Biomedical subjects

Terence Hwa

Publications and source records attributed to Terence Hwa.

18 recordsLinked to original sources

PubMed2005

A novel method distinguishes between mutation rates and fixation biases in patterns of single-nucleotide substitution.

Analysis of the genome-wide patterns of single-nucleotide substitution reveals that the human GC content structure is out of equilibrium. The substitutions are decreasing the overall GC content (GC), at the same time making its range narrower. Investigation of single-nucleotide polymorphisms (SNPs) revealed that presently the decrease in GC content is due to a uniform mutational preference for A:T pairs, while its projected range is due to a variability in the fixation preference for G:C pairs. However, it is important to determine whether lessons learned about evolutionary processes operating at the present time (that is reflected in the SNP data) can be extended back into the evolutionary past. We describe here a new approach to this problem that utilizes the juxtaposition of forward and reverse substitution rates to determine the relative importance of variability in mutation rates and fixation probabilities in shaping long-term substitutional patterns. We use this approach to demonstrate that the forces shaping GC content structure over the recent past (since the appearance of the SNPs) extend all the way back to the mammalian radiation approximately 90 million years ago. In addition, we find a small but significant effect that has not been detected in the SNP data-relatively high rates of C:G-->A:T germline mutation in low-GC regions of the genome.

Base Composition↗

PubMed2005

Nonlinear protein degradation and the function of genetic circuits.

The functions of most genetic circuits require a sufficient degree of cooperativity in the circuit components. Although mechanisms of cooperativity have been studied most extensively in the context of transcriptional initiation control, cooperativity from other processes involved in the operation of the circuits can also play important roles. In this work, we examine a simple kinetic source of cooperativity stemming from the nonlinear degradation of multimeric proteins. Ample experimental evidence suggests that protein subunits can degrade less rapidly when associated in multimeric complexes, an effect we refer to as "cooperative stability." For dimeric transcription factors, this effect leads to a concentration-dependence in the degradation rate because monomers, which are predominant at low concentrations, will be more rapidly degraded. Thus, cooperative stability can effectively widen the accessible range of protein levels in vivo. Through theoretical analysis of two exemplary genetic circuits in bacteria, we show that such an increased range is important for the robust operation of genetic circuits as well as their evolvability. Our calculations demonstrate that a few-fold difference between the degradation rate of monomers and dimers can already enhance the function of these circuits substantially. We discuss molecular mechanisms of cooperative stability and their occurrence in natural or engineered systems. Our results suggest that cooperative stability needs to be considered explicitly and characterized quantitatively in any systematic experimental or theoretical study of gene circuits.

Bacteria↗

PubMed2005

Substantial regional variation in substitution rates in the human genome: importance of GC content, gene density, and telomere-specific effects.

This study presents the first global, 1-Mbp-level analysis of patterns of nucleotide substitutions along the human lineage. The study is based on the analysis of a large amount of repetitive elements deposited into the human genome since the mammalian radiation, yielding a number of results that would have been difficult to obtain using the more conventional comparative method of analysis. This analysis revealed substantial and consistent variability of rates of substitution, with the variability ranging up to twofold among different regions. The rates of substitutions of C or G nucleotides with A or T nucleotides vary much more sharply than the reverse rates, suggesting that much of that variation is due to differences in mutation rates rather than in the probabilities of fixation of C/G vs. A/T nucleotides across the genome. For all types of substitution we observe substantially more hotspots than coldspots, with hotspots showing substantial clustering over tens of Mbp's. Our analysis revealed that GC-content of surrounding sequences is the best predictor of the rates of substitution. The pattern of substitution appears very different near telomeres compared to the rest of the genome and cannot be explained by the genome-wide correlations of the substitution rates with GC content or exon density. The telomere pattern of substitution is consistent with natural selection or biased gene conversion acting to increase the GC-content of the sequences that are within 10-15 Mbp away from the telomere.

Base Composition↗

PubMed2005

Identification and measurement of neighbor-dependent nucleotide substitution processes.

MOTIVATION: Neighbor-dependent substitution processes generated specific pattern of dinucleotide frequencies in the genomes of most organisms. The CpG-methylation-deamination process is, e.g. a prominent process in vertebrates (CpG effect). Such processes, often with unknown mechanistic origins, need to be incorporated into realistic models of nucleotide substitutions. RESULTS: Based on a general framework of nucleotide substitutions we developed a method that is able to identify the most relevant neighbor-dependent substitution processes, estimate their relative frequencies and judge their importance in order to be included into the modeling. Starting from a model for neighbor independent nucleotide substitution we successively added neighbor-dependent substitution processes in the order of their ability to increase the likelihood of the model describing given data. The analysis of neighbor-dependent nucleotide substitutions based on repetitive elements found in the genomes of human, zebrafish and fruit fly is presented. AVAILABILITY: A web server to perform the presented analysis is freely available at: http://evogen.molgen.mpg.de/server/substitution-analysis

Algorithms↗

PubMed2005

Transcriptional regulation by the numbers: applications.

With the increasing amount of experimental data on gene expression and regulation, there is a growing need for quantitative models to describe the data and relate them to their respective context. Thermodynamic models provide a useful framework for the quantitative analysis of bacterial transcription regulation. This framework can facilitate the quantification of vastly different forms of gene expression from several well-characterized bacterial promoters that are regulated by one or two species of transcription factors; it is useful because it requires only a few parameters. As such, it provides a compact description useful for higher-level studies (e.g. of genetic networks) without the need to invoke the biochemical details of every component. Moreover, it can be used to generate hypotheses on the likely mechanisms of transcriptional control.

Animals↗

PubMed2005

Transcriptional regulation by the numbers: models.

The expression of genes is regularly characterized with respect to how much, how fast, when and where. Such quantitative data demands quantitative models. Thermodynamic models are based on the assumption that the level of gene expression is proportional to the equilibrium probability that RNA polymerase (RNAP) is bound to the promoter of interest. Statistical mechanics provides a framework for computing these probabilities. Within this framework, interactions of activators, repressors, helper molecules and RNAP are described by a single function, the "regulation factor". This analysis culminates in an expression for the probability of RNA polymerase binding at the promoter of interest as a function of the number of regulatory proteins in the cell.

Gene Expression Regulation↗

PubMed2004

Regional and time-resolved mutation patterns of the human genome.

MOTIVATION: Substantial regional variations of substitutional processes have recently been reported from human/mouse comparisons. However, several features including the C + G dependence and the CpG-based transition effect remain obscure. RESULTS: Utilizing the vast amount of transposable elements in the human genome, we performed detailed analysis of the substitutional and insertion/deletion patterns along the human lineage in a regional and time-resolved fashion. We observed a drastic increase in the CpG-based transition frequency at about the time of the mammalian radiation. We also observed clear regional biases of substitution patterns, most notably a bias to enrich the C+G content toward the telomeres. AVAILABILITY: The programs used are available upon request from the authors.

Algorithms↗

PubMed2004

Analytical study of the effect of recombination on evolution via DNA shuffling.

DNA shuffling is an evolutionary protocol wherein cycles of selection, recombination, mutation, and amplification are employed to evolve proteins and DNA sequences. Experiments have shown its superiority to traditional protocols which do not employ recombination. Motivated by DNA shuffling, we investigate a multilocus evolutionary model that incorporates selection, recombination, and point mutations. Due to simplicity of the model, for the case of an infinite population we can obtain a full analytical treatment of both its dynamical and equilibrium properties, and study the benefit of recombination explicitly and quantitatively. We also briefly discuss finite-population size corrections.

Animals↗

PubMed2004

Translocation of structured polynucleotides through nanopores.

We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic barriers for the translocation process. We show that this circumstance may be exploited to determine the full basepairing pattern of polynucleotides, including RNA pseudoknots. The crucial requirement is that the translocation dynamics (i.e. the length of the translocated molecular segment) needs to be recorded as a function of time with a spatial resolution of a few nucleotides. This could be achieved, for instance, by applying a mechanical driving force for translocation and recording force-extension curves (FECs) with a device such as an atomic force microscope or optical tweezers. Our analysis suggests that, with this added spatial resolution, nanopores could be transformed into a powerful experimental tool to study the folding of nucleic acids.

Animals↗

PubMed2003

Distinct changes of genomic biases in nucleotide substitution at the time of Mammalian radiation.

Differences in the regional substitution patterns in the human genome created patterns of large-scale variation of base composition known as genomic isochores. To gain insight into the origin of the genomic isochores, we develop a maximum-likelihood approach to determine the history of substitution patterns in the human genome. This approach utilizes the vast amount of repetitive sequence deposited in the human genome over the past approximately 250 Myr. Using this approach, we estimate the frequencies of seven types of substitutions: the four transversions, two transitions, and the methyl-assisted transition of cytosine in CpG. Comparing substitutional patterns in repetitive elements of various ages, we reconstruct the history of the base-substitutional process in the different isochores for the past 250 Myr. At around 90 MYA (around the time of the mammalian radiation), we find an abrupt fourfold to eightfold increase of the cytosine transition rate in CpG pairs compared with that of the reptilian ancestor. Further analysis of nucleotide substitutions in regions with different GC content reveals concurrent changes in the substitutional patterns. Although the substitutional pattern was dependent on the regional GC content in such ways that it preserved the regional GC content before the mammalian radiation, it lost this dependence afterward. The substitutional pattern changed from an isochore-preserving to an isochore-degrading one. We conclude that isochores have been established before the radiation of the eutherian mammals and have been subject to the process of homogenization since then.

CpG Islands↗

PubMed2003

On schemes of combinatorial transcription logic.

Cells receive a wide variety of cellular and environmental signals, which are often processed combinatorially to generate specific genetic responses. Here we explore theoretically the potentials and limitations of combinatorial signal integration at the level of cis-regulatory transcription control. Our analysis suggests that many complex transcription-control functions of the type encountered in higher eukaryotes are already implementable within the much simpler bacterial transcription system. Using a quantitative model of bacterial transcription and invoking only specific protein-DNA interaction and weak glue-like interaction between regulatory proteins, we show explicit schemes to implement regulatory logic functions of increasing complexity by appropriately selecting the strengths and arranging the relative positions of the relevant protein-binding DNA sequences in the cis-regulatory region. The architectures that emerge are naturally modular and evolvable. Our results suggest that the transcription regulatory apparatus is a "programmable" computing machine, belonging formally to the class of Boltzmann machines. Crucial to our results is the ability to regulate gene expression at a distance. In bacteria, this can be achieved for isolated genes via DNA looping controlled by the dimerization of DNA-bound proteins. However, if adopted extensively in the genome, long-distance interaction can cause unintentional intergenic cross talk, a detrimental side effect difficult to overcome by the known bacterial transcription-regulation systems. This may be a key factor limiting the genome-wide adoption of complex transcription control in bacteria. Implications of our findings for combinatorial transcription control in eukaryotes are discussed.

Bacteria↗

PubMed2003

Localization of denaturation bubbles in random DNA sequences.

We study the thermodynamic and dynamic behaviors of twist-induced denaturation bubbles in a long, stretched random sequence of DNA. The small bubbles associated with weak twist are delocalized. Above a threshold torque, the bubbles of several tens of bases or larger become preferentially localized to AT-rich segments. In the localized regime, the bubbles exhibit "aging" and move around subdiffusively with continuously varying dynamic exponents. These properties are derived by using results of large-deviation theory together with scaling arguments and are verified by Monte Carlo simulations.

Base Composition↗

PubMed2003

Dynamics of competitive evolution on a smooth landscape.

We study competitive DNA sequence evolution directed by in vitro protein binding. The steady-state dynamics of this process is well described by a shape-preserving pulse which decelerates and eventually reaches equilibrium. We explain this dynamical behavior within a continuum mean-field framework. Analytical results obtained on the motion of the pulse agree with simulations. Furthermore, finite population correction to the mean-field results are found to be insignificant.

Binding, Competitive↗

PubMed2003

Mechanically probing the folding pathway of single RNA molecules.

We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating the experimentally determined free energy rules for RNA secondary structure, whereas exterior single-stranded regions are modeled as freely jointed chains. For exemplary RNA sequences (hairpins and the Tetrahymena thermophila group I intron), we compute the quasiequilibrium fluctuations in the end-to-end distance as the molecule is unfolded by pulling on opposite ends. Unlike the average quasiequilibrium force-extension curves, these fluctuations reveal clear signatures from the unfolding of individual structural elements. We find that the resolution of these signatures depends on the spring constant of the force-measuring device, with an optimal value intermediate between very rigid and very soft. We compare and relate our results to recent experiments by Liphardt et al. (2001).

Animals↗

PubMed2003

DNA sequence evolution with neighbor-dependent mutation.

We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of models is developed by adopting well-known methods of nonlinear dynamics. Results are presented for the CpG-methylation-deamination process, which dominates point substitutions in vertebrates. The dinucleotide frequencies generated by the model (using empirically obtained mutation rates) match the overall pattern observed in noncoding DNA. A web-based tool has been constructed to compute single- and dinucleotide frequencies for arbitrary neighbor-dependent mutation rates. Also provided is the backward procedure to infer the mutation rates using maximum likelihood analysis given the observed single- and dinucleotide frequencies. Reasonable estimates of the mutation rates can be obtained very efficiently, using generic noncoding DNA sequences as input, after masking out long homonucleotide subsequences. Our method is much more convenient and versatile to use than the traditional method of deducing mutation rates by counting mutation events in carefully chosen sequences. More generally, our approach provides a more realistic but still tractable description of noncoding genomic DNA and may be used as a null model for various sequence analysis applications.

DNA↗

PubMed2002

Physical constraints and functional characteristics of transcription factor-DNA interaction.

We study theoretical "design principles" for transcription factor (TF)-DNA interaction in bacteria, focusing particularly on the statistical interaction of the TFs with the genomic background (i.e., the genome without the target sites). We introduce and motivate the concept of programmability, i.e., the ability to set the threshold concentration for TF binding over a wide range merely by mutating the binding sequence of a target site. This functional demand, together with physical constraints arising from the thermodynamics and kinetics of TF-DNA interaction, leads us to a narrow range of "optimal" interaction parameters. We find that this parameter set agrees well with experimental data for the interaction parameters of a few exemplary prokaryotic TFs, which indicates that TF-DNA interaction is indeed programmable. We suggest further experiments to test whether this is a general feature for a large class of TFs.

Bacterial Proteins↗

PubMed2002

On the selection and evolution of regulatory DNA motifs.

The mutation and selection of regulatory DNA sequences are presented as an ideal model system of molecular evolution where genotype, phenotype, and fitness can be explicitly and independently characterized. In this theoretical study, we construct an explicit model for the evolution of regulatory sequences, making use of the known biophysics of the binding of regulatory proteins to DNA sequences, under the assumption that fitness of a sequence depends only on its binding affinity to the regulatory protein. The model is confined to the mean field (i.e., infinite population size) limit. Using realistic values for all parameters, we determine the minimum fitness advantage needed to maintain a binding sequence, demonstrating explicitly the "error threshold" below which a binding sequence cannot survive the accumulated effect of mutation over long time. The commonly observed "fuzziness" in binding motifs arises naturally as a consequence of the balance between selection and mutation in our model. In addition, we devise a simple model for the evolution of multiple binding sequences in a given regulatory region. We find the number of evolutionarily stable binding sequences to increase in a step-like fashion with increasing fitness advantage, if multiple regulatory proteins can synergistically enhance gene transcription. We discuss possible experimental approaches to resolve open questions raised by our study.

Binding Sites↗

PubMed2002

Hybrid alignment: high-performance with universal statistics.

The score statistics of a recently introduced 'hybrid alignment' algorithm is studied in detail numerically. An extensive survey across the 2216 models of protein domains contained in the Pfam v5.4 database (Bateman et al., Nucleic Acids Res., 28, 263-266, 2000) verifies the theoretical predictions: For the position-specific scoring functions used in the Pfam models, the score statistics of hybrid alignment obey the Gumbel distribution, with the key Gumbel parameter lambda taking on the asymptotic value 1 universally for all models. Thus, the use of hybrid alignment eliminates the time-consuming computer simulations normally needed to assign p-values to alignment scores, freeing the users to experiment with different scoring parameters and functions. The performance of the hybrid algorithm in detecting sequence homology is also studied. For protein sequences from the SCOP database (Murzin et al., J. Mol. Biol., 247, 536-540, 1995) using uniform scoring functions, the performance is found to be comparable to the best of the existing methods. Preliminary results using the PfamA database suggest that the hybrid algorithm achieves similar performance as existing methods for position-specific scoring systems as well. Hybrid alignment is thereby established as a high performance alignment algorithm with well-characterized, universal statistics.

Algorithms↗