Transcription mediated insulation and interference direct gene cluster expression switches
- University of Oxford, United Kingdom
- European Molecular Biology Laboratory, Germany
Figures
Figure 1 with 4 supplements
Reciprocal switching of expression by carbon source reveals links to the YMC.
(A) The distribution of all ORF-Ts into different YMC phases. OX, oxidative phase; RB, reductive building phase; RC, reductive charging phase of the YMC. (B, C, F) YMC profiles (SCEPTRANS; http://mom…
Figure 1—figure supplement 1
Exemplary tandem gene clusters and their regulation by carbon source and the YMC.
Supplements 1A–D, 2A–D, 3A–C show examples of tandem gene clusters with reciprocal switching of transcription by carbon source, di-cistrons, and antisense transcripts. Supplements 3D and 4A–D show …
Figure 1—figure supplement 2
Exemplary tandem gene clusters and their regulation by carbon source and the YMC.
Supplements 1A–D, 2A–D, 3A–C show examples of tandem gene clusters with reciprocal switching of transcription by carbon source, di-cistrons, and antisense transcripts. Supplements 3D and 4A–D show …
Figure 1—figure supplement 3
Exemplary tandem gene clusters and their regulation by carbon source and the YMC.
Supplements 1A–D, 2A–D, 3A–C show examples of tandem gene clusters with reciprocal switching of transcription by carbon source, di-cistrons, and antisense transcripts. Supplements 3D and 4A–D show …
Figure 1—figure supplement 4
Exemplary tandem gene clusters and their regulation by carbon source and the YMC.
Supplements 1A–D, 2A–D, 3A–C show examples of tandem gene clusters with reciprocal switching of transcription by carbon source, di-cistrons, and antisense transcripts. Supplements 3D and 4A–D show …
Figure 2 with 1 supplement
Characterization of transcripts around the HMS2:BAT2 locus (A).
Visualizing HMS2 transcripts using RNA fluorescence in situ hybridization (RNA FISH) in single cells using a combination of four, 50 nt DNA probes labelled with four fluorophores, either Cy5 (sense) …
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Figure 2—Source data 1
(A) Source data for Figure 2B, (B) Source data for Figure 2—Supplement 1B.
- https://doi.org/10.7554/eLife.03635.009
Figure 2—figure supplement 1
Characterization of transcripts around the HMS2:BAT2 locus.
(A) Map of transcripts. (B) Histogram showing quantitation of the Northern blot in (C) Figure 2—source data 1B. (C) Northern blot showing carbon source regulation of HMS2, SUT650, and BAT2 …
Figure 3
HMS2 mediates transcriptional interference of BAT2.
(A) Schematic showing constructs and transcripts at the WT HMS2:BAT2 locus and after insertion of the ADH1 terminator (T). (B) Exemplarily autoradiographs of Northern blots of total RNA prepared …
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Figure 3—source data 1
- https://doi.org/10.7554/eLife.03635.012
Figure 4 with 1 supplement
SUT650 antisense transcription insulates BAT2 from interference by HMS2.
(A) Schematic showing transcripts after replacement of the HMS2 coding region (top) with the URA3 coding region (middle) or URA3 plus a transcription terminator (T) (bottom). Transcripts resulting …
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Figure 4—source data 1
- https://doi.org/10.7554/eLife.03635.014
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Figure 4—source data 2
Source data for Figure 4G.
- https://doi.org/10.7554/eLife.03635.015
Figure 4—figure supplement 1
No SUT650 antisense transcription in either GLU or GAL in the HMS2:URA3 strain.
(A) Schematic showing transcripts after replacement of the HMS2 coding region (top) with the URA3 coding region (bottom). (B) Northern blots of total RNA in WT strain or with the HMS2 coding region …
Figure 5 with 1 supplement
HMS2 sense transcription represses the HMS2 antisense transcript and BAT2.
(A) Schematic showing transcripts when expression of HMS2 is regulated by the GAL1 promoter (pGAL1) in glucose (antisense-dominant state) or galactose (sense-dominant state) or when the HMS2 coding …
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Figure 5—source data 1
- https://doi.org/10.7554/eLife.03635.018
Figure 5—figure supplement 1
Mapping the 3′ ends of the pGAL.HMS2 antisense transcript isoforms.
(A) Schematic of the pGAL1.HMS2 transcription unit. (B) 3′RACE performed on the galactose-inducible HMS2 strain in glucose displays evidence of two poly(A) tails, one consistent with the short, BG2, …
Figure 6 with 1 supplement
General and specific transcription factors control state switching at HMS2.
(A, C, D) Northern blots showing sense or antisense-dominant state at HMS2 in strains lacking general or specific transcription factors. (A) Strains were cultured in YPD depleted for tryptophan. (B) …
Figure 6—figure supplement 1
The effect of deletion or ablation of transcription factors with putative binding sites at the HMS2:BAT2 intergenic region on HMS2:BAT2 transcripts.
(A) Schematic of transcripts. (B, C) Northern blot analysis in the strains indicated. (B) In the top panel strains were grown in glucose (−) or for 1 hr in galactose (GAL, +). In the bottom panel, …
Figure 7 with 1 supplement
The plasticity of transcription units.
(A, C) Schematic of constructs showing transcripts and position of probes. Transcripts resulting from the pTEF:kanMX:TEFt insertion, the same construct with the ADH1 terminator (pink box), or the TEF…
Figure 7—figure supplement 1
Creating and characterizing an interleaved locus around HMS2.
(A) Schematic (i) and estimated sizes (ii) of transcripts in the HMS2.kan, HMS2 TEFΔ1.kan, and HMS2.ADH disruption strains. (B) Dissection of the 5′ region of the TEF promoter. The TEF promoter can …
Additional files
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Supplementary file 1
(A) Genome-wide NET-seq (NET) and poly(A)+ RNA hybridised to microarray (mi). (B) Data for Pie Charts in Figure 1. (C) YMC genes (Coloured in columns A, C, and E) that overlap with genes whose transcription changes >threefold on the GLU to GAL shift (Column G—complete list colour coded). (D) Gene Ontology (GO) associated with genes that change >threefold on the GLU to GAL shift. (E) Annotated CUTs and SUTs that change >threefold on GLU to GAL shift (from Supplementary file 1A). (F) Extracted data from genome-wide simulation of gene type, orientation, and regulation. (G). Gene Groups from genome-wide annotations of OX.RC, RC.OX, and non-cycling (NC) pairs in tandem—used to provide information for Supplementary file 1J and to derive the distinct environments surrounding pairs of cycling or non-cycling genes. (H) Selected genes from Supplementary file 1A and analysis of their environment. (I) Genes that change >threefold on the GLU/GAL shift that also have an annotated antisense CUT or SUT that also changes >threefold on the GLU/GAL shift. (J) Selected gene clusters resembling HMS2:BAT2. (K) Transcription-related factors enriched at the promoters of RC or OX genes. (L) Genotype of yeast strains used in this study. (M) Primers used for 3′RACE. (N) Primers used to generate strand-specific probes for Northern blot analysis. The T7 promoter sequence is shown in parentheses. (O) RNA FISH probes. (P) Primers used for real-time PCR.
- https://doi.org/10.7554/eLife.03635.024
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Source Code 1
Source Codes in MATLAB 'simulation_gene_orientation_and_expression'.
- https://doi.org/10.7554/eLife.03635.025
