1. Departments of Developmental Biology and Genetics, Stanford University Medical Center, Stanford, California 94305, USA
2. Stanford Medical Informatics, 251 Campus Drive, MSOB X-215, Stanford, California 94305, USA

Correspondence to: Stuart K. Kim¹ Correspondence and requests for materials should be addressed to S.K.K. (e-mail: Email: kim@cmgm.stanford.edu).

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 expressed¹. Classic examples of open chromatin domains include 'puffs' on polytene chromosomes in Drosophila and extended loops from lampbrush chromosomes^{2, 3}. 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 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 genes along the chromosome is correlated with their expression in specific tissues.