITE COLLAR-independent frequency transcription by histone H3 lysine 36 methyltransferase SET-2 is necessary for clock function in Neurospora. J Biol Chem. 2016;291(21):11055–63. https://doi.org/10.1074/jbc.M115.711333.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xue Z, Ye Q, Anson SR, Yang J, Xiao G, Kowbel D, et al. Transcriptional interference by antisense RNA is required for circadian clock function. Nature. 2014;514(7524):650–3. https://doi.org/10.1038/nature13671.
Article
CAS
PubMed
PubMed Central
Google Scholar
Reyes-Dominguez Y, Bok JW, Berger H, Shwab EK, Basheer A, Gallmetzer A, et al. Heterochromatic marks are associated with the repression of secondary metabolism clusters in Aspergillus nidulans. Mol Microbiol. 2010;76(6):1376–86. https://doi.org/10.1111/j.1365-2958.2010.07051.x.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gacek-Matthews A, Berger H, Sasaki T, Wittstein K, Gruber C, Lewis ZA, et al. KdmB, a Jumonji histone H3 demethylase, regulates genome-wide H3K4 Trimethylation and is required for Normal induction of secondary metabolism in Aspergillus nidulans. PLoS Genet. 2016;12(8):e1006222. https://doi.org/10.1371/journal.pgen.1006222.
Article
CAS
PubMed
PubMed Central
Google Scholar
DeGennaro CM, Alver BH, Marguerat S, Stepanova E, Davis CP, Bahler J, et al. Spt6 regulates intragenic and antisense transcription, nucleosome positioning, and histone modifications genome-wide in fission yeast. Mol Cell Biol. 2013;33(24):4779–92. https://doi.org/10.1128/MCB.01068-13.
Article
CAS
PubMed
PubMed Central
Google Scholar
Suzuki S, Kato H, Suzuki Y, Chikashige Y, Hiraoka Y, Kimura H, et al. Histone H3K36 trimethylation is essential for multiple silencing mechanisms in fission yeast. Nucleic Acids Res. 2016;44(9):4147–62. https://doi.org/10.1093/nar/gkw008.
Article
CAS
PubMed
PubMed Central
Google Scholar
Colot HV, Park G, Turner GE, Ringelberg C, Crew CM, Litvinkova L, et al. A high-throughput gene knockout procedure for Neurospora reveals functions for multiple transcription factors. Proc Natl Acad Sci U S A. 2006;103(27):10352–7. https://doi.org/10.1073/pnas.0601456103.
Article
CAS
PubMed
PubMed Central
Google Scholar
Davis RH, de Serres FJ. [4] genetic and microbiological research techniques for Neurospora crassa. Methods Enzymol. 1970;17:79–143. https://doi.org/10.1016/0076-6879(71)17168-6.
Article
Google Scholar
Lamb TM, Vickery J, Bell-Pedersen D. Regulation of gene expression in Neurospora crassa with a copper responsive promoter. G3 (Bethesda). 2013;3(12):2273–80.
Article
Google Scholar
Honda S, Selker EU. Tools for fungal proteomics: multifunctional neurospora vectors for gene replacement, protein expression and protein purification. Genetics. 2009;182(1):11–23. https://doi.org/10.1534/genetics.108.098707.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bardiya N, Shiu PK. Cyclosporin A-resistance based gene placement system for Neurospora crassa. Fungal Genet Biol. 2007;44(5):307–14. https://doi.org/10.1016/j.fgb.2006.12.011.
Article
CAS
PubMed
Google Scholar
Seymour M, Ji L, Santos AM, Kamei M, Sasaki T, Basenko EY, et al. Histone H1 Limits DNA Methylation in Neurospora crassa. G3 (Bethesda). 2016;6(7):1879–89.
Article
CAS
Google Scholar
Ferraro AR, Lewis ZA. ChIP-Seq analysis in Neurospora crassa. Methods Mol Biol. 1775;2018:241–50.
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012;9(4):357–9. https://doi.org/10.1038/nmeth.1923.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lawrence M, Huber W, Pages H, Aboyoun P, Carlson M, Gentleman R, et al. Software for computing and annotating genomic ranges. PLoS Comput Biol. 2013;9(8):e1003118. https://doi.org/10.1371/journal.pcbi.1003118.
Article
CAS
PubMed
PubMed Central
Google Scholar
Team RC: R Core Team. R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing; 2014. URL http://wwwR-projectorg/ 2014
Google Scholar
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841–2. https://doi.org/10.1093/bioinformatics/btq033.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. https://doi.org/10.1186/gb-2008-9-9-r137.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ruepp A, Zollner A, Maier D, Albermann K, Hani J, Mokrejs M, et al. The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res. 2004;32(18):5539–45. https://doi.org/10.1093/nar/gkh894.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ramirez F, Ryan DP, Gruning B, Bhardwaj V, Kilpert F, Richter AS, et al. DeepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 2016;44(W1):W160–5. https://doi.org/10.1093/nar/gkw257.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yu G, Wang LG, He QY. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics. 2015;31(14):2382–3. https://doi.org/10.1093/bioinformatics/btv145.
Article
CAS
PubMed
Google Scholar
Zhu LJ, Gazin C, Lawson ND, Pages H, Lin SM, Lapointe DS, et al. ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics. 2010;11(1):237. https://doi.org/10.1186/1471-2105-11-237.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015;12(4):357–60. https://doi.org/10.1038/nmeth.3317.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liao Y, Smyth GK, Shi W. The subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Res. 2013;41(10):e108. https://doi.org/10.1093/nar/gkt214.
Article
CAS
PubMed
PubMed Central
Google Scholar
Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010;38(4):576–89. https://doi.org/10.1016/j.molcel.2010.05.004.
Article
CAS
PubMed
PubMed Central
Google Scholar