1
|
Liu D, Myers EA, Xuan S, Prichard LE, Donahue LI, Ellison EE, Starker CG, Voytas DF. Heritable, multinucleotide deletions in plants using viral delivery of a repair exonuclease and guide RNAs. PLANT PHYSIOLOGY 2024; 194:2229-2239. [PMID: 38243587 DOI: 10.1093/plphys/kiae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 01/21/2024]
Abstract
CRISPR/Cas9-mediated mutagenesis typically results in short insertion/deletion mutations, which are often too small to disrupt the function of cis-acting regulatory elements. Here, we describe a highly efficient in planta gene editing approach called VirTREX2-HLDel that achieves heritable multinucleotide deletions in both protein-coding genes and noncoding DNA regulatory elements. VirTREX2-HLDel uses RNA viruses to deliver both the 3 prime repair exonuclease 2 (TREX2) and single-guide RNAs. Our method enables recovery of multiplexed heritable deletions and increases the heritable gene editing frequency at poorly edited sites. We identified functional conservation and divergence of MICRORNA164 (miR164) in Nicotiana benthamiana and tomato (Solanum lycopersicum) using VirTREX2-HLDel and observed previously uncharacterized phenotypes in plants with large deletions at this locus. Our viral delivery method reduces the need for tissue culture and will accelerate the understanding of protein-coding and regulatory regions in plants.
Collapse
Affiliation(s)
- Degao Liu
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN 55108, USA
| | - Erik A Myers
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN 55108, USA
| | - Shuya Xuan
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN 55108, USA
| | - Lynn E Prichard
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN 55108, USA
| | - Lilee I Donahue
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN 55108, USA
| | - Evan E Ellison
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN 55108, USA
| | - Colby G Starker
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN 55108, USA
| | - Daniel F Voytas
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN 55108, USA
| |
Collapse
|
2
|
Xu Y, Bush SJ, Yang X, Xu L, Wang B, Ye K. Evolutionary analysis of conserved non-coding elements subsequent to whole-genome duplication in opium poppy. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1804-1824. [PMID: 37706612 DOI: 10.1111/tpj.16466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/28/2023] [Accepted: 09/05/2023] [Indexed: 09/15/2023]
Abstract
Whole-genome duplication (WGD) leads to the duplication of both coding and non-coding sequences within an organism's genome, providing an abundant supply of genetic material that can drive evolution, ultimately contributing to plant adaptation and speciation. Although non-coding sequences contain numerous regulatory elements, they have been understudied compared to coding sequences. In order to address this gap, we explored the evolutionary patterns of regulatory sequences, coding sequences and transcriptomes using conserved non-coding elements (CNEs) as regulatory element proxies following the recent WGD event in opium poppy (Papaver somniferum). Our results showed similar evolutionary patterns in subgenomes of regulatory and coding sequences. Specifically, the biased or unbiased retention of coding sequences reflected the same pattern as retention levels in regulatory sequences. Further, the divergence of gene expression patterns mediated by regulatory element variations occurred at a more rapid pace than that of gene coding sequences. However, gene losses were purportedly dependent on relaxed selection pressure in coding sequences. Specifically, the rapid evolution of tissue-specific benzylisoquinoline alkaloid production in P. somniferum was associated with regulatory element changes. The origin of a novel stem-specific ACR, which utilized ancestral cis-elements as templates, is likely to be linked to the evolutionary trajectory behind the transition of the PSMT1-CYP719A21 cluster from high levels of expression solely in P. rhoeas root tissue to its elevated expression in P. somniferum stem tissue. Our findings demonstrate that rapid regulatory element evolution can contribute to the emergence of new phenotypes and provide valuable insights into the high evolvability of regulatory elements.
Collapse
Affiliation(s)
- Yu Xu
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Stephen J Bush
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xinyi Yang
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Linfeng Xu
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Bo Wang
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Kai Ye
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Genome Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| |
Collapse
|
3
|
Pereira WJ, Knaack S, Chakraborty S, Conde D, Folk RA, Triozzi PM, Balmant KM, Dervinis C, Schmidt HW, Ané J, Roy S, Kirst M. Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen-fixing clade. THE NEW PHYTOLOGIST 2022; 234:634-649. [PMID: 35092309 PMCID: PMC9302667 DOI: 10.1111/nph.18006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 01/16/2022] [Indexed: 06/14/2023]
Abstract
Nitrogen is one of the most inaccessible plant nutrients, but certain species have overcome this limitation by establishing symbiotic interactions with nitrogen-fixing bacteria in the root nodule. This root-nodule symbiosis (RNS) is restricted to species within a single clade of angiosperms, suggesting a critical, but undetermined, evolutionary event at the base of this clade. To identify putative regulatory sequences implicated in the evolution of RNS, we evaluated the genomes of 25 species capable of nodulation and identified 3091 conserved noncoding sequences (CNS) in the nitrogen-fixing clade (NFC). We show that the chromatin accessibility of 452 CNS correlates significantly with the regulation of genes responding to lipochitooligosaccharides in Medicago truncatula. These included 38 CNS in proximity to 19 known genes involved in RNS. Five such regions are upstream of MtCRE1, Cytokinin Response Element 1, required to activate a suite of downstream transcription factors necessary for nodulation in M. truncatula. Genetic complementation of an Mtcre1 mutant showed a significant decrease of nodulation in the absence of the five CNS, when they are driving the expression of a functional copy of MtCRE1. CNS identified in the NFC may harbor elements required for the regulation of genes controlling RNS in M. truncatula.
Collapse
Affiliation(s)
- Wendell J. Pereira
- School of Forest, Fisheries and Geomatics SciencesUniversity of FloridaGainesvilleFL32611USA
| | - Sara Knaack
- Wisconsin Institute for DiscoveryUniversity of Wisconsin‐MadisonMadisonWI53715USA
| | | | - Daniel Conde
- School of Forest, Fisheries and Geomatics SciencesUniversity of FloridaGainesvilleFL32611USA
| | - Ryan A. Folk
- Department of Biological SciencesMississippi State UniversityStarkvilleMS39762USA
| | - Paolo M. Triozzi
- School of Forest, Fisheries and Geomatics SciencesUniversity of FloridaGainesvilleFL32611USA
| | - Kelly M. Balmant
- School of Forest, Fisheries and Geomatics SciencesUniversity of FloridaGainesvilleFL32611USA
| | - Christopher Dervinis
- School of Forest, Fisheries and Geomatics SciencesUniversity of FloridaGainesvilleFL32611USA
| | - Henry W. Schmidt
- School of Forest, Fisheries and Geomatics SciencesUniversity of FloridaGainesvilleFL32611USA
| | - Jean‐Michel Ané
- Department of BacteriologyUniversity of Wisconsin‐MadisonMadisonWI53706USA
- Department of AgronomyUniversity of Wisconsin‐MadisonMadisonWI53706USA
| | - Sushmita Roy
- Wisconsin Institute for DiscoveryUniversity of Wisconsin‐MadisonMadisonWI53715USA
- Department of Biostatistics and Medical InformaticsUniversity of Wisconsin‐MadisonMadisonWI53715USA
| | - Matias Kirst
- School of Forest, Fisheries and Geomatics SciencesUniversity of FloridaGainesvilleFL32611USA
- Genetics InstituteUniversity of FloridaGainesvilleFL32611USA
| |
Collapse
|
4
|
Li L, Wu Q, Fang L, Wu K, Li M, Zeng S. Comparative Chloroplast Genomics and Phylogenetic Analysis of Thuniopsis and Closely Related Genera within Coelogyninae (Orchidaceae). Front Genet 2022; 13:850201. [PMID: 35401668 PMCID: PMC8987740 DOI: 10.3389/fgene.2022.850201] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/22/2022] [Indexed: 11/17/2022] Open
Abstract
The genus Thuniopsis was recently proposed for a rare orchid species T. cleistogama formerly classified in the genus Thunia. The relationships between Thuniopsis and its related genera have not yet been conclusively resolved. Recognition of the genus provides a new perspective to illustrate the morphological diversity and plastome evolution within Coelogyninae. In this study, we sequenced and assembled complete chloroplast (cp) genomes for three accessions of Thuniopsis cleistogama and two accessions of Thunia alba. A total of 135 genes were annotated for each cp genome, including 89 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The ENC-plot and neutrality plot analyses revealed that natural selection dominated over mutation pressure in their evolutionary process. Specially, we found that selection played a vital role in shaping the codon usage in Thunia alba cp genome. General characteristics of the cp genomes were further analyzed and compared with those published plastomes of four other related species. Despite the conserved organization and structure, the whole individual cp genome size ranged from 158,394 bp to 159,950 bp. In all the examined plastomes, sequences in the inverted repeat (IR) regions were more conserved than those in the small single copy (SSC) and large single copy (LSC) regions. However, close examination identified contraction and expansion of the IR/SSC boundary regions, which might be the main reason for the cp genome size variation. Our comparative analysis of the cp genomes revealed that single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) provided valuable information for identifying genetic variations within and among genera. Furthermore, sequence variations in the protein-coding regions were more conserved than those in the non-coding regions. We selected eight divergence hotspots with nucleotide sequence diversities (Pi values) higher than 0.08. Most of these polymorphisms were located in the intergenic regions. Phylogenomic analyses recovered largely congruent relationships among major clades and strongly supported the monophyly of Thuniopsis. The results obtained in this study can improve our understanding of the classification of this enigmatic genus. The chloroplast genomic data presented here provide valuable insights into the phylogeny and evolutionary patterns of the Coelogyninae as well as the orchids as a whole.
Collapse
Affiliation(s)
- Lin Li
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Qiuping Wu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lin Fang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Kunlin Wu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Mingzhi Li
- Guangzhou Bio and Data Biotechnology Co., Ltd., Guangzhou, China
| | - Songjun Zeng
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- *Correspondence: Songjun Zeng,
| |
Collapse
|
5
|
Yocca AE, Edger PP. Current status and future perspectives on the evolution of cis-regulatory elements in plants. CURRENT OPINION IN PLANT BIOLOGY 2022; 65:102139. [PMID: 34837823 DOI: 10.1016/j.pbi.2021.102139] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/20/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
Cis-regulatory elements (CREs) are short stretches (∼5-15 base pairs) of DNA capable of being bound by a transcription factor and influencing the expression of nearby genes. These regions are of great interest to anyone studying the relationship between phenotype and genotype as these sequences often dictate genes' spatio-temporal expression. Indeed, several associative signals between genotype and phenotype are known to lie outside of protein-coding regions. Therefore, a key to understand evolutionary biology requires their characterization in current and future genome assemblies. In this review, we cover some recent examples of how CRE variation contributes to phenotypic evolution, discuss evidence for the selective pressures experienced by non-coding regions of the genome, and consider several studies on accessible chromatin regions in plants and what they can tell us about CREs. Finally, we discuss how current advances in sequencing technologies will improve our knowledge of CRE variation.
Collapse
Affiliation(s)
- Alan E Yocca
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA; Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA; Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, 48824, USA.
| |
Collapse
|
6
|
Kramer MC, Kim HJ, Palos KR, Garcia BA, Lyons E, Beilstein MA, Nelson ADL, Gregory BD. A Conserved Long Intergenic Non-coding RNA Containing snoRNA Sequences, lncCOBRA1, Affects Arabidopsis Germination and Development. FRONTIERS IN PLANT SCIENCE 2022; 13:906603. [PMID: 35693169 PMCID: PMC9175010 DOI: 10.3389/fpls.2022.906603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/04/2022] [Indexed: 05/04/2023]
Abstract
Long non-coding RNAs (lncRNAs) are an increasingly studied group of non-protein coding transcripts with a wide variety of molecular functions gaining attention for their roles in numerous biological processes. Nearly 6,000 lncRNAs have been identified in Arabidopsis thaliana but many have yet to be studied. Here, we examine a class of previously uncharacterized lncRNAs termed CONSERVED IN BRASSICA RAPA (lncCOBRA) transcripts that were previously identified for their high level of sequence conservation in the related crop species Brassica rapa, their nuclear-localization and protein-bound nature. In particular, we focus on lncCOBRA1 and demonstrate that its abundance is highly tissue and developmental specific, with particularly high levels early in germination. lncCOBRA1 contains two snoRNAs domains within it, making it the first sno-lincRNA example in a non-mammalian system. However, we find that it is processed differently than its mammalian counterparts. We further show that plants lacking lncCOBRA1 display patterns of delayed germination and are overall smaller than wild-type plants. Lastly, we identify the proteins that interact with lncCOBRA1 and propose a novel mechanism of lincRNA action in which it may act as a scaffold with the RACK1A protein to regulate germination and development, possibly through a role in ribosome biogenesis.
Collapse
Affiliation(s)
- Marianne C. Kramer
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Hee Jong Kim
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA, United States
| | - Kyle R. Palos
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Eric Lyons
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States
- CyVerse Inc., Tucson, AZ, United States
| | - Mark A. Beilstein
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States
| | | | - Brian D. Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- *Correspondence: Brian D. Gregory,
| |
Collapse
|
7
|
Zemlyanskaya EV, Dolgikh VA, Levitsky VG, Mironova V. Transcriptional regulation in plants: Using omics data to crack the cis-regulatory code. CURRENT OPINION IN PLANT BIOLOGY 2021; 63:102058. [PMID: 34098218 DOI: 10.1016/j.pbi.2021.102058] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 06/12/2023]
Abstract
Innovative omics technologies, advanced bioinformatics, and machine learning methods are rapidly becoming integral tools for plant functional genomics, with tremendous recent advances made in this field. In transcriptional regulation, an initial lag in the accumulation of plant omics data relative to that of animals stimulated the development of computational methods capable of extracting maximum information from the available data sets. Recent comprehensive studies of transcription factor-binding profiles in Arabidopsis and maize and the accumulation of uniformly processed omics data in public databases have brought plant biologists into the big leagues, with many cutting-edge methods available. Here, we summarize the state-of-the-art bioinformatics approaches used to predict or infer the cis-regulatory code behind transcriptional gene regulation, focusing on their plant research applications.
Collapse
Affiliation(s)
- Elena V Zemlyanskaya
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia; Novosibirsk State University, Novosibirsk, 630090, Russia.
| | - Vladislav A Dolgikh
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Victor G Levitsky
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia; Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Victoria Mironova
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia; Novosibirsk State University, Novosibirsk, 630090, Russia; Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, the Netherlands.
| |
Collapse
|
8
|
Leypold NA, Speicher MR. Evolutionary conservation in noncoding genomic regions. Trends Genet 2021; 37:903-918. [PMID: 34238591 DOI: 10.1016/j.tig.2021.06.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/25/2021] [Accepted: 06/07/2021] [Indexed: 12/28/2022]
Abstract
Humans may share more genomic commonalities with other species than previously thought. According to current estimates, ~5% of the human genome is functionally constrained, which is a much larger fraction than the ~1.5% occupied by annotated protein-coding genes. Hence, ~3.5% of the human genome comprises likely functional conserved noncoding elements (CNEs) preserved among organisms, whose common ancestors existed throughout hundreds of millions of years of evolution. As whole-genome sequencing emerges as a standard procedure in genetic analyses, interpretation of variations in CNEs, including the elucidation of mechanistic and functional roles, becomes a necessity. Here, we discuss the phenomenon of noncoding conservation via four dimensions (sequence, regulatory conservation, spatiotemporal expression, and structure) and the potential significance of CNEs in phenotype variation and disease.
Collapse
Affiliation(s)
- Nicole A Leypold
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, 8010 Graz, Austria.
| | - Michael R Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, 8010 Graz, Austria; BioTechMed-Graz, Graz, Austria.
| |
Collapse
|
9
|
Fang J, Guo T, Xie Z, Chun Y, Zhao J, Peng L, Zafar SA, Yuan S, Xiao L, Li X. The URL1-ROC5-TPL2 transcriptional repressor complex represses the ACL1 gene to modulate leaf rolling in rice. PLANT PHYSIOLOGY 2021; 185:1722-1744. [PMID: 33793928 PMCID: PMC8133684 DOI: 10.1093/plphys/kiaa121] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 12/13/2020] [Indexed: 05/31/2023]
Abstract
Moderate leaf rolling is beneficial for leaf erectness and compact plant architecture. However, our understanding regarding the molecular mechanisms of leaf rolling is still limited. Here, we characterized a semi-dominant rice (Oryza sativa L.) mutant upward rolled leaf 1 (Url1) showing adaxially rolled leaves due to a decrease in the number and size of bulliform cells. Map-based cloning revealed that URL1 encodes the homeodomain-leucine zipper (HD-Zip) IV family member RICE OUTERMOST CELL-SPECIFIC 8 (ROC8). A single-base substitution in one of the two conserved complementary motifs unique to the 3'-untranslated region of this family enhanced URL1 mRNA stability and abundance in the Url1 mutant. URL1 (UPWARD ROLLED LEAF1) contains an ethylene-responsive element binding factor-associated amphiphilic repression motif and functions as a transcriptional repressor via interaction with the TOPLESS co-repressor OsTPL2. Rather than homodimerizing, URL1 heterodimerizes with another HD-ZIP IV member ROC5. URL1 could bind directly to the promoter and suppress the expression of abaxially curled leaf 1 (ACL1), a positive regulator of bulliform cell development. Knockout of OsTPL2 or ROC5 or overexpression of ACL1 in the Url1 mutant partially suppressed the leaf-rolling phenotype. Our results reveal a regulatory network whereby a transcriptional repression complex composed of URL1, ROC5, and the transcriptional corepressor TPL2 suppresses the expression of the ACL1 gene, thus modulating bulliform cell development and leaf rolling in rice.
Collapse
Affiliation(s)
- Jingjing Fang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tingting Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Hunan Provincial Key Laboratory of Phytohormones, Hunan Provincial Key Laboratory for Crop Germplasm Innovation and Utilization, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
- College of Agriculture and Biotechnology, Hunan University of Humanities, Science and Technology, Loudi 417000, China
| | - Zhiwei Xie
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yan Chun
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jinfeng Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lixiang Peng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Syed Adeel Zafar
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shoujiang Yuan
- Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Langtao Xiao
- Hunan Provincial Key Laboratory of Phytohormones, Hunan Provincial Key Laboratory for Crop Germplasm Innovation and Utilization, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Xueyong Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| |
Collapse
|
10
|
Yocca AE, Lu Z, Schmitz RJ, Freeling M, Edger PP. Evolution of Conserved Noncoding Sequences in Arabidopsis thaliana. Mol Biol Evol 2021; 38:2692-2703. [PMID: 33565589 PMCID: PMC8233505 DOI: 10.1093/molbev/msab042] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Recent pangenome studies have revealed a large fraction of the gene content within a species exhibits presence-absence variation (PAV). However, coding regions alone provide an incomplete assessment of functional genomic sequence variation at the species level. Little to no attention has been paid to noncoding regulatory regions in pangenome studies, though these sequences directly modulate gene expression and phenotype. To uncover regulatory genetic variation, we generated chromosome-scale genome assemblies for thirty Arabidopsis thaliana accessions from multiple distinct habitats and characterized species level variation in Conserved Noncoding Sequences (CNS). Our analyses uncovered not only PAV and positional variation (PosV) but that diversity in CNS is nonrandom, with variants shared across different accessions. Using evolutionary analyses and chromatin accessibility data, we provide further evidence supporting roles for conserved and variable CNS in gene regulation. Additionally, our data suggests that transposable elements contribute to CNS variation. Characterizing species-level diversity in all functional genomic sequences may later uncover previously unknown mechanistic links between genotype and phenotype.
Collapse
Affiliation(s)
- Alan E Yocca
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA.,Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Zefu Lu
- Department of Genetics, University of Georgia, Athens, GA, USA
| | | | - Michael Freeling
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, USA.,Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI, USA
| |
Collapse
|
11
|
Molecular and evolutionary processes generating variation in gene expression. Nat Rev Genet 2020; 22:203-215. [PMID: 33268840 DOI: 10.1038/s41576-020-00304-w] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2020] [Indexed: 12/18/2022]
Abstract
Heritable variation in gene expression is common within and between species. This variation arises from mutations that alter the form or function of molecular gene regulatory networks that are then filtered by natural selection. High-throughput methods for introducing mutations and characterizing their cis- and trans-regulatory effects on gene expression (particularly, transcription) are revealing how different molecular mechanisms generate regulatory variation, and studies comparing these mutational effects with variation seen in the wild are teasing apart the role of neutral and non-neutral evolutionary processes. This integration of molecular and evolutionary biology allows us to understand how the variation in gene expression we see today came to be and to predict how it is most likely to evolve in the future.
Collapse
|
12
|
Han J, Wang P, Wang Q, Lin Q, Chen Z, Yu G, Miao C, Dao Y, Wu R, Schnable JC, Tang H, Wang K. Genome-Wide Characterization of DNase I-Hypersensitive Sites and Cold Response Regulatory Landscapes in Grasses. THE PLANT CELL 2020; 32:2457-2473. [PMID: 32471863 PMCID: PMC7401015 DOI: 10.1105/tpc.19.00716] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 05/11/2020] [Accepted: 05/23/2020] [Indexed: 05/05/2023]
Abstract
Deep sequencing of DNase-I treated chromatin (DNase-seq) can be used to identify DNase I-hypersensitive sites (DHSs) and facilitates genome-scale mining of de novo cis-regulatory DNA elements. Here, we adapted DNase-seq to generate genome-wide maps of DHSs using control and cold-treated leaf, stem, and root tissues of three widely studied grass species: Brachypodium distachyon, foxtail millet (Setaria italica), and sorghum (Sorghum bicolor). Functional validation demonstrated that 12 of 15 DHSs drove reporter gene expression in transiently transgenic B. distachyon protoplasts. DHSs under both normal and cold treatment substantially differed among tissues and species. Intriguingly, the putative DHS-derived transcription factors (TFs) are largely colocated among tissues and species and include 17 ubiquitous motifs covering all grass taxa and all tissues examined in this study. This feature allowed us to reconstruct a regulatory network that responds to cold stress. Ethylene-responsive TFs SHINE3, ERF2, and ERF9 occurred frequently in cold feedback loops in the tissues examined, pointing to their possible roles in the regulatory network. Overall, we provide experimental annotation of 322,713 DHSs and 93 derived cold-response TF binding motifs in multiple grasses, which could serve as a valuable resource for elucidating the transcriptional networks that function in the cold-stress response and other physiological processes.
Collapse
Affiliation(s)
- Jinlei Han
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Pengxi Wang
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Qiongli Wang
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Qingfang Lin
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Zhiyong Chen
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Guangrun Yu
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Chenyong Miao
- Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
| | - Yihang Dao
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Ruoxi Wu
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - James C Schnable
- Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
| | - Haibao Tang
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Kai Wang
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| |
Collapse
|
13
|
Tian F, Yang DC, Meng YQ, Jin J, Gao G. PlantRegMap: charting functional regulatory maps in plants. Nucleic Acids Res 2020; 48:D1104-D1113. [PMID: 31701126 PMCID: PMC7145545 DOI: 10.1093/nar/gkz1020] [Citation(s) in RCA: 275] [Impact Index Per Article: 68.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/17/2019] [Accepted: 10/21/2019] [Indexed: 11/18/2022] Open
Abstract
With the goal of charting plant transcriptional regulatory maps (i.e. transcription factors (TFs), cis-elements and interactions between them), we have upgraded the TF-centred database PlantTFDB (http://planttfdb.cbi.pku.edu.cn/) to a plant regulatory data and analysis platform PlantRegMap (http://plantregmap.cbi.pku.edu.cn/) over the past three years. In this version, we updated the annotations for the previously collected TFs and set up a new section, ‘extended TF repertoires’ (TFext), to allow users prompt access to the TF repertoires of newly sequenced species. In addition to our regular TF updates, we are dedicated to updating the data on cis-elements and functional interactions between TFs and cis-elements. We established genome-wide conservation landscapes for 63 representative plants and then developed an algorithm, FunTFBS, to screen for functional regulatory elements and interactions by coupling the base-varied binding affinities of TFs with the evolutionary footprints on their binding sites. Using the FunTFBS algorithm and the conservation landscapes, we further identified over 20 million functional TF binding sites (TFBSs) and two million functional interactions for 21 346 TFs, charting the functional regulatory maps of these 63 plants. These resources are publicly available at PlantRegMap (http://plantregmap.cbi.pku.edu.cn/) and a cloud-based mirror (http://plantregmap.gao-lab.org/), providing the plant research community with valuable resources for decoding plant transcriptional regulatory systems.
Collapse
Affiliation(s)
- Feng Tian
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, China.,Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - De-Chang Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, China.,Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China
| | - Yu-Qi Meng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, China.,Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China
| | - Jinpu Jin
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, China.,Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China
| | - Ge Gao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, China.,Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing 100871, China
| |
Collapse
|
14
|
Li Q, Sapkota M, van der Knaap E. Perspectives of CRISPR/Cas-mediated cis-engineering in horticulture: unlocking the neglected potential for crop improvement. HORTICULTURE RESEARCH 2020; 7:36. [PMID: 32194972 PMCID: PMC7072075 DOI: 10.1038/s41438-020-0258-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/09/2020] [Accepted: 02/11/2020] [Indexed: 05/14/2023]
Abstract
Directed breeding of horticultural crops is essential for increasing yield, nutritional content, and consumer-valued characteristics such as shape and color of the produce. However, limited genetic diversity restricts the amount of crop improvement that can be achieved through conventional breeding approaches. Natural genetic changes in cis-regulatory regions of genes play important roles in shaping phenotypic diversity by altering their expression. Utilization of CRISPR/Cas editing in crop species can accelerate crop improvement through the introduction of genetic variation in a targeted manner. The advent of CRISPR/Cas-mediated cis-regulatory region engineering (cis-engineering) provides a more refined method for modulating gene expression and creating phenotypic diversity to benefit crop improvement. Here, we focus on the current applications of CRISPR/Cas-mediated cis-engineering in horticultural crops. We describe strategies and limitations for its use in crop improvement, including de novo cis-regulatory element (CRE) discovery, precise genome editing, and transgene-free genome editing. In addition, we discuss the challenges and prospects regarding current technologies and achievements. CRISPR/Cas-mediated cis-engineering is a critical tool for generating horticultural crops that are better able to adapt to climate change and providing food for an increasing world population.
Collapse
Affiliation(s)
- Qiang Li
- College of Horticultural Science and Engineering, Shandong Agricultural University, Tai’an, China
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA USA
| | - Manoj Sapkota
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA USA
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA USA
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA USA
- Department of Horticulture, University of Georgia, Athens, GA USA
| |
Collapse
|
15
|
Wang HLV, Chekanova JA. Novel mRNAs 3' end-associated cis-regulatory elements with epigenomic signatures of mammalian enhancers in the Arabidopsis genome. RNA (NEW YORK, N.Y.) 2019; 25:1242-1258. [PMID: 31311821 PMCID: PMC6800480 DOI: 10.1261/rna.071209.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 07/04/2019] [Indexed: 06/10/2023]
Abstract
The precise spatial and temporal control of gene expression requires the coordinated action of genomic cis-regulatory elements (CREs), including transcriptional enhancers. However, our knowledge of enhancers in plants remains rudimentary and only a few plant enhancers have been experimentally defined. Here, we screened the Arabidopsis thaliana genome and identified >1900 unique candidate CREs that carry the genomic signatures of mammalian enhancers. These were termed putative enhancer-like elements (PEs). Nearly all PEs are intragenic and, unexpectedly, most associate with the 3' ends of protein-coding genes. PEs are hotspots for transcription factor binding and harbor motifs resembling cleavage/polyadenylation signals, potentially coupling 3' end processing to the transcriptional regulation of other genes. Hi-C data showed that 24% of PEs are located at regions that can interact intrachromosomally with other protein-coding genes and, surprisingly, many of these target genes interact with PEs through their 3' UTRs. Examination of the genomes of 1135 sequenced Arabidopsis accessions showed that PEs are conserved. Our findings suggest that the identified PEs may serve as transcriptional enhancers and sites for mRNA 3' end processing, and constitute a novel group of CREs in Arabidopsis.
Collapse
Affiliation(s)
- Hsiao-Lin V Wang
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Julia A Chekanova
- Mycological Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| |
Collapse
|
16
|
Rubin BER, Jones BM, Hunt BG, Kocher SD. Rate variation in the evolution of non-coding DNA associated with social evolution in bees. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180247. [PMID: 31154980 PMCID: PMC6560270 DOI: 10.1098/rstb.2018.0247] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2019] [Indexed: 11/12/2022] Open
Abstract
The evolutionary origins of eusociality represent increases in complexity from individual to caste-based, group reproduction. These behavioural transitions have been hypothesized to go hand in hand with an increased ability to regulate when and where genes are expressed. Bees have convergently evolved eusociality up to five times, providing a framework to test this hypothesis. To examine potential links between putative gene regulatory elements and social evolution, we compare alignable, non-coding sequences in 11 diverse bee species, encompassing three independent origins of reproductive division of labour and two elaborations of eusocial complexity. We find that rates of evolution in a number of non-coding sequences correlate with key social transitions in bees. Interestingly, while we find little evidence for convergent rate changes associated with independent origins of social behaviour, a number of molecular pathways exhibit convergent rate changes in conjunction with subsequent elaborations of social organization. We also present evidence that many novel non-coding regions may have been recruited alongside the origin of sociality in corbiculate bees; these loci could represent gene regulatory elements associated with division of labour within this group. Thus, our findings are consistent with the hypothesis that gene regulatory innovations are associated with the evolution of eusociality and illustrate how a thorough examination of both coding and non-coding sequence can provide a more complete understanding of the molecular mechanisms underlying behavioural evolution. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
Collapse
Affiliation(s)
- Benjamin E. R. Rubin
- Department of Ecology and Evolutionary Biology; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Beryl M. Jones
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois, Urbana, IL, USA
| | - Brendan G. Hunt
- Department of Entomology, University of Georgia, Griffin, GA, USA
| | - Sarah D. Kocher
- Department of Ecology and Evolutionary Biology; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| |
Collapse
|
17
|
Pandiarajan R, Grover A. In vivo promoter engineering in plants: Are we ready? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 277:132-138. [PMID: 30466578 DOI: 10.1016/j.plantsci.2018.10.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 09/13/2018] [Accepted: 10/11/2018] [Indexed: 05/27/2023]
Abstract
Engineering plant promoter sequence for optimal expression of a gene has been a long standing goal for plant scientists. In recent times, Sequence Specific Nucleases (SSNs) like CRISPR/Cas9 are enabling researchers to achieve this goal, in vivo in the genome. It is well known that SSNs have met with unprecedented success in rapid transgene free crop improvement largely by targeting the coding sequence. Here, we discuss the strategies being employed by plant scientists in targeting SSNs to non-coding promoter regions/Cis Regulatory Elements (CRE). We collectively refer all such endeavors as in vivo promoter engineering (IPE). We further classify the IPE efforts into CRE addition, CRE deletion/disruption, promoter swap/insertion and targeted promoter polymorphism. Till date, IPE has proven useful in altering plant architecture in tomato, developing resistance against Xanthomonas sp in rice and citrus, and engineering drought tolerance in maize. However it is quite challenging to achieve predictable changes in gene expression using IPE at this point. In future years, data generated from high throughput techniques to investigate non coding genome may immensely augment the efforts in this direction. As IPE does not involve addition of the transgene for modifying crop traits, it will be relatively more conducive to public acceptance in crop improvement programs.
Collapse
Affiliation(s)
- Ramakrishnan Pandiarajan
- Department of Plant Molecular Biology, South Campus, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021, India
| | - Anil Grover
- Department of Plant Molecular Biology, South Campus, University of Delhi, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021, India.
| |
Collapse
|
18
|
Marinov GK, Kundaje A. ChIP-ping the branches of the tree: functional genomics and the evolution of eukaryotic gene regulation. Brief Funct Genomics 2018; 17:116-137. [PMID: 29529131 PMCID: PMC5889016 DOI: 10.1093/bfgp/ely004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Advances in the methods for detecting protein-DNA interactions have played a key role in determining the directions of research into the mechanisms of transcriptional regulation. The most recent major technological transformation happened a decade ago, with the move from using tiling arrays [chromatin immunoprecipitation (ChIP)-on-Chip] to high-throughput sequencing (ChIP-seq) as a readout for ChIP assays. In addition to the numerous other ways in which it is superior to arrays, by eliminating the need to design and manufacture them, sequencing also opened the door to carrying out comparative analyses of genome-wide transcription factor occupancy across species and studying chromatin biology in previously less accessible model and nonmodel organisms, thus allowing us to understand the evolution and diversity of regulatory mechanisms in unprecedented detail. Here, we review the biological insights obtained from such studies in recent years and discuss anticipated future developments in the field.
Collapse
Affiliation(s)
- Georgi K Marinov
- Corresponding author: Georgi K. Marinov, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA. E-mail:
| | | |
Collapse
|
19
|
Liang P, Saqib HSA, Zhang X, Zhang L, Tang H. Single-Base Resolution Map of Evolutionary Constraints and Annotation of Conserved Elements across Major Grass Genomes. Genome Biol Evol 2018; 10:473-488. [PMID: 29378032 PMCID: PMC5798027 DOI: 10.1093/gbe/evy006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2018] [Indexed: 12/20/2022] Open
Abstract
Conserved noncoding sequences (CNSs) are evolutionarily conserved DNA sequences that do not encode proteins but may have potential regulatory roles in gene expression. CNS in crop genomes could be linked to many important agronomic traits and ecological adaptations. Compared with the relatively mature exon annotation protocols, efficient methods are lacking to predict the location of noncoding sequences in the plant genomes. We implemented a computational pipeline that is tailored to the comparisons of plant genomes, yielding a large number of conserved sequences using rice genome as the reference. In this study, we used 17 published grass genomes, along with five monocot genomes as well as the basal angiosperm genome of Amborella trichopoda. Genome alignments among these genomes suggest that at least 12.05% of the rice genome appears to be evolving under constraints in the Poaceae lineage, with close to half of the evolutionarily constrained sequences located outside protein-coding regions. We found evidence for purifying selection acting on the conserved sequences by analyzing segregating SNPs within the rice population. Furthermore, we found that known functional motifs were significantly enriched within CNS, with many motifs associated with the preferred binding of ubiquitous transcription factors. The conserved elements that we have curated are accessible through our public database and the JBrowse server. In-depth functional annotations and evolutionary dynamics of the identified conserved sequences provide a solid foundation for studying gene regulation, genome evolution, as well as to inform gene isolation for cereal biologists.
Collapse
Affiliation(s)
- Pingping Liang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Center for Genomics and Biotechnology, Ministry of Education; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, China
| | - Hafiz Sohaib Ahmed Saqib
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xingtan Zhang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Center for Genomics and Biotechnology, Ministry of Education; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liangsheng Zhang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Center for Genomics and Biotechnology, Ministry of Education; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Haibao Tang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Center for Genomics and Biotechnology, Ministry of Education; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
20
|
Polychronopoulos D, King JWD, Nash AJ, Tan G, Lenhard B. Conserved non-coding elements: developmental gene regulation meets genome organization. Nucleic Acids Res 2018; 45:12611-12624. [PMID: 29121339 PMCID: PMC5728398 DOI: 10.1093/nar/gkx1074] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/24/2017] [Indexed: 12/20/2022] Open
Abstract
Comparative genomics has revealed a class of non-protein-coding genomic sequences that display an extraordinary degree of conservation between two or more organisms, regularly exceeding that found within protein-coding exons. These elements, collectively referred to as conserved non-coding elements (CNEs), are non-randomly distributed across chromosomes and tend to cluster in the vicinity of genes with regulatory roles in multicellular development and differentiation. CNEs are organized into functional ensembles called genomic regulatory blocks–dense clusters of elements that collectively coordinate the expression of shared target genes, and whose span in many cases coincides with topologically associated domains. CNEs display sequence properties that set them apart from other sequences under constraint, and have recently been proposed as useful markers for the reconstruction of the evolutionary history of organisms. Disruption of several of these elements is known to contribute to diseases linked with development, and cancer. The emergence, evolutionary dynamics and functions of CNEs still remain poorly understood, and new approaches are required to enable comprehensive CNE identification and characterization. Here, we review current knowledge and identify challenges that need to be tackled to resolve the impasse in understanding extreme non-coding conservation.
Collapse
Affiliation(s)
- Dimitris Polychronopoulos
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - James W D King
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Alexander J Nash
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Ge Tan
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Boris Lenhard
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK.,Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway
| |
Collapse
|
21
|
Edwards SV, Cloutier A, Baker AJ. Conserved Nonexonic Elements: A Novel Class of Marker for Phylogenomics. Syst Biol 2017; 66:1028-1044. [PMID: 28637293 PMCID: PMC5790140 DOI: 10.1093/sysbio/syx058] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 06/03/2017] [Accepted: 06/06/2017] [Indexed: 01/12/2023] Open
Abstract
Noncoding markers have a particular appeal as tools for phylogenomic analysis because, at least in vertebrates, they appear less subject to strong variation in GC content among lineages. Thus far, ultraconserved elements (UCEs) and introns have been the most widely used noncoding markers. Here we analyze and study the evolutionary properties of a new type of noncoding marker, conserved nonexonic elements (CNEEs), which consists of noncoding elements that are estimated to evolve slower than the neutral rate across a set of species. Although they often include UCEs, CNEEs are distinct from UCEs because they are not ultraconserved, and, most importantly, the core region alone is analyzed, rather than both the core and its flanking regions. Using a data set of 16 birds plus an alligator outgroup, and ∼3600-∼3800 loci per marker type, we found that although CNEEs were less variable than bioinformatically derived UCEs or introns and in some cases exhibited a slower approach to branch resolution as determined by phylogenomic subsampling, the quality of CNEE alignments was superior to those of the other markers, with fewer gaps and missing species. Phylogenetic resolution using coalescent approaches was comparable among the three marker types, with most nodes being fully and congruently resolved. Comparison of phylogenetic results across the three marker types indicated that one branch, the sister group to the passerine + falcon clade, was resolved differently and with moderate (>70%) bootstrap support between CNEEs and UCEs or introns. Overall, CNEEs appear to be promising as phylogenomic markers, yielding phylogenetic resolution as high as for UCEs and introns but with fewer gaps, less ambiguity in alignments and with patterns of nucleotide substitution more consistent with the assumptions of commonly used methods of phylogenetic analysis.
Collapse
Affiliation(s)
- Scott V. Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, 26 Oxford Street, Harvard University, Cambridge, MA 02138 USA
| | - Alison Cloutier
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, 26 Oxford Street, Harvard University, Cambridge, MA 02138 USA
- Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, Ontario, M5S 2C6 Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcox Street, Toronto, Ontario, M5S 3B2 Canada
| | - Allan J. Baker
- Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, Ontario, M5S 2C6 Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcox Street, Toronto, Ontario, M5S 3B2 Canada
| |
Collapse
|
22
|
Buffry AD, Mendes CC, McGregor AP. The Functionality and Evolution of Eukaryotic Transcriptional Enhancers. ADVANCES IN GENETICS 2016; 96:143-206. [PMID: 27968730 DOI: 10.1016/bs.adgen.2016.08.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Enhancers regulate precise spatial and temporal patterns of gene expression in eukaryotes and, moreover, evolutionary changes in these modular cis-regulatory elements may represent the predominant genetic basis for phenotypic evolution. Here, we review approaches to identify and functionally analyze enhancers and their transcription factor binding sites, including assay for transposable-accessible chromatin-sequencing (ATAC-Seq) and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9, respectively. We also explore enhancer functionality, including how transcription factor binding sites combine to regulate transcription, as well as research on shadow and super enhancers, and how enhancers can act over great distances and even in trans. Finally, we discuss recent theoretical and empirical data on how transcription factor binding sites and enhancers evolve. This includes how the function of enhancers is maintained despite the turnover of transcription factor binding sites as well as reviewing studies where mutations in enhancers have been shown to underlie morphological change.
Collapse
Affiliation(s)
- A D Buffry
- Oxford Brookes University, Oxford, United Kingdom
| | - C C Mendes
- Oxford Brookes University, Oxford, United Kingdom
| | - A P McGregor
- Oxford Brookes University, Oxford, United Kingdom
| |
Collapse
|
23
|
Banf M, Rhee SY. Computational inference of gene regulatory networks: Approaches, limitations and opportunities. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:41-52. [PMID: 27641093 DOI: 10.1016/j.bbagrm.2016.09.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 09/08/2016] [Accepted: 09/08/2016] [Indexed: 10/21/2022]
Abstract
Gene regulatory networks lie at the core of cell function control. In E. coli and S. cerevisiae, the study of gene regulatory networks has led to the discovery of regulatory mechanisms responsible for the control of cell growth, differentiation and responses to environmental stimuli. In plants, computational rendering of gene regulatory networks is gaining momentum, thanks to the recent availability of high-quality genomes and transcriptomes and development of computational network inference approaches. Here, we review current techniques, challenges and trends in gene regulatory network inference and highlight challenges and opportunities for plant science. We provide plant-specific application examples to guide researchers in selecting methodologies that suit their particular research questions. Given the interdisciplinary nature of gene regulatory network inference, we tried to cater to both biologists and computer scientists to help them engage in a dialogue about concepts and caveats in network inference. Specifically, we discuss problems and opportunities in heterogeneous data integration for eukaryotic organisms and common caveats to be considered during network model evaluation. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
Collapse
Affiliation(s)
- Michael Banf
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford 93405, United States.
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford 93405, United States.
| |
Collapse
|
24
|
Van de Velde J, Van Bel M, Vaneechoutte D, Vandepoele K. A Collection of Conserved Noncoding Sequences to Study Gene Regulation in Flowering Plants. PLANT PHYSIOLOGY 2016; 171:2586-98. [PMID: 27261064 PMCID: PMC4972296 DOI: 10.1104/pp.16.00821] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 05/31/2016] [Indexed: 05/03/2023]
Abstract
Transcription factors (TFs) regulate gene expression by binding cis-regulatory elements, of which the identification remains an ongoing challenge owing to the prevalence of large numbers of nonfunctional TF binding sites. Powerful comparative genomics methods, such as phylogenetic footprinting, can be used for the detection of conserved noncoding sequences (CNSs), which are functionally constrained and can greatly help in reducing the number of false-positive elements. In this study, we applied a phylogenetic footprinting approach for the identification of CNSs in 10 dicot plants, yielding 1,032,291 CNSs associated with 243,187 genes. To annotate CNSs with TF binding sites, we made use of binding site information for 642 TFs originating from 35 TF families in Arabidopsis (Arabidopsis thaliana). In three species, the identified CNSs were evaluated using TF chromatin immunoprecipitation sequencing data, resulting in significant overlap for the majority of data sets. To identify ultraconserved CNSs, we included genomes of additional plant families and identified 715 binding sites for 501 genes conserved in dicots, monocots, mosses, and green algae. Additionally, we found that genes that are part of conserved mini-regulons have a higher coherence in their expression profile than other divergent gene pairs. All identified CNSs were integrated in the PLAZA 3.0 Dicots comparative genomics platform (http://bioinformatics.psb.ugent.be/plaza/versions/plaza_v3_dicots/) together with new functionalities facilitating the exploration of conserved cis-regulatory elements and their associated genes. The availability of this data set in a user-friendly platform enables the exploration of functional noncoding DNA to study gene regulation in a variety of plant species, including crops.
Collapse
Affiliation(s)
- Jan Van de Velde
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (J.V.d.V., M.V.B., D.V., K.V.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (J.V.d.V., M.V.B., D.V., K.V.)
| | - Michiel Van Bel
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (J.V.d.V., M.V.B., D.V., K.V.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (J.V.d.V., M.V.B., D.V., K.V.)
| | - Dries Vaneechoutte
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (J.V.d.V., M.V.B., D.V., K.V.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (J.V.d.V., M.V.B., D.V., K.V.)
| | - Klaas Vandepoele
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (J.V.d.V., M.V.B., D.V., K.V.); andDepartment of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (J.V.d.V., M.V.B., D.V., K.V.)
| |
Collapse
|
25
|
Hoffmann RD, Palmgren M. Purifying selection acts on coding and non-coding sequences of paralogous genes in Arabidopsis thaliana. BMC Genomics 2016; 17:456. [PMID: 27296049 PMCID: PMC4906602 DOI: 10.1186/s12864-016-2803-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 05/27/2016] [Indexed: 01/13/2023] Open
Abstract
Background Whole-genome duplications in the ancestors of many diverse species provided the genetic material for evolutionary novelty. Several models explain the retention of paralogous genes. However, how these models are reflected in the evolution of coding and non-coding sequences of paralogous genes is unknown. Results Here, we analyzed the coding and non-coding sequences of paralogous genes in Arabidopsis thaliana and compared these sequences with those of orthologous genes in Arabidopsis lyrata. Paralogs with lower expression than their duplicate had more nonsynonymous substitutions, were more likely to fractionate, and exhibited less similar expression patterns with their orthologs in the other species. Also, lower-expressed genes had greater tissue specificity. Orthologous conserved non-coding sequences in the promoters, introns, and 3′ untranslated regions were less abundant at lower-expressed genes compared to their higher-expressed paralogs. A gene ontology (GO) term enrichment analysis showed that paralogs with similar expression levels were enriched in GO terms related to ribosomes, whereas paralogs with different expression levels were enriched in terms associated with stress responses. Conclusions Loss of conserved non-coding sequences in one gene of a paralogous gene pair correlates with reduced expression levels that are more tissue specific. Together with increased mutation rates in the coding sequences, this suggests that similar forces of purifying selection act on coding and non-coding sequences. We propose that coding and non-coding sequences evolve concurrently following gene duplication. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2803-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Robert D Hoffmann
- Center for Membrane Pumps in Cells and Disease - PUMPKIN, Danish National Research Foundation, Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark.
| | - Michael Palmgren
- Center for Membrane Pumps in Cells and Disease - PUMPKIN, Danish National Research Foundation, Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg C, Denmark
| |
Collapse
|
26
|
Freeling M, Scanlon MJ, Fowler JE. Fractionation and subfunctionalization following genome duplications: mechanisms that drive gene content and their consequences. Curr Opin Genet Dev 2015; 35:110-8. [PMID: 26657818 DOI: 10.1016/j.gde.2015.11.002] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 11/09/2015] [Accepted: 11/09/2015] [Indexed: 12/11/2022]
Abstract
A gene's duplication relaxes selection. Loss of duplicate, low-function DNA (fractionation) sometimes follows, mostly by deletion in plants, but mostly via the pseudogene pathway in fish and other clades with smaller population sizes. Subfunctionalization--the founding term of the Xfunctionalization lexicon--while not the general cause of differences in duplicate gene retention, becomes primary as the number of a gene's cis-regulatory sites increases. Balanced gene drive explains retention for the average gene. Both maintenance-of-balance and subfunctionalization drive gene content nonrandomly, and currently fall outside of our accepted Theory of Evolution. The 'typical' mutation encountered by a gene duplicate is not a neutral loss-of-function; dominant mutations (Muller's lexicon; these are not neutral) abound, and confound X functionalization terms like 'neofunctionalization'. Confusion of words may cause confusion of thought. As with many plants, fish tetraploidies provide a higher throughput surrogate-genetic method to infer function from human and other vertebrate ENCODE-like regulatory sites.
Collapse
Affiliation(s)
- Michael Freeling
- Department of Plant and Microbial Biology, Univ. California, Berkeley, CA 94720, United States.
| | - Michael J Scanlon
- Section of Plant Biology, Cornell University, Ithaca, NY 14853, United States
| | - John E Fowler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, United States
| |
Collapse
|
27
|
Burgess DG, Xu J, Freeling M. Advances in understanding cis regulation of the plant gene with an emphasis on comparative genomics. CURRENT OPINION IN PLANT BIOLOGY 2015; 27:141-7. [PMID: 26247124 DOI: 10.1016/j.pbi.2015.07.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 06/26/2015] [Accepted: 07/07/2015] [Indexed: 05/07/2023]
Abstract
The plant gene model remains largely an extrapolation from animals, with the cis functional unit, the gene, cast as a dynamic looping structure. Molecular genetics with model plants continues to make advances; highlighted here are quantitative-occupancy results from the Arabidopsis thaliana (Arabidopsis) Phytochrome-Interacting bHLH transcription Factors (PIF) quartet. Compared to this complex snapshot, results from chromatin occupancy and other Encyclopedia of DNA Elements (ENCODE)-like approaches increase our transcription factor-motif cognate library, but regulation cannot by itself be inferred from binding. Complementary published Arabidopsis conserved noncoding sequence lists are compared, evaluated, merged, and released. Comparative genomic approaches have identified a cis modifier of a gene's expression-hypothetically, a transposon-based 'rheostat'-that works in all cells, times and places.
Collapse
Affiliation(s)
- Diane G Burgess
- Department of Plant and Microbial Biology, University of California, Berkeley 94720, United States.
| | - Jie Xu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan 611130, China
| | - Michael Freeling
- Department of Plant and Microbial Biology, University of California, Berkeley 94720, United States
| |
Collapse
|
28
|
Freeling M, Xu J, Woodhouse M, Lisch D. A Solution to the C-Value Paradox and the Function of Junk DNA: The Genome Balance Hypothesis. MOLECULAR PLANT 2015; 8:899-910. [PMID: 25743198 DOI: 10.1016/j.molp.2015.02.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 02/03/2015] [Accepted: 02/18/2015] [Indexed: 05/11/2023]
Abstract
The Genome Balance Hypothesis originated from a recent study that provided a mechanism for the phenomenon of genome dominance in ancient polyploids: unique 24nt RNA coverage near genes is greater in genes on the recessive subgenome irrespective of differences in gene expression. 24nt RNAs target transposons. Transposon position effects are now hypothesized to balance the expression of networked genes and provide spring-like tension between pericentromeric heterochromatin and microtubules. The balance (coordination) of gene expression and centromere movement is under selection. Our hypothesis states that this balance can be maintained by many or few transposons about equally well. We explain known balanced distributions of junk DNA within genomes and between subgenomes in allopolyploids (and our hypothesis passes "the onion test" for any so-called solution to the C-value paradox). Importantly, when the allotetraploid maize chromosomes delete redundant genes, their nearby transposons are also lost; this result is explained if transposons near genes function. The Genome Balance Hypothesis is hypothetical because the position effect mechanisms implicated are not proved to apply to all junk DNA, and the continuous nature of the centromeric and gene position effects have not yet been studied as a single phenomenon.
Collapse
Affiliation(s)
- Michael Freeling
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
| | - Jie Xu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA; Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan 611130, China
| | - Margaret Woodhouse
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| |
Collapse
|