Characterizing the Tissue-specific and Epigenetic Gene Regulation of Transcriptional and Post-transcriptional Responses in Maize

Characterizing the Tissue-specific and Epigenetic Gene Regulation of Transcriptional and Post-transcriptional Responses in Maize PDF Author: Lauren Michelle Schulte
Publisher:
ISBN:
Category : Biology
Languages : en
Pages : 80

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Book Description
Plants regulate gene expression at the transcriptional and post-transcriptional levels to produce a variety of functionally diverse cells and tissues that ensure normal growth, development, and environmental response. Although distinct gene expression patterns have been characterized between different plant tissues, it is unclear if transcriptional regulation drives the development of these plant tissues. Additionally, transcriptional gene silencing pathways, like the RNA-directed DNA Methylation (RdDM) pathway, regulate the transcriptional silencing of a variety of loci across the genome influencing gene expression. However, the effects of the RdDM pathway on genes are not always direct or immediate and need to be explored further. RNA-seq, while widely used to assay for changes in transcript abundance, does not discriminate between differential expression caused by mRNA degradation and active transcription. Recently, the presence of intron sequences in RNA-seq analysis of libraries constructed with total RNA has been found to coincide with genes undergoing active transcription. In one study, I adapted the intron RNA-sequencing (iRNA-seq) analysis to determine genome-wide transcriptional activity in two different maize (Zea mays) tissues: husk and V2-inner stem tissue. A total of 5,341 genes were predicted to be transcriptionally differentially expressed between the two tissues, including many genes expected to have biological activity relative to the identity of each tissue. Correlations with transcriptional enhancer and transcription factor activity support the validity of iRNA-seq predictions of transcriptional regulation. A subset of transcription factors were further analyzed using gene regulatory network analysis to determine the impact of their tissue-specific activation. The predicted regulatory patterns between these genes were used to model a potential tissue-specific gene regulatory network of transcription factors and regulatory targets. In another study, iRNA-seq analysis was used to determine genome-wide transcriptional activity in two maize RdDM mutants: mop1-1 and mop3-1. MEDIATOR OF PARAMUTATION 1 (MOP1) is an RNA-dependent RNA polymerase required for the progression of the RdDM pathway and MOP3 is the largest subunit of RNA polymerase IV (Pol IV), the initiating polymerase of the RdDM pathway. The loss of RdDM machinery seen in RdDM mutants illustrates the influence of RdDM activity on gene expression. However, due to the nature of silencing activity, a cascade of gene regulatory effects could be influenced, making the characterization of RdDM protein coding gene targets challenging. Genes predicted to undergo changes in transcriptional activity via iRNA-seq analysis in these RdDM mutants have the potential to be RdDM gene targets. In some cases, these changes in transcriptional activity were found to associate with RdDM produced small interfering RNAs (siRNAs). Differentially expressed genes with an siRNA association were further evaluated for additional regulatory activity using a gene regulatory network analysis, leading to the development of a model for RdDM activity that describes RdDM immediate and secondary gene regulatory effects. These studies provide a new maize bioinformatic tool, increasing the resources available to maize researchers, and increase our understanding of gene regulation in maize through the prediction of various regulatory mechanisms and their targets.

Transposable Elements

Transposable Elements PDF Author: Heinz Saedler
Publisher: Springer Science & Business Media
ISBN: 3642797954
Category : Science
Languages : en
Pages : 234

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Book Description
Most genes are lined up on chromosomes like pearls on a string. However, a certain class of genes differ by being highly mobile; and the mecha they are termed transposons. Their properties of transposition will be described in this book. nism is the rule, irregularities like a spot on a Where uniformity plain-coloured surface strike the eye. Thus the phenomenon of has long been a source of fascina variegation among organisms In plants, variegation is most easily recognised as irregulari tion. in pigment patterns on leaves, flowers and seeds, but other ties as leaf or flower form might also show characteristics such In 1588, such a variegation pattern was described in variegation. kernels of Zea mays by Jacob Theodor of Bergzabern, a village is so detailed that if south of Strasbourg. The report by Theodor one counts the different kernel phenotypes described it be is looking at a Mendelian segrega comes clear that the author had tion. It goes without saying that Latin-American Indians already bred such variegated material much earlier, but no descriptions have yet been uncovered. Meanwhile, genetically heritable variegation patterns have been described at many different loci in more than 34 different plant species.

Engineering Tolerance in Crop Plants Against Abiotic Stress

Engineering Tolerance in Crop Plants Against Abiotic Stress PDF Author: Shah Fahad
Publisher: CRC Press
ISBN: 1000462137
Category : Science
Languages : en
Pages : 310

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Book Description
Despite significant progress in increasing agricultural production, meeting the changing dietary preferences and increasing food demands of future populations remains a significant challenge. Salinity, drought, water logging, high temperature and toxicity are abiotic stresses that affect the crop yield and production. Tolerance for stress is a important characteristic that plants need to have in order to survive. Identification of proper techniques at a proper time can make it easy for scientists to increase crop productivity and yield. In Engineering Tolerance in Crop Plants against Abiotic Stress we have discussed the possible stresses and their impact on crops and portrayed distinctive abiotic stress tolerance in response to different techniques that can improve the performance of crops. Features of the Book: Provide a state-of-the-art description of the physiological, biochemical, and molecular status of the understanding of abiotic stress in plants. Address factors that threaten future food production and provide potential solution to these factors. Designed to cater to the needs of the students engaged in the field of environmental sciences, soil sciences, agricultural microbiology, plant pathology, and agronomy. New strategies for better crop productivity and yield. Understanding new techniques pointed out in this book will open the possibility of genetic engineering in crop plants with the concomitant improved stress tolerance.

The Salvia miltiorrhiza Genome

The Salvia miltiorrhiza Genome PDF Author: Shanfa Lu
Publisher: Springer Nature
ISBN: 3030247163
Category : Science
Languages : en
Pages : 192

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Book Description
This is the first book on the genome of Salvia miltiorrhiza, summarizing the research advances in the molecular mapping, whole genome sequencing, chloroplast and mitochondria genomes, epigenetics, transcriptomics and functional genomics of this emerging model plant with great economic and medicinal value. It also describes its distribution, taxonomy and morphology and provides useful information on its cultivation and breeding. Further, it highlights the biosynthetic pathways of tanshinones and phenolic acids – two main classes of bioactive components produced in this plant species – and reviews and discusses the technology of hairy root induction, tissue culture and genetic transformation of S. miltiorrhiza. The book is a valuable resource for students, teachers and researchers in academia and industry interested in medicinal plants and pharmacy.

Index Medicus

Index Medicus PDF Author:
Publisher:
ISBN:
Category : Medicine
Languages : en
Pages : 1926

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Book Description


Plant Biotechnology and Agriculture

Plant Biotechnology and Agriculture PDF Author: Arie Altman
Publisher: Academic Press
ISBN: 0123814669
Category : Medical
Languages : en
Pages : 586

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Book Description
As the oldest and largest human intervention in nature, the science of agriculture is one of the most intensely studied practices. From manipulation of plant gene structure to the use of plants for bioenergy, biotechnology interventions in plant and agricultural science have been rapidly developing over the past ten years with immense forward leaps on an annual basis. This book begins by laying the foundations for plant biotechnology by outlining the biological aspects including gene structure and expression, and the basic procedures in plant biotechnology of genomics, metabolomics, transcriptomics and proteomics. It then focuses on a discussion of the impacts of biotechnology on plant breeding technologies and germplasm sustainability. The role of biotechnology in the improvement of agricultural traits, production of industrial products and pharmaceuticals as well as biomaterials and biomass provide a historical perspective and a look to the future. Sections addressing intellectual property rights and sociological and food safety issues round out the holistic discussion of this important topic. Includes specific emphasis on the inter-relationships between basic plant biotechnologies and applied agricultural applications, and the way they contribute to each other Provides an updated review of the major plant biotechnology procedures and techniques, their impact on novel agricultural development and crop plant improvement Takes a broad view of the topic with discussions of practices in many countries

Characterizing the Tissue-specific and Epigenetic Gene Regulation of Transcriptional and Post-transcriptional Responses in Maize

Characterizing the Tissue-specific and Epigenetic Gene Regulation of Transcriptional and Post-transcriptional Responses in Maize PDF Author: Lauren Michelle Schulte
Publisher:
ISBN:
Category : Biology
Languages : en
Pages : 80

View

Book Description
Plants regulate gene expression at the transcriptional and post-transcriptional levels to produce a variety of functionally diverse cells and tissues that ensure normal growth, development, and environmental response. Although distinct gene expression patterns have been characterized between different plant tissues, it is unclear if transcriptional regulation drives the development of these plant tissues. Additionally, transcriptional gene silencing pathways, like the RNA-directed DNA Methylation (RdDM) pathway, regulate the transcriptional silencing of a variety of loci across the genome influencing gene expression. However, the effects of the RdDM pathway on genes are not always direct or immediate and need to be explored further. RNA-seq, while widely used to assay for changes in transcript abundance, does not discriminate between differential expression caused by mRNA degradation and active transcription. Recently, the presence of intron sequences in RNA-seq analysis of libraries constructed with total RNA has been found to coincide with genes undergoing active transcription. In one study, I adapted the intron RNA-sequencing (iRNA-seq) analysis to determine genome-wide transcriptional activity in two different maize (Zea mays) tissues: husk and V2-inner stem tissue. A total of 5,341 genes were predicted to be transcriptionally differentially expressed between the two tissues, including many genes expected to have biological activity relative to the identity of each tissue. Correlations with transcriptional enhancer and transcription factor activity support the validity of iRNA-seq predictions of transcriptional regulation. A subset of transcription factors were further analyzed using gene regulatory network analysis to determine the impact of their tissue-specific activation. The predicted regulatory patterns between these genes were used to model a potential tissue-specific gene regulatory network of transcription factors and regulatory targets. In another study, iRNA-seq analysis was used to determine genome-wide transcriptional activity in two maize RdDM mutants: mop1-1 and mop3-1. MEDIATOR OF PARAMUTATION 1 (MOP1) is an RNA-dependent RNA polymerase required for the progression of the RdDM pathway and MOP3 is the largest subunit of RNA polymerase IV (Pol IV), the initiating polymerase of the RdDM pathway. The loss of RdDM machinery seen in RdDM mutants illustrates the influence of RdDM activity on gene expression. However, due to the nature of silencing activity, a cascade of gene regulatory effects could be influenced, making the characterization of RdDM protein coding gene targets challenging. Genes predicted to undergo changes in transcriptional activity via iRNA-seq analysis in these RdDM mutants have the potential to be RdDM gene targets. In some cases, these changes in transcriptional activity were found to associate with RdDM produced small interfering RNAs (siRNAs). Differentially expressed genes with an siRNA association were further evaluated for additional regulatory activity using a gene regulatory network analysis, leading to the development of a model for RdDM activity that describes RdDM immediate and secondary gene regulatory effects. These studies provide a new maize bioinformatic tool, increasing the resources available to maize researchers, and increase our understanding of gene regulation in maize through the prediction of various regulatory mechanisms and their targets.

Cumulated Index Medicus

Cumulated Index Medicus PDF Author:
Publisher:
ISBN:
Category : Medicine
Languages : en
Pages : 1844

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Book Description


Transposable Elements

Transposable Elements PDF Author: Heinz Saedler
Publisher: Springer Science & Business Media
ISBN: 3642797954
Category : Science
Languages : en
Pages : 234

View

Book Description
Most genes are lined up on chromosomes like pearls on a string. However, a certain class of genes differ by being highly mobile; and the mecha they are termed transposons. Their properties of transposition will be described in this book. nism is the rule, irregularities like a spot on a Where uniformity plain-coloured surface strike the eye. Thus the phenomenon of has long been a source of fascina variegation among organisms In plants, variegation is most easily recognised as irregulari tion. in pigment patterns on leaves, flowers and seeds, but other ties as leaf or flower form might also show characteristics such In 1588, such a variegation pattern was described in variegation. kernels of Zea mays by Jacob Theodor of Bergzabern, a village is so detailed that if south of Strasbourg. The report by Theodor one counts the different kernel phenotypes described it be is looking at a Mendelian segrega comes clear that the author had tion. It goes without saying that Latin-American Indians already bred such variegated material much earlier, but no descriptions have yet been uncovered. Meanwhile, genetically heritable variegation patterns have been described at many different loci in more than 34 different plant species.

Bibliography of Agriculture

Bibliography of Agriculture PDF Author:
Publisher:
ISBN:
Category : Agriculture
Languages : en
Pages :

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Book Description


Engineering Tolerance in Crop Plants Against Abiotic Stress

Engineering Tolerance in Crop Plants Against Abiotic Stress PDF Author: Shah Fahad
Publisher: CRC Press
ISBN: 1000462137
Category : Science
Languages : en
Pages : 310

View

Book Description
Despite significant progress in increasing agricultural production, meeting the changing dietary preferences and increasing food demands of future populations remains a significant challenge. Salinity, drought, water logging, high temperature and toxicity are abiotic stresses that affect the crop yield and production. Tolerance for stress is a important characteristic that plants need to have in order to survive. Identification of proper techniques at a proper time can make it easy for scientists to increase crop productivity and yield. In Engineering Tolerance in Crop Plants against Abiotic Stress we have discussed the possible stresses and their impact on crops and portrayed distinctive abiotic stress tolerance in response to different techniques that can improve the performance of crops. Features of the Book: Provide a state-of-the-art description of the physiological, biochemical, and molecular status of the understanding of abiotic stress in plants. Address factors that threaten future food production and provide potential solution to these factors. Designed to cater to the needs of the students engaged in the field of environmental sciences, soil sciences, agricultural microbiology, plant pathology, and agronomy. New strategies for better crop productivity and yield. Understanding new techniques pointed out in this book will open the possibility of genetic engineering in crop plants with the concomitant improved stress tolerance.

Bibliography of Agriculture with Subject Index

Bibliography of Agriculture with Subject Index PDF Author:
Publisher:
ISBN:
Category : Agriculture
Languages : en
Pages :

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Book Description


The Salvia miltiorrhiza Genome

The Salvia miltiorrhiza Genome PDF Author: Shanfa Lu
Publisher: Springer Nature
ISBN: 3030247163
Category : Science
Languages : en
Pages : 192

View

Book Description
This is the first book on the genome of Salvia miltiorrhiza, summarizing the research advances in the molecular mapping, whole genome sequencing, chloroplast and mitochondria genomes, epigenetics, transcriptomics and functional genomics of this emerging model plant with great economic and medicinal value. It also describes its distribution, taxonomy and morphology and provides useful information on its cultivation and breeding. Further, it highlights the biosynthetic pathways of tanshinones and phenolic acids – two main classes of bioactive components produced in this plant species – and reviews and discusses the technology of hairy root induction, tissue culture and genetic transformation of S. miltiorrhiza. The book is a valuable resource for students, teachers and researchers in academia and industry interested in medicinal plants and pharmacy.

Index Medicus

Index Medicus PDF Author:
Publisher:
ISBN:
Category : Medicine
Languages : en
Pages : 1926

View

Book Description


Plant Biotechnology and Agriculture

Plant Biotechnology and Agriculture PDF Author: Arie Altman
Publisher: Academic Press
ISBN: 0123814669
Category : Medical
Languages : en
Pages : 586

View

Book Description
As the oldest and largest human intervention in nature, the science of agriculture is one of the most intensely studied practices. From manipulation of plant gene structure to the use of plants for bioenergy, biotechnology interventions in plant and agricultural science have been rapidly developing over the past ten years with immense forward leaps on an annual basis. This book begins by laying the foundations for plant biotechnology by outlining the biological aspects including gene structure and expression, and the basic procedures in plant biotechnology of genomics, metabolomics, transcriptomics and proteomics. It then focuses on a discussion of the impacts of biotechnology on plant breeding technologies and germplasm sustainability. The role of biotechnology in the improvement of agricultural traits, production of industrial products and pharmaceuticals as well as biomaterials and biomass provide a historical perspective and a look to the future. Sections addressing intellectual property rights and sociological and food safety issues round out the holistic discussion of this important topic. Includes specific emphasis on the inter-relationships between basic plant biotechnologies and applied agricultural applications, and the way they contribute to each other Provides an updated review of the major plant biotechnology procedures and techniques, their impact on novel agricultural development and crop plant improvement Takes a broad view of the topic with discussions of practices in many countries

Nucleic Acids Abstracts

Nucleic Acids Abstracts PDF Author:
Publisher:
ISBN:
Category : Nucleic acids
Languages : en
Pages :

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Book Description