Maintenance of long-range DNA interactions after inhibition of ongoing RNA polymerase II transcription

Abstract

A relationship exists between nuclear architecture and gene activity and it has been proposed that the activity of ongoing RNA polymerase II transcription determines genome organization in the mammalian cell nucleus. Recently developed 3C and 4C technology allowed us to test the importance of transcription for nuclear architecture. We demonstrate that upon transcription inhibition binding of RNA polymerase II to gene regulatory elements is severely reduced. However, contacts between regulatory DNA elements and genes in the beta-globin locus are unaffected and the locus still interacts with the same genomic regions elsewhere on the chromosome. This is a general phenomenon since the great majority of intra- and interchromosomal interactions with the ubiquitously expressed Rad23a gene are also not affected. Our data demonstrate that without transcription the organization and modification of nucleosomes at active loci and the local binding of specific trans-acting factors is unaltered. We propose that these parameters, more than transcription or RNA polymerase II binding, determine the maintenance of long-range DNA interactions.

Figure 1. Transcription is efficiently inhibited by DRB and α-amanitin.

(A) Schematic presentation of the murine β-globin locus. Red arrows and ellipses depict the individual HSs. The globin genes are indicated by black triangles. The white boxes indicate the olfactory receptor (OR) genes (5′OR1-6 and 3′OR1-4). Distances (roman numerals) are in kb counting from the site of initiation of the εy gene. (B) Primary RNA-FISH of DRB and α-amanitin treated cells. Red bars indicate percentage of cells expressing β-globin and green bars indicate percentage of cells expressing α-globin. Representative examples of images are shown. (C) Reduction of the active elongating form of RNAPII as detected by western blot. Top panel using an antibody against the RPB1 subunit of RNAPII (N20). IIO represent the phosphorylated form of RNAPII, IIA the unphosporylated form. Bottom panel using an antibody against the Ser2 phosphorylated CTD of RNAPII (H5). (D) RNAPII binding at the β-major gene and hypersensitive sites of the LCR. Enrichment is relative to amylase. Blue bars depict untreated samples, red bars DRB treated samples, green bars α-amanitin treated samples. (E) RNAPII binding at regulatory elements within the Rad23a locus upon DRB and α-amanitin treatment. Enrichment is relative to amylase. Blue bars depict untreated samples, red bars DRB treated samples and green bars α-amanitin treated samples. Error bars indicate standard error of mean.

Figure 2. LCR-gene interactions in the β-globin locus are not dependent on ongoing transcription.

(A–B) Locus wide cross-linking frequencies observed in untreated fetal liver cells (blue) DRB treated fetal liver cells (red) and α-amanitin treated fetal livers (green) are shown. The murine β-globin locus is depicted on top of each graph. X-axis shows position in the locus. Black shading shows the position and size of the ‘fixed’ HindIII fragment. Grey shading indicates position and size of other HindIII fragments analyzed. Standard-error-of-mean is indicated. Cross-linking frequencies are normalized to the highest interaction within an experiment and give an arbitrary value of 1. (A) Cross-linking frequencies for a restriction fragment containing the β-globin promoter. High crosslinking frequencies with restriction fragments containing the hypersensitive sites of the LCR are observed in all samples, indicating close proximity between the β-globin promoter and LCR (B) Cross-linking frequencies for a restriction fragment containing HS2 of the β-globin LCR. High crosslinking frequencies with the restriction fragment containing the β-globin promoter is observed in all samples, indicating close proximity between HS2 of the LCR and the β-globin promoter. (C) Bar graphs of cross-linking frequencies for a restriction fragment containing the CTCF-binding HS4/5 of the β-globin LCR with other selected CTCF-binding sites within the β-globin locus (i.e. HS-85.5, HS-62.5/-60.7 and 3′HS1). Blue bars depict untreated samples, red bars DRB treated samples and green bars α-amanitin treated samples. Cross-linking frequencies are normalized to the highest interaction within the experiment and give an arbitrary value of 1. Error bars indicate standard error of mean.

Figure 3. The tissue specific β-globin locus does not switch its nuclear environment upon transcription inhibition.

(A) Running mean data for two untreated fetal liver (blue) and α-amanitin treated fetal liver (green) samples are shown. Peaks of interaction of the β-globin promoter that are above the threshold (dashed line) with several regions on chromosome 7 are observed. (B) Zoom in of the running mean data plotted along a 12-Mb region centered around 114.5 MB on chromosome 7. False discovery rate was set at 5% (dashed line). Highly reproducible clusters of interactions with the β-globin locus are observed in the two untreated fetal liver samples and the two α-amanitin treated fetal liver samples. Vertical bars indicate interactions that reach threshold levels in both duplicates. Chromosomal positions were based on National Center for Biotechnology (NCBI) build m34. (C) Indicated are the percentages of interacting regions on chromosome 7 observed for the β-globin locus in untreated fetal liver that are identified in both, a single or none of the α-amanitin treated fetal liver samples. (D) Schematic representation of cryo-FISH results. Grey shading indicates the regions identified (positive in both replicates) in untreated fetal livers, black shading indicates the regions identified (positive in both replicates) in α-amanitin treated fetal liver cells. Percentages of interaction with β-globin are indicated above the chromosome for untreated fetal liver cells or below the chromosome for α-amanitin treated fetal liver cells (black numbers indicate interacting, red non-interacting). Green bars indicate regions that are identified to be positive in both replicates by 4C technology. Red bars indicate regions identified to be negative in both replicates. Regions that are identified to be positive in only one replicate are indicated by a combined red and green bar. (E) Regions that score single positive after treatment while being double positive in untreated samples represent genuine interacting regions. Box plots representing our collective cryo-FISH data obtained for negative, single positive and double positive 4C regions for 102 different loci in different cell types scoring a total of 26733 alleles. Left panel depicts data obtained for interactions in Cis, right panel depicts data obtained for interactions in Trans. Horizontal bars represent the 10^th, 25^th, 50^th (median), 75^th and 90^th percentiles, and p values for pairs of samples are indicated. The p value for a pair of samples was determined by an independent samples t-test for equality of means. Circles represent single values identified as outliers.

Figure 4. The housekeeping gene Rad23a does not switch its nuclear environment upon transcription inhibition.

(A) Running mean data for two untreated fetal liver (blue) and α-amanitin treated fetal liver (green) samples is shown. Peaks of interaction of the Rad23a promoter above the threshold (dashed line) with several regions on chromosome 8 can be observed. False discovery rate was set at 5% (dashed line). Chromosomal positions were based on NCBI build m34. (B) Indicated are the percentages of interacting regions observed for Rad23a in cis on chromosome 8 in untreated fetal liver that are identified in both, a single or none of the α-amanitin treated fetal liver samples. (C) Indicated is the percentages of trans-interacting regions observed for Rad23a in untreated fetal liver that are identified in both, a single or none of the α-amanitin treated fetal liver samples.

Figure 5. Key erythroid transcription factors remain bound to regulatory sites of the β-globin locus.

Binding of (A) EKLF, (B) GATA-1, (C) NF-E2 and (D) CBP at β-globin regulatory elements. Blue bars depict untreated fetal liver samples, red bars DRB treated fetal liver samples and green bars α-amanitin treated fetal liver samples. Enrichment is relative to amylase. Error bars indicate standard error of mean.

Figure 6. The chromatin of loci remains in an active state after transcription inhibition.

(A) Acetylation of histone H3 at regulatory sites of the β-globin and Rad23a locus (B) dimethylation of lysine 9 and 27 of histone H3 at regulatory sites of the β-globin and Rad23a locus (C) Trimethylation of lysine 4 of histone H3 at regulatory sites of the β-globin and Rad23a locus. (D) Detection of histone depleted chromatin at regulatory elements of the β-globin locus using FAIRE. Enrichment is relative to amylase. Grey bars depict fetal brain samples, blue bars depict untreated fetal liver samples, red bars depict DRB treated fetal liver samples and green bars α-amanitin treated fetal liver samples. Error bars indicate standard error of mean.