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Davis-Turak J, Johnson TL, Hoffmann A. Mathematical modeling identifies potential gene structure determinants of co-transcriptional control of alternative pre-mRNA splicing. Nucleic Acids Res 2019; 46:10598-10607. [PMID: 30272246 PMCID: PMC6237756 DOI: 10.1093/nar/gky870] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 09/17/2018] [Indexed: 01/22/2023] Open
Abstract
The spliceosome catalyzes the removal of introns from pre-messenger RNA (mRNA) and subsequent pairing of exons with remarkable fidelity. Some exons are known to be skipped or included in the mature mRNA in a cell type- or context-dependent manner (cassette exons), thereby contributing to the diversification of the human proteome. Interestingly, splicing is initiated (and sometimes completed) co-transcriptionally. Here, we develop a kinetic mathematical modeling framework to investigate alternative co-transcriptional splicing (CTS) and, specifically, the control of cassette exons' inclusion. We show that when splicing is co-transcriptional, default splice patterns of exon inclusion are more likely than when splicing is post-transcriptional, and that certain exons are more likely to be regulatable (i.e. cassette exons) than others, based on the exon-intron structure context. For such regulatable exons, transcriptional elongation rates may affect splicing outcomes. Within the CTS paradigm, we examine previously described hypotheses of co-operativity between splice sites of short introns (i.e. 'intron definition') or across short exons (i.e. 'exon definition'), and find that models encoding these faithfully recapitulate observations in the fly and human genomes, respectively.
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Affiliation(s)
- Jeremy Davis-Turak
- San Diego Center for Systems Biology (SDCSB), University of California, San Diego, La Jolla, CA 92093, USA
| | - Tracy L Johnson
- San Diego Center for Systems Biology (SDCSB), University of California, San Diego, La Jolla, CA 92093, USA.,Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA.,Molecular Biology Institute (MBI), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Alexander Hoffmann
- San Diego Center for Systems Biology (SDCSB), University of California, San Diego, La Jolla, CA 92093, USA.,Molecular Biology Institute (MBI), University of California, Los Angeles, Los Angeles, CA 90095, USA.,Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles, CA 90095, USA.,Institute for Quantitative and Computational Biosciences (QCB) University of California, Los Angeles, Los Angeles, CA 90095, USA
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Murugan R. Theory of Site-Specific DNA-Protein Interactions in the Presence of Nucleosome Roadblocks. Biophys J 2019; 114:2516-2529. [PMID: 29874603 DOI: 10.1016/j.bpj.2018.04.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 03/13/2018] [Accepted: 04/24/2018] [Indexed: 01/19/2023] Open
Abstract
We show that nucleosomes exert a maximal amount of hindrance to the one-dimensional diffusion of transcription factors (TFs) when they are present between TFs and their cognate sites on DNA. The effective one-dimensional diffusion coefficient of TFs (χTF) decreases with a rise in the free-energy barrier (μNU) of the sliding of nucleosomes as χTF∝exp(-μNU). The average time (ηL) required by TFs to slide over L sites on DNA increases with μNU as ηL∝exp(μNU). When TFs move close to nucleosomes, then they exhibit typical subdiffusion. Nucleosomes can enhance the search dynamics of TFs when TFs are present between nucleosomes and TF binding sites. These results suggest that nucleosome-depleted regions around the cognate sites of TFs are mandatory for efficient site-specific binding of TFs. Remarkably, the genome-wide in vivo positioning pattern of TFs shows a maximum at their specific binding sites where the occupancy of nucleosomes shows a minimum. This could be a consequence of an increasing level of breathing dynamics of nucleosome cores and decreasing levels of fluctuations in the DNA binding domains of TFs as they move across TF binding sites. The dynamics of TFs becomes slow as they approach their cognate sites so that TFs form a tight site-specific complex, whereas the dynamics of nucleosomes becomes rapid so that they quickly pass through the cognate sites of TFs. Several in vivo data sets on the genome-wide positioning pattern of nucleosomes and TFs agree well with our arguments. The retarding effects of nucleosomes can be minimized when the degree of condensation of DNA is such that it can permit a jump size associated with the dynamics of TFs beyond ∼160-180 bp.
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Affiliation(s)
- Rajamanickam Murugan
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India.
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Niranjani G, Murugan R. Theory on the mechanism of site-specific DNA-protein interactions in the presence of traps. Phys Biol 2016; 13:046003. [PMID: 27434174 DOI: 10.1088/1478-3975/13/4/046003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The speed of site-specific binding of transcription factor (TFs) proteins with genomic DNA seems to be strongly retarded by the randomly occurring sequence traps. Traps are those DNA sequences sharing significant similarity with the original specific binding sites (SBSs). It is an intriguing question how the naturally occurring TFs and their SBSs are designed to manage the retarding effects of such randomly occurring traps. We develop a simple random walk model on the site-specific binding of TFs with genomic DNA in the presence of sequence traps. Our dynamical model predicts that (a) the retarding effects of traps will be minimum when the traps are arranged around the SBS such that there is a negative correlation between the binding strength of TFs with traps and the distance of traps from the SBS and (b) the retarding effects of sequence traps can be appeased by the condensed conformational state of DNA. Our computational analysis results on the distribution of sequence traps around the putative binding sites of various TFs in mouse and human genome clearly agree well the theoretical predictions. We propose that the distribution of traps can be used as an additional metric to efficiently identify the SBSs of TFs on genomic DNA.
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Affiliation(s)
- G Niranjani
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
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Davis-Turak JC, Allison K, Shokhirev MN, Ponomarenko P, Tsimring LS, Glass CK, Johnson TL, Hoffmann A. Considering the kinetics of mRNA synthesis in the analysis of the genome and epigenome reveals determinants of co-transcriptional splicing. Nucleic Acids Res 2014; 43:699-707. [PMID: 25541195 PMCID: PMC4333389 DOI: 10.1093/nar/gku1338] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
When messenger RNA splicing occurs co-transcriptionally, the potential for kinetic control based on transcription dynamics is widely recognized. Indeed, perturbation studies have reported that when transcription kinetics are perturbed genetically or pharmacologically splice patterns may change. However, whether kinetic control is contributing to the control of splicing within the normal range of physiological conditions remains unknown. We examined if the kinetic determinants for co-transcriptional splicing (CTS) might be reflected in the structure and expression patterns of the genome and epigenome. To identify and then quantitatively relate multiple, simultaneous CTS determinants, we constructed a scalable mathematical model of the kinetic interplay of RNA synthesis and CTS and parameterized it with diverse next generation sequencing (NGS) data. We thus found a variety of CTS determinants encoded in vertebrate genomes and epigenomes, and that these combine variously for different groups of genes such as housekeeping versus regulated genes. Together, our findings indicate that the kinetic basis of splicing is functionally and physiologically relevant, and may meaningfully inform the analysis of genomic and epigenomic data to provide insights that are missed when relying on statistical approaches alone.
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Affiliation(s)
- Jeremy C Davis-Turak
- San Diego Center for Systems Biology (SDCSB), University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Karmel Allison
- San Diego Center for Systems Biology (SDCSB), University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Maxim N Shokhirev
- San Diego Center for Systems Biology (SDCSB), University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Petr Ponomarenko
- San Diego Center for Systems Biology (SDCSB), University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Lev S Tsimring
- San Diego Center for Systems Biology (SDCSB), University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA BioCircuits Institute, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Christopher K Glass
- San Diego Center for Systems Biology (SDCSB), University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Tracy L Johnson
- San Diego Center for Systems Biology (SDCSB), University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Alexander Hoffmann
- San Diego Center for Systems Biology (SDCSB), University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA BioCircuits Institute, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California at Los Angeles, Los Angeles, CA 90095, USA Institute for Quantitative and Computational Biosciences (QCB), University of California at Los Angeles, Los Angeles, CA 90095, USA
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