arXiv subjects

Weiqun Peng

Publications and source records attributed to Weiqun Peng.

8 recordsLinked to original sources

arXiv2013

H3K4 mono- and di-methyltransferase MLL4 is required for enhancer activation during cell differentiation

Enhancers play a central role in cell-type-specific gene expression and are marked by H3K4me1/2. Active enhancers are further marked by H3K27ac. However, the methyltransferases responsible for H3K4me1/2 on enhancers remain elusive. Furthermore, how these enzymes function on enhancers to regulate cell-type-specific gene expression is unclear. Here we identify MLL4 (KMT2D) as a major mammalian H3K4 mono- and di-methyltransferase with partial functional redundancy with MLL3 (KMT2C). Using adipogenesis and myogenesis as model systems, we show that MLL4 exhibits cell-type- and differentiation-stage-specific genomic binding and is predominantly localized on enhancers. MLL4 co-localizes with lineage-determining transcription factors (TFs) on active enhancers during differentiation. Deletion of MLL4 markedly decreases H3K4me1/2, H3K27ac, Polymerase II and Mediator levels on enhancers and leads to severe defects in cell-type-specific gene expression and cell differentiation. Together, these findings identify MLL4 as a major mammalian H3K4 mono- and di-methyltransferase essential for enhancer activation during cell differentiation.

q-bio.GN↗

arXiv2003

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

We investigate a multi-locus evolutionary model which is based on the DNA shuffling protocol widely applied in \textit{in vitro} directed evolution. This model incorporates selection, recombination and point mutations. The simplicity of the model allows us to obtain a full analytical treatment of both its dynamical and equilibrium properties, for the case of an infinite population. We also briefly discuss finite population size corrections.

physics.bio-ph↗

arXiv2003

Dynamics of Competitive Evolution on a Smooth Landscape

We study competitive DNA sequence evolution directed by {\it 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.

cond-mat.stat-mech↗

arXiv2001

Connecting the vulcanization transition to percolation

The vulcanization transition is addressed via a minimal replica-field-theoretic model. The appropriate long-wave-length behavior of the two- and three-point vertex functions is considered diagrammatically, to all orders in perturbation theory, and identified with the corresponding quantities in the Houghton-Reeve-Wallace field-theoretic approach to the percolation critical phenomenon. Hence, it is shown that percolation theory correctly captures the critical phenomenology of the vulcanization transition associated with the liquid and critical states.

cond-mat.dis-nn↗

arXiv2000

Density-correlator signatures of the vulcanization transition

Certain density correlators, measurable via various experimental techniques, are studied in the context of the vulcanization transition. It is shown that these correlators contain essential information about both the vulcanization transition and the emergent amorphous solid state. Contact is made with various physical ingredients that have featured in experimental studies of amorphous colloidal and gel systems and in theoretical studies of the glassy state.

cond-mat.dis-nn↗

arXiv1999

Correlations near the vulcanization transition: A renormalization-group approach

Correlators describing the vulcanization transition are constructed and explored via a renormalization group approach. This approach is based on a minimal model that accounts for the thermal motion of constituents and the quenched random constraints imposed on their motion by crosslinks. Critical exponents associated with the correlators are obtained near six dimensions, and found to equal those governing analogous entities in percolation theory. Some expectations for how the vulcanization transition is realized in two dimensions, developed with H. E. Castillo, are discussed.

cond-mat.dis-nn↗

arXiv1999

Renormalization-Group Approach to the Vulcanization Transition

The vulcanization transition - the crosslink-density-controlled equilibrium phase transition from the liquid to the amorphous solid state - is explored analytically from a renormalization group perspective. The analysis centers on a minimal model that accounts for both the thermal motion of the constituents and the quenched random constraints imposed on their motion by the crosslinks, as well as particle-particle repulsion which suppresses density fluctuations. A correlation function involving fluctuations of the amorphous solid order parameter, the behavior of which signals the vulcanization transition, is examined, its physical meaning is elucidated, and the associated susceptibility is constructed and analyzed. A Ginzburg criterion for the width (in crosslink density) of the critical region is derived and is found to be consistent with a prediction due to de Gennes. Certain universal critical exponents characterizing the vulcanization transition are computed, to lowest nontrivial order, within the framework of an expansion around the upper critical dimension of six. This expansion shows that the connection between vulcanization and percolation extends beyond mean-field theory, at least to first order in the departure from the upper critical dimension. The relationship between the present approach to vulcanized matter and other approaches is explored in the light of this connection. To conclude, some expectations for how the vulcanization transition is realized in two dimensions, developed with H. E. Castillo, are discussed.

cond-mat.dis-nn↗

arXiv1997

Universality and its Origins at the Amorphous Solidification Transition

Systems undergoing an equilibrium phase transition from a liquid state to an amorphous solid state exhibit certain universal characteristics. Chief among these are the fraction of particles that are randomly localized and the scaling functions that describe the order parameter and (equivalently) the statistical distribution of localization lengths for these localized particles. The purpose of this Paper is to discuss the origins and consequences of this universality, and in doing so, three themes are explored. First, a replica-Landau-type approach is formulated for the universality class of systems that are composed of extended objects connected by permanent random constraints and undergo amorphous solidification at a critical density of constraints. This formulation generalizes the cases of randomly cross-linked and end-linked macromolecular systems, discussed previously. The universal replica free energy is constructed, in terms of the replica order parameter appropriate to amorphous solidification, the value of the order parameter is obtained in the liquid and amorphous solid states, and the chief universal characteristics are determined. Second, the theory is reformulated in terms of the distribution of local static density fluctuations rather than the replica order parameter. It is shown that a suitable free energy can be constructed, depending on the distribution of static density fluctuations, and that this formulation yields precisely the same conclusions as the replica approach. Third, the universal predictions of the theory are compared with the results of extensive numerical simulations of randomly cross-linked macromolecular systems, due to Barsky and Plischke, and excellent agreement is found.

cond-mat.dis-nn↗