Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans

Abstract

Chromosomes are divided into domains of open chromatin, where genes have the potential to be expressed, and domains of closed chromatin, where genes are not expressed. Classic examples of open chromatin domains include 'puffs' on polytene chromosomes in Drosophila and extended loops from lampbrush chromosomes. If multiple genes were typically expressed together from a single open chromatin domain, the position of co-expressed genes along the chromosomes would appear clustered. To investigate whether co-expressed genes are clustered, we examined the chromosomal positions of the genes expressed in the muscle of Caenorhabditis elegans at the first larval stage. Here we show that co-expressed genes in C. elegans are clustered in groups of 2-5 along the chromosomes, suggesting that expression from a chromatin domain can extend over several genes. These observations reveal a higher-order organization of the structure of the genome, in which the order of the genes along the chromosome id correlated with their expression in specific tissues.

Endosperm: an integrator of seed growth and development

“…This will be overcome in the future, however, by utilizing recent advances in 'genomics' tools, including new sampling techniques, such as laser-assisted micro-dissection, or mRNA-tagging approaches [43,44]. The establishment of general as well as spatial and temporal transcriptomes or proteomes is likely to lead to the generation of specific profiles for each reproductive cell type and will be a new source of information [45,46].…”

Analysis of 101 nuclear transcriptomes reveals 23 distinct regulons and their relationship to metabolism, chromosomal gene distribution and co-ordination of nuclear and plastid gene expression

“…In eukaryotes, transcription rates are modulated by transcription factors, by remodelling of local chromatin structure through histone modification, as well as by transcriptional activation of euchromatic chromosomal regions. Finally, regulation of sets of adjacent genes has been demonstrated in a number of cases, including groups of co-expressed pairs or triplets of adjacent genes (Cohen et al, 2000), or larger clusters of co-regulated genes (Caron et al, 2001;Roy et al, 2002;Spellman and Rubin, 2002). From the evolutionary standpoint, the case of transcriptional control of gene expression presented in this paper has wide relevance for the understanding of how gene co-ordination has been achieved during the co-evolution of chloroplasts and their host cells.…”

“…Proteins encoded by members of a regulon can have a coherent function, or even be physically associated, like the components of the ribosome, proteasome and nucleosome (Brown and Botstein, 1999). In human, Drosophila, Caenorhabditis and budding yeast, co-regulated genes have been shown to cluster in the genome (Cohen et al, 2000;Caron et al, 2001;Roy et al, 2002;Spellman and Rubin, 2002).…”

Function prediction and protein networks

“…The evidence for functional interactions between the proteins encoded by such polycistronic transcripts is, however, anecdotal. A second observation is the chromosomal clustering of co-expressed genes in Caenorhabditis elegans at a higher level than that of the polycistronic RNAs [48]. Also in Homo sapiens highly expressed genes are clustered in the genome [49].…”