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Publications


2015

Li Q, Gent JI, Zynda G, Song J, Makarevitch I, Hirsch CD, Hirsch CN, Dawe RK, Madzima TF, McGinnis KM, Lisch D, Schmitz RJ, Vaughn MW, Springer NM. (In press) RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome.  Proc Natl Acad Sci USA. In press.

Hirsch C, Springer NM, Hirsch CN. 2015. Genomic limitations to RNAseq expression profiling.  Plant Journal 84: 491–503.

Springer NM, McGinnis KM. 2015. Paramutation in evolution, population genetics and breeding.  Semin Cell Dev Biol. doi: 10.1016/j.semcdb.2015.08.010.

Brady S, Burow M, Busch W, Carlborg O, Denby K, Glazebrook J, Hamilton E, Maloof J, Springer N, Kliebenstein D. 2015. Reassess the t-test: interact with all your data via ANOVA.  Plant Cell 27(8):2088-94.

Eichten SR, Springer NM 2015. Minimal evidence for consistent changes in maize DNA methylation patterns following environmental stress. Frontiers in Plant genetics and Genomics 6:308.

Li Q, Song J, West PT, Zynda G, Eichten SR, Vaughn MW, Springer NM. 2015. Examining the causes and consequences of context-specific differential DNA methylation in maize.  Plant Physiology 168(4):1262-1274.

Li Q, Suzuki M, Wendt J, Patterson N, Eichten SR, Hermanson PJ, Green D, Jeddeloh J, Richmond T, Rosenbaum H, Burgess D, Springer NM, Greally JM.  2015. Post-conversion targeted capture of modified cytosines in mammalian and plant genomes. Nucleic Acids Research 43(12):e81.

Springer NM. 2015. Transposable elements: Microbiomes in the genomes. Nature Plants 1:15004.

Makarevitch I, Waters AJ, West PT, Stitzer M, Ross-Ibarra J, Springer NM.  2015. Transposable elements contribute to activation of maize genes in response to abiotic stress. PLoS Genetics 11:e1004915.

 

 

2014

Li Q, Eichten SR, Hermanson PJ, Zaunbrecher V, Song J, Wendt J, Rosenbaum H, Madzima TF, Sloan AE, Huang J, Burgess D, Richman TA, Kaeppler SM, McGinnis KM, Meeley RB, Danilevskaya ON, Vaughn MW, Jeddeloh JA, Springer NM. 2014. Genetic perturbation of the maize methylome.  Plant Cell 26:4602-4616.

Belova T, Grønvold L, Kumar A, Kianian S, He X, Lillemo M, Springer NM, Lien S, Olsen O, Sandve S (2014) Utilization of deletion bins to anchor and order sequences along the wheat 7B chromosome. Theor Appl Genet. Theor Appl Genet. 127(9):2029-2040.

West PT, Li Q, Ji L, Eichten SR, Song J, Vaughn MW, Schmitz RJ, Springer NM.  2014. Genomic distribution of H3K9me2 and DNA methylation in a maize genome.  PLoS One 9: e105267.

Hirsch CN, Flint-Garcia SA, Beissinger TM, Eichten SR, Deshpande S, Barry K, McMullen MD, Holland JB, Buckler ES, Springer NM, Buell CR, de Leon N, Kaeppler SM (2014) Insights into the effects of long-term artificial selection on seed size in maize.  Genetics pii: genetics.114.167155

Thompson AM, Crants JE, Schnable PS, Yu J, Timmermans MC, Springer NM, Scanlon MJ, Muehlbauer GJ. 2014. Genetic Control of Maize Shoot Apical Meristem Architecture. G3 4: 1327-1337.

Shaefer RJ, Briskine R, Springer NM, Myers CL (2014) Discovering Functional Modules Across Diverse Maize Transcriptional Datasets Using COB, The Co-expression Browser. PLoS One 9(6):e99193.

Stelpflug SC, Eichten SR, Hermanson PJ, Springer NM, Kaeppler SM. 2014. Consistent and heritable alterations of DNA methylation are induced by tissue culture in maize.  Genetics pii: genetics.114.165480.

Penning BW, Sykes RW, Babcock NC, Dugard CK, Held MA, Klimek JF, Shreve JT, Fowler M, Ziebell A, Davis MF, Decker SR, Turner GB, Mosier NS, Springer NM, Thimmapuram J, Weil CF, McCann MC, Carpita NC.  2014. Genetic determinants for enzymatic digestion of lignocellulosic biomass are independent of those for lignin abundance in a maize recombinant inbred population. Plant Physiology pii: pp.114.242446.

Eichten SR, Schmitz, RS, Springer NM.  2014.  Epigenetics, more than chromatin modifications and complex regulatory systems.  Plant Physiology 165: 933-947.

Lin Q, Eichten SR, Hermanson PJ, Springer NM.  2014. Inheritance patterns and stability of DNA methylation variation in maize near-isogenic lines.  Genetics. 196(3)667-676.

Lin L, Eichten SR, Shimizu R, Petsch K, Yeh C-T, Wu W, Scanlon MJ, Yu J, Schnable PS, Timmermans MCP, Springer NM, Muehlbauer GJ.  2014. Genome-wide discovery and characterization of maize long non-coding RNAs (lncRNAs). Genome Biology. 15(2):R40.


2013

Waters AJ, Bilinski P, Eichten SR, Vaughn MW, Ross-Ibarra J, Gehring M, Springer NM. 2013.  Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species.  Proc Natl Acad Sci USA 110(48):19639-44.

Eichten SR, Briskine R, Song J, Li Q, Swanson-Wagner R, Hermanson PJ, Waters AJ, Starr E, West PT, Tiffin P, Myers CL, Vaughn MW, Springer NM. 2013. Epigenetic and genetic influences on DNA methylation variation in maize populations.  Plant Cell.


Sekhon RS, Briskine R, Hirsch CN, Myers CL, Springer NM, Buell CR, de Leon N, Kaeppler SM. 2013. Maize Gene Atlas Developed by RNA Sequencing and Comparative Evaluation of Transcriptomes Based on RNA Sequencing and Microarrays.  PLoS One 8(4):e61005.


Muñoz-Amatriaín M, Eichten SR, Wicker T, Richmond TA, Mascher M, Steuernagel B, Scholz U, Ariyadasa R, Spannagl M, Nussbaumer T, Mayer KF, Taudien S, Platzer M, Jeddeloh JA, Springer NM, Muehlbauer GJ, Stein N. 2013. Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome. Genome Biol. 14(6):R65.


Makarevitch I, Eichten SR, Briskine R, Danilevskaya ON, Meeley RB, Myers C, Vaughn MW, Springer NM.  2013. Genomic distribution of maize facultative heterochromatin marked by trimethylation of H3K27. Plant Cell. 25(3): 780-793.


Schnable PS, Springer NM. 2013. Progress Toward Understanding Heterosis in Crop Plants. Annu Rev Plant Biol. 64:71-88.


Li L, Petsch K, Shimizu R, Liu S, Xu W, Ying K, Schnable PS, Yu J, Timmermans MCP, Scanlon MJ, Springer NM, Muehlbauer GJ. 2013. Mendelian and non-Mendelian regulation of gene expression in maize.  PLoS Genetics 9(1): e1003202


Springer NM. 2013. Epigenetics and crop improvement. Trends in Genetics 29(4):241-247.


2012


Eichten SR, Ellis NA, Makarevtich I, Yeh C-T, Gent JI, Guo L, McGinnis KM, Zhang X, Schnable PS, Vaughn MW, Dawe RK, Springer NM.  2012. Spreading of heterochromatin is limited to specific families of maize retrotransposons. PLoS Genet 8(12): e1003127.  


Swanson-Wagner RA, Briskine R, Schaefer R, Hufford MB, Ross-Ibarra J, Myers CL, Tiffin P, Springer NM.  2012. Reshaping of the maize transcriptome by domestication.  Proc Natl Acad Sci USA, 109(29):11878-11883.


Eichten SR, Vaughn MW, Hermanson PJ, Springer NM. 2013. Variation in DNA methylation patterns is more common among maize inbreds than among tissues.  The Plant Genome doi: 10.3835/plantgenome2012.06.0009


Liu S, Ying K, Yeh C-T, Yang J, Swanson-Wagner RA, Wu W, Richmond T, Gerhardt DJ, Albert TJ, Lai J, Springer NM, Nettleton D, Jeddeloh JA, Schnable PS.  Changes in genome content generated via segregation of non-allelic homologs. The Plant Journal 72:390-399


Hufford MB, Xu X, van Heerwaarden J, Pyhajarvi T, Chia J-M, Cartwright RA, Elshire RJ, Glaubitz JC, Guill KE, Kaeppler SM, Lai J, Morrell PL, Shannon LM, Song C, Springer NM, Swanson-Wagner RA, Tiffin P, Wang J, Zhang G, Doebley J, McMullen MD, Ware D, Buckler ES, Yang S, Ross-Ibarra J.  2012.  Comparative population genomics of maize domestication and improvement. Nature Genetics 44(7):808-811.


Makarevitch I, Thompson A, Muehlbauer GJ, Springer NM. 2012.  Brd1 gene in maize encodes a brassinosteroid C-6 oxidase. PLoS One 7: e30798.


2011


Waters A, Makarevitch I, Eichten SR, Swanson-Wagner RA, Gehring M, Hermanson PJ, Yeh C-T, Schnable PS, Vaughn MW, Springer NM. 2011. Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm. Plant Cell 23: 4221-4233.


Eichten SR, Swanson-Wagner RA, Schnable JC, Waters AJ, Hermanson PJ, Liu S, Yeh C-T, Jia Y, Freeling M, Schnable PS, Springer NM, Vaughn MW 2011.  Heritable epigenetic variation among maize inbreds.  PLoS Genetics 7: e1002372.


Eichten SR, Foerster J, de Leon, N, Kai, Y, Yeh C-T, Liu S, Jeddeloh J, Schnable PS, Kaeppleer SM, Springer NM (2011).  B73-Mo17 near isogenic lines (NILs) demonstrate dispersed structural variation in maize.  Plant Physiology 156(4): 1679-1690.


Schnable J, Springer NM, Freeling M.  2011. Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss.  Proc Natl Acad Sci USA 108:4069-4074.


St Pierre S, Springer NM, Muehlbauer GJ.  2011.  Density stress has minimal impacts on the barley or maize seedling transcriptome.  The Plant Genome 4:47-54


2010


Fu Y, Springer NM, Ying K, Yeh C-T, Iniguez, AL, Richmond T, Wu W, Barbazuk WB, Nettleton D, Jeddeloh J, Schnable PS.  2010. High-resolution genotyping via whole genome hybridizations to microarrays containing long oligonucleotide probes.  PLoS One 5(12):e14178.


Haun WJ, Hyten DL, Xu WW, Gerhardt DJ, Albert TJ, Richmond T, Jeddeloh JA, Jia G, Springer NM, Vance CP, Stupar RM. 2011. The composition and origins of intravarietal genomic heterogeneity in soybean.  Plant Physiology 155: 645-655.


Lai J, Li R, Xu X, Jin W, Xu M, Zhao H, Xiang Z, Song W, Ying K, Zhang M, Jiao Y, Ni P, Zhang J, Li D, Guo X, Ye K, Jian M, Wang B, Zheng H, Liang H, Zhang X, Wang S, Chen S, Li J, Fu Y, Springer NM, Yang H, Wang J, Dai J, Schnable PS, Wang J (2010) Genome-wide genetic variation among elite maize inbreds: implications for crop improvement.  Nature Genetics 42(11):1027-1030.


Swanson-Wagner RA, Eichten SR, Kumari S, Tiffin P, Stein JC, Ware D, Springer NM.  2010. Pervasive gene content variation and copy number variation in both maize and its undomesticated progenitor.  Genome Research 20(12):1689-99.


Springer NM. 2010. Shaping a better rice plant. Nat Genet 42(6); 475-476.


Springer NM, Jackson SA. 2010. Realizing the potential of genomics for crop improvement.  Brief Func Genomic Proteomic 9(2) 93-94.


Douglas RN, Wiley D, Sarkar A, Springer NM, Timmermans MCP, Scanlon MJ. 2010. ragged sedling2 encodes an ARGONAUTE7-like protein required for mediolateral expansion, but not dorsiventrality, of maize leaves. Plant Cell 22(5)1441-5.


Fu Y, Springer NM, Gerhardt D, Ying K, Yeh C-T, Wei W, Swanson-Wagner R, D’Ascenzo M, Millard T, Freeberg L, Aoyama N, Kitzman J, Burgess D, Richmond T,  Albert T, Barbazuk WB, Jeddeloh J, Schnable PS. 2010. Repeat subtraction-mediated sequence capture from a complex genome.  Plant Journal 62(5):898-909.


2009


Springer NM, Eichten S, Smith A, Papa CM, Steinway S, Kaeppler SM. 2009. Characterization of a novel maize retrotransposon family SPRITE that shows high levels of variability among maize inbred lines. Maydica 54: 417-428.


Schnable PS, D Ware, RS Fulton, JC Stein, F Wei, S Pasternak, C Liang, J Zhang, L Fulton, TA Graves, P Minx, AD Reily, L Courtney, SS Kruchowski, C Tomlinson, C Strong, K Delehaunty, C Fronick, W Courtney, SM Rock, E Belter, F Du, K Kim, RM Abbott, M Cotton, A Levy, P Marchetto, K Ochoa, SM Jackson, B Gillam, W Chen, L Yan, J Higginbotham, M Cardenas, J Waligorski, E Applebaum, L Phelps, J Falcone, K Kanchi, T Thane, A Scimone, N Thane, J Henke, T Wang, J Ruppert, N Shah, K Rotter, J Hodges, E Ingenthron, M Cordes, S Kohlberg,  J Sgro,  B Delgado,  K Mead,  A Chinwalla,  S Leonard,  K Crouse,  K Collura,  D Kudrna,  J Currie,  R He,  A Angelova,  S Rajasekar,  T Mueller,  R Lomeli,  G Scara,  A Ko,  K Delaney,  M Wissotski,  G Lopez,  D Campos,  M Braidotti,  E Ashley,  W Golser,  H Kim,  S Lee,  J Lin,  Z Dujmic,  W Kim,  J Talag,  A Zuccolo,  C Fan,  A Sebastian,  M Kramer,  L Spiegel,  L Nascimento,  T Zutavern,  B Miller,  C Ambroise,  S Muller,  W Spooner,  A Narechania,  L Ren,  S Wei,  S Kumari,  B Faga,  M Levy,  L McMahan,  PV Buren,  MW Vaughn,  K Ying,  CT Yeh,  SJ Emrich,  Y Jia,  A Kalyanaraman,  AP Hsia,  WB Barbazuk,  RS Baucom,  TP Brutnell,  NC Carpita,  C Chaparro,  J Chia,  J Deragon,  JC Estill,  Y Fu,  JA Jeddeloh,  Y Han,  H Lee,  P Li,  DR Lisch,  S Liu,  Z Liu,  DH Nagel,  MC McCann,  P SanMiguel,  AM Myers,  DS Nettleton,  J Nguyen,  BW Penning,  L Ponnala,  KL Schneider,  DC Schwartz,  A Sharma,  C Soderlund,  NM Springer,  Q Sun,  H Wang,  M Waterman,  R Westerman,  TK Wolfgruber,  L Yang,  Y Yu,  L Zhang,  S Zhou,  Q Zhu,  JL Bennetzen,  RK Dawe,  J Jiang,  N Jiang,  GG Presting,  SR Wessler,  S Aluru,  RA Martienssen,  SW Clifton,  WR McCombie,  RA Wing,  RK Wilson. 2009. The B73 maize genome: complexity, diversity and dynamics. Science, 326(5956): 1112-1115.


Springer NM, Ying K, Fu Y, Ji T, Yeh C-T, Jia Y, Wu W, Richmond T, Kitzman J, Rosenbaum H, Iniguez AL, Barbazuk WB, Jeddeloh JA, Nettleton D, Schnable PS. 2009. Maize Inbreds Exhibit High Levels of CNV and Presence/Absence Differences in Genome Content. PLoS Genetics 5(11): e1000734.


Liu S, Chen HD, Makarevitch I, Shirmer R, Emrich SJ, Dietrich CR, Barbazuk WB, Springer NM, Schnable PS. 2010. High-Throughput Genetic Mapping of Mutants via Quantitative SNP-typing. Genetics 184:19-26.  PMID: 19884313


Flint-Garcia SA, Buckler ES, Tiffin P, Ersoz E, Springer NM. 2009. Heterosis is prevalent for multiple traits in diverse maize germplasm. PLoS One 4:e7433. PMID: 19823591


Springer NM. 2009. Small RNAs: how seeds remember to obey their mother. Curr Biol. 19:R649-51.


Johnson KJ, Springer NM, Bielinsky AK, Largaespada DA, Ross JA. 2009. Developmental origins of cancer. Cancer Res. 69:6375-6377.


Gray J, Bevan M, Brutnell T, Buell CR, Cone K, Hake S, Jackson D, Kellogg E, Lawrence C, McCouch S, Mockler T, Moose S, Paterson A, Peterson T, Rokshar D, Souza GM, Springer N, Stein N, Timmermans M, Wang GL, Grotewold E. 2009.  A recommendation for naming transcription factor proteins in the grasses. Plant Physiol. 149:4-6.


Haun WJ, Danilevskaya O, Meeley RM, Springer NM.  2009.  Disruption of Imprinting by Mu Transposon Insertions in the 5' Proximal Regions of the Zea mays Mez1 Locus.  Genetics 181:1229-1237.


Chaudhary B, Flagel L, Stupar RM, Udall JA, Verma N, Springer NM, Wendel J.  2009.  Reciprocal silencing, transcriptional bias and functional divergence of homoeologs in polyploid cotton (Gossypium).  Genetics 182:503-517.


2008


Haun WJ, Springer NM.  2008.  Maternal and paternal alleles exhibit differential histone methylation and acetylation at the maize imprinted genes.  The Plant Journal 56: 903-912


Stupar RM, Gardiner JG, Oldre AG, Haun WJ, Chandler VL, Springer NM.  2008.  Gene expression analyses in maize inbreds and hybrids with varying levels of heterosis.  BMC Plant Biology 8:33.


Springer NM, Stupar RM.  2007.  Allele-specific expression analysis reveals prevalent cis-acting variation and parent-of-origin affects on gene expression in maize.  Plant Cell 19: 2391-2402.


Makarevitch I, Phillips RL, Springer NM.  2008.  Profiling expression changes caused by a segmental aneuploid in maize.  BMC Genomics 9:7.


2007


Stupar RM, Hermanson PJ, Springer NM.  2007.  Nonadditive expression and parent-of-origin effects identified by microarray and allele-specific expression profiling of maize endosperm.  Plant Physiology 145: 411-425.


Makarevitch I, Stupar RM, Iniguez AL, Haun WJ, Barbazuk WB, Kaeppler SM, Springer NM.  2007.  Natural variation for alleles under epigenetic control by the maize chromomethylase Zmet2.  Genetics 177:749-60.


McGinnis K, Murphy N, Carlson AR, Akula A, Akula C, Basinger H, Carlson M, Hermanson PJ, Kovacevic N, McGill MA, Seshadri V, Yoyokie J, Cone KC, Kaeppler HF, Kaeppler SM, Springer NM.  2007.  Assessing the efficiency of RNA interference for maize functional genomics.  Plant Physiology 143:1441-51.


Springer NM, Stupar RM.  2007.  Allelic variation and heterosis in maize: How do two halves make more than a whole?  Gen. Res.  17:264-75.


Haun WJ, Laoueille-Duprat S, O’Connell MJ, Spillane C, Grossniklaus U, Phillips AR, Kaeppler SM, Springer NM. 2007. Genomic imprinting, methylation and molecular evolution of maize Enhancer of zeste (Mez) homologs.  The Plant Journal 49: 325-337.


2006


Stupar RM, Springer NM.  2006.  Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression patterns in the F1 hybrid.  Genetics 173:2199-2210.


2005


Springer NM, Kaeppler SM.  2005.  Evolutionary divergence of monocot and dicot methyl-CpG-binding domain proteins.  Plant Physiol. 138(1):92-104.


McGinnis K, Chandler V, Cone K, Kaeppler H, Kaeppler S, Kerschen A, Pikaard C, Richards E, Sidorenko L, Smith T, Springer N, Wulan T. 2005.  Transgene-induced RNA interference as a Tool for Plant Functional Genomics. In RNA Interference Methods in Enzymology eds. John Rossi and David Engelke. Methods Enzymol 392:1-24.


2004


Till BJ, Reynolds SH, Weil C, Springer NM, Burtner C, Young K, Bowers E, Codomo CA, Enns LC, Odden AR, Greene EA, Comai L, Henikoff S. 2004.  Discovery of induced point mutations in maize genes by TILLING.  BMC Plant Biol. 4(1):12


Springer NM, Xu X, Barbazuk WB.  2004.  Utility of different gene-enrichment approaches towards identifying and sequencing the maize gene space.  Plant Physiol. 136(2):3023-33


2003


Springer NM, Napoli CA, Selinger DA, Pandey R, Cone KC, Chandler VL, Kaeppler HF, Kaeppler SM. 2003.  Comparative Analysis of SET Domain Proteins in Maize and Arabidopsis Reveals Multiple Duplications Preceding the Divergence of Monocots and Dicots.  Plant Physiol. 132:907-925


2002


Springer NM, Danilevskaya O, Hermon P, Helentjaris T, Phillips RL, Kaeppler HF, Kaeppler SM. 2002. Sequence Relationships, Conserved Domains, and Expression Patterns for Zea mays Homologs of the Drosophila Polycomb Group Genes E(z), esc, and E(Pc). Plant Phys.  128: 1332-1345


2001


Papa CM, Springer NM, Muszynski MG, Meeley R, Kaeppler SM. 2001. Maize chromomethylase Zea methyltransferase2 is required for CpNpG methylation. Plant Cell 13: 1919-1928.


2000


Cao X, Springer NM,  Muszynski MG, Phillips RL, Kaeppler SM, Jacobsen SE. 2000. Conserved plant genes with similarity to mammalian de novo DNA methyltransferases. Proc. Natl. Acad. Sci. 9:4979-4984



BOOK CHAPTERS:


Springer NM, Kaeppler SM. 2008. Epigenetics: The Second Genetic Code.  In Advances in Agronomy: Volume 100 (Ed. Donald Sparks) Academic Press. San Diego, CA.


Hollick J, Springer NM. 2008.  Paramutation, imprinting and epigenomics in maize.  In Epigenomics (Eds. Martienssen R, Greally J, Anne Ferguson-Smith A) Springer-Verlag. New York


Springer NM, Gutierrez-Marcos JF. 2008.  Imprinting in maize.  In The Maize handbook. (Eds. Hake S, Bennetzen J)  Springer-Verlag. New York.


Grotewold E, Springer NM. 2008.  Decoding the transcriptional hardwiring of the plant genome.  In The Annual Plant Biology Review – Systems Biology (Eds. Coruzzi G, Gutierrez R).  Blackwell, Oxford UK.


Springer NM. 2007.  Isolation of DNA from plants.  In Genetic Variation: A Laboratory Manual (ed. Michael Weiner) Cold Spring Harbor Press, Cold Spring Harbor New York.


Kaeppler, S.M., N.M. Springer.  2002.  Silence of the genes: Epigenetic gene silencing as a tool in genetic research and cultivar development.  Proceedings of the 56th Annual Corn and Sorghum Research Conference.