Nucleotide-level linkage of transcriptional elongation and polyadenylation
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, United States
- RNA Bioscience Initiative, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, United States
Figures
Figure 1 with 2 supplements
Isoforms in yeast 3’ untranslated regions (UTRs) are clustered.
(A) Polyadenylation profile of ATG27, a typical yeast gene, illustrating that major isoforms appear in clusters (represented as C1, C2, and C3 in red lettering). (B) Frequency distribution of …
Figure 1—figure supplement 1
Frequency distributions of naturally occurring and randomized clusters as a function of different cluster definitions.
Cluster definition was altered to reflect either lower (n≤3; top left) or higher (n≤5, top right; n≤6, bottom left; n≤7, bottom right) maximal isoform spacing relative to the cluster definition used …
Figure 1—figure supplement 2
Pol II elongation rate does not affect isoform clustering in 3’ untranslated regions (UTRs).
(Left panel) Frequency distribution of clusters (all isoforms in cluster ≤4 nt apart) containing the indicated number of isoforms in either the randomized or genomic population. The number and …
Figure 2 with 1 supplement
Pol II elongation rate drives poly(A) cluster formation.
(A) Examples of poly(A) profiles in which ‘slower’/wild-type (WT) major isoform ratios (purple) decrease more rapidly within clusters than between clusters. Individual isoforms are defined by the …
Figure 2—figure supplement 1
The link between Pol II elongation rate and poly(A) cluster formation is independent of exact cluster definition.
Median relative ratios (downstream/upstream isoform) of genome-wide ‘slower’/wild-type Pol II utilization at major isoform pairs as a function of nucleotide spacing either within clusters (circles) …
Figure 3 with 1 supplement
Pol II elongation rate drives poly(A) cluster formation.
(A) Example poly(A) profile in which ‘faster’/wild-type (WT) major isoform ratios (purple) increase more rapidly within clusters than between clusters. Clusters and inter-cluster regions are …
Figure 3—figure supplement 1
The link between Pol II elongation rate and poly(A) cluster formation is independent of exact cluster definition.
Median relative ratios (downstream/upstream isoform) of genome-wide ‘faster’/wild-type Pol II utilization at major isoform pairs as a function of nucleotide spacing either within clusters (circles) …
Figure 4 with 2 supplements
Poly(A) cluster formation is also linked to Pol II elongation rate in human cell lines.
(A) An example of a poly(A) profile in which R749H/wild-type (WT) major isoform ratios (purple) decrease more rapidly within a cluster than between clusters. Clusters and inter-cluster regions are …
Figure 4—figure supplement 1
Correlation of wild-type (WT) or R749H Pol II biological replicates.
Axes in bottom left panels represent log10 of isoform reads. Each pairwise comparison panel contains >49,000 (WT) or >32,000 (R749H) isoforms with non-zero reads in both replicates. Upper right …
Figure 4—figure supplement 2
The link between Pol II elongation rate and poly(A) cluster formation is independent of the exact cluster definition in mammalian cells.
Median relative ratios (downstream/upstream isoform) of genome-wide R749H/wild-type (WT) Pol II utilization at major isoform pairs as a function of nucleotide spacing either within clusters …
Figure 5
Cluster-independent link between Pol II elongation rate and poly(A) formation.
(A) Median utilization difference (downstream isoform mutant/wild-type expression ratio minus upstream isoform mutant/wild-type expression ratio) is plotted for either ‘slower’/wild-type (gray bars) …
Figure 6
GC-rich region just downstream of isoform clusters.
(A) GC content in a region downstream of clusters is correlated to cluster slopes in ‘slow’/wild-type (upper left), ‘slower’/wild-type (bottom left), ‘fast’/wild-type (top left), and …
Figure 7 with 1 supplement
Pol II occupancy and AT composition at either READS poly(A) or decoy intronic AATAAA sites in human HEK293 cell lines harboring either wild-type (‘WT’) or slow (‘R749H’) Pol II variants.
(A) eNETseq signal for WT (black; right axis) and R749H (red; right axis) at 2989 READS poly(A) sites (≥20 reads/site in both WT and R749H). Percent AT composition is in blue with the scale on the …
Figure 7—figure supplement 1
Correlation of eNETseq biological replicates at poly(A) and decoy intronic AATAAA sites.
For the wild-type Pol II (‘WT’; left panels) and R749H (right panels) cell lines, the log2 of the total number of eNETseq reads at each site ±100 nt is plotted for each replicate. Pearson …
Figure 8
Schematic of the link between Pol II elongation rate and poly(A) formation.
(A) Nucleotide-level link between Pol II elongation and cleavage/polyadenylation (CpA). As the Pol II machinery (dark blue) elongates the nascent RNA one nucleotide at a time, upstream sequences of …
Additional files
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Supplementary file 1
Supplemental file showing all clusters in YPD.
- https://cdn.elifesciences.org/articles/83153/elife-83153-supp1-v2.xlsx
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MDAR checklist
- https://cdn.elifesciences.org/articles/83153/elife-83153-mdarchecklist1-v2.docx
