Genomic and expression analysis of transition proteins in Drosophila

References

• Jayaramaiah Raja S, Renkawitz-Pohl R. Replacement by Drosophila melanogaster protamines and Mst77F of histones during chromatin condensation in late spermatids and role of sesame in the removal of these proteins from the male pronucleus. Mol Cell Biol 2005; 25:6165-77; PMID:15988027; http://dx.doi.org/10.1128/MCB.25.14.6165-6177.2005
   PubMed Web of Science ®Google Scholar
• Tirmarche S, Kimura S, Sapey-Triomphe L, Sullivan W, Landmann F, Loppin B. Drosophila protamine-like Mst35Ba and Mst35Bb are required for proper sperm nuclear morphology but are dispensable for male fertility. G3 (Bethesda) 2014; 4:2241-5; PMID:25236732; http://dx.doi.org/full_text
   PubMedGoogle Scholar
• Balhorn R. The protamine family of sperm nuclear proteins. Genome Biol 2007; 8:227; PMID:17903313; http://dx.doi.org/10.1186/gb-2007-8-9-227
   PubMed Web of Science ®Google Scholar
• Rathke C, Baarends WM, Jayaramaiah-Raja S, Bartkuhn M, Renkawitz R, Renkawitz-Pohl R. Transition from a nucleosome-based to a protamine-based chromatin configuration during spermiogenesis in Drosophila. J Cell Sci 2007; 120:1689-700; PMID:17452629; http://dx.doi.org/10.1242/jcs.004663
   PubMed Web of Science ®Google Scholar
• Rathke C, Baarends WM, Awe S, Renkawitz-Pohl R. Chromatin dynamics during spermiogenesis. Biochim Biophys Acta 2014; 1839:155-68; PMID:24091090; http://dx.doi.org/10.1016/j.bbagrm.2013.08.004
   PubMed Web of Science ®Google Scholar
• Rathke C, Barckmann B, Burkhard S, Jayaramaiah-Raja S, Roote J, Renkawitz-Pohl R. Distinct functions of Mst77F and protamines in nuclear shaping and chromatin condensation during Drosophila spermiogenesis. Eur J Cell Biol 2010; 89:326-38; PMID:20138392; http://dx.doi.org/10.1016/j.ejcb.2009.09.001
   PubMed Web of Science ®Google Scholar
• Ausio J. Histone H1 and evolution of sperm nuclear basic proteins. J Biol Chem 1999; 274:31115-8; PMID:10531297; http://dx.doi.org/10.1074/jbc.274.44.31115
   PubMed Web of Science ®Google Scholar
• Kasinsky HE, Eirin-Lopez JM, Ausio J. Protamines: structural complexity, evolution and chromatin patterning. Protein Pept Lett 2011; 18:755-71; PMID:21443489; http://dx.doi.org/10.2174/092986611795713989
   PubMed Web of Science ®Google Scholar
• Yan W, Ma L, Burns KH, Matzuk MM. HILS1 is a spermatid-specific linker histone H1-like protein implicated in chromatin remodeling during mammalian spermiogenesis. Proc Natl Acad Sci U S A 2003; 100:10546-51; PMID:12920187; http://dx.doi.org/10.1073/pnas.1837812100
   PubMed Web of Science ®Google Scholar
• Bianchi F, Rousseaux-Prevost R, Bailly C, Rousseaux J. Interaction of human P1 and P2 protamines with DNA. Biochem Biophys Res Commun 1994; 201:1197-204; PMID:8024562; http://dx.doi.org/10.1006/bbrc.1994.1832
   PubMed Web of Science ®Google Scholar
• Kanippayoor RLA JH, Moehring AJ. Protamines and spermatogenesis in Drosophila and Homo sapiens: a comparative analysis. Spermatogenesis 2013; 1-7.
   Google Scholar
• Saperas N, Chiva M, Casas MT, Campos JL, Eirin-Lopez JM, Frehlick LJ, Prieto C, Subirana JA, Ausio J. A unique vertebrate histone H1-related protamine-like protein results in an unusual sperm chromatin organization. FEBS J 2006; 273:4548-61; PMID:16965539; http://dx.doi.org/10.1111/j.1742-4658.2006.05461.x
   PubMed Web of Science ®Google Scholar
• Alvi ZA, Chu TC, Schawaroch V, Klaus AV. Protamine-like proteins in 12 sequenced species of Drosophila. Protein Pept Lett 2013; 20:17-35; PMID:22789106; http://dx.doi.org/10.2174/092986613804096847
   PubMed Web of Science ®Google Scholar
• Lewis JD, Ausio J. Protamine-like proteins: evidence for a novel chromatin structure. Biochem Cell Biol 2002; 80:353-61; PMID:12123288; http://dx.doi.org/10.1139/o02-083
   PubMed Web of Science ®Google Scholar
• Zhang F, Lewis JD, Ausio J. Cysteine-containing histone H1-like (PL-I) proteins of sperm. Mol Reprod Dev 1999; 54:402-9; PMID:10542381; http://dx.doi.org/10.1002/(SICI)1098-2795(199912)54:4%3c402::AID-MRD11%3e3.0.CO;2-X
   PubMed Web of Science ®Google Scholar
• Lewis JD, Saperas N, Song Y, Zamora MJ, Chiva M, Ausio J. Histone H1 and the origin of protamines. Proc Natl Acad Sci U S A 2004; 101:4148-52; PMID:15024099; http://dx.doi.org/10.1073/pnas.0308721101
   PubMed Web of Science ®Google Scholar
• Zini AA. A. Sperm Chromatin Biological and Clinical Applications in Male Infertility and Assisted Reproduction. New York: Springer, 2011.
   Google Scholar
• White-Cooper H. Studying how flies make sperm–investigating gene function in Drosophila testes. Molecular and Cellular Endocrinology 2009; 306:66-74; PMID:19101606; http://dx.doi.org/10.1016/j.mce.2008.11.026
   PubMed Web of Science ®Google Scholar
• Ricketts PG, Minimair M, Yates RW, Klaus AV. The effects of glutathione, insulin and oxidative stress on cultured spermatogenic cysts. Spermatogenesis 2011; 1:159-71; PMID:22319665; http://dx.doi.org/10.4161/spmg.1.2.17031
   PubMedGoogle Scholar
• Decotto E, Spradling AC. The Drosophila ovarian and testis stem cell niches: similar somatic stem cells and signals. Dev Cell 2005; 9:501-10; PMID:16198292; http://dx.doi.org/10.1016/j.devcel.2005.08.012
   PubMed Web of Science ®Google Scholar
• Eirin-Lopez JM, Frehlick LJ, Ausio J. Protamines, in the footsteps of linker histone evolution. J Biol Chem 2006; 281:1-4; PMID:16243843; http://dx.doi.org/10.1074/jbc.R500018200
   PubMed Web of Science ®Google Scholar
• Eirin-Lopez JM, Lewis JD, Howe le A, Ausio J. Common phylogenetic origin of protamine-like (PL) proteins and histone H1: Evidence from bivalve PL genes. Mol Biol Evol 2006; 23:1304-17; PMID:16613862; http://dx.doi.org/10.1093/molbev/msk021
   PubMed Web of Science ®Google Scholar
• Barckmann B, Chen X, Kaiser S, Jayaramaiah-Raja S, Rathke C, Dottermusch-Heidel C, Fuller MT, Renkawitz-Pohl R. Three levels of regulation lead to protamine and Mst77F expression in Drosophila. Dev Biol 2013; 377:33-45; PMID:23466740; http://dx.doi.org/10.1016/j.ydbio.2013.02.018
   PubMed Web of Science ®Google Scholar
• Cho C, Willis WD, Goulding EH, Jung-Ha H, Choi YC, Hecht NB, Eddy EM. Haploinsufficiency of protamine-1 or -2 causes infertility in mice. Nat Genet 2001; 28:82-6; PMID:11326282
   PubMed Web of Science ®Google Scholar
• Dorus S, Freeman ZN, Parker ER, Heath BD, Karr TL. Recent origins of sperm genes in Drosophila. Mol Biol Evol 2008; 25:2157-66; PMID:18653731; http://dx.doi.org/10.1093/molbev/msn162
   PubMed Web of Science ®Google Scholar
• Yu KKaJ. Modified Nel and Van der Merwe test for the multivariate Behrens–Fisher problem. Statistics & Probability Letters 2004; 66:161-9; http://dx.doi.org/10.1016/j.spl.2003.10.012
   Web of Science ®Google Scholar
• Jeanteur P. Epigenetics and Chromatin. Berlin: Springer, 2005.
   Google Scholar
• Niu L, Huang W, Umbach DM, Li L. IUTA: a tool for effectively detecting differential isoform usage from RNA-Seq data. BMC Genomics 2014; 15:862; PMID:25283306; http://dx.doi.org/10.1186/1471-2164-15-862
   PubMed Web of Science ®Google Scholar
• Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, et al. Ensembl 2014. Nucleic Acids Res 2014; 42:D749-55; PMID:24316576; http://dx.doi.org/10.1093/nar/gkt1196
   PubMed Web of Science ®Google Scholar
• mod EC, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 2010; 330:1787-97; PMID:21177974; http://dx.doi.org/10.1126/science.1198374
   PubMed Web of Science ®Google Scholar
• St Pierre SE, Ponting L, Stefancsik R, McQuilton P, FlyBase C. FlyBase 102–advanced approaches to interrogating FlyBase. Nucleic Acids Res 2014; 42:D780-8; PMID:24234449; http://dx.doi.org/10.1093/nar/gkt1-092
   PubMedGoogle Scholar
• Begun DJ, Lindfors HA, Kern AD, Jones CD. Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade. Genetics 2007; 176:1131-7; PMID:17435230; http://dx.doi.org/10.1534/genetics.106.069245
   PubMed Web of Science ®Google Scholar
• Begun DJ, Lindfors HA, Thompson ME, Holloway AK. Recently evolved genes identified from Drosophila yakuba and D. erecta accessory gland expressed sequence tags. Genetics 2006; 172:1675-81; PMID:16361246; http://dx.doi.org/10.1534/genetics.105.050336
   PubMed Web of Science ®Google Scholar
• VanKuren NW, Vibranovski MD. A novel dataset for identifying sex-biased genes in Drosophila. J Genomics 2014; 2:64-7; PMID:25031657; http://dx.doi.org/10.7150/jgen.7955
   PubMedGoogle Scholar
• Wheeler WC. Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data. Systematic Biology 1995; 44:321-31; http://dx.doi.org/10.1093/sysbio/44.3.321
   Web of Science ®Google Scholar
• de Pinna MCC. Concepts and tests of homology in the cladistic paradigm. Cladistics 1991; 7:367-94; http://dx.doi.org/10.1111/j.1096-0031.1991.tb00045.x
   Web of Science ®Google Scholar
• Brower AVZ, Schawaroch V. Three steps of homology assesment. Cladistics 1996; 12:265-72.
   PubMed Web of Science ®Google Scholar
• Gatsey J, DeSalle R, Wheeler WC. Alignment ambiguous nucleotide sites and the exclusion of systematic data. Molecular Phylogenetics and Evolution 1994; 2:152-7; http://dx.doi.org/10.1006/mpev.1993.1015
   Web of Science ®Google Scholar
• Akama K, Oka S, Tobita T, Hayashi H. The amino acid sequence of a boar transition protein 3. J Biochem 1994; 115:58-65; PMID:8188637
   PubMed Web of Science ®Google Scholar
• Grimes SR, Jr., Platz RD, Meistrich ML, Hnilica LS. Partial characterization of a new basic nuclear protein from rat testis elongated spermatids. Biochem Biophys Res Commun 1975; 67:182-9; PMID:1201018; http://dx.doi.org/10.1016/0006-291X(75)90300-9
   PubMed Web of Science ®Google Scholar
• Singh J, Rao MR. Interaction of rat testis protein, TP, with nucleic acids in vitro. Fluorescence quenching, UV absorption, and thermal denaturation studies. J Biol Chem 1987; 262:734-40; PMID:3805005
   PubMed Web of Science ®Google Scholar
• Eirin-Lopez JM, Ausio J. Origin and evolution of chromosomal sperm proteins. Bioessays 2009; 31:1062-70; PMID:19708021; http://dx.doi.org/10.1002/bies.200900050
   PubMedGoogle Scholar
• Birkhead TRH DJ, Pitnick S. Sperm Biology: An Evolutionary Perspective. Amsterdam: Elsevier/Academic, 2009.
   Google Scholar
• Meistrich ML, Mohapatra B, Shirley CR, Zhao M. Roles of transition nuclear proteins in spermiogenesis. Chromosoma 2003; 111:483-8; PMID:12743712; http://dx.doi.org/10.1007/s00412-002-0227-z
   PubMed Web of Science ®Google Scholar
• Cheng WM, An L, Wu ZH, Zhu YB, Liu JH, Gao HM, Li XH, Zheng SJ, Chen DB, Tian JH. Effects of disulfide bond reducing agents on sperm chromatin structural integrity and developmental competence of in vitro matured oocytes after intracytoplasmic sperm injection in pigs. Reproduction 2009; 137:633-43; PMID:19155332; http://dx.doi.org/10.1530/REP-08-0143
   PubMed Web of Science ®Google Scholar
• McBride AA, Klausner RD, Howley PM. Conserved cysteine residue in the DNA-binding domain of the bovine papillomavirus type 1 E2 protein confers redox regulation of the DNA-binding activity in vitro. Proc Natl Acad Sci U S A 1992; 89:7531-5; PMID:1323841; http://dx.doi.org/10.1073/pnas.89.16.7531
   PubMed Web of Science ®Google Scholar
• Wagner CR, Hamana K, Elgin SC. A high-mobility-group protein and its cDNAs from Drosophila melanogaster. Mol Cell Biol 1992; 12:1915-23; PMID:1373803; http://dx.doi.org/10.1128/MCB.12.5.1915
   PubMed Web of Science ®Google Scholar
• Qin J, Kang W, Leung B, McLeod M. Ste11p, a high-mobility-group box DNA-binding protein, undergoes pheromone- and nutrient-regulated nuclear-cytoplasmic shuttling. Mol Cell Biol 2003; 23:3253-64; PMID:12697825; http://dx.doi.org/10.1128/MCB.23.9.3253-3264.2003
   PubMed Web of Science ®Google Scholar
• Travers AA. Priming the nucleosome: a role for HMGB proteins? EMBO Rep 2003; 4:131-6; PMID:12612600; http://dx.doi.org/10.1038/sj.embor.embor741
   PubMed Web of Science ®Google Scholar
• Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, et al. The Pfam protein families database. Nucleic Acids Res 2004; 32:D138-41; PMID:14681378; http://dx.doi.org/10.1093/nar/gkh121
   PubMed Web of Science ®Google Scholar
• Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010; 26:139-40; PMID:19910308; http://dx.doi.org/10.1093/bioinformatics/btp616
   PubMed Web of Science ®Google Scholar
• Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol 2010; 11:R106; PMID:20979621; http://dx.doi.org/10.1186/gb-2010-11-10-r106
   PubMed Web of Science ®Google Scholar
• Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 2012; 7:562-78; PMID:22383036; http://dx.doi.org/10.1038/nprot.2012.016
   PubMed Web of Science ®Google Scholar
• Goff LTR, Kelley D. cummeRbund: Analysis, exploration, manipulation, and visualization of cufflinks high-throughput sequencing data. 2013.
   Google Scholar
• Ashburner M, Golic KG, Hawley RS. Drosophila: a laboratory handbook, 2nd Edition. Cold Spring Harbor Laboratory. 2005. pp. 1123-1283.
   Google Scholar
• Drosophila 12 Genomes C, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature 2007; 450:203-18; PMID:17994087; http://dx.doi.org/10.1038/nature06341
   PubMed Web of Science ®Google Scholar
• Di Tommaso P, Moretti S, Xenarios I, Orobitg M, Montanyola A, Chang JM, Taly JF, Notredame C. T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. Nucleic Acids Res 2011; 39:W13-7; PMID:21558174; http://dx.doi.org/10.1093/nar/gkr245
   PubMed Web of Science ®Google Scholar
• Kumar M, Gromiha MM, Raghava GP. Identification of DNA-binding proteins using support vector machines and evolutionary profiles. BMC Bioinformatics 2007; 8:463; PMID:18042272; http://dx.doi.org/10.1186/1471-2105-8-463
   PubMed Web of Science ®Google Scholar
• Wang L, Huang C, Yang MQ, Yang JY. BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features. BMC Syst Biol 2010; 4Suppl 1:S3; PMID:20522253; http://dx.doi.org/10.1186/1752-0509-4-S1-S3
   PubMedGoogle Scholar
• Zhu X, Ericksen SS, Mitchell JC. DBSI: DNA-binding site identifier. Nucleic Acids Res 2013; 41:e160; PMID:23873960; http://dx.doi.org/10.1093/nar/gkt617
   PubMedGoogle Scholar
• Hwang S, Gou Z, Kuznetsov IB. DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins. Bioinformatics 2007; 23:634-6; PMID:17237068; http://dx.doi.org/10.1093/bioinformatics/btl672
   PubMed Web of Science ®Google Scholar
• Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 2010; 330:1775-87; PMID:21177976; http://dx.doi.org/10.1126/science.1196914
   PubMed Web of Science ®Google Scholar
• Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R. InterProScan: protein domains identifier. Nucleic Acids Res 2005; 33:W116-20; PMID:15980438; http://dx.doi.org/10.1093/nar/gki442
   PubMed Web of Science ®Google Scholar
• Finn RD, Clements J, Eddy SR. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 2011; 39:W29-37; PMID:21593126; http://dx.doi.org/10.1093/nar/gkr367
   PubMed Web of Science ®Google Scholar
• Kelley LA, Sternberg MJ. Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc 2009; 4:363-71; PMID:19247286; http://dx.doi.org/10.1038/nprot.2009.2
   PubMed Web of Science ®Google Scholar
• Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114-20; PMID:24695404; http://dx.doi.org/10.1093/bioinformatics/btu170
   PubMed Web of Science ®Google Scholar
• Goff SA, Vaughn M, McKay S, Lyons E, Stapleton AE, Gessler D, Matasci N, Wang L, Hanlon M, Lenards A, et al. The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Front Plant Sci 2011; 2:34; PMID:22645531; http://dx.doi.org/10.3389/fpls.2011.00034
   PubMed Web of Science ®Google Scholar
• Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 2013; 14:R36; PMID:23618408; http://dx.doi.org/10.1186/gb-2013-14-4-r36
   PubMed Web of Science ®Google Scholar
• Roberts A, Pimentel H, Trapnell C, Pachter L. Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics 2011; 27:2325-9; PMID:21697122; http://dx.doi.org/10.1093/bioinformatics/btr355
   PubMed Web of Science ®Google Scholar
• Anders S, Pyl PT, Huber W. HTSeq–a Python framework to work with high-throughput sequencing data. Bioinformatics 2015; 31:166-9; PMID:25260700; http://dx.doi.org/10.1093/bio-informatics/btu638
   PubMed Web of Science ®Google Scholar
• Muni S, Srivastava SK, Yutaka Kano. A two sample test in high dimensional data. Journal of Multivariate Analysis 2013; 114:349-58; http://dx.doi.org/10.1016/j.jmva.2012.08.014
   Web of Science ®Google Scholar
• Qin SXCaY-L. A two-sample test for high-dimensional data with applications to gene-set testing. The Annals of Statistics 2010; 38:808-35; http://dx.doi.org/10.1214/09-AOS716
   Web of Science ®Google Scholar
• Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 2013; 30:2725-9; PMID:24132122; http://dx.doi.org/10.1093/molbev/mst197
   PubMed Web of Science ®Google Scholar
• Thompson JD, Gibson TJ, Higgins DG. Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics 2002; Chapter 2:Unit 2 3; PMID:18792934
   PubMedGoogle Scholar
• Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony (*and other methods), version 4.0a147. 2016.
   Google Scholar