Transcription within condensed chromatin: Steric hindrance facilitates elongation

Abstract

During eukaryotic transcription, RNA-polymerase activity generates torsional stress in DNA, having a negative impact on the elongation process. Using our previous studies of chromatin fiber structure and conformational transitions, we suggest that this torsional stress can be alleviated, thanks to a tradeoff between the fiber twist and nucleosome conformational transitions into an activated state named "reversome". Our model enlightens the origin of polymerase pauses, and leads to the counterintuitive conclusion that chromatin-organized compaction might facilitate polymerase progression. Indeed, in a compact and well-structured chromatin loop, steric hindrance between nucleosomes enforces sequential transitions, thus ensuring that the polymerase always meets a permissive nucleosomal state.

Figure 1

(Color online) Free-energy landscape for the nucleosome conformation. The reaction coordinate (abscissa Lk) is the linking number of nucleosomal DNA; this choice appears relevant to investigate the landscape changes when a torque Γ is applied to the DNA (see subsection Linking Number Conservation: Accounting for Mechanical Constraints). The two main states are sketched here: the current nucleosome, with two substates N and P according to the relative positions of the linkers (negative or positive crossing); and an activated state, the reversome, in which the histone core partially unfolds and the nucleosomal DNA adopts a right-handed path around the histone core. (Courtesy of Hua Wong.)

Figure 2

(Color online) The n-start fiber structure (with n = 4, corresponding to a repeat length of n_repeat = 87 bps (25)). Note the close and regular nucleosome stacking along each start, preventing the transition to reversome of a single nucleosome, and instead enforcing a concerted sequential transition. (Courtesy of Julien Mozziconacci.)

Figure 3

Relative positions along the chromatin fiber. The polymerase moves to the right, X(t) being its position at time t. The value l₀ is the length of the loop region downstream of the initiation site X(0) = 0, and l(t) = l₀ – X(t) is the length remaining at time t between the polymerase and the downstream boundary.

Figure 4

(Color online) RNA-polymerase processing within condensed chromatin fiber. (a) The supercoiling generated by the polymerase activity is trapped within the loop delineated by topological boundaries (the thin black regions are outside the loop). The ensuing torsional constraints trigger the sequential transition of nucleosomes (in green) into reversomes (in yellow). (b) Illustration of the domino effect: after 1 s, the fifth nucleosome downstream of the polymerase (green in panel a) has turned into a reversome (yellow in panel b); after one more second, the sixth nucleosome has turned into a reversome. (c) Reversome density profile: in the bold yellow region [0, x^∗], the reversome density ξ(x, t) equals 1. The wavefront is located at x^∗ and propagates downstream ∼10 times faster than the polymerase progression. In the polymerase wake, the nucleosomes turn to the negative state (dashed blue in panel a) to ensure the conservation of the total linking number of the loop.