The Role of Insulation in Patterning Gene Expression

Abstract

Development is orchestrated by regulatory elements that turn genes ON or OFF in precise spatial and temporal patterns. Many safety mechanisms prevent inappropriate action of a regulatory element on the wrong gene promoter. In flies and mammals, dedicated DNA elements (insulators) recruit protein factors (insulator binding proteins, or IBPs) to shield promoters from regulatory elements. In mammals, a single IBP called CCCTC-binding factor (CTCF) is known, whereas genetic and biochemical analyses in Drosophila have identified a larger repertoire of IBPs. How insulators function at the molecular level is not fully understood, but it is currently thought that they fold chromosomes into conformations that affect regulatory element-promoter communication. Here, we review the discovery of insulators and describe their properties. We discuss recent genetic studies in flies and mice to address the question: Is gene insulation important for animal development? Comparing and contrasting observations in these two species reveal that they have different requirements for insulation, but that insulation is a conserved and critical gene regulation strategy.

Drosophilaarchitectural protein CTCF is not essential for fly survival and is able to function independently of CP190

“…CTCF sites are commonly found in mammalian genomes, and CTCF inactivation typically results in cell death and embryonic mortality, in addition to significantly disturbing the chromosomal architecture [16,24,25]. However, the inactivation of hCTCF only affects the expression of a small number of genes [16], which is consistent with a model in which CTCF is the primary but not the only architectural protein in mammals.…”

CTCF loss has limited effects on global genome architecture in Drosophila despite critical regulatory functions

“…CTCF may also function redundantly with other insulator-binding proteins in Drosophila to limit regulatory crosstalk in this compact genome. Unlike what is known in mammals, flies have a family of insulator-binding proteins, many of which have DNA binding domains with which they target specific loci 56 .…”

A Phosphorylated Histone H2A Variant Displays Properties of Chromatin Insulator Proteins inDrosophila

“…One such example of this is a TAD boundary that flanks a TAD containing the homeotic gene Abdominal A ( Abd-A ). Like other boundaries associated with the homeobox gene cluster (Postika et al , 2018, Ozdemir and Gambetta, 2019), this boundary is enriched in the insulator proteins Su(Hw), Modifier of Mdg4, CP190, CTCF, and HIPP1. Here, we show this boundary is equally enriched in γH2Av (Figure 10F).…”

“…These interactions create domains that may be restricted from interacting with each other, and are based on specific interactions between chromatin-binding proteins (van Berkum et al , 2010, Rao et al , 2014, Fudenberg et al , 2016). Chromatin insulators represent a class of protein/DNA complexes associated to specific sequences in the genome that work through two general functions: to restrict communication between enhancers and promoters through physical separation into different genomic domains and to prevent the spread of heterochromatin into euchromatic regions of the genome (Harrison et al, 1989, Geyer and Corces, 1992, Bell et al, 1999, Schoborg and Labrador, 2014, Ozdemir and Gambetta, 2019). The presence of insulators in the genome is conserved among eukaryotes, with the CTCF insulator being the only known insulator regulating the human genome (Heger and Wiehe, 2014).…”