Genomic organization of Polycomb Response Elements and its functional implication in Drosophila and other insects

The epigenetic memory is an essential aspect of multicellular organisms to maintain several cell types and their geneexpression pattern. This complex process uses a number of protein factors and specific DNA elements within thedevelopmental cues to achieve this. The protein factors involved in the process are the Polycomb group (PcG)members, and, accordingly, the DNA sequences that interact with these proteins are called Polycomb ResponseElements (PREs). Since the PcG proteins are highly conserved among higher eukaryotes, including insects, andfunction at thousands of sites in the genomes, it is expected that PREs may also be present across the genome. However,the studies on PREs in insect species, other thanDrosophila, is currently lacking.We took a bioinformatics approach todevelop an inclusive PRE prediction tool, ‘PRE Mapper’, to address this need. By applying this tool on the Drosophilamelanogaster genome, we predicted[20,000 PREs. When compared with the available PRE prediction methods, thistool shows far better performance by correctly identifying the in vivo binding sites of PcG proteins, identified bygenome-scale ChIP experiments. Further analysis of the predicted PREs shows their cohabitation with chromatindomain boundary elements at several places in the Drosophila genome, possibly defining a composite epigeneticmodule. We analysed 10 insect genomes in this context and find several conserved features in PREs across the insectspecies with some variations in their occurrence frequency. These analyses leading to the identification of PRE in insectgenomes contribute to our understanding of epigenetic mechanisms in these organisms.

Cromosomas, vehcculos en la organización y transmisión de los caracteres / Chromosomes as Vehicle in Organization and Transmission of Characters

Uno de los aspectos fundamentales en los genomas es la organización de los genes en paquetes conocidos como cromosomas. Todos los organismos, desde los más simples, hasta los más complejos tienen estas estructuras, siendo la morfología y número de estos una característica de cada especie. Las mutaciones cromosómicas son cambios, que pueden ser originados por errores en la mitosis o meiosis en un individuo, y que pueden ser fijadas en la población durante la evolución si representa alguna ventaja selectiva, en caso contrario, si tienen efectos negativos severos en el fenotipo y/o en la fertilidad de los portadores, se manifestará como una anomalía o síndrome genético que será eliminado de la población. En este artículo de reflexión se muestra como a la luz de las técnicas citogenéticas clásicas y moleculares, se ha venido entendiendo el papel de los rearreglos cromosómicos en la diferenciación de especies, así como que fallas puntuales o cambios individuales en su morfología o número pueden ocasionar serias disfunciones reconocidas como síndromes genéticos.

One of the fundamental aspects of genomes is the organization of the genes in packages known as chromosomes. All organisms from the simplest to the most complex possess chromosomes as part of their genome and they are characterized by a particular morphology and a characteristic number of each species. Chromosome mutations induce changes that can originate in mitotic o meiotic errors in an individual, and these can become fixed in the population during evolution. This results either if the particular changes represent a selective advantage, or they may result in severe effects on the phenotype and fertility of its carriers that may be manifested as a genetic syndrome. In this essay I demonstrate how, using conventional and recent cytogenetic and molecular techniques we have begun understanding the function of chromosome arrangements in the differentiation of species and how particular defects or individual changes in the morphology or number of chromosomes can result in serious dysfunctions that are recognized as genetic syndromes.

Mitochondrial genome organization and cytoplasmic male sterility in plants.

Plant mitochondrial genomes are much larger and more complex than those of other eukaryotic organisms. They contain a very active recombination system and have a multipartite genome organization with a master circle resolving into two or more subgenomic circles by recombination through repeated sequences. Their protein coding capacity is very low and is comparable to that of animal and fungal systems. Several subunits of mitochondrial functional complexes, a complete set of tRNAs and 26S, 18S and 5S rRNAs are coded by the plant mitochondrial genome. The protein coding genes contain group II introns. The organelle genome contains stretches of DNA sequences homologous to chloroplast DNA. It also contains actively transcribed DNA sequences having open reading frames. Plasmid like DNA molecules are found in mitochondria of some plants Cytoplasmic male sterility in plants, characterized by failure to produce functional pollen grains, is a maternally inherited trait. This phenomenon has been found in many species of plants and is conveniently used for hybrid plant production. The genetic determinants for cytoplasmic male sterility reside in the mitochondrial genome. Some species of plants exhibit more than one type of cytoplasmic male sterility. Several nuclear genes are known to control expression of cytoplasmic male sterility. Different cytoplasmic male sterility types are distinguished by their specific nuclear genes (rfs) which restore pollen fertility. Cytoplasmic male sterility types are also characterized by mitochondrial DNA restriction fragment length polymorphism patterns, variations in mitochondrial RNAs, differences in protein synthetic profiles, differences in sensitivity to fungal toxins and insecticides, presence of plasmid DNAs or RNAs and also presence of certain unique sequences in the genome. Recently nuclear male sterility systems based on (i) over expression of agrobacterial rol C gene and (ii) anther specific expression of an RNase gene have been developed in tobacco and Brassica by genetic engineering methods.