Plant epigenetics : methods and protocols / edited by Igor Kovalchuk, Franz J. Zemp.

Contributor(s): Kovalchuk, Igor | Zemp, Franz J
Material type: TextTextSeries: Springer protocols (Series): ; Methods in molecular biology (Clifton, N.J.): v. 631.Publisher: New York : Humana Press, ©2010Description: 1 online resource (x, 273 pages) : illustrationsContent type: text Media type: computer Carrier type: online resourceISBN: 9781607616467; 1607616467Subject(s): Plant genetic regulation | Epigenesis | Epigenesis, Genetic | Gene Expression Regulation, Plant | Gene Silencing | Gene Expression Regulation | Genetic Phenomena | Phenomena and Processes | Epigenesis | Plant genetic regulation | planten | plants | epigenetica | epigenetics | moleculaire genetica | molecular genetics | dna methylation | bioinformatics | histonen | histones | dna sequencing | transgene planten | transgenic plants | laboratoriummethoden | laboratory methods | protocollen | protocols | Biological Techniques | Biologische techniekenGenre/Form: Electronic books. Additional physical formats: Print version:: Plant epigenetics.DDC classification: 572.8652 LOC classification: QK981.4 | .P53 2010Online resources: Click here to access online
Contents:
Analysis of DNA methylation in plants by bisulfite sequencing / Andrea Foerster and Ortrun Mittelsten Scheid -- Analysis of bisulfite sequencing data from plant DNA using CyMATE / Andrea M. Foerster [and others] -- Analysis of locus-specific changes in methylation patterns using a COBRA (combined bisulfite restriction analysis) assay / Alex Boyko and Igor Kovalchuk -- Detection of changes in global genome methylation using the cytosine-extension assay / Alex Boyko and Igor Kovalchuk -- In situ analysis of DNA methylation in plants / Palak Kathiria and Igor Kovalchuk -- Analysis of mutation/rearrangement frequencies and methylation patterns at a given DNA locus using restriction fragment length polymorphism / Alex Boyko and Igor Kovalchuk -- Isoschizomers and amplified fragment length polymorphism for the detection of specific cytosine methylation changes / Leonor Ruiz-García [and others] -- Analysis of small RNA populations using hybridization to DNA tiling arrays / Martine Boccara [and others] -- Northern blotting techniques for small RNAs / Todd Blevins -- qRT-PCR of small RNAs / Erika Varkonyi-Gasic and Roger P. Hellens -- Cloning new small RNA sequences / Yuko Tagami, Naoko Inaba, and Yuichiro Watanabe -- Genome-wide mapping of protein-DNA interaction by chromatin immunoprecipitatino and DNA microarray hybridization (ChIP-chip). Part A : ChiP-chip molecular methods / Julia J. Reimer and Franziska Turck. Part B : ChIP-chip data analysis / Ulrike Göbel, Julia Reimer, and Franziska Turck -- Metaanalysis of ChIP-chip data / Julia Engelhorn and Franziska Turck -- Chromatin immunoprecipitation protocol for histone modifications and protein-DNA binding analyses in Arabidopsis / Stéphane Pien and Ueli Grossniklaus -- cDNA libraries for virus-induced gene silencing / Andrea T. Todd, Enwu Liu, and Jonathan E. Page -- Detection and quantification of DNA strand breaks using the ROPS (random oligonucleotide primed synthesis) assay / Alex Boyko and Igor Kovalchuk -- Reporter gene-based recombination lines for studies of genome stability / Palak Kathiria and Igor Kovalchuk -- Plant transgenesis / Alicja Ziemienowicz.
Summary: The past fifteen years have witnessed major advances in epigenetics, one of the most popular and quickly evolving fields of modern science. In Plant Epigenetics: Methods and Protocols, expert researchers explore the most recent developments, examining in great detail the contribution of epigenetic regulation to cell function in plants. Chapters include a variety of protocols for studying the function of small non-coding RNAs, DNA methylation, and histone modifications in plants, often in different degrees of complexity. This volume describes bioinformatic approaches to the analysis of high-throughput data, such as bisulfite sequencing and Chip-on-chip assays. It features much-desired protocols for plant transgenesis and the analysis of genome stability, with a detailed discussion of their applications to epigenetic studies. Composed in the highly successful Methods in Molecular Biology series format, each chapter contains a brief introduction, step-by-step methods, a list of necessary materials, and a Notes section which shares tips on troubleshooting and avoiding known pitfalls. Wide-ranging and innovative, Plant Epigenetics: Methods and Protocols is an invaluable manual designed to help researchers uncover the undiscovered and unexplained phenomena in plant biology.
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Includes bibliographical references and index.

Analysis of DNA methylation in plants by bisulfite sequencing / Andrea Foerster and Ortrun Mittelsten Scheid -- Analysis of bisulfite sequencing data from plant DNA using CyMATE / Andrea M. Foerster [and others] -- Analysis of locus-specific changes in methylation patterns using a COBRA (combined bisulfite restriction analysis) assay / Alex Boyko and Igor Kovalchuk -- Detection of changes in global genome methylation using the cytosine-extension assay / Alex Boyko and Igor Kovalchuk -- In situ analysis of DNA methylation in plants / Palak Kathiria and Igor Kovalchuk -- Analysis of mutation/rearrangement frequencies and methylation patterns at a given DNA locus using restriction fragment length polymorphism / Alex Boyko and Igor Kovalchuk -- Isoschizomers and amplified fragment length polymorphism for the detection of specific cytosine methylation changes / Leonor Ruiz-García [and others] -- Analysis of small RNA populations using hybridization to DNA tiling arrays / Martine Boccara [and others] -- Northern blotting techniques for small RNAs / Todd Blevins -- qRT-PCR of small RNAs / Erika Varkonyi-Gasic and Roger P. Hellens -- Cloning new small RNA sequences / Yuko Tagami, Naoko Inaba, and Yuichiro Watanabe -- Genome-wide mapping of protein-DNA interaction by chromatin immunoprecipitatino and DNA microarray hybridization (ChIP-chip). Part A : ChiP-chip molecular methods / Julia J. Reimer and Franziska Turck. Part B : ChIP-chip data analysis / Ulrike Göbel, Julia Reimer, and Franziska Turck -- Metaanalysis of ChIP-chip data / Julia Engelhorn and Franziska Turck -- Chromatin immunoprecipitation protocol for histone modifications and protein-DNA binding analyses in Arabidopsis / Stéphane Pien and Ueli Grossniklaus -- cDNA libraries for virus-induced gene silencing / Andrea T. Todd, Enwu Liu, and Jonathan E. Page -- Detection and quantification of DNA strand breaks using the ROPS (random oligonucleotide primed synthesis) assay / Alex Boyko and Igor Kovalchuk -- Reporter gene-based recombination lines for studies of genome stability / Palak Kathiria and Igor Kovalchuk -- Plant transgenesis / Alicja Ziemienowicz.

Print version record.

The past fifteen years have witnessed major advances in epigenetics, one of the most popular and quickly evolving fields of modern science. In Plant Epigenetics: Methods and Protocols, expert researchers explore the most recent developments, examining in great detail the contribution of epigenetic regulation to cell function in plants. Chapters include a variety of protocols for studying the function of small non-coding RNAs, DNA methylation, and histone modifications in plants, often in different degrees of complexity. This volume describes bioinformatic approaches to the analysis of high-throughput data, such as bisulfite sequencing and Chip-on-chip assays. It features much-desired protocols for plant transgenesis and the analysis of genome stability, with a detailed discussion of their applications to epigenetic studies. Composed in the highly successful Methods in Molecular Biology series format, each chapter contains a brief introduction, step-by-step methods, a list of necessary materials, and a Notes section which shares tips on troubleshooting and avoiding known pitfalls. Wide-ranging and innovative, Plant Epigenetics: Methods and Protocols is an invaluable manual designed to help researchers uncover the undiscovered and unexplained phenomena in plant biology.

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Plant epigenetics : ©2017
Plant epigenetics : ©2017

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