The Impact of Local Genome Sequence on Defining Heterochromatin Domains

Abstract

Characterizing how genomic sequence interacts with trans-acting regulatory factors to implement a program of gene expression in eukaryotic organisms is critical to understanding genome function. One means by which patterns of gene expression are achieved is through the differential packaging of DNA into distinct types of chromatin. While chromatin state exerts a major influence on gene expression, the extent to which cis-acting DNA sequences contribute to the specification of chromatin state remains incompletely understood. To address this, we have used a fission yeast sequence element (L5), known to be sufficient to nucleate heterochromatin, to establish de novo heterochromatin domains in the Schizosaccharomyces pombe genome. The resulting heterochromatin domains were queried for the presence of H3K9 di-methylation and Swi6p, both hallmarks of heterochromatin, and for levels of gene expression. We describe a major effect of genomic sequences in determining the size and extent of such de novo heterochromatin domains. Heterochromatin spreading is antagonized by the presence of genes, in a manner that can occur independent of strength of transcription. Increasing the dosage of Swi6p results in increased heterochromatin proximal to the L5 element, but does not result in an expansion of the heterochromatin domain, suggesting that in this context genomic effects are dominant over trans effects. Finally, we show that the ratio of Swi6p to H3K9 di-methylation is sequence-dependent and correlates with the extent of gene repression. Taken together, these data demonstrate that the sequence content of a genomic region plays a significant role in shaping its response to encroaching heterochromatin and suggest a role of DNA sequence in specifying chromatin state.

Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin

“…3), embryos, and fly tissues (arms 2L and 3L, Supplemental Fig. 3) argues against a mechanism involving strict sequence-based boundary elements, as observed in S. pombe (Scott et al 2006;Wheeler et al 2009). We favor the hypothesis that border positions depend on the ''epigenetic balance'' between euchromatic and heterochromatic chromatin components, as suggested by studies of rearranged chromosomes (Ebert et al 2004;Rudolph et al 2007).…”

RNAi-dependent formation of heterochromatin and its diverse functions

“…This process, impacted by the chromosomal context [44], involves a complex interplay between histone-modifying activities and proteins that bind to modified histones [5]. Spreading of heterochromatin has been reported to require RNAi [45].…”

A Barrier-Type Insulator Forms a Boundary between Active and Inactive Chromatin at the Murine TCRβ Locus

“…Here, we identified an LTR at the border between these chromatin domains, and showed that LTR-containing DNA functions as a barrier-type insulator that can protect a transgene from negative chromosomal position effects. This LTR colocalizes with a peak of histone modification H3K4me2, suggesting that it may share with other barrier-type insulators the capacity to recruit histone modifying enzymes that can block the propagation of silent chromatin (16–19). We suggest that by functioning in this way, this LTR helps to maintain the integrity of the E β -regulated chromatin domain in the murine Tcrb locus.…”

“…In vertebrates, enhancer-blocking is mediated by the DNA binding protein CTCF (CCCTC-binding protein), which is thought to function by promoting the formation of chromatin loops (13–15). Several mechanisms have been proposed to explain barrier activity, but a common theme is the recruitment of histone modifying enzymes that deliver activating chromatin modifications which can interrupt the propagation of silent chromatin (16–19). While transcriptional activity has been demonstrated for many yeast insulators with barrier function, transcription is not an absolute requirement for this function (20–21).…”