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Imashimizu M, Tokunaga Y, Afek A, Takahashi H, Shimamoto N, Lukatsky DB. Control of Transcription Initiation by Biased Thermal Fluctuations on Repetitive Genomic Sequences. Biomolecules 2020; 10:biom10091299. [PMID: 32916947 PMCID: PMC7564750 DOI: 10.3390/biom10091299] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/23/2020] [Accepted: 09/04/2020] [Indexed: 12/12/2022] Open
Abstract
In the process of transcription initiation by RNA polymerase, promoter DNA sequences affect multiple reaction pathways determining the productivity of transcription. However, the question of how the molecular mechanism of transcription initiation depends on the sequence properties of promoter DNA remains poorly understood. Here, combining the statistical mechanical approach with high-throughput sequencing results, we characterize abortive transcription and pausing during transcription initiation by Escherichia coli RNA polymerase at a genome-wide level. Our results suggest that initially transcribed sequences, when enriched with thymine bases, contain the signal for inducing abortive transcription, whereas certain repetitive sequence elements embedded in promoter regions constitute the signal for inducing pausing. Both signals decrease the productivity of transcription initiation. Based on solution NMR and in vitro transcription measurements, we suggest that repetitive sequence elements within the promoter DNA modulate the nonlocal base pair stability of its double-stranded form. This stability profoundly influences the reaction coordinates of the productive initiation via pausing.
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Affiliation(s)
- Masahiko Imashimizu
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan;
- Correspondence: (M.I.); (D.B.L.); Tel.: +81-3-3599-8232 (M.I.); +972-8642-8370 (D.B.L.)
| | - Yuji Tokunaga
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan;
| | - Ariel Afek
- Center for Genomic and Computational Biology, Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27708, USA;
| | - Hiroki Takahashi
- Medical Mycology Research Center, Chiba University, Chiba 260-8673, Japan;
- Molecular Chirality Research Center, Chiba University, Chiba 263-8522, Japan
- Plant Molecular Science Center, Chiba University, Chiba 260-8675, Japan
| | - Nobuo Shimamoto
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan;
| | - David B. Lukatsky
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Correspondence: (M.I.); (D.B.L.); Tel.: +81-3-3599-8232 (M.I.); +972-8642-8370 (D.B.L.)
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2
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Roßmanith J, Weskamp M, Narberhaus F. Design of a Temperature-Responsive Transcription Terminator. ACS Synth Biol 2018; 7:613-621. [PMID: 29191010 DOI: 10.1021/acssynbio.7b00356] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
RNA structures regulate various steps in gene expression. Transcription in bacteria is typically terminated by stable hairpin structures. Translation initiation can be modulated by metabolite- or temperature-sensitive RNA structures, called riboswitches or RNA thermometers (RNATs), respectively. RNATs control translation initiation by occlusion of the ribosome binding site at low temperatures. Increasing temperatures destabilize the RNA structure and facilitate ribosome access. In this study, we exploited temperature-responsive RNAT structures to design regulatory elements that control transcription termination instead of translation initiation in Escherichia coli. In order to mimic the structure of factor-independent intrinsic terminators, naturally occurring RNAT hairpins were genetically engineered to be followed by a U-stretch. Functional temperature-responsive terminators (thermoterms) prevented mRNA synthesis at low temperatures but resumed transcription after a temperature upshift. The successful design of temperature-controlled terminators highlights the potential of RNA structures as versatile gene expression control elements.
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Affiliation(s)
| | - Mareen Weskamp
- Microbial Biology, Ruhr University Bochum, 44780 Bochum, Germany
| | - Franz Narberhaus
- Microbial Biology, Ruhr University Bochum, 44780 Bochum, Germany
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3
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Huang Y, Russu IM. Dynamic and Energetic Signatures of Adenine Tracts in a rA-dT RNA-DNA Hybrid and in Homologous RNA-DNA, RNA-RNA, and DNA-DNA Double Helices. Biochemistry 2017; 56:2446-2454. [PMID: 28430414 DOI: 10.1021/acs.biochem.6b01122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclear magnetic resonance spectroscopy and proton exchange are being used to characterize the opening reactions of individual base pairs in the RNA-DNA hybrid 5'-rGCGAUAAAAAGGCC-3'/5'-dGGCCTTTTTATCGC-3'. The hybrid contains a central tract of five rA-dT base pairs. The rates and the equilibrium constant of the opening reaction for each base pair are determined from the dependence of the exchange rates of imino protons on ammonia concentration, at 10 °C. The results are compared to those previously obtained by our laboratory for three homologous duplexes of the same base sequence (except for the appropriate T/U substitution), containing tracts of dA-rU, rA-rU, or dA-dT base pairs. The rA-dT tract is distinguished by an enhanced propensity of the base pairs to exist in the extrahelical state. The opening rates of rA-dT base pairs also exhibit a strong dependence on the location of the base pair in the structure; namely, as one advances into the tract, the opening rates of rA-dT base pairs gradually decrease. The local stability of each rA-dT base pair within the tract is the same as that of the corresponding rA-rU base pair in the homologous RNA-only duplex but differs from the stabilities of dA-dT and dA-rU base pairs in the other two duplexes (namely, dA-dT > rA-dT > dA-rU). These results demonstrate that, in nucleic acid double helices with the same base sequence, the opening dynamics and the energetics of individual base pairs are strongly influenced by the nature of the strand and by the structural context of the base pair.
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Affiliation(s)
- Yuegao Huang
- Department of Chemistry and Molecular Biophysics Program, Wesleyan University , Middletown, Connecticut 06459, United States
| | - Irina M Russu
- Department of Chemistry and Molecular Biophysics Program, Wesleyan University , Middletown, Connecticut 06459, United States
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4
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Szulik M, Pallan PS, Nocek B, Voehler M, Banerjee S, Brooks S, Joachimiak A, Egli M, Eichman BF, Stone MP. Differential stabilities and sequence-dependent base pair opening dynamics of Watson-Crick base pairs with 5-hydroxymethylcytosine, 5-formylcytosine, or 5-carboxylcytosine. Biochemistry 2015; 54:1294-305. [PMID: 25632825 PMCID: PMC4325598 DOI: 10.1021/bi501534x] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
5-Hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) form during active demethylation of 5-methylcytosine (5mC) and are implicated in epigenetic regulation of the genome. They are differentially processed by thymine DNA glycosylase (TDG), an enzyme involved in active demethylation of 5mC. Three modified Dickerson-Drew dodecamer (DDD) sequences, amenable to crystallographic and spectroscopic analyses and containing the 5'-CG-3' sequence associated with genomic cytosine methylation, containing 5hmC, 5fC, or 5caC placed site-specifically into the 5'-T(8)X(9)G(10)-3' sequence of the DDD, were compared. The presence of 5caC at the X(9) base increased the stability of the DDD, whereas 5hmC or 5fC did not. Both 5hmC and 5fC increased imino proton exchange rates and calculated rate constants for base pair opening at the neighboring base pair A(5):T(8), whereas 5caC did not. At the oxidized base pair G(4):X(9), 5fC exhibited an increase in the imino proton exchange rate and the calculated kop. In all cases, minimal effects to imino proton exchange rates occurred at the neighboring base pair C(3):G(10). No evidence was observed for imino tautomerization, accompanied by wobble base pairing, for 5hmC, 5fC, or 5caC when positioned at base pair G(4):X(9); each favored Watson-Crick base pairing. However, both 5fC and 5caC exhibited intranucleobase hydrogen bonding between their formyl or carboxyl oxygens, respectively, and the adjacent cytosine N(4) exocyclic amines. The lesion-specific differences observed in the DDD may be implicated in recognition of 5hmC, 5fC, or 5caC in DNA by TDG. However, they do not correlate with differential excision of 5hmC, 5fC, or 5caC by TDG, which may be mediated by differences in transition states of the enzyme-bound complexes.
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Affiliation(s)
- Marta
W. Szulik
- Department
of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt
Ingram Cancer Center, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Pradeep S. Pallan
- Department
of Biochemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt
Ingram Cancer Center, and Center for Structural Biology, School of
Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Boguslaw Nocek
- Bioscience
Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Markus Voehler
- Department
of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt
Ingram Cancer Center, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Surajit Banerjee
- Northeastern
Collaborative Access Team and Department of Chemistry and Chemical
Biology, Cornell University, Argonne National
Laboratory, Argonne, Illinois 60439, United
States
| | - Sonja Brooks
- Department
of Biological Sciences, Vanderbilt Institute of Chemical Biology,
and Center for Structural Biology, Vanderbilt
University, Nashville, Tennessee 37235, United States
| | - Andrzej Joachimiak
- Bioscience
Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Martin Egli
- Department
of Biochemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt
Ingram Cancer Center, and Center for Structural Biology, School of
Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Brandt F. Eichman
- Department
of Biological Sciences, Vanderbilt Institute of Chemical Biology,
and Center for Structural Biology, Vanderbilt
University, Nashville, Tennessee 37235, United States
| | - Michael P. Stone
- Department
of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt
Ingram Cancer Center, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States,(M.P.S.) Tel.: 615-322-2589; E-mail:
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Schaughency P, Merran J, Corden JL. Genome-wide mapping of yeast RNA polymerase II termination. PLoS Genet 2014; 10:e1004632. [PMID: 25299594 PMCID: PMC4191890 DOI: 10.1371/journal.pgen.1004632] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 07/21/2014] [Indexed: 12/22/2022] Open
Abstract
Yeast RNA polymerase II (Pol II) terminates transcription of coding transcripts through the polyadenylation (pA) pathway and non-coding transcripts through the non-polyadenylation (non-pA) pathway. We have used PAR-CLIP to map the position of Pol II genome-wide in living yeast cells after depletion of components of either the pA or non-pA termination complexes. We show here that Ysh1, responsible for cleavage at the pA site, is required for efficient removal of Pol II from the template. Depletion of Ysh1 from the nucleus does not, however, lead to readthrough transcription. In contrast, depletion of the termination factor Nrd1 leads to widespread runaway elongation of non-pA transcripts. Depletion of Sen1 also leads to readthrough at non-pA terminators, but in contrast to Nrd1, this readthrough is less processive, or more susceptible to pausing. The data presented here provide delineation of in vivo Pol II termination regions and highlight differences in the sequences that signal termination of different classes of non-pA transcripts. Transcription termination is an important regulatory event for both non-coding and coding transcripts. Using high-throughput sequencing, we have mapped RNA Polymerase II's position in the genome after depletion of termination factors from the nucleus. We found that depletion of Ysh1 and Sen1 cause build up of polymerase directly downstream of coding and non-coding genes, respectively. Depletion of Nrd1 causes an increase in polymerase that is distributed up to 1,000 bases downstream of non-coding genes. The depletion of Nrd1 helped us to identify more than 250 unique termination regions for non-coding RNAs. Within this set of newly identified non-coding termination regions, we are further able to classify them based on sequence motif similarities, suggesting a functional role for different terminator motifs. The role of these factors in transcriptional termination of coding and/or non-coding transcripts can be inferred from the effect of polymerase's position downstream of given termination sites. This method of depletion and sequencing can be used to further elucidate other factors whose importance to transcription has yet to be determined.
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Affiliation(s)
- Paul Schaughency
- Department of Molecular Biology and Genetics, Johns Hopkins Medical School, Baltimore, Maryland, United States of America
| | - Jonathan Merran
- Department of Molecular Biology and Genetics, Johns Hopkins Medical School, Baltimore, Maryland, United States of America
| | - Jeffry L. Corden
- Department of Molecular Biology and Genetics, Johns Hopkins Medical School, Baltimore, Maryland, United States of America
- * E-mail:
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6
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Zhang J, Russu IM. Site-Resolved Structural Energetics of the T7 Concatemer Junction. Biochemistry 2014; 53:4806-13. [DOI: 10.1021/bi500393q] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jie Zhang
- Department of Chemistry and
Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459, United States
| | - Irina M. Russu
- Department of Chemistry and
Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459, United States
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7
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Szulik MW, Voehler MW, Ganguly M, Gold B, Stone MP. Site-specific stabilization of DNA by a tethered major groove amine, 7-aminomethyl-7-deaza-2'-deoxyguanosine. Biochemistry 2013; 52:7659-68. [PMID: 24131376 PMCID: PMC3812902 DOI: 10.1021/bi400695r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
A cationic
7-aminomethyl-7-deaza-2′-deoxyguanosine (7amG)
was incorporated site-specifically into the self-complementary duplex
d(G1A2G3A4X5C6G7C8T9C10T11C12)2 (X = 7amG). This construct placed two positively charged amines adjacent
to the major groove edges of two symmetry-related guanines, providing
a model for probing how cation binding in the major groove modulates
the structure and stability of DNA. Molecular dynamics calculations
restrained by nuclear magnetic resonance (NMR) data revealed that
the tethered cationic amines were in plane with the modified base
pairs. The tethered amines did not form salt bridges to the phosphodiester
backbone. There was also no indication of the amines being capable
of hydrogen bonding to flanking DNA bases. NMR spectroscopy as a function
of temperature revealed that the X5 imino resonance remained
sharp at 55 °C. Additionally, two 5′-neighboring base
pairs, A4:T9 and G3:C10, were stabilized with respect to the exchange of their imino protons
with solvent. The equilibrium constant for base pair opening at the
A4:T9 base pair determined by magnetization
transfer from water in the absence and presence of added ammonia base
catalyst decreased for the modified duplex compared to that of the
A4:T9 base pair in the unmodified duplex, which
confirmed that the overall fraction of the A4:T9 base pair in the open state of the modified duplex decreased. This
was also observed for the G3:C10 base pair,
where αKop for the G3:C10 base pair in the modified duplex was 3.0 × 106 versus 4.1 × 106 for the same base pair in
the unmodified duplex. In contrast, equilibrium constants for base
pair opening at the X5:C8 and C6:G7 base pairs did not change at 15 °C. These results argue
against the notion that electrostatic interactions with DNA are entirely
entropic and suggest that major groove cations can stabilize DNA via
enthalpic contributions to the free energy of duplex formation.
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Affiliation(s)
- Marta W Szulik
- Department of Chemistry and Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37235, United States
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Chen YJ, Liu P, Nielsen AAK, Brophy JAN, Clancy K, Peterson T, Voigt CA. Characterization of 582 natural and synthetic terminators and quantification of their design constraints. Nat Methods 2013; 10:659-64. [DOI: 10.1038/nmeth.2515] [Citation(s) in RCA: 344] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 05/06/2013] [Indexed: 01/20/2023]
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Huang Y, Weng X, Russu IM. Enhanced base-pair opening in the adenine tract of a RNA double helix. Biochemistry 2011; 50:1857-63. [PMID: 21250663 DOI: 10.1021/bi1014997] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Proton exchange and nuclear magnetic resonance spectroscopy are being used to characterize the kinetics and energetics of base-pair opening in two nucleic acid double helices. One is the RNA duplex 5'-r(GCGAUAAAAAGGCC)-3'/5'-r(GGCCUUUUUAUCGC)-3', which contains a central tract of five AU base pairs. The other is the homologous DNA duplex with a central tract of five AT base pairs. The rates and the equilibrium constants of the opening reaction of each base pair are measured from the dependence of the exchange rates of imino protons on ammonia concentration, at 10 °C. The results reveal that the tract of AU base pairs in the RNA duplex differs from the homologous tract of AT base pairs in DNA in several ways. The rates of opening of AU base pairs in RNA are high and increase progressively along the tract, reaching their largest values at the 3'-end of the tract. In contrast, the opening rates of AT base pairs in DNA are much lower than those of AU base pairs. Within the tract, the largest opening rate is observed for the AT base pair at the 5'-end of the tract. These differences in opening kinetics are paralleled by differences in the stabilities of individual base pairs. All AU base pairs in the RNA are less stable than the AT base pairs in the DNA. The presence of the tract enhances these differences by increasing the stability of AT base pairs in DNA while decreasing the stability of AU base pairs in RNA. Due to these divergent trends, along the tracts, the AU base pairs become progressively less stable than AT base pairs. These findings demonstrate that tracts of AU base pairs in RNA have specific dynamic and energetic signatures that distinguish them from similar tracts of AT base pairs in DNA.
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Affiliation(s)
- Yuegao Huang
- Department of Chemistry and Molecular Biophysics Program, Wesleyan University, Middletown, Connecticut 06459, United States
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