About this project (CSAGRIM/NUPRIME)

This is the homepage of an NSF-funded project that investigates the structure, organization, and dynamics of chromatin in maize. This website houses information that relates to this project, which include:

• Research - A description of the project aims, methods, and findings.
• Data - A collection of data and links to data produced by this research.
• Outreach - Past and future public outreach programs employed through this project.
• People - A list of project members and contact information.
  
• Protocols - Lab/Workshop Protocols for MNase Profiling via DNS-seq
  

Understanding how genomes are organized functionally is a major challenge in biology. Structurally, the genomes of eukaryotes are organized into chromatin, which is a complex of DNA, the genetic material, and various chromosomal proteins. The basic subunit of chromatin is the nucleosome, comprising approximately 150 base pairs of DNA wrapped around eight histone proteins. Nucleosome positioning and chromatin modifications are known to contribute to changes in gene expression levels, yet the exact nature and role of chromatin structure remains a challenge to discern. The overall goal of this project is to characterize the chromatin structure of the maize genome in relation to function, specifically with respect to nucleosome occupancy and genome-wide in situ chromatin architecture. The project combines expertise from researchers at FSU and FAMU to achieve these goals, using computational, biochemical, genetic, and microscopic methods.

Florida State NEWS article describing the project's inception. The primary objectives are:

1. Develop DNA microarrays for genome-wide studies of chromatin structure in maize, using technologies first developed to study the human genome. We plan to map nucleosome positions at high resolution, map large-domain chromatin accessibility. The resulting empirical data will be used to train computational models for DNA-sequence based predictions of nucleosome positions in maize and other flowering plant species such as rice, Arabidopsis, and soybean.
2. Employ these technologies to investigate how the chromatin structure of the maize genome responds to the mop1 (mediator of paramutation1) mutation. The maize Mop1 gene is an RNA-dependent RNA polymerase whose function is thought to regulate chromatin structure through small RNAs and by silencing potentially deleterious genome changes.
3. Investigate the changes in chromosome topology and nuclear architecture associated with the genome responses measured using DNA microarrays or next generation sequencing. The in situ assays will employ multi-color 3D molecular cytology (FISH), and provide a means of integration of observations from the molecular to the cellular level, a vastly understudied area in contemporary genome research.

Key Findings This Project: (more on Research page)

• (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) 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 in maize. Plant Cell doi/10.1105/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 ]
• (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).
• (*2020) Parvathaneni RK, Bertolini E, Shamimuzzaman M, Vera DL, Lung P-Y, Rice BR, Zhang J, Brown PJ, Lipka AE, Bass HW, and Eveland AL. "The regulatory landscape of early maize inflorescence development." Genome Biology 2020 Jul 6;21(1):165. (DOI: 10.1186/s13059-020-02070-8).
• (*2020) Wheeler E, Brooks AM, Concia L, Vera DL, Wear EE, LeBlanc C, Ramu U, Vaughn MW, Bass HW, Martienssen RA, Thompson WF, and Hanley-Bowdoin L. "Arabidopsis DNA replication initiates in intergenic, AT-rich open chromatin" Plant Physiology 183:206-220. (DOI: 10.1104/pp.19.01520).

Books, Chapters, & Collaborative Publications Supported in Part by This Project:

• (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) 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

• (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 i (eds. WP Pawlowski, M Grelon, and S Armstrong); Springer New York Volume 990, pp 53-66.

• (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 durin g plant development. Journal of Experimental Botany 10.1093/jxb/ert470.

• (2019) Gumber HK, McKenna JF, Estrada AL, Tolmie AF, Graumann K, and Bass HW. "Identification and characterization of genes encoding the nuclear envelope LINC complex in the monocot species Zea mays" Journal of Cell Science 132(3):jcs221390. (DOI: 10.1242/jcs.221390).
  Feature article: First Person - Hardeep Gumber.

• (2021) McKenna** JF, Gumber** HK, Turpin ZM, Jalovec AM, Kartick AC, Graumann K, and Bass HW. "Maize (Zea mays L.) nucleoskeletal proteins regulate nuclear envelope remodeling and function in stomatal complex development and pollen viability." (** for co-1st Authors); Frontiers in Plant Science February 2021 | Volume 12 | Article 645218. (DOI: doi: 10.3389/fpls.2021.645218).

• (2019) Bass, H. W., & Onokpise, K. (Eds.). Crazy Lazy Corn!!!: A Book about Plant Genetics for Students and Future Scientists. SokheChapke Publishing.

Project Poster Presentations at National and International Conferencesi:

2010 (* presenting authors)
• JH Dennis, JA Fincher, KM McGinnis*, and HW Bass* Nucleosome Mapping and Chromatin Structure in Maize, a Novel Platform for Genome Response Assays. 52nd Annual Maize Genetics Conference; Riva del Garda, Italy; March 18-21, 2010.

• HW Bass*, JH Dennis, KM McGinnis, OU Onokpise, & JA Fincher. Nucleosome Mapping and Chromatin Structure in Maize, a Novel Platform for Genome Response Assays. NSF Plant Genome Research Program Awardee Meeting. Arlington, VA, September, 2010.

  2011

• HW Bass*, JA Fincher, KM McGinnis, and JH Dennis. Nucleosome Mapping And Chromatin Structure In Maize, A Novel Platform For Genome Response Assays. Plant and Animal Genome XIX Conference; San Diego, CA; January 15-18, 2011.

• JA Fincher*, BL Bremen, TZ Sen, JH Dennis, and HW Bass. Using a Support Vector Machine to Predict Nucleosome Occupancy Likelihood (NOL) in the Maize Genome. 53rd Annual Maize Genetics Conference; St. Charles, IL; March 17-20, 2011.

• PM Alam, DL Vera, JA Fincher, KM McGinnis, HW Bass, and JH Dennis*. Nucleosome distribution and promoter architecture at 400 genes in the maize genome. 53rd Annual Maize Genetics Conference; St. Charles, IL; March 17-20, 2011.

• DL Vera*, KM McGinnis, JH Dennis, and HW Bass. Analysis of Chromatin Accessibility in the Maize Interphase Nucleus. 53rd Annual Maize Genetics Conference; St. Charles, IL; March 17-20, 2011.

• JA Fincher*, DL Vera, HW Bass, JH Dennis. Overlapping but distinct DNA sequence features drive nucleosome organization in maize and humans. Dynamic DNA Packaging Across Kingdoms: Chromatin and Beyond; Biophysical Society; Asilomar, CA; July 5-5, 2011.

• HW Bass*, JH Dennis, KM McGinnis, OU Onokpise, JA Fincher, DL Vera, JD Labonne, MP Alam, TF Madzima, and GG Hoffman Nucleosome Mapping and Chromatin Structure in Maize, a Novel Platform for Genome Response Assays. NSF Plant Genome Program (PGRP) Awardee meeting; Arlington VA; September 8-9, 2011.

  2012

• DL Vera*, HW Bass, JH Dennis. (POSTER) Chromatin accessibility is largely unaltered by the transition to mitotic chromosomes. Keystone Symposia: Epigenomics; Keystone, CO; January 17-22, 2012.

• JDJ Labonne, DL Vera, AM Parwez, TF Madzima, GG Hoffman*, JH Dennis, KM McGinnis, & HW Bass. (POSTER) Development of a robust method for microscopic and molecular assays of nuclear architecture and chromatin structure in maize.54th Annual Maize Genetics Conference; Portland, OR; March 15-18, 2012.

• DL Vera*, DD Hughes, JH Dennis, & HW Bass. Defining the chromatin domain organization of the maize genome.54th Annual Maize Genetics Conference; Portland, OR; March 15-18, 2012.

• HW Bass*, DL Vera, DD Hughes, JA Fincher, PM Alam, JDJ Labonne, TF Madzima, Z Wiggins, OU Onokpise, SP Moose, KM McGinnis, & JH Dennis. Tissue- specific nucleosome occupancy in the promoter/TSS region of 400 classical maize genes 54th Annual Maize Genetics Conference; Portland, OR; March 15-18, 2012.

• DL Vera*, JH Dennis, HW Bass. Using empirical maize chromatin data to train a support vector machine to predict nucleosome occupancy likelihood (NOL). 54th Annual Maize Genetics Conference; Portland, OR; March 15-18, 2012.

• HW Bass*, DL Vera, DD Hughes, JA Fincher, AM Parwez, JDJ Labonne, TF Madzima, ZJ Wiggins, OU Onokpise, GH Hoffman, KM McGinnis, & JH Dennis. Chromatin Structure and Genome Response in Maize. NSF Plant Genome Research Program Awardee Meeting; Arlington, VA; September 6-7, 2012.