1
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Deans NC, Talbot JERB, Li M, Sáez-González C, Hövel I, Heavens D, Stam M, Hollick JB. Paramutation at the maize pl1 locus is associated with RdDM activity at distal tandem repeats. PLoS Genet 2024; 20:e1011296. [PMID: 38814980 PMCID: PMC11166354 DOI: 10.1371/journal.pgen.1011296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 06/11/2024] [Accepted: 05/08/2024] [Indexed: 06/01/2024] Open
Abstract
Exceptions to Mendelian inheritance often highlight novel chromosomal behaviors. The maize Pl1-Rhoades allele conferring plant pigmentation can display inheritance patterns deviating from Mendelian expectations in a behavior known as paramutation. However, the chromosome features mediating such exceptions remain unknown. Here we show that small RNA production reflecting RNA polymerase IV function within a distal downstream set of five tandem repeats is coincident with meiotically-heritable repression of the Pl1-Rhoades transcription unit. A related pl1 haplotype with three, but not one with two, repeat units also displays the trans-homolog silencing typifying paramutations. 4C interactions, CHD3a-dependent small RNA profiles, nuclease sensitivity, and polyadenylated RNA levels highlight a repeat subregion having regulatory potential. Our comparative and mutant analyses show that transcriptional repression of Pl1-Rhoades correlates with 24-nucleotide RNA production and cytosine methylation at this subregion indicating the action of a specific DNA-dependent RNA polymerase complex. These findings support a working model in which pl1 paramutation depends on trans-chromosomal RNA-directed DNA methylation operating at a discrete cis-linked and copy-number-dependent transcriptional regulatory element.
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Affiliation(s)
- Natalie C. Deans
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- Centers for Applied Plant Sciences and RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Joy-El R. B. Talbot
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Mowei Li
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- Centers for Applied Plant Sciences and RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Cristian Sáez-González
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Iris Hövel
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Amsterdam, The Netherlands
| | | | - Maike Stam
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, Amsterdam, The Netherlands
| | - Jay B. Hollick
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- Centers for Applied Plant Sciences and RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
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2
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Gumber HK, McKenna JF, Tolmie AF, Jalovec AM, Kartick AC, Graumann K, Bass HW. MLKS2 is an ARM domain and F-actin-associated KASH protein that functions in stomatal complex development and meiotic chromosome segregation. Nucleus 2019; 10:144-166. [PMID: 31221013 PMCID: PMC6649574 DOI: 10.1080/19491034.2019.1629795] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/13/2019] [Accepted: 05/28/2019] [Indexed: 01/25/2023] Open
Abstract
The linker of nucleoskeleton and cytoskeleton (LINC) complex is an essential multi-protein structure spanning the eukaryotic nuclear envelope. The LINC complex functions to maintain nuclear architecture, positioning, and mobility, along with specialized functions in meiotic prophase and chromosome segregation. Members of the LINC complex were recently identified in maize, an important scientific and agricultural grass species. Here we characterized Maize LINC KASH AtSINE-like2, MLKS2, which encodes a highly conserved SINE-group plant KASH protein with characteristic N-terminal armadillo repeats (ARM). Using a heterologous expression system, we showed that actively expressed GFP-MLKS2 is targeted to the nuclear periphery and colocalizes with F-actin and the endoplasmic reticulum, but not microtubules in the cell cortex. Expression of GFP-MLKS2, but not GFP-MLKS2ΔARM, resulted in nuclear anchoring. Genetic analysis of transposon-insertion mutations, mlks2-1 and mlks2-2, showed that the mutant phenotypes were pleiotropic, affecting root hair nuclear morphology, stomatal complex development, multiple aspects of meiosis, and pollen viability. In male meiosis, the mutants showed defects for bouquet-stage telomere clustering, nuclear repositioning, perinuclear actin accumulation, dispersal of late prophase bivalents, and meiotic chromosome segregation. These findings support a model in which the nucleus is connected to cytoskeletal F-actin through the ARM-domain, predicted alpha solenoid structure of MLKS2. Functional conservation of MLKS2 was demonstrated through genetic rescue of the misshapen nuclear phenotype of an Arabidopsis (triple-WIP) KASH mutant. This study establishes a role for the SINE-type KASH proteins in affecting the dynamic nuclear phenomena required for normal plant growth and fertility. Abbreviations: FRAP: Fluorescence recovery after photobleaching; DPI: Days post infiltration; OD: Optical density; MLKS2: Maize LINC KASH AtSINE-like2; LINC: Linker of nucleoskeleton and cytoskeleton; NE: Nuclear envelope; INM: Inner nuclear membrane; ONM: Outer nuclear membrane.
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Affiliation(s)
- Hardeep K. Gumber
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Joseph F. McKenna
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Andrea F. Tolmie
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Alexis M. Jalovec
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Andre C. Kartick
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Katja Graumann
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Hank W. Bass
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
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3
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Stroud LK, McGinnis KM. Altered nucleosome positions in maize haplotypes and mutants of a subset of SWI/SNF-like proteins. PLANT DIRECT 2017; 1:e00019. [PMID: 31245667 PMCID: PMC6508530 DOI: 10.1002/pld3.19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 08/07/2017] [Accepted: 09/25/2017] [Indexed: 06/09/2023]
Abstract
Chromatin remodelers alter DNA-histone interactions in eukaryotic organisms and have been well characterized in yeast and Arabidopsis. While there are maize proteins with similar domains as known remodelers, the ability of the maize proteins to alter nucleosome position has not been reported. Mutant alleles of several maize proteins (RMR1, CHR101, CHR106, CHR127, and CHR156) with similar functional domains to known chromatin remodelers were identified. Altered gene expression of Chr101, Chr106, Chr127, and Chr156 was demonstrated in plants homozygous for the mutant alleles. These mutant genotypes were subjected to nucleosome position analysis to determine whether misregulation of putative maize chromatin proteins would lead to altered DNA-histone interactions. Nucleosome position changes were observed in plants homozygous for chr101, chr106, chr127, and chr156 mutant alleles, suggesting that CHR101, CHR106, CHR127, and CHR156 may affect chromatin structure. The role of RNA polymerases in altering DNA-histone interactions was also tested. Changes in nucleosome position were demonstrated in homozygous mop2-1 individuals. These changes were demonstrated at the b1 tandem repeats and at newly identified loci. Additionally, differential DNA-histone interactions and altered gene expression of putative chromatin remodelers were demonstrated between different maize haplotypes.
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Affiliation(s)
- Linda K. Stroud
- Department of Biological ScienceFlorida State UniversityTallahasseeFLUSA
| | - Karen M. McGinnis
- Department of Biological ScienceFlorida State UniversityTallahasseeFLUSA
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4
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Chen J, Li E, Zhang X, Dong X, Lei L, Song W, Zhao H, Lai J. Genome-wide Nucleosome Occupancy and Organization Modulates the Plasticity of Gene Transcriptional Status in Maize. MOLECULAR PLANT 2017; 10:962-974. [PMID: 28487258 DOI: 10.1016/j.molp.2017.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 04/28/2017] [Accepted: 05/01/2017] [Indexed: 05/16/2023]
Abstract
Nucleosomes are fundamental units of chromatin that play critical roles in gene regulation by modulating DNA accessibility. However, their roles in regulating tissue-specific gene transcription are poorly understood. Here, we present genome-wide nucleosome maps of maize shoot and endosperm generated by sequencing the micrococcal nuclease digested nucleosomal DNA. The changes of gene transcriptional status between shoot and endosperm were accompanied by preferential nucleosome loss from the promoters and shifts in the first nucleosome downstream of the transcriptional start sites (+1 nucleosome) and upstream of transcriptional termination sites (-1 nucleosome). Intrinsically DNA-encoded nucleosome organization was largely associated with the capacity of a gene to alter its transcriptional status among different tissues. Compared with tissue-specific genes, constitutively expressed genes showed more pronounced 5' and 3' nucleosome-depleted regions as well as further +1 nucleosome to transcriptional start sites and -1 nucleosome to transcriptional termination sites. Moreover, nucleosome organization was more highly correlated with the plasticity of gene transcriptional status than with its expression level when examined using in vivo and predicted nucleosome data. In addition, the translational efficiencies of tissue-specific genes appeared to be greater than those of constitutively expressed genes. Taken together, our results indicate that intrinsically DNA-encoded nucleosome organization is important, beyond its role in regulating gene expression levels, in determining the plasticity of gene transcriptional status.
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Affiliation(s)
- Jian Chen
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P. R. China
| | - En Li
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P. R. China
| | - Xiangbo Zhang
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P. R. China
| | - Xiaomei Dong
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P. R. China
| | - Lei Lei
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P. R. China
| | - Weibin Song
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P. R. China
| | - Haiming Zhao
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P. R. China
| | - Jinsheng Lai
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, P. R. China.
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5
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Epigenetic Control of Gene Expression in Maize. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2017; 328:25-48. [DOI: 10.1016/bs.ircmb.2016.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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6
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Böhmdorfer G, Wierzbicki AT. Control of Chromatin Structure by Long Noncoding RNA. Trends Cell Biol 2016; 25:623-632. [PMID: 26410408 DOI: 10.1016/j.tcb.2015.07.002] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 05/22/2015] [Accepted: 07/17/2015] [Indexed: 12/11/2022]
Abstract
Long noncoding RNA (lncRNA) is a pivotal factor regulating various aspects of genome activity. Genome regulation via DNA methylation and post-translational histone modifications is a well-documented function of lncRNA in plants, fungi, and animals. Here, we summarize evidence showing that lncRNA also controls chromatin structure, including nucleosome positioning and chromosome looping. We focus on data from plant experimental systems, discussed in the context of other eukaryotes. We explain the mechanisms of lncRNA-controlled chromatin remodeling and the implications of the functional interplay between noncoding transcription and several different chromatin remodelers. We propose that the unique properties of RNA make it suitable for controlling chromatin modifications and structure.
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Affiliation(s)
- Gudrun Böhmdorfer
- University of Michigan, Department of Molecular, Cellular, and Developmental Biology, Ann Arbor, MI 48109, USA
| | - Andrzej T Wierzbicki
- University of Michigan, Department of Molecular, Cellular, and Developmental Biology, Ann Arbor, MI 48109, USA.
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7
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Gent JI, Madzima TF, Bader R, Kent MR, Zhang X, Stam M, McGinnis KM, Dawe RK. Accessible DNA and relative depletion of H3K9me2 at maize loci undergoing RNA-directed DNA methylation. THE PLANT CELL 2014; 26:4903-17. [PMID: 25465407 PMCID: PMC4311197 DOI: 10.1105/tpc.114.130427] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 11/03/2014] [Accepted: 11/18/2014] [Indexed: 05/18/2023]
Abstract
RNA-directed DNA methylation (RdDM) in plants is a well-characterized example of RNA interference-related transcriptional gene silencing. To determine the relationships between RdDM and heterochromatin in the repeat-rich maize (Zea mays) genome, we performed whole-genome analyses of several heterochromatic features: dimethylation of lysine 9 and lysine 27 (H3K9me2 and H3K27me2), chromatin accessibility, DNA methylation, and small RNAs; we also analyzed two mutants that affect these processes, mediator of paramutation1 and zea methyltransferase2. The data revealed that the majority of the genome exists in a heterochromatic state defined by inaccessible chromatin that is marked by H3K9me2 and H3K27me2 but that lacks RdDM. The minority of the genome marked by RdDM was predominantly near genes, and its overall chromatin structure appeared more similar to euchromatin than to heterochromatin. These and other data indicate that the densely staining chromatin defined as heterochromatin differs fundamentally from RdDM-targeted chromatin. We propose that small interfering RNAs perform a specialized role in repressing transposons in accessible chromatin environments and that the bulk of heterochromatin is incompatible with small RNA production.
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Affiliation(s)
- Jonathan I. Gent
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
| | - Thelma F. Madzima
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306
| | - Rechien Bader
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Matthew R. Kent
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
| | - Xiaoyu Zhang
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
| | - Maike Stam
- Swammerdam Institute for Life Sciences, Universiteit van Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Karen M. McGinnis
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306
| | - R. Kelly Dawe
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
- Department of Genetics, University of Georgia, Athens, Georgia 30602
- Address correspondence to
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8
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Vera DL, Madzima TF, Labonne JD, Alam MP, Hoffman GG, Girimurugan SB, Zhang J, McGinnis KM, Dennis JH, Bass HW. Differential nuclease sensitivity profiling of chromatin reveals biochemical footprints coupled to gene expression and functional DNA elements in maize. THE PLANT CELL 2014; 26:3883-93. [PMID: 25361955 PMCID: PMC4247582 DOI: 10.1105/tpc.114.130609] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 10/03/2014] [Accepted: 10/14/2014] [Indexed: 05/19/2023]
Abstract
The eukaryotic genome is organized into nucleosomes, the fundamental units of chromatin. The positions of nucleosomes on DNA regulate protein-DNA interactions and in turn influence DNA-templated events. Despite the increasing number of genome-wide maps of nucleosome position, how global changes in gene expression relate to changes in nucleosome position is poorly understood. We show that in nucleosome occupancy mapping experiments in maize (Zea mays), particular genomic regions are highly susceptible to variation introduced by differences in the extent to which chromatin is digested with micrococcal nuclease (MNase). We exploited this digestion-linked variation to identify protein footprints that are hypersensitive to MNase digestion, an approach we term differential nuclease sensitivity profiling (DNS-chip). Hypersensitive footprints were enriched at the 5' and 3' ends of genes, associated with gene expression levels, and significantly overlapped with conserved noncoding sequences and the binding sites of the transcription factor KNOTTED1. We also found that the tissue-specific regulation of gene expression was linked to tissue-specific hypersensitive footprints. These results reveal biochemical features of nucleosome organization that correlate with gene expression levels and colocalize with functional DNA elements. This approach to chromatin profiling should be broadly applicable to other species and should shed light on the relationships among chromatin organization, protein-DNA interactions, and genome regulation.
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Affiliation(s)
- Daniel L Vera
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295
| | - Thelma F Madzima
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295
| | - Jonathan D Labonne
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295
| | - Mohammad P Alam
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295
| | - Gregg G Hoffman
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295
| | - S B Girimurugan
- Department of Statistics, Florida State University, Tallahassee, Florida 32306
| | - Jinfeng Zhang
- Department of Statistics, Florida State University, Tallahassee, Florida 32306
| | - Karen M McGinnis
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295
| | - Jonathan H Dennis
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295
| | - Hank W Bass
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295
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9
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Diverse gene-silencing mechanisms with distinct requirements for RNA polymerase subunits in Zea mays. Genetics 2014; 198:1031-42. [PMID: 25164883 DOI: 10.1534/genetics.114.168518] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In Zea mays, transcriptional regulation of the b1 (booster1) gene requires a distal enhancer and MEDIATOR OF PARAMUTATION1 (MOP1), MOP2, and MOP3 proteins orthologous to Arabidopsis components of the RNA-dependent DNA methylation pathway. We compared the genetic requirements for MOP1, MOP2, and MOP3 for endogenous gene silencing by two hairpin transgenes with inverted repeats of the a1 (anthocyaninless1) gene promoter (a1pIR) and the b1 gene enhancer (b1IR), respectively. The a1pIR transgene induced silencing of endogenous A1 in mop1-1 and mop3-1, but not in Mop2-1 homozygous plants. This finding suggests that transgene-derived small interfering RNAs (siRNAs) circumvented the requirement for MOP1, a predicted RNA-dependent RNA polymerase, and MOP3, the predicted largest subunit of RNA polymerase IV (Pol IV). Because the Arabidopsis protein orthologous to MOP2 is the second largest subunit of Pol IV and V, our results may indicate that hairpin-induced siRNAs cannot bypass the requirement for the predicted scaffolding activity of Pol V. In contrast to a1pIR, the b1IR transgene silenced endogenous B1 in all three homozygous mutant genotypes--mop1-1, Mop2-1, and mop3-1--suggesting that transgene mediated b1 silencing did not involve MOP2-containing Pol V complexes. Based on the combined results for a1, b1, and three previously described loci, we propose a speculative hypothesis of locus-specific deployment of Pol II, MOP2-containing Pol V, or alternative versions of Pol V with second largest subunits other than MOP2 to explain the mechanistic differences in silencing at specific loci, including one example associated with paramutation.
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10
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Madzima TF, Huang J, McGinnis KM. Chromatin structure and gene expression changes associated with loss of MOP1 activity in Zea mays. Epigenetics 2014; 9:1047-59. [PMID: 24786611 PMCID: PMC4143406 DOI: 10.4161/epi.29022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Though the mechanisms governing nuclear organization are not well understood, it is apparent that epigenetic modifications coordinately modulate chromatin organization as well as transcription. In maize, MEDIATOR OF PARAMUTATION1 (MOP1) is required for 24 nt siRNA-mediated epigenetic regulation and transcriptional gene silencing via a putative Pol IV- RdDM pathway. To elucidate the mechanisms of nuclear chromatin organization, we investigated the relationship between chromatin structure and transcription in response to loss of MOP1 function. We used a microarray based micrococcal nuclease sensitivity assay to identify genome-wide changes in chromatin structure in mop1-1 immature ears and observed an increase in chromatin accessibility at chromosome arms associated with loss of MOP1 function. Within the many genes misregulated in mop1 mutants, we identified one subset likely to be direct targets of epigenetic transcriptional silencing via Pol-IV RdDM. We found that target specificity for MOP1-mediated RdDM activity is governed by multiple signals that include accumulation of 24 nt siRNAs and the presence of specific classes of gene-proximal transposons, but neither of these attributes alone is sufficient to predict transcriptional misregulation in mop1-1 homozygous mutants. Our results suggest a role for MOP1 in regulation of higher-order chromatin organization where loss of MOP1 activity at a subset of loci triggers a broader cascade of transcriptional consequences and genome-wide changes in chromatin structure.
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Affiliation(s)
- Thelma F Madzima
- Department of Biological Science; Florida State University; Tallahassee, FL USA
| | - Ji Huang
- Department of Biological Science; Florida State University; Tallahassee, FL USA
| | - Karen M McGinnis
- Department of Biological Science; Florida State University; Tallahassee, FL USA
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11
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Fincher JA, Vera DL, Hughes DD, McGinnis KM, Dennis JH, Bass HW. Genome-wide prediction of nucleosome occupancy in maize reveals plant chromatin structural features at genes and other elements at multiple scales. PLANT PHYSIOLOGY 2013; 162:1127-41. [PMID: 23572549 PMCID: PMC3668044 DOI: 10.1104/pp.113.216432] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The nucleosome is a fundamental structural and functional chromatin unit that affects nearly all DNA-templated events in eukaryotic genomes. It is also a biochemical substrate for higher order, cis-acting gene expression codes and the monomeric structural unit for chromatin packaging at multiple scales. To predict the nucleosome landscape of a model plant genome, we used a support vector machine computational algorithm trained on human chromatin to predict the nucleosome occupancy likelihood (NOL) across the maize (Zea mays) genome. Experimentally validated NOL plots provide a novel genomic annotation that highlights gene structures, repetitive elements, and chromosome-scale domains likely to reflect regional gene density. We established a new genome browser (http://www.genomaize.org) for viewing support vector machine-based NOL scores. This annotation provides sequence-based comprehensive coverage across the entire genome, including repetitive genomic regions typically excluded from experimental genomics data. We find that transposable elements often displayed family-specific NOL profiles that included distinct regions, especially near their termini, predicted to have strong affinities for nucleosomes. We examined transcription start site consensus NOL plots for maize gene sets and discovered that most maize genes display a typical +1 nucleosome positioning signal just downstream of the start site but not upstream. This overall lack of a -1 nucleosome positioning signal was also predicted by our method for Arabidopsis (Arabidopsis thaliana) genes and verified by additional analysis of previously published Arabidopsis MNase-Seq data, revealing a general feature of plant promoters. Our study advances plant chromatin research by defining the potential contribution of the DNA sequence to observed nucleosome positioning and provides an invariant baseline annotation against which other genomic data can be compared.
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