The events of the cell cycle of most organisms are ordered into dependent pathways in which the initiation of late events is dependent on the completion of early events. In eukaryotes, for example, mitosis is dependent on the completion of DNA synthesis. Some dependencies can be relieved by mutation (mitosis may then occur before completion of DNA synthesis), suggesting that the dependency is due to a control mechanism and not an intrinsic feature of the events themselves. Control mechanisms enforcing dependency in the cell cycle are here called checkpoints. Elimination of checkpoints may result in cell death, infidelity in the distribution of chromosomes or other organelles, or increased susceptibility to environmental perturbations such as DNA damaging agents. It appears that some checkpoints are eliminated during the early embryonic development of some organisms; this fact may pose special problems for the fidelity of embryonic cell division.

https://science.sciencemag.org/content/sci/246/4930/629.full.pdf

Checkpoints: controls that ensure the order of cell cycle events

The spatiotemporal expression of genes in an organism is determined by regulatory systems that involve a large number of genes connected through a complex network of interactions. As an intuitive understanding of the behavior of these systems is hard to obtain, computer tools for the modeling and simulation of genetic regulatory networks will be indispensable. This report reviews formalisms that have been employed in mathematical biology and bioinformatics to describe genetic regulatory systems, in particular directed graphs, Bayesian networks, ordinary and partial differential equations, stochastic equations, Boolean networks and their generalizations, qualitative differential equations, and rule-based formalisms. In addition, the report discusses how these formalisms have been used in the modeling and simulation of regulatory systems.

/pdf/modeling-and-simulation-of-genetic-regulatory-systems-a-2pgggkutcb.pdf

Modeling and simulation of genetic regulatory systems: a literature review.

Local, Efflux-Dependent Auxin Gradients as a Common Module for Plant Organ Formation

Publisher Summary This chapter reviews the current state of the knowledge of transcription and translation in Caenorhabditis elegans. Transcription in eukaryotes is accomplished by three RNA polymerases, each transcribing a particular type of RNA; RNA polymerase I transcribes ribosomal RNA, RNA polymerase II transcribes mRNAs and snRNAs, and RNA polymerase III transcribes tRNAs and other low-molecular-weight RNAs. The chapter focuses on RNA polymerase II transcription. The C. elegans gene for the large subunit of RNA polymerase II has been cloned, and has shown to encode a protein that resembles its vertebrate counterparts. For most polymerase II transcribed genes in C. elegans, a sequence fitting the consensus TATA element about 30 bp upstream of the transcriptional start site is found. Recently, a cDNA encoding the TATA box binding protein, or TATA binding protein (TBP) subunit of transcription factor II D (TFIID), has been identified in the nematode. This protein shows extended regions of sequence similarity to vertebrate TBP, binds to a TATA box sequence and can substitute for vertebrate TFIID basal activity in in vitro extracts. These results illustrate a high degree of evolutionary conservation in the basic transcription machinery.

Transcription and translation.

mRNA stability in mammalian cells.

https://www.cell.com/cell/pdf/0092-8674(86)90009-7.pdf

Parameters controlling transcriptional activation during early drosophila development

https://www.cell.com/cell/pdf/0092-8674(86)90771-3.pdf

Cell cycle control by the nucleo-cytoplasmic ratio in early Drosophila development

Repression and turnover pattern fushi tarazu RNA in the early Drosophila embryo.

Drosophila imaginal disc cells can switch fates by transdetermining from one determined state to another. We analyzed the expression profiles of cells induced by ectopic Wingless expression to transdetermine from leg to wing by dissecting transdetermined cells and hybridizing probes generated by linear RNA amplification to DNA microarrays. Changes in expression levels implicated a number of genes: lamina ancestor, CG12534 (a gene orthologous to mouse augmenter of liver regeneration), Notch pathway members, and the Polycomb and trithorax groups of chromatin regulators. Functional tests revealed that transdetermination was significantly affected in mutants for lama and seven different PcG and trxG genes. These results validate our methods for expression profiling as a way to analyze developmental programs, and show that modifications to chromatin structure are key to changes in cell fate. Our findings are likely to be relevant to the mechanisms that lead to disease when homologs of Wingless are expressed at abnormal levels and to the manifestation of pluripotency of stem cells.

/pdf/regulation-of-cellular-plasticity-in-drosophila-imaginal-4gx2ohgy9g.pdf

Gerold Schubiger

Papers

Parameters controlling transcriptional activation during early drosophila development

Cell cycle control by the nucleo-cytoplasmic ratio in early Drosophila development

Repression and turnover pattern fushi tarazu RNA in the early Drosophila embryo.

Regulation of cellular plasticity in Drosophila imaginal disc cells by the Polycomb group, trithorax group and lama genes

Peripodial cells regulate proliferation and patterning of Drosophila imaginal discs.