scholarly journals The Mechanisms of Generation, Recognition, and Erasure of DNA 5-Methylcytosine and Thymine Oxidations

2015 ◽  
Vol 290 (34) ◽  
pp. 20723-20733 ◽  
Author(s):  
Hideharu Hashimoto ◽  
Xing Zhang ◽  
Paula M. Vertino ◽  
Xiaodong Cheng
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Cytosine Methylation ◽  
Epigenetic Modifications ◽  
Dna Bases ◽  
Oxidation States ◽  
Control Of Gene Expression ◽  
Methylation Of Dna ◽  
Recent Developments ◽  
Base Excision

One of the most fundamental questions in the control of gene expression in mammals is how the patterns of epigenetic modifications of DNA are generated, recognized, and erased. This includes covalent cytosine methylation of DNA and its associated oxidation states. An array of AdoMet-dependent methyltransferases, Fe(II)- and α-ketoglutarate-dependent dioxygenases, base excision glycosylases, and sequence-specific transcription factors is responsible for changing, maintaining, and interpreting the modification status of specific regions of chromatin. This review focuses on recent developments in characterizing the functional and structural links between the modification status of two DNA bases 5-methylcytosine and thymine (5-methyluracil).

Principles of Molecular Biology

2013 ◽  
pp. 76-87
Author(s):  
Steven E. Hyman ◽  
Eric J. Nestler
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Molecular Biology ◽  
Cell Surface ◽  
Environmental Context ◽  
Molecular Processes ◽  
Control Of Gene Expression ◽  
Extracellular Signals ◽  
Gene Environment

This chapter provides an overview of the fundamental molecular processes by which information is encoded in the genome and how this information is expressed within an environmental context. We describe what genes are, how they function, and how their expression into RNA and protein is regulated by signals from outside the cell. Particular attention is given to a series of stimulus-regulated transcription factors, which play important roles in transducing information from the cell surface to the nucleus. Work in this area has shown that the control of gene expression by extracellular signals is a critical arena for gene–environment interactions that are highly relevant to psychiatry.

The control of gene expression and cell proliferation by the epithelial apical junctional complex

2012 ◽  
Vol 53 ◽  
pp. 83-93 ◽  
Author(s):  
Domenica Spadaro ◽  
Rocio Tapia ◽  
Pamela Pulimeno ◽  
Sandra Citi
Keyword(s):  
Gene Expression ◽  
Cell Proliferation ◽  
Transcription Factors ◽  
Protein Complexes ◽  
Regulation Of Gene Expression ◽  
Small Gtpases ◽  
Junctional Complex ◽  
Nucleotide Exchange ◽  
Control Of Gene Expression ◽  
Apical Junctional Complex

The AJC (apical junctional complex) of vertebrate epithelial cells orchestrates cell–cell adhesion and tissue barrier function. In addition, it plays a pivotal role in signalling. Several protein components of the AJC, e.g. the cytoplasmic proteins β-catenin, p120-catenin and ZO (Zonula Occludens)-2, can shuttle to the nucleus, where they interact with transcription factors to regulate gene expression and cell proliferation. Other junctional proteins, e.g. angiomotin, α-catenin and cingulin, are believed to act by sequestering either transcription factors, such as YAP (Yes-associated protein), or regulators of small GTPases, such as GEF (guanine-nucleotide-exchange factor)-H1, at junctions. The signalling activities of AJC proteins are triggered by different extracellular and intracellular cues, including cell density, and physiological or pathological activation of developmentally regulated pathways, such as the Wnt pathway. The interplay between junctional protein complexes, the actin cytoskeleton and signalling pathways is of crucial importance in the regulation of gene expression and cell proliferation.

scholarly journals Spatial Control of Gene Expression by miR319-Regulated TCP Transcription Factors in Leaf Development

2017 ◽  
Vol 176 (2) ◽  
pp. 1694-1708 ◽  
Author(s):  
Edgardo G. Bresso ◽  
Uciel Chorostecki ◽  
Ramiro E. Rodriguez ◽  
Javier F. Palatnik ◽  
Carla Schommer
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Leaf Development ◽  
Control Of Gene Expression ◽  
Spatial Control

Intranuclear trafficking of transcription factors: Requirements for vitamin D-mediated biological control of gene expression

2002 ◽  
Vol 88 (2) ◽  
pp. 340-355 ◽  
Author(s):  
Gary S. Stein ◽  
Jane B. Lian ◽  
Janet L. Stein ◽  
André J. van Wijnen ◽  
Martin Montecino ◽  
...  
Keyword(s):  
Gene Expression ◽  
Biological Control ◽  
Vitamin D ◽  
Transcription Factors ◽  
Control Of Gene Expression

scholarly journals The histone H3K4 demethylase JARID1A directly interacts with haematopoietic transcription factor GATA1 in erythroid cells through its second PHD domain

2020 ◽  
Vol 7 (1) ◽  
pp. 191048 ◽  
Author(s):  
Dimple Karia ◽  
Robert C. G. Gilbert ◽  
Antonio J. Biasutto ◽  
Catherine Porcher ◽  
Erika J. Mancini
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Blood Cells ◽  
Physical Contact ◽  
Histone Demethylases ◽  
Control Of Gene Expression ◽  
Histone H3k4 ◽  
Lineage Specific Genes ◽  
Phd Domain

Chromatin remodelling and transcription factors play important roles in lineage commitment and development through control of gene expression. Activation of selected lineage-specific genes and repression of alternative lineage-affiliated genes result in tightly regulated cell differentiation transcriptional programmes. However, the complex functional and physical interplay between transcription factors and chromatin-modifying enzymes remains elusive. Recent evidence has implicated histone demethylases in normal haematopoietic differentiation as well as in malignant haematopoiesis. Here, we report an interaction between H3K4 demethylase JARID1A and the haematopoietic-specific master transcription proteins SCL and GATA1 in red blood cells. Specifically, we observe a direct physical contact between GATA1 and the second PHD domain of JARID1A. This interaction has potential implications for normal and malignant haematopoiesis.

scholarly journals Nfat

2002 ◽  
Vol 156 (5) ◽  
pp. 771-774 ◽  
Author(s):  
Valerie Horsley ◽  
Grace K. Pavlath
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
Transcription Factors ◽  
Immune System ◽  
Cell Types ◽  
Cytokine Gene Expression ◽  
Nuclear Factor ◽  
Cytokine Gene ◽  
Activated T Cells ◽  
Control Of Gene Expression

The nuclear factor of activated T cells (NFAT) proteins are a family of transcription factors whose activation is controlled by calcineurin, a Ca2+-dependent phosphatase. Originally identified in T cells as inducers of cytokine gene expression, NFAT proteins play varied roles in cells outside of the immune system. This review addresses the recent data implicating NFAT in the control of gene expression influencing the development and adaptation of numerous mammalian cell types.

The marks, mechanisms and memory of epigenetic states in mammals

2001 ◽  
Vol 356 (1) ◽  
pp. 1-10 ◽  
Author(s):  
Vardhman K. RAKYAN ◽  
Jost PREIS ◽  
Hugh D. MORGAN ◽  
Emma WHITELAW
Keyword(s):  
Gene Expression ◽  
Genetic Linkage ◽  
Cytosine Methylation ◽  
Epigenetic Inheritance ◽  
Epigenetic Modifications ◽  
Strict Sense ◽  
Know How ◽  
The Past ◽  
Dna Nucleotide Sequence ◽  
Developmental Noise

It is well recognized that there is a surprising degree of phenotypic variation among genetically identical individuals, even when the environmental influences, in the strict sense of the word, are identical. Genetic textbooks acknowledge this fact and use different terms, such as ‘intangible variation’ or ‘developmental noise’, to describe it. We believe that this intangible variation results from the stochastic establishment of epigenetic modifications to the DNA nucleotide sequence. These modifications, which may involve cytosine methylation and chromatin remodelling, result in alterations in gene expression which, in turn, affects the phenotype of the organism. Recent evidence, from our work and that of others in mice, suggests that these epigenetic modifications, which in the past were thought to be cleared and reset on passage through the germline, may sometimes be inherited to the next generation. This is termed epigenetic inheritance, and while this process has been well recognized in plants, the recent findings in mice force us to consider the implications of this type of inheritance in mammals. At this stage we do not know how extensive this phenomenon is in humans, but it may well turn out to be the explanation for some diseases which appear to be sporadic or show only weak genetic linkage.

scholarly journals DNA Methylation and Chromatin: Role(s) of Methyl-CpG-Binding Protein ZBTB38

2018 ◽  
Vol 11 ◽  
pp. 251686571881111 ◽  
Author(s):  
Maud de Dieuleveult ◽  
Benoit Miotto
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Transcription Factors ◽  
Dna Sequences ◽  
Mammalian Cells ◽  
Expression Patterns ◽  
Control Of Gene Expression ◽  
Methylated Dna

DNA methylation plays an essential role in the control of gene expression during early stages of development as well as in disease. Although many transcription factors are sensitive to this modification of the DNA, we still do not clearly understand how it contributes to the establishment of proper gene expression patterns. We discuss here the recent findings regarding the biological and molecular function(s) of the transcription factor ZBTB38 that binds methylated DNA sequences in vitro and in cells. We speculate how these findings may help understand the role of DNA methylation and DNA methylation–sensitive transcription factors in mammalian cells.

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