Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction
Mooijman D, Dey SS (co-first author), Boisset JC, Crosetto N, van Oudenaarden A
Nature Biotechnology 34:852-856 (2016).

The epigenetic DNA modification 5-hydroxymethylcytosine (5hmC) has crucial roles in development and gene regulation. Quantifying the abundance of this epigenetic mark at the single-cell level could enable us to understand its roles. We present a single-cell, genome-wide and strand-specific 5hmC sequencing technology, based on 5hmC glucosylation and glucosylation-dependent digestion of DNA, that reveals pronounced cell-to-cell variability in the abundance of 5hmC on the two DNA strands of a given chromosome. We develop a mathematical model that reproduces the strand bias and use this model to make two predictions. First, the variation in strand bias should decrease when 5hmC turnover increases. Second, the strand bias of two sister cells should be strongly anti-correlated. We validate these predictions experimentally, and use our model to reconstruct lineages of two- and four-cell mouse embryos, showing that single-cell 5hmC sequencing can be used as a lineage reconstruction tool.

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Genome-wide maps of nuclear lamina interactions in single human cells
Kind J, Pagie L, de Vries SS, Nahidiazar L, Dey SS, Bienko M, Zhan Y, Lajoie B, de Graaf CA, Amendola M, Fudenberg G, Imakaev M, Mirny L, Jalink K, Dekker J, van Oudenaarden A, van Steensel B
Cell 163:134-147 (2015).

Mammalian interphase chromosomes interact with the nuclear lamina (NL) through hundreds of large lamina-associated domains (LADs). We report a method to map NL contacts genome-wide in single human cells. Analysis of nearly 400 maps reveals a core architecture consisting of gene-poor LADs that contact the NL with high cell-to-cell consistency, interspersed by LADs with more variable NL interactions. The variable contacts tend to be cell-type specific and are more sensitive to changes in genome ploidy than the consistent contacts. Single-cell maps indicate that NL contacts involve multivalent interactions over hundreds of kilobases. Moreover, we observe extensive intra-chromosomal coordination of NL contacts, even over tens of megabases. Such coordinated loci exhibit preferential interactions as detected by Hi-C. Finally, the consistency of NL contacts is inversely linked to gene activity in single cells and correlates positively with the heterochromatic histone modification H3K9me3. These results highlight fundamental principles of single-cell chromatin organization.

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Orthogonal control of expression mean and variance by epigenetic features at different genomic loci
Dey SS, Foley JE (co-first author), Limsirichai P, Schaffer DV, Arkin AP
Molecular Systems Biology 11:806 (2015).

While gene expression noise has been shown to drive dramatic phenotypic variations, the molecular basis for this variability in mammalian systems is not well understood. Gene expression has been shown to be regulated by promoter architecture and the associated chromatin environment. However, the exact contribution of these two factors in regulating expression noise has not been explored. Using a dual-reporter lentiviral model system, we deconvolved the influence of the promoter sequence to systematically study the contribution of the chromatin environment at different genomic locations in regulating expression noise. By integrating a large-scale analysis to quantify mRNA levels by smFISH and protein levels by flow cytometry in single cells, we found that mean expression and noise are uncorrelated across genomic locations. Furthermore, we showed that this independence could be explained by the orthogonal control of mean expression by the transcript burst size and noise by the burst frequency. Finally, we showed that genomic locations displaying higher expression noise are associated with more repressed chromatin, thereby indicating the contribution of the chromatin environment in regulating expression noise.

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Integrated genome and transcriptome sequencing of the same cell
Dey SS, Kester L (co-first author), Spanjaard B, Bienko M, van Oudenaarden A
Nature Biotechnology 33:285-289 (2015).

Single-cell genomics and single-cell transcriptomics have emerged as powerful tools to study the biology of single cells at a genome-wide scale. However, a major challenge is to sequence both genomic DNA and mRNA from the same cell, which would allow direct comparison of genomic variation and transcriptome heterogeneity. We describe a quasilinear amplification strategy to quantify genomic DNA and mRNA from the same cell without physically separating the nucleic acids before amplification. We show that the efficiency of our integrated approach is similar to existing methods for single-cell sequencing of either genomic DNA or mRNA. Further, we find that genes with high cell-to-cell variability in transcript numbers generally have lower genomic copy numbers, and vice versa, suggesting that copy number variations may drive variability in gene expression among individual cells. Applications of our integrated sequencing approach could range from gaining insights into cancer evolution and heterogeneity to understanding the transcriptional consequences of copy number variations in healthy and diseased tissues.

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Quantitative evaluation and optimization of co-drugging to improve anti-HIV latency therapy
Wong VC, Fong LE (co-first author), Adams NM, Xue Q, Dey SS, Miller-Jensen K
Cellular and Molecular Bioengineering 7:320-333 (2014).

Human immunodeficiency virus 1 (HIV) latency remains a significant obstacle to curing infected patients. One promising therapeutic strategy is to purge the latent cellular reservoir by activating latent HIV with latency-reversing agents (LRAs). In some cases, co-drugging with multiple LRAs is necessary to activate latent infections, but few studies have established quantitative criteria for determining when co-drugging is required. Here we systematically quantified drug interactions between histone deacetylase inhibitors and transcriptional activators of HIV and found that the need for co-drugging is determined by the proximity of latent infections to the chromatin-regulated viral gene activation threshold at the viral promoter. Our results suggest two classes of latent viral integrations: those far from the activation threshold that benefit from co-drugging, and those close to the threshold that are efficiently activated by a single drug. Using a primary T cell model of latency, we further demonstrated that the requirement for co-drugging was donor dependent, suggesting that the host may set the level of repression of latent infections. Finally, we showed that single drug or co-drugging doses could be optimized, via repeat stimulations, to minimize unwanted side effects while main- taining robust viral activation. Our results motivate further study of patient-specific latency-reversing strategies.

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Chromatin accessibility at the HIV-1 LTR promoter sets a threshold for NF-κB mediated viral gene expression
Miller-Jensen K, Dey SS (co-first author), Pham N, Foley JE, Arkin AP, Schaffer DV
Integrative Biology 4:661-671 (2012).

Higher order chromatin structure in eukaryotes can lead to differential gene expression in response to the same transcription factor; however, how transcription factor inputs integrate with quantitative features of the chromatin environment to regulate gene expression is not clear. In vitro models of HIV gene regulation, in which repressive mechanisms acting locally at an integration site keep proviruses transcriptionally silent until appropriately stimulated, provide a powerful system to study gene expression regulation in different chromatin environments. Here we quantified HIV expression as a function of activating transcription factor nuclear factor-κB RelA/ p65 (RelA) levels and chromatin features at a panel of viral integration sites. Variable RelA overexpression demonstrated that the viral genomic location sets a threshold RelA level necessary to induce gene expression. However, once the induction threshold is reached, gene expression increases similarly for all integration sites. Furthermore, we found that higher induction thresholds are associated with repressive histone marks and a decreased sensitivity to nuclease digestion at the LTR promoter. Increasing chromatin accessibility via inhibition of histone deacetylation or DNA methylation lowered the induction threshold, demonstrating that chromatin accessibility sets the level of RelA required to activate gene expression. Finally, a functional relationship between gene expression, RelA level, and chromatin accessibility accurately predicted synergistic HIV activation in response to combinatorial pharmacological perturbations. Different genomic environments thus set a threshold for transcription factor activation of a key viral promoter, which may point toward biological principles that underlie selective gene expression and inform strategies for combinatorial therapies to combat latent HIV.

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Mutual information analysis reveals coevolving residues in Tat that compensate for two distinct functions in HIV-1 gene expression
Dey SS, Xue Y, Joachimiak MP, Friedland GD, Burnett JC, Zhou Q, Arkin AP, Schaffer DV
Journal of Biological Chemistry 287:7945-7955 (2012).

Viral genomes are continually subjected to mutations, and functionally deleterious ones can be rescued by reversion or additional mutations that restore fitness. The error prone nature of HIV-1 replication has resulted in highly diverse viral sequences, and it is not clear how viral proteins such as Tat, which plays a critical role in viral gene expression and replication, retain their complex functions. Although several important amino acid positions in Tat are conserved, we hypothesized that it may also harbor functionally important residues that may not be individually conserved yet appear as correlated pairs, whose analysis could yield new mechanistic insights into Tat function and evolution. To identify such sites, we combined mutual information analysis and experimentation to identify coevolving positions and found that residues 35 and 39 are strongly correlated. Mutation of either residue of this pair into amino acids that appear in numerous viral isolates yields a defective virus; however, simultaneous introduction of both mutations into the heterologous Tat sequence restores gene expression close to wild-type Tat. Furthermore, in contrast to most coevolving protein residues that contribute to the same function, structural modeling and biochemical studies showed that these two residues contribute to two mechanistically distinct steps in gene expression: binding P-TEFb and promoting P-TEFb phosphorylation of the C-terminal domain in RNAPII. Moreover, Tat variants that mimic HIV-1 subtypes B or C at sites 35 and 39 have evolved orthogonal strengths of P-TEFb binding versus RNAPII phosphorylation, suggesting that subtypes have evolved alternate transcriptional strategies to achieve similar gene expression levels.

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Varying Virulence: Epigenetic control of expression noise and disease processes
Miller-Jensen K, Dey SS (co-first author), Schaffer DV, Arkin AP
Trends in Biotechnology 29:517-525 (2011).

Gene expression noise is a significant source of phenotypic heterogeneity in otherwise identical populations of cells. Phenotypic heterogeneity can cause reversible drug resistance in diseased cells, and thus a better understanding of its origins might improve treatment strategies. In eukaryotes, data strongly suggest that intrinsic noise arises from transcriptional bursts caused by slow, random transitions between inactive and active gene states that are mediated by chromatin remodeling. In this review, we consider how chromatin modifications might modulate gene expression noise and lead to phenotypic diversity in diseases as varied as viral infection and cancer. Additionally, we argue that this fundamental information can be applied to develop innovative therapies that counteract ‘pathogenic noise’ and sensitize all diseased cells to therapeutic intervention.

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Opportunities for chemical engineering thermodynamics in biotechnology: Some examples
Dey SS, Prausnitz JM
Industrial & Engineering Chemistry Research 50:3-15 (2011).

Because of its generality, thermodynamics is applicable to all substances, including biomacromolecules. To illustrate how thermodynamics can contribute to biotechnology, each of six examples gives a brief summary of pertinent, previously published research. Each example indicates that familiar concepts in chemical engineering thermodynamics can be applied to contribute toward solution of a practical problem. These examples are discussed here to encourage thermodynamically oriented chemical engineers to devote their talents toward helping to advance industrial biotechnology.

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(1S*,2S*,4S*,5S*)-Cyclohexane-1,2,4,5-tetrol monohydrate
Mehta G, Sen S, Dey SS
Acta Crystallographica Section C 61 (Pt 6):o358-360 (2005).

In the title compound, C6H12O4.H2O, 1,4/2,5-cyclohexane-tetrol and water molecules are seen to possess twofold symmetry. All four hydroxyl groups of the tetrol participate in extensive intermolecular O—H…O hydrogen bonding to form molecular tapes propagating along the a axis. Translationally related tapes along the c axis are held together by four coordinated water molecules.

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Mehta G, Sen S, Dey SS
Acta Crystallographica Section E 61 (Pt 4):o920-922 (2005).

The title compound, C6H12O4, exists in a chair form, with three of the four OH groups equatorially disposed. All four hydroxy groups participate in extensive intermolecular O—H…O hydrogen bonding.

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