Transcription Factor Protocols

Transcription Factor Protocols

Author: Martin J. Tymms

Publisher: Springer Science & Business Media

Published: 2008-02-03

Total Pages: 304

ISBN-13: 159259686X

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The effort to sequence the human genome is now moving toward a c- clusion. As all of the protein coding sequences are described, an increasing emphasis will be placed on understanding gene function and regulation. One important aspect of this analysis is the study of how transcription factors re- late transcriptional initiation by RNA polymerase II, which is responsible for transcribing nuclear genes encoding messenger RNAs. The initiation of Class II transcription is dependent upon transcription factors binding to DNA e- ments that include the core or basal promoter elements, proximal promoter elements, and distal enhancer elements. General initiation factors are involved in positioning RNA polymerase II on the core promoter, but the complex - teraction of these proteins and transcriptional activators binding to DNA e- ments outside the core promoter regulate the rate of transcriptional initiation. This initiation process appears to be a crucial step in the modulation of mRNA levels in response to developmental and environmental signals. Transcription Factor Protocols provides step-by-step procedures for key techniques that have been developed to study DNA sequences and the protein factors that regulate the transcription of protein encoding genes. This volume is aimed at providing researchers in the field with the well-detailed protocols that have been the hallmark of previous volumes of the Methods in Molecular TM Biology series.


Transcription Factor Regulatory Networks

Transcription Factor Regulatory Networks

Author: Etsuko Miyamoto-Sato

Publisher: Humana

Published: 2014-06-14

Total Pages: 220

ISBN-13: 9781493908042

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Transcription Factor Regulatory Methods details various techniques ranging from cutting-edge to general techniques use to study transcription factor regulatory networks. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Transcription Factor Regulatory Methods aids scientists in the further study into post-genomic or the personal genomic era.


Transcription Factors

Transcription Factors

Author: Paul J. Higgins

Publisher: Humana

Published: 2016-08-23

Total Pages: 426

ISBN-13: 9781493957156

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In the last few years, significant breakthroughs in transcription research expanded our appreciation for the complexity of molecular controls on gene expression in mammalian cells. In Transcription Factors: Methods and Protocols, experts in the field describe state-of-the-art approaches that investigators can use to probe critical mechanisms underlying transcription factor nuclear-cytoplasmic trafficking as well as to assess the functional impact of post-translational modifications on transcription factor function. The chapters are written by prominent scientists, many of whom developed these methods, and highlight protocols that focus on specific transcription factor family members with particular relevance to human disease. Composed in the highly successful Methods in Molecular BiologyTM 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. Comprehensive and current, Transcription Factors: Methods and Protocols compiles the latest techniques for elucidating controls on transcription factor intracellular localization and activity, and consequently is unlike any other methods-based text on transcriptional regulation today.


Transcription Factor Regulatory Networks

Transcription Factor Regulatory Networks

Author: Qi Song

Publisher: Springer Nature

Published: 2022-10-20

Total Pages: 229

ISBN-13: 1071628151

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This book covers various state-of-the-art techniques regarding the associations between transcription factors (TFs) and genes, with a focus on providing methodological and practical references for researchers. The contents cover diverse protocols and summaries of TFs including screening of TF-DNA interactions, detection of open chromatin regions, identification of epigenetic regulations, engineering TFs with genome editing tools, detection of transcriptional activities, computational analysis of TF networks, functions and druggabilities of TFs in biomedical research, and much more. Written for the highly successful Methods in Molecular Biology series, chapters feature the kind of detailed implementation advice from the experts to ensure successful research results. Authoritative and cutting-edge, Transcription Factor Regulatory Networks aims to benefit readers who are interested in using state-of-the-art techniques to study TFs and their myriad effects in cellular life.


Transcription Factor Regulatory Networks

Transcription Factor Regulatory Networks

Author: Etsuko Miyamoto-Sato

Publisher: Humana Press

Published: 2014-06-14

Total Pages: 220

ISBN-13: 9781493908066

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Transcription Factor Regulatory Methods details various techniques ranging from cutting-edge to general techniques use to study transcription factor regulatory networks. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Transcription Factor Regulatory Methods aids scientists in the further study into post-genomic or the personal genomic era.


Transcriptional Regulation

Transcriptional Regulation

Author: Ales Vancura

Publisher: Humana

Published: 2016-08-23

Total Pages: 627

ISBN-13: 9781493958542

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Through many recent remarkable developments, perhaps the most significant advancements in the study of transcriptional regulation are the development of genome-wide approaches for measuring gene expression, exemplified by gene chips (chip), and chromatin immunoprecipitation assays (ChIP) for measuring in vivo protein-DNA interactions at any genomic loci. Transcriptional Regulation: Methods and Protocols takes this progress and builds upon it with a collection of key protocols used in expert laboratories around the world. Divided into four convenient sections, this detailed volume explores promoter elements, transcription factors, and preinitiation complex (PIC) assembly, chromatin structure, chromatin modifying complexes, and RNA synthesis and regulation. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and vital tips on troubleshooting and avoiding known pitfalls. Comprehensive and accessible, Transcriptional Regulation: Methods and Protocols equally serves senior researchers and scientists experienced in transcriptional regulation as well as graduate students and scientists who wish to study transcriptional regulation for the first time.


Plant Transcription Factors

Plant Transcription Factors

Author: Nobutoshi Yamaguchi

Publisher: Humana

Published: 2019-08-08

Total Pages: 396

ISBN-13: 9781493993567

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This detailed book provides general protocols and technologies that plant biologists worldwide often utilize for the purpose of accelerating research progress in the field of plant transcription factors. Beginning with a brief introduction, the volume continues by exploring methods in the preparation of plant materials, detection of expression levels, interaction tests, and chromatin analyses. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Plant Transcription Factors: Methods and Protocols aims to answer a wide range of questions related to transcription factors commonly raised by plant biologists.


Transcription Factors

Transcription Factors

Author: David Latchman

Publisher: OUP Oxford

Published: 1999-04-08

Total Pages: 326

ISBN-13: 0191565792

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Since the publication of the first edition five years ago, a wide range of new methodologies have been developed to facilitate studies on both isolated parts of the genome and the genome as a whole. This new edition has been updated and expanded so that it provides a comprehensive guide to the methods currently available to characterize the function and activity of an individual transcription factor. All the original chapters have been fully updated or rewritten and additional chapters cover the use of in vitro transcription assays, analysis of chromatin structure, use of the genomic binding site assay and analysis of transcription factor modifications. As with the previous edition, the book starts with a series of chapters concerned with characterizing the proteins binding to a specific DNA sequence and then a chapter on more detailed characterization of the protein itself. The next two chapters describe the isolation of cDNA clones encoding a transcription factor using oligonucleotides predicted from protein sequence and screening of a cDNA expression library. Chapter 6 deals with identification of transcription factors based on sequence homology analysis by both experimental screening and database searches. Chapter 7 is a new chapter that describes methods of identifying the target genes of a previously uncharacterized factor. The next chapters deal with analysis of transcription factor function. Chapter 8 deals with general techniques, and then the following chapters cover the specialized techniques of in vitro transcription assays using transcriptionally active nuclear extracts derived from rat brain, and analysis of the effect of transcription factors on chromatin structure. The final chapter describes methods for detecting the phosphorylation and glycosylation state of transcription factors.