Decoding gene regulatory pathways by evolutionary systems biology

The Yanai Lab moved in 2016 from the Faculty of Biology at the Technion to New York University’s School of Medicine. The NYU lab is currently situated in the West Alexandria tower (courtesy of the Institute of Systems Genetics), and we are scheduled to move into the 8th floor of the New Science Building in early 2018.

Some of our interests include:

  1. Single-cell transcriptomics. Our lab developed CEL-Seq, a popular method for single-cell RNA-Seq that is highly-multiplexed and uses linear amplification by in vitro transcription. We have shown that our latest CEL-Seq2 protocol is the most sensitive method for singe-cell transcriptomics. We have also adapted this method to capture intracellular bacterial pathogens and have rendered it high-throughput for studying thousands of cells.
  2. Gene expression atlas construction. We identified the time and germ-layer of expression of all genes throughout the embryonic development of the C. elegans nematode. Using this information, we were able to infer the evolutionary history of the endoderm germ layer. We are now identifying the expression of all cells throughout C. elegans embryogenesis and have also extended our atlas construction to the mammalian pancreas and melanoma tumors.
  3. Evolution of developmental gene expression programs. Comparing developmental transcriptome across species, we discovered that developmental milestones punctuate gene expression. Recently, we examined the development at the transcriptome level of ten different species, each of a different phylum, and discovered a universal mid-developmental transition.
  4. Genome evolution and the genetic basis of genotype-environment interactions. We have analyzed the transcriptomes of five C. elegans strains cultivated in five growth conditions and characterized the genotype-environment interactions. We also study how novelty is patterned in the genome and we reported a relationship between gene duplication and alternative splicing. We found that a gene’s length and expression level together control its fate of either accumulating splice variants or multiplying by gene duplication.

The precise regulation of gene expression leads to such spectacular achievements as the construction of an animal’s body, the function of a complex organ, and a coordinated response to infection. The genome contains crucial information about the time, place, and condition under which genes are expressed, yet this program is not, at present, intelligible to us from a study of the DNA sequence alone. Our best hope of inferring gene regulation on a genomic scale may be the coupling of (1) a systems-biology approach integrating computational methods with high-resolution whole-genomic data and (2) an evolutionary-theoretic approach identifying constraints through species comparisons. Combining these two strategies holds great promise for discovering the principles of gene regulation and may ultimately reveal the ways in which such regulation might be reprogrammed.

Our lab uses the tractable C. elegans embryo as an experimental system. One of our goals is to make a comprehensive determination of gene expression in every cell in this nematode. We are computationally analyzing this complete atlas to infer gene regulatory pathways. One future goal is to compare gene expression patterns across disparate metazoan phyla, searching for how the various signaling pathways and transcription factor (TF) modules are differentially expressed in patterning distinct body plans. In addition to embryonic development, we aim to reveal the spatial and conditional aspects of gene regulatory pathways by studying an organ (the human pancreas), tumorigenesis (zebrafish melanoma), and host-pathogen interaction (human Salmonella), through a collaborative approach that will also include the development of novel methods for spatial transcriptomics. We will also extend our analysis to regulatory pathways involving—in addition to mRNA—small RNA such as miRNAs and piRNAs, as well as lincRNAs. By providing insight into the structure, function, and plasticity of gene regulatory networks, this research will impact the fields of developmental, ecological, and evolutionary biology. 

About 1Figure 1. The evolution of gene regulatory pathways. (a) Single-cell RNA-Seq can be used to decipher the transcriptome of all cells and together with computational methods enable pathway inference. (b) Comparative analysis of molecular pathways in five additional model systems. (c) Evolution of developmental pathways. Circles represent TFs, boxes represent differentiation genes. Shadings and shape indicate the identity of the genes. Change may occur at different levels of the pathway as well as by deletion or intercalation of regulation.

Deciphering developmental gene pathways. The ideal way to study how gene regulatory pathways are orchestrated to achieve embryonic development would be to possess the complete gene expression program: that is, the expression of all genes in all cells at all times. This is impossible for most organisms at present, owing to the immense number of cells involved. But in the nematode C. elegans only 1,341 cells occur throughout embryogenesis. An additional benefit to using the C. elegans model system is that the cell-fate lineage was completely worked out by Sir John Sulston, who shared a 2002 Nobel Prize for this effort. Using our CEL-Seq method for single-cell RNA-Seq will uncover, for the first time in any animal, the expression of each gene in all cells (Figure 1a). Using this dataset we will be in a position to test a range of important, unsolved questions about embryogenesis. For example, do cells arrive at the same fate by a similar molecular pathway even if they originate from different regions in the embryo? Is there a correspondence between the cell’s transcriptomes and the described cell-types? Is a cell more similar to its sister than to its cellular analog in another embryo? After addressing these and other questions, an ambitious project in itself, we will employ this method routinely to study developmental pathway reprogramming using perturbations such as over-expression and elimination of crucial regulators.

Evolution of developmental gene pathways. The presence of a pathway reveals nothing about the reason for its particular manifestation. To form such an explanation requires an uncovering of the organizational principles of gene pathways. Evolutionary analyses carried out by comparing developmental processes across species, are crucial for revealing properties such as their robustness, constraints and plasticity. Previously, we led efforts comparing gene expression across strains and across species of the same genus. Most recently, a comparison across the ten major phyla led us to propose a far-reaching conclusion regarding the universality of embryogenesis: we found a conserved stage in mid-embryogenesis that corresponds to the time during which the body plan is set up. Our lab will build upon this discovery to unravel the sub-circuits in different parts of the embryo occurring at this stage, at the single-cell level, in five phyla in addition to our nematodes work: Annelida, Ctenophora, Cnidaria, Tardigrada, and Echinodermata (Figure 1b). These comparisons will allow us to explore how pathways are deployed across development in different species, to see which stages are highly conserved and where there are points of plasticity (Figure 1c). Through this research, we expect to gain insight into the principles governing gene regulatory pathways and how these pathways might be reprogrammed. The ability to systematically reprogram pathways will be of great medical importance, as in the case of cancer research.

When Charles Darwin introduced natural selection in his magnum opus “On the Origin of Species” as the process by which we may account for the staggering diversity of the living world, he did so by analogy to the artificial selection employed by British hobbyists for breeding fancy pigeons. Over 150 years later, this research program seeks to chart the opposite path: leading from a molecular understanding of gene expression pathways we are seeking to learn how genetic interactions are to be rewired to arrive at an alternative phenotype. Essentially, we aim to uncover the principles by which developmental pathways evolve, with the ultimate goals of predicting 1. the features of development from genomes alone, and 2. the modes available to us for their reprogramming. A main goal in our lab is a systematic and comprehensive description of gene regulation in the cell, including analysis of different types of non-coding RNA and their patterns of cross-regulation (Figure 2). Throughout, we make broad use of the comparative approach, studying multiple species at both the developmental and genomic levels. As our methods improve for revealing transcription—the first phenotype of the organism—at the resolution of individual cells throughout the life-cycle of the organism and across the various physiological conditions, our lab will seek to also better decipher gene pathways. We will next achieve proficiency in mapping these pathways back to the genome, thereby reverse engineering the genomic code. An understanding of pathway evolvability promises to highlight the principles of reprogramming of these for the betterment of human health.

About 2Figure 2. Evidenced and hypothesized regulatory interactions among RNA classes. The genomic view of diverse RNA classes is shown at the bottom. On the left, the vertical arrows indicate transcription and translation of mRNA and protein. In the middle and right, transcription of lincRNA and miRNA are shown, respectively. Intermediate processing steps are omitted for simplicity. The regulations stemming and arriving at lincRNAs are mostly hypothesized interactions.



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