Genomic Looping: A Key Principle of Chromatin Organization

Abstract

The effective volume occupied by the genomes of all forms of life far exceeds that of the cells in which they are contained. Therefore, all organisms have developed mechanisms for compactly folding and functionally organizing their genetic material. Through recent advances in fluorescent microscopy and 3C-based technologies, we finally have a first glimpse into the complex mechanisms governing the 3-D folding of genomes. A key feature of genome organization in all domains of life is the formation of DNA loops. Here, we describe the main players in DNA organization with a focus on DNA-bridging proteins. Specifically, we discuss the properties of the bacterial DNA-bridging protein H-NS. Via two different modes of binding to DNA, this protein is a key driver of bacterial genome organization and provides a link between 3-D organization and transcription regulation. Importantly, H-NS function is modulated in response to environmental cues, which are translated into adapted gene expression patterns. We delve into the mechanisms underlying DNA looping and explore the complex and subtle modulation of these diverse, yet difficult-to-study, structures. DNA looping is universal and a conserved mechanism of genome organization throughout all domains of life.

Mechanism of environmentally driven conformational changes that modulate H-NS DNA-bridging activity

“…A key protein in nucleoid organization of Gram-negative bacteria is the Histone-like Nucleoid Structuring protein (H-NS). Genome-wide binding studies have revealed that H-NS binds along the genome in long patches ( Grainger et al, 2006 ; Kahramanoglou et al, 2011 ; Lucchini et al, 2006 ; Navarre, 2006 ; Oshima et al, 2006 ), which have been proposed to mediate the formation of genomic loops ( Noom et al, 2007 ; van der Valk et al, 2014 ). H-NS is also an important regulator of global gene expression, implied in mediating global transcriptional responses to environmental stimuli (osmolarity, pH, temperature) ( Atlung and Ingmer, 1997 ), and operating as xenogeneic silencer, silencing horizontally integrated DNA ( Navarre et al, 2006 ).…”

Environment driven conformational changes modulate H-NS DNA bridging activity

“…Mg 2+ alters H-NS structure. To investigate the role of Mg 2+ on individual H-NS dimers we carried out MD simulations of an H-NS dimer in both the absence and presence of Mg 2+ , using our previously established model of a full-length H-NS dimer 14 . Visual inspection of the H-NS dimer simulations at 50 mM KCl reveals that H-NS changes from an "open" extended conformation into more compact "closed" shapes (see figure 2a for snapshots from these simulations or figure 2 -figure supplement 2 for a movie of one such simulation).…”

“…The starting conformation of the full length H-NS dimer was constructed as described previously 14 . The system was placed in a periodic dodecahedron box with a distance of at least 0.8 nm between the box edge and the most extended atom of the protein dimer, followed by the addition of water and ions.…”

“…A key protein in nucleoid organization of Gram-negative bacteria is the Histone-like Nucleoid Structuring protein (H-NS). Genomewide binding studies have revealed that H-NS binds along the genome in long patches [8][9][10][11][12] , which have been proposed to mediate the formation of genomic loops 13,14 . H-NS is also an important regulator of global gene expression, implied in mediating global transcriptional responses to environmental stimuli (osmolarity, pH, temperature) 15 .…”

Quantitative Determination of DNA Bridging Efficiency of Chromatin Proteins

“…These loops may operate locally with regulatory functions at specific single genes [1,2], or over longer distances, enabling the organism to co-regulate genes that are in terms of genomic position far apart [3,4]. Although studies involving DNA looping have a rich history [3,[5][6][7][8][9][10][11][12], in recent years, numerous new insights have become available through the application of new biochemical and biophysical techniques.…”