Research Findings from the CSAGRIM/NUPRIME Project

Primary Literature Resulting from Research Fully or Partialy Supported by this Project

• (2012) Howe ES, Clemente TE, and Bass HW. Maize histone H2B-mCherry, a new fluorescent chromatin marker for somatic and meiotic chromosome research. DNA and Cell Biology 31(6):925-938. (DOI: 10.1089/dna.2011.1514) [PubMed 22662764 | Journal Online | PDF | Supp. 3D Image Movies ]
• (2013) Fincher JA, Vera DL, Hughes DD, McGinnis KM, Dennis JH, and Bass HW. Genome-wide prediction of nucleosome occupancy in maize (Zea mays L.) highlights chromatin structural features at multiple scales. Plant Physiology 162(2):1127-1141 (PDF).
• (2013) Labonne JDJ, Dorweiler JE, and McGinnis KM. Changes in nucleosome position at transcriptional start sites of specific genes in Zea mays mediator of paramutation1 mutants. Epigenetics 8(4):1-11. (DOI: dx.doi.org/10.4161/epi.24199 | PDF)
• (2014) Bass HW, Wear EE, Lee T-J, Hoffman GG, Gumber HK, Allen GC, Thompson WF, Hanley-Bowdoin L. A maize root tip system to study DNA replication programmes in somatic and endocycling nuclei during plant development. Journal of Experimental Botany 10.1093/jxb/ert470.

• (2014) Madzima TF, Huang J, and McGinnis KM. Chromatin structure and gene expression changes associated with loss of MOPl activity in Zea mays. Epigenetics May 1;9(7). [doi 10.4161/epi.29022 | PubMed ]
• (2014) Vera DL, Madzima TF, Labonne JD, Alam MP, Hoffman GG, Girimurugan SB, Zhang J, McGinnis KM, Dennis K M, and Bass HW. Differential nuclease sensitivity profiling of chromatin reveals biochemical footprints coupled to gene expression and functional DNA elements. Plant Cell tpc.114.130609.

• (2016) Rodgers-Melnick E, Vera DL, Bass HW, and Buckler ES. Open Chromatin Reveals the Functional Maize Genome. Proc Nat Acad Sci, USA 113(22):E3177-E3184. [doi: 10.1073/pnas.1525244113 | PubMed 27185945 ]
• (2017) Savadel SD and Bass HW. "Review: Take a Look at Plant DNA Replication: Recent Insights and New Questions." Plant Signaling & Behavior, 12:4, e1311437 (DOI: 10.1080/15592324.2017.1311437).
  Public images on omero at bio for teaching and reseaerch; https://goo.gl/CTI06F view as Public omero
  
• (2018) Griffin BD and Bass HW. "Review: Plant G-quadruplex (G4) motifs in DNA and RNA; abundant, intriguing sequences of unknown f unction." Plant Science 269:143-147
  (DOI: 10.1016/j.plantsc i.2018.01.011 [PDF via DiginNole!).
• (2018) Girimurugan SB, Liu Y, Lung P-Y, Vera DL, Dennis JH, Bass HW, and Zhang "iSeg: an efficient algorithm for segmentation of genomic and epigenomic data." BMC Bioinformatics 19:131(15pp) (DOI: 10.1186/s12859-018-2140-3).
• (2018) Turpin ZM, Vera DL, Savadel SD, Lung, P-Y, Wear EE, Mickelson-Young L, Thompson, WF, Hanley-Bowdoin L, Dennis, JH, Zhang J, and Bass HW. "Chromatin Structure Profile Data from DNS-seq: Differential Nuclease Sensitivity Mapping of Four Reference Tissues of B73 Maize (Zea mays L)." Data in Brief 20:358-363 (DOI: 10.1016/j.dib.2018.08.015).

Book Chapters:

• (2011) Figueroa DM, Amarillo FE, and Bass HW. "Cytogenetic Mapping in Plants"; in Plant Cytogenetics (eds. HW Bass and JA Birchler); Springer New York, NY.

• (2011) Fincher JA and Dennis JH "DNA sequence contribution to nucleosome distribution"; in Epigenetics: A reference manual (eds. JM Craig and NC Wong); Norwich, UK: Horizon Scientific Press, pp 133-142.

• (2011) Murphy SP and Bass HW "Genetics and Cytology of Meiotic Chromosome Behavior in Plants"; in Plant Cytogenetics (eds. HW Bass and JA Birchler); Springer New York, NY

• (2011) Spetman B, Lueking S, Druliner BR, and Dennis JH. "Microarray mapping of nucleosome position"; in Epigenetics: A reference manual (eds. JM Craig and NC Wong); Norwich, UK: Horizon Scientific Press, pp 337-347.
• (2013) Howe ES, Murphy SP, and Bass HW. "Three-dimensional acrylamide fluorescence in situ hybridization (FISH) for plant cells"; in Methods in Molecular Biology: Plant Meiosis (eds. WP Pawlowski, M Grelon, and S Armstrong); Springer New York Volume 990, pp 53-66.

Recent Presentations (Posters, Talks, etc)

2016
• Bass HW, DL Vera, E Rodgers-Melnick, and ES Buckler. (TALK) Functional Genomics in Maize using Differential Nuclease Sensitivity (DNS-seq) Chromatin Profiling. Workshop #3288; New England Biolabs - Recent advances in NGS sample prep. Plant and Animal Genome XXIV Conference; San Diego, CA, USA; January 9-13, 2016.

Bass HW, DL Vera, E Rodgers-Melnick, and ES Buckler. (TALK) Investigating Chromatin Structure at Multiple Scales in Maize. Workshop #3086; EPIC: the Plant Epigenome Project. Plant and Animal Genome XXIV Conference; San Diego, CA, USA; January 9-13, 2016.
• Bass, HW, DL Vera, ZD Wiggins, K Yu, JH Dennis, J Zhang, and OU Onokpise. (POSTER) DNS - NUPRIME: Differential Nuclease Sensitivity for Nuclease Profiling as an Integrative Resource for Maize Epigenomics. 58th Annual Maize Genetics Conference, Jacksonville, FL, USA, March 17-20, 2016.

• Easterling KA, HW Bass, DL Vera, and T. Brutnell (and the W22 Consortium). (POSTER). W22 Chromosomes and Chromatin: A Pachytene FISH Karyotype and Genome-wide Differential Nuclease Sensitivity Profile. 58th Annual Maize Genetics Conference, Jacksonville, FL, USA, March 17-20, 2016.

• Estrada AL, IC Bass, OU Onokpise, and HW Bass. (POSTER) Genome strolling through the Maize-10-Maze; a living museum outreach project exhibiting select mutants of maize. 58th Annual Maize Genetics Conference, Jacksonville, FL, USA, March 17-20, 2016.

• Farran AE, ZM Turpin, and HW Bass. (POSTER) Does hypoxia signal transduction involve targeted ROS-mediated oxidative base modification (8-oxoG) at G4 DNA elements in maize? 58th Annual Maize Genetics Conference, Jacksonville, FL, USA, March 17-20, 2016.

• Griffin BD, and HW Bass. (POSTER) Producing Reporter Gene Constructs for Investigating the Role of G-Quadruplex (G4) DNA elements in Gene Regulation. 58th Annual Maize Genetics Conference, Jacksonville, FL, USA, March 17-20, 2016.

• Hoffman GG, T-J Lee, EE Wear, SR Joseph, GC Allen, WF Thompson, L Hanley-Bowdoin, and HW Bass. (POSTER) The spatiotemporal patterns of DNA replication and endoreduplication as defined by 3D microscopy of nuclei from developing maize root tip nuclei. 58th Annual Maize Genetics Conference, Jacksonville, FL, USA, March 17-20, 2016.

• Bass HW. (KEYNOTE LECTURE) in Dynamic Organisation of the Nucleus session; Exploring maize nuclear structure-function relationships operative at multiple scales. Society for Experimental Biology, SEB Brighton 2016, Brighton, UK; July 4-7, 2016.

• 2017

• Parvathaneni RK, Shamimuzzaman, Md, Kovar LL, Vera, DL, Bass HW, and A Eveland. (POSTER) Defining gene regulatory networks controlling early inflorescence development in maize. 59th Annual Maize Genetics Conference, St. Louis, MO, USA, March 9-12, 2017.

• Vera DL, Kyle K, and H Bass (POSTER) Genomaize, a UCSC genome browser for maize genomes. 59th Annual Maize Genetics Conference, St. Louis, MO, USA, March 9-12, 2017.

• Turpin ZM, Vera DL, and HW Bass. (POSTER) Chromatin structure profile (MNase DNS-seq) for 15-DAP endosperm, a B73 core reference tissue. 59th Annual Maize Genetics Conference, St. Louis, MO, USA, March 9-12, 2017.

• Griffin BD, Winn MN, and HW Bass. (POSTER) Producing reporter gene constructs for investigating the role of G-Quadruplex (G4) DNA elements in gene regulation. 59th Annual Maize Genetics Conference, St. Louis, MO, USA, March 9-12, 2017.

• Savadel SD and HW Bass. (POSTER) Taking a look at plant DNA replication: recent insights, new questions, and data sharing through OMERO.bio.fsu.edu. 59th Annual Maize Genetics Conference, St. Louis, MO, USA, March 9-12, 2017.

  2018

• Bass HW, Vera DL, Lung P-L, Liu Y, Girimurugan SB, Turpin ZM, Savadel SD, Kyle KE, Dennis JH, and J Zhang. (POSTER-PDF) The NUPRIME Project: Nuclease Profiling of Four Reference Tissues as a Resource for Maize Epigenomics. 60th Annual Maize Genetics Conference, Saint-Malo, France, March 22-25, 2018.

• Savadel SD, Vera DL, Lung P-Y, Zhang, J, and Bass HW. (POSTER-PDF) MOA (MNase Open Access) Mapping: A New and Efficient Method for Genome-Wide Open Chromatin Profiling in Maize, Demonstrated with Developing Earshoots. 60th Annual Maize Genetics Conference, Saint-Malo, France, March 22-25, 2018.