Browsing by Author "Gao, Yuan"

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Open Access
A paired-end sequencing strategy to map the complex landscape of transcription initiation.
(Nature methods, 2010-07) Ni, Ting; Corcoran, David L; Rach, Elizabeth A; Song, Shen; Spana, Eric P; Gao, Yuan; Ohler, Uwe; Zhu, Jun
Recent studies using high-throughput sequencing protocols have uncovered the complexity of mammalian transcription by RNA polymerase II, helping to define several initiation patterns in which transcription start sites (TSSs) cluster in both narrow and broad genomic windows. Here we describe a paired-end sequencing strategy, which enables more robust mapping and characterization of capped transcripts. We used this strategy to explore the transcription initiation landscape in the Drosophila melanogaster embryo. Extending the previous findings in mammals, we found that fly promoters exhibited distinct initiation patterns, which were linked to specific promoter sequence motifs. Furthermore, we identified many 5' capped transcripts originating from coding exons; our analyses support that they are unlikely the result of alternative TSSs, but rather the product of post-transcriptional modifications. We demonstrated paired-end TSS analysis to be a powerful method to uncover the transcriptional complexity of eukaryotic genomes.
Open Access
Microphase Separation of Stimulus-Responsive Block-co-Polypeptides on Surfaces
(2018) Gao, Yuan
Among soft matter materials, block copolymers can form ordered structures with high regularity by microphase separation, triggered by the selective incompatibility of the blocks with each other. Many current studies of block-co-polypeptides are focused on their self-assembly in dilute solutions. This work expands previous research on the self-assembly of block-co-polypeptides into micellar structures in dilute solutions to the microphase separation in concentrated solutions and on surfaces, by using a model family of resilin-like/elastin-like block-co-polypeptides. The effects of four parameters, including relative block lengths, temperature, concentration, and deposition methods, on microphase separation are investigated. The results show that the presence of microphase separation and the morphologies of microphase separated structures are predictable from our study of thermodynamic theory. This work provides an understanding of how sequence design of stimulus-responsive block-co-polypeptides is related to their microphase separation.
Open Access
Non-local SPDE limits of spatially-correlated-noise driven spin systems derived to sample a canonical distribution
Gao, Yuan; Marzuola, Jeremy L; Mattingly, Jonathan C; Newhall, Katherine A
We study the macroscopic behavior of a stochastic spin ensemble driven by a discrete Markov jump process motivated by the Metropolis-Hastings algorithm where the proposal is made with spatially correlated (colored) noise, and hence fails to be symmetric. However, we demonstrate a scenario where the failure of proposal symmetry is a higher order effect. Hence, from these microscopic dynamics we derive as a limit as the proposal size goes to zero and the number of spins to infinity, a non-local stochastic version of the harmonic map heat flow (or overdamped Landau-Lipshitz equation). The equation is both mathematically well-posed and samples the canonical/Gibbs distribution related to the kinetic energy. The failure of proposal symmetry due to interaction between the confining geometry of the spin system and the colored noise is in contrast to the uncorrelated, white-noise, driven system. Specifically, the choice of projection of the noise to conserve the magnitude of the spins is crucial to maintaining the proper equilibrium distribution. Numerical simulations are included to verify convergence properties and demonstrate the dynamics.
Open Access
The prevalence and regulation of antisense transcripts in Schizosaccharomyces pombe.
(PLoS One, 2010-12-20) Ni, Ting; Tu, Kang; Wang, Zhong; Song, Shen; Wu, Han; Xie, Bin; Scott, Kristin C; Grewal, Shiv I; Gao, Yuan; Zhu, Jun
A strand-specific transcriptome sequencing strategy, directional ligation sequencing or DeLi-seq, was employed to profile antisense transcriptome of Schizosaccharomyces pombe. Under both normal and heat shock conditions, we found that polyadenylated antisense transcripts are broadly expressed while distinct expression patterns were observed for protein-coding and non-coding loci. Dominant antisense expression is enriched in protein-coding genes involved in meiosis or stress response pathways. Detailed analyses further suggest that antisense transcripts are independently regulated with respect to their sense transcripts, and diverse mechanisms might be potentially involved in the biogenesis and degradation of antisense RNAs. Taken together, antisense transcription may have profound impacts on global gene regulation in S. pombe.