from Yuk Jing Loke and Jeffrey M. Craig writing in Epigenetics: A Reference Manual:
Epigenetics can appear as an impenetrable subject; not just to those encountering it for the first time, but to those within the field too. However, epigenetics, like any subject can be made easier to understand using a combination of clear language, creative illustrations and even animations and film clips. This chapter aims to point readers of all experiences towards helpful and easy-to-read resources that educate about epigenetics. It is split into two main sections, the first aimed at a lay audience including teachers and high school students and the second, at graduate and postgraduate students and beyond. Each section contains summaries of published articles and web sites. The chapter ends with a short section on epigenetic societies and research networks and a summary table of resources. It is intended to provide a sample of some of the best short to medium length reviews on general topics within the field of epigenetics and while we cover a wide variety of themes, we apologise for any areas not covered. We cite the URLs of freely-available articles wherever possible, but many articles will require library access. We also urge readers to contact authors or publishers if they wish to distribute any of the articles for teaching purposes.
Further reading: Epigenetics: A Reference Manual
from Karlijn C. Bastiaansen, Wilbert Bitter and María A. Llamas writing in Bacterial Regulatory Networks:
Gene expression in bacteria is mainly controlled at the level of transcription initiation. To achieve this process a number of different mechanisms have evolved, one of which is the utilization of alternative sigma factors. Sigma factors are small proteins that associate with the RNA polymerase core enzyme (RNAPc) and direct it to specific promoter sequences, where they initiate gene transcription. Bacteria are able to regulate transcription initiation by synthesizing and activating different sigma factors that recognize different promoter consensus sequences. The largest group of alternative sigma factors consists of the so-called extracytoplasmic function (ECF) sigma factors that regulate gene expression in response to cell envelope stresses or environmental stimuli. The activity of ECF sigma factors is controlled by anti-sigma factors and a complex cascade of regulated (proteolytic) modifications. In gram-negative bacteria, ECF sigma factors are also controlled by cell-surface signalling (CSS), a regulatory system that includes an outer membrane receptor in the signal transduction pathway. In this chapter we will discuss the general composition and function of ECF sigma factors and their role in cell envelope stress responses and CSS.
Further reading: Bacterial Regulatory Networks Related publications
from Moshe Szyf writing in Epigenetics: A Reference Manual:
The DNA molecule contains within its chemical structure two layers of information. The DNA sequence that bears the ancestral genetic information and the pattern of distribution of covalently bound methyl groups to cytosines in DNA. While the genetic information is similar in all tissues in the individual, the pattern of distribution of methylation across the genome is cell-type specific. DNA methylation is an important regulator of gene function. Recent data that will be discussed here that supports the hypothesis that DNA methylation is a reversible biological signal. This expands the potential role of DNA methylation beyond embryogenesis to other time-points in life and to post mitotic tissues such as the brain. DNA methylation is proposed to act as a genomic response to both physical and social signals from the environment at different time points in life and to serve as a genomic memory of these exposures at different time scales, stably altering gene expression programming and thus modulating the physical and behavioral phenotypes to respond to these environments. It is hypothesized that DNA methylation provides within the structure of the DNA a dynamic interface between the changing world around us and the relatively fixed and stable genome.
Further reading: Epigenetics: A Reference Manual
from Scott B. Vande Pol writing in Small DNA Tumour Viruses:
Papillomavirus E6 oncoproteins are small zinc-binding proteins with a bewildering array of biological activities, including modulation of apoptosis, cellular transcription, host cell differentiation, growth factor dependence, DNA damage responses, and cell cycle progression. How can such a tiny protein do so much? This review examines insights from studies of oncogenic human papillomavirus E6 and bovine papillomavirus E6 to illuminate the mechanism by which E6 proteins interact with cellular binding partners. The origins of E6 and the history of its investigation are presented with the discovery of the major interaction partners that mediate E6 effects on DNA damage responses, cellular transcription, and modulation of keratinocyte differentiation.
Further reading: Small DNA Tumour Viruses Related publications
from Begoña Carrasco, Paula P. Cardenas, Cristina Cañas, Tribuhwuan Yadav, Carolina E. César, Silvia Ayora and Juan C. Alonso writing in Bacillus: Cellular and Molecular Biology (Second edition):
All organisms have developed a variety of DNA repair mechanisms to cope with DNA lesions. Homologous recombination (HR), which uses a homologous template to restore lost information at the break site, is the ultimate step for repair of one- or two-ended double strands breaks (DSBs) and for promoting the re-establishment of replication forks. Genetic and cytological approaches were used to analyze the requirements of exponentially growing Bacillus subtilis cells to survive chemical or physical agents that generate one- or two-ended DSBs and the choreography of DSB repair. The damage-induced multi-protein complex (recombinosome), organised into focal assemblies, has been confirmed by biochemical approaches. HR is coordinated with other essential processes, such as DNA replication, transcription and chromosomal segregation. When DSB recognition or end resection is severely impaired or an intact homologous template is not available the DNA ends of two-ended DSBs are repaired via non-homologous end joining.
Further reading: Bacillus: Cellular and Molecular Biology (Second edition)
from Eivind Almaas, Per Bruheim, Rahmi Lale and Svein Valla writing in Systems Microbiology: Current Topics and Applications:
The functional repertoire of an organism's metabolic network is closely linked to its phenotype and potential for utility in metabolic engineering applications. In this chapter, we discuss a systems biology view of Escherichia coli metabolism by integrating current genome-scale computational modelling approaches with available molecular genetics tools, as well as the experimental framework for metabolite and metabolic flux determination.
Further reading: Systems Microbiology Related publications