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Review
. 2012 Jun;28(6):285-94.
doi: 10.1016/j.tig.2012.02.005. Epub 2012 Mar 31.

Overcoming the nucleosome barrier during transcript elongation

Steven J Petesch  1 , John T Lis
Affiliations
Review

Overcoming the nucleosome barrier during transcript elongation

Steven J Petesch et al. Trends Genet. 2012 Jun.

Abstract

RNA polymerase II (Pol II) must break the nucleosomal barrier to gain access to DNA and transcribe genes efficiently. New single-molecule techniques have elucidated many molecular details of nucleosome disassembly and what happens once Pol II encounters a nucleosome. Our review highlights mechanisms that Pol II utilizes to transcribe through nucleosomes, including the roles of chromatin remodelers, histone chaperones, post-translational modifications of histones, incorporation of histone variants into nucleosomes, and activation of the poly(ADP-ribose) polymerase (PARP) enzyme. Future studies need to assess the molecular details and the contribution of each of these mechanisms, individually and in combination, to transcription across the genome to understand how cells are able to regulate transcription in response to developmental, environmental and nutritional cues.

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Figures

Figure 1
Figure 1. The nucleosome contains specific interactions that provide a barrier to transcript elongation and can be disassembled through chromatin remodelers
(a) The crystal structure of the nucleosome as visualized from PDBid 1AOI [72]. The nucleosome consists of 147 bp of DNA (strands colored black) wrapped 1.7 times around a core octamer of histone proteins with 2 H2A (yellow) H2B (red) dimers associated with an H3 (blue) H4 (green) tetramer. All the subsequent depictions of nucleosomes will use the color coordination depicted here unless otherwise noted. The strongest DNA contacts that exist between the DNA and histones are marked by asterisks with the first being 30 bp into the nucleosome where DNA contacts the H2A-H2B dimer interface and 70 bp into the nucleosome at the nucleosome dyad. This perspective of the nucleosome also shows the direction of DNA movement when breathing, a process whereby DNA spontaneously breaks contact with the histones, which occurs once every 250 ms 20 bp into the nucleosome but once every 10 minutes 40 bp into the nucleosome. The figure on the right is rotated to show the same nucleosome looking at the nucleosome dyad, which is the perspective Pol II takes when it engages the nucleosome. This is the perspective sketched in (b) and subsequent figures. (b) Diagram depicting the reversible process of nucleosome disassembly/assembly as determined by FRET assays. The first step depicts the H2A-H2B dimers breaking contact with the H3-H4 tetramer in the intact nucleosome state (i) and opening up to form the intermediate shown in (ii). The second step shows the dissociation of the H2A-H2B dimers from the DNA template leaving just the H3-H4 template as shown in (iii). The last step includes the dissociation of the H3-H4 tetramer from the DNA template resulting in naked DNA (iv). (c) Chromatin remodelers contain multiple functions which result in either changes in the nucleosome position or composition. These four functions are depicted as reversible processes that can be achieved independently of one another. Chromatin remodelers are capable of sliding nucleosomes along a DNA template to change nucleosome positions (i), ejecting individual histones (ii), exchanging new histones into the nucleosome (H2A.Z is shown to be exchanged as an example in pink) (iii), or completely ejecting a full histone octamer (iv).
Figure 2
Figure 2. Transcriptionally Active Genes are Associated with Specific Histone Post-Translational Modifications that can Trigger the Enzymatic Activity of Poly(ADP-Ribose) Polymerase to Facilitate Transcript elongation
(a) A transcriptionally active gene is shown with the transcription start site of the gene indicated by the arrow, and a representative profile of Pol II density along the gene is shown above in a red line trace. The promoter region of most genes contains a nucleosome depleted region with flanking nucleosomes on either side that are enriched in the histone variants H2A.Z (pink) and H3.3 (purple) which have a higher rate of exchange than their canonical histones found further into the open reading frame. Nucleosomes are periodically spaced flanking the nucleosome-depleted region and may be the result of chromatin remodelers that evenly space the nucleosomes such as Chd1 and ISWI. Additionally, PTMs of histones that correlate positively with gene transcription are depicted above the gene. These include histone acetylation of the N-terminal tails of both H3 and H4, such as H3K9, H4K5, H4K8, H4K12, and H4K16, which are found near the promoters of genes (blue dome) and trimethylated at H3K4 (orange triangles), which are present on nucleosomes flanking the promoter in a monotonically decreasing fashion. Finally, the open reading frames of active genes are progressively modified by H3K36Me3, H3K79Me2, and H2BK123Ub (gold triangle). (b) Model of PARP activation at heat shock loci summarizing [86, 87]. (i) Before heat shock, the Drosophila Hsp70 gene contains a transcriptionally engaged, paused Pol II (red) and inactive PARP (gray) present near the first well-positioned nucleosome after the transcription start site, indicated by the arrow. Hsp70 is known to contain the Drosophila H2A.Z variant, H2Av (pink), at the 5’ end of the gene before heat shock. It is not known if the C-terminal S137 of H2Av is already in a phosphorylated state. (ii) After heat shock, the master transcriptional activator, heat shock factor (HSF, orange), is recruited to the promoter of Hsp70 as a trimer. HSF in turn is responsible for recruiting the dTip60 complex (purple cloud), which is part of a chromatin remodeling complex containing a protein homologous to Swr1. dTip60 is responsible for acetylating H2AK5 near the 5’ end of the gene. (iii) Following acetylation of H2AK5, the dTip60 complex is likely to exchange out the H2Av variant as it is known to do in vitro with H2Av that is acetylated at K5 and phosphorylated at S137. The combination of the acetylation of H2AK5 and the exchange of H2A triggers activation of PARP's enzymatic activity (now shown in blue). (iv) The activation of PARP (blue) results in the formation of PAR (blue lines) and the redistribution of PARP throughout the coding region and beyond, but halts at nearby natural chromatin insulating elements (not shown). This rapid, domain-wide process leads to a buildup of PAR throughout the region that locally disrupts and strips histones from the gene allowing for efficient transcript elongation and robust gene activation.
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