Preprint: Lalit F and Jose AM. Selecting genes for analysis using historically contingent progress: from RNA changes to protein-protein interactions. bioRxiv. (Online May 3, 2024 with an update on 6/9/2024). Download pdf.
Progress in biology has generated numerous lists of genes that share some property. But, advancing from these lists of genes to understanding their roles is slow and unsystematic. This study uses RNA silencing in C. elegans to illustrate an approach for identifying understudied genes. Many proteins encoded by the understudied genes are predicted to physically interact with known regulators of RNA silencing. These predicted influencers of RNA-regulated expression could be used for feedback regulation, which is essential for the homeostasis observed in all living systems. These discoveries suggest that the analysis of perturbed transcripts and potential interactions of the proteins they encode could help prioritize candidate regulators of any process.
Preprint: Chey MS, Raman P, Ettefa F, and Jose AM. Evidence for multiple forms of heritable RNA silencing. bioRxiv. (Online Apr 29, 2024). Download pdf.
Heritable gene silencing has been proposed to rely on DNA methylation, histone modifications, and/or non-coding RNAs in different organisms. This study demonstrates that multiple RNA-mediated mechanisms with distinct and easily detectable molecular signatures can underlie heritable silencing of the same open-reading frame in the nematode C. elegans. Three cases of gene-selective silencing in two-gene operons provide support for the transmission of heritable epigenetic changes through different mechanisms of RNA silencing independent of changes in chromatin that would affect all genes of an operon equally. Different heritable epigenetic states of a gene were associated with distinct populations of stabilized mRNA fragments with untemplated poly-UG (pUG) tails, which are known intermediates of RNA silencing. These ‘pUG signatures’ provide a way to distinguish the multiple mechanisms that can drive heritable RNA silencing of a single gene.
2024: Knudsen DR, Raman P, Ettefa F, DeRavin L, and Jose AM. Target-specific requirements for RNA interference can arise through restricted RNA amplification despite the lack of specialized pathways. eLife. 13:RP97487 (Online on Feb 8, 2023 with update on 3/1/2024 on bioRxiv). Download pdf.
This study analyzes how an intrinsically disordered protein, a Maelstrom domain, and an Argonaute can work together in a single regulatory network to cause RNA interference (RNAi) such that there are target-specific genetic requirements for silencing. A quantitative model for RNAi provides explanations and predictions: 1. Key intermediates of RNAi such as 1º siRNAs, 2º siRNAs, and pUG RNAs undergo turnover. 2. Small RNA levels cannot predict knockdown efficiency. 3. A target mRNA with high turnover is difficult to knockdown. In testing the model, we show that animals recover after a pulse of double-stranded RNA (dsRNA), pUG RNAs are made chiefly upon targeting by 1º siRNAs, and enhanced dsRNA processing can overcome the requirement for a specific secondary Argonaute. Insights from this study inform choice of targets for RNAi-based interventions in Agriculture and Medicine to forestall the development of resistance and avoid futile cycles of innovation.
Reviewed Preprint: Shugarts N, Sathya A, Yi AL, Chan WM, Marré JA, Jose AM. Intergenerational transport of double-stranded RNA limits heritable epigenetic changes. eLife. 13:RP99149 (Online Oct 6, 2021 with revisions on 2/12/2023 and 4/23/2024). Download pdf.
This study dissects the intergenerational path taken by dsRNA from parental circulation and discovers that cytosolic entry in the parental germline and/or developing progeny through the dsRNA importer SID-1 varies based on developmental time and dsRNA substrates. Temporary loss of SID-1 causes changes in the expression of the sid-1-dependent gene sdg-1 that can last for more than 100 generations. The SDG-1 protein is enriched in perinuclear Z granules required for heritable RNA silencing, but it is expressed from a retrotransposon targeted by such RNA silencing. This auto-inhibitory loop reveals how retrotransposons could persist over evolutionary time by hosting genes that regulate their own silencing.
2024: Jose AM. Heritable epigenetic changes are constrained by the dynamics of regulatory architectures. eLife. 12:RP92093. (Online Jun 9, 2023 on bioRxiv). Download pdf.
Interacting molecules create regulatory architectures that can persist despite turnover of molecules. Although epigenetic changes occur within the context of such architectures, there is limited understanding of how they can influence the heritability of changes. This study develops criteria for the heritability of regulatory architectures and uses quantitative simulations of interacting regulators parsed as entities, their sensors and the sensed properties to analyze how architectures influence heritable epigenetic changes. Broadly, these results provide a foundation for analyzing the inheritance of epigenetic changes within the context of the regulatory architectures implemented using diverse molecules in different living systems.
2022: Chey M, Jose AM. Heritable epigenetic changes at single genes: challenges and opportunities in Caenorhabditis elegans. Trends in Genetics 38(2):116-119. (Online Sep 4, 2021). Download pdf.
This short review highlights the three key questions that need to be answered to explain any heritable epigenetic change: 1) How many generations does it last? 2) What molecules are required? 3) What change in regulatory architecture accounts for its nature and duration? It also outlines the opportunities and challenges for analyzing RNA-mediated epigenetic changes at single genes in C. elegans.
2021: Devanapally S*, Raman P*, Chey M, Allgood S, Ettefa F, Diop M, Lin Y, Cho YE, Jose AM. Mating can initiate stable RNA silencing that overcomes epigenetic recovery. Nature Communications 12:4239. (Online Jan 7, 2020, BioRxiv). *equal contribution Download pdf.
This study reports a way to initiate >300 generations of silencing simply by mating. Such heritable RNA silencing occurs only for a rare set of transgenes when males with the transgene are mated with wild-type animals without the transgene. It also demonstrates that recovery from epigenetic change does not depend on the sequence targeted by RNA silencing but rather on the regulatory context provided by the gene containing the target sequence. Such gene-specific epigenetic repair mechanisms that preserve the epigenome are thus analogous to DNA repair mechanisms that preserve the genome. We speculate that such recovery is the reason why form and function of organisms are largely preserved in successive generations. News reports on this work were highlighted on websites including Maryland Today, Technology Networks, and What is epigenetics?.
2020: Galford KF, Jose AM. The FDA-approved drugs ticlopidine, sertaconazole, and dexlansoprazole can cause morphological changes in C. elegans. Chemosphere 261:127756. (Online Apr 11, 2020, bioRxiv) Download pdf.
This study reports the serendipitous discovery of three FDA-approved drugs causing obvious morphological changes in C. elegans. Ticlopidine and Sertaconazole cause accumulations & lethality upon acute exposure. Dexlansoprazole causes defects in molting upon exposure during larval development. These changes provide opportunities for using an animal model system to explore additional aspects of these drugs that have been collectively prescribed to millions of humans. See associated press release and interview of Kyle on 17 minutes of Science.
2020: Jose AM. The analysis of living systems can generate both knowledge and illusions. eLife 9:e56354. Download pdf.
This article proposes that six complementary approaches are available for the analysis of any living system: perturbation, visualization, substitution, characterization, reconstitution, and simulation. Combining results from these approaches can lead to acceptance of knowledge that later turns out to be unreliable. Awareness of this taxonomy and the limitations of each approach could improve reliability of inferences, enhance fairness of review, and limit presistent illusions of knowledge.
2020: Jose AM. A framework for parsing heritable information. Journal of the Royal Society Interface 17:20200154 (Online Mar 2, 2020, arXiv). Download pdf.
This study develops a single framework for all heritable information in living systems by parsing the molecules in the bottleneck stage between generations into entities, their sensors, and the sensed properties. This framework is a useful guide for understanding how life evolves and how the storage of information has itself evolved with complexity since before the origin of life. News reports on this work were published on many websites, including Maryland Today, LabRoots.com, Genetic Engineering & Biotechnology News, phys.org (a top story of the week), and others around the world (e.g., Galileu in Brazil, ABC in Spain, Trust My Science, editorial in RTFlash: Recherche et Technologie, and one of '60 new ways to see the world' according to Science & Vie in France, Evolution Tree in Turkey, 4everScience in Ukraine, BioNews in the UK). It also sparked discussions among diverse groups (e.g., Hacker News, Uncommon Descent, and Phys.org).
2020: Jose AM. Heritable epigenetic changes alter transgenerational waveforms maintained by cycling stores of information. BioEssays 1900254. Download pdf.
This essay elucidates how transgenerational epigenetic inheritance can be associated with chemical changes in molecules, physical changes in molecules, or changes in the system alone. Regardless of the kind of change, all need to alter the waveforms traced across generations by the cycling stores of information that are recreated during successive bottleneck stages. This paper is complementary to work presented in Jose AM, J. R. Soc. Interface, 2020, with which it was co-published.
2019: Ravikumar S, Devanapally S, Jose AM. Gene silencing by double-stranded RNA from C. elegans neurons reveals functional mosaicism of RNA interference. Nucleic Acids Research. 47(19):10059-71. (Online Aug 16, 2018 with revision on Jul 27, 2019, BioRxiv). Download pdf.
This study reveals random variation in the mechanism(s) used for RNA interference. We found that dsRNA from neurons can silence cells throughout the animal using a mechanism that can differ from that used by other sources of dsRNA. Single-cell resolution measurements of silencing revealed that the identities of intestinal cells requiring a particular RNA-dependent RNA polymerase for this silencing can vary from animal to animal. This is an illustration of functional equivalence allowing underlying mosaicism, whereby the same function - gene silencing - is achieved using different molecules in random sets of cells. News reports on this work were published on many websites including University of Maryland's website, TechnologyNetworks.com, The Southern Maryland Chronicle, Genetic Engineering & Biotechnology News, and BioOptics World. Highlighted on the National Institutes of General Medical Sciences, NIH website.
2018: Jose AM. Replicating and cycling stores of information perpetuate life. BioEssays. 40(4):1700161. (Online on 6/14/2017 with revisions on 7/30/2017 and 8/26/2017, BioRxiv) See video abstract, Download pdf. [Inside front cover]
This essay integrates insights from the history of biology to bring into sharp relief what we do not know about the fundamental nature of living things: all the information that is necessary to perpetuate life. Information is held within cells in two distinct forms: (1) the well-studied genome sequence; and (2) the under-explored changing arrangement of all molecules within a cell that return to a similar configuration at the start of each generation. Together, they form the cell code - the interdependent and coevolving arrangement of molecules that perpetuates the organism. While we do not know the entire cell code of any organism, clearly seeing the relationship between an organism and its cell code has broad implications for our understanding of evolution, the origins of inherited diseases, and the potential synthesis of living things.
2017: Raman P, Zaghab S, Traver EC, Jose AM. The double-stranded RNA binding protein RDE-4 can act cell autonomously during feeding RNAi in C. elegans. Nucleic Acids Research. 45(14):8463-73. (Online on 12/2/2016, BioRxiv) Download pdf.
This study analyzes the organismal fate of ingested dsRNA and discovers the general reduction in silencing by ingested dsRNA that occurs within cells that express repetitive DNA.
2017: Choi YS, Edwards LO, DiBello A, Jose AM. Removing bias against short sequences enables northern blotting to better complement RNA-seq for the study of small RNAs. Nucleic Acids Research. 45(10):e87. (Online on 8/16/2016, BioRxiv) Download pdf.
This study highlights the need for approaches that complement RNA-seq, discovers that northern blotting of small RNAs is biased against short sequences, and develops a protocol that removes this bias.
2016: Marré JA, Traver EC, Jose AM. Extracellular RNA is transported from one generation to the next in C. elegans. Proceedings of the National Academy of Sciences USA. 113(44):12496-501. Download pdf. [Also see 2017: Marré J and Jose A. Inheritance of extracellular nutrition and information in Caenorhabditis elegans. Mol. Reprod. Dev. 84(4):283. Download pdf.]
This study demonstrates that extracellular RNA from a parent can be imported into oocytes, be held within intracellular vesicles, and reach progeny to cause gene silencing. This work was highlighted in This Week in PNAS. News reports on this work were published on many websites including BioTechniques News, University of Maryland's website, Epigenie.com, LabRoots.com, and Genetic Engineering & Biotechnology News.
2016: Le HH, Looney M, Strauss B, Bloodgood M, Jose AM. Tissue homogeneity requires inhibition of unequal gene silencing during development. Journal of Cell Biology. 214(3):319-31. Download pdf.
This study develops a paradigm for answering the fundamental question: given the numerous components of a cell, how do animals keep any two cells equal? As part of this study, we collaborated with a computer scientist from Center for Advanced Study of Language (Dr. Michael Bloodgood) for the use of machine learning approaches. This work was highlighted as the In Focus article of the issue. News reports on this work were published on many websites including University of Maryland's website.
2016: Blumenfeld AL, Jose AM. Reproducible features of small RNAs in C. elegans reveal NU RNAs and provide insights into 22G RNAs and 26G RNAs. RNA. 22:184-92 Download pdf.
This study analyzes small RNAs in C. elegans, identifies a class of RNAs smaller than 18 nucleotides called NU RNAs (pronounced "new RNAs"), and makes the case for RNAs smaller than 18 nucleotides being used for sequence-specific gene regulation. PACER (Programs for Analysis of C. elegans small RNAs) is a collection of all the scripts and programs used in this paper and wrapped by Rex Ledesma.
2015: Jose AM. Movement of regulatory RNA between animal cells. genesis. 53(7): 395-416. Download pdf.
This invited review summarizes the state of the field, highlights unanswered questions, and suggests future directions.
2015: Devanapally S, Ravikumar S, Jose AM. Double-stranded RNA made in C. elegans neurons can enter the germline and cause transgenerational gene silencing. Proceedings of the National Academy of Sciences USA. 112(7):2133-8. Download pdf.
This study demonstrates for the first time the transport of sequence-specific information from neurons to germ cells in an animal. This work was highlighted in This Week in PNAS and Science Signaling. News reports on this work were published on many websites including University of Maryland's website, the Diamondback newspaper, Epigenie.com, and Biomedical picture of the day. Highlighted in She has her mother’s laugh, one of New York Times 100 notable books of 2018 - read summary in The Atlantic.
2012: Jose AM*, Kim YA*, Leal-Ekman S, Hunter CP. A conserved tyrosine kinase promotes the import of silencing RNAs into C. elegans cells. Proceedings of the National Academy of Sciences USA. 109(36):14520-5.*equal contribution. Download pdf.
This study demonstrates that the import of RNA into animal cells is regulated by a conserved tyrosine kinase that likely responds to environmental changes. Undergraduate Yunsoo Kim won the Henderson prize and the Hoopes prize for her thesis as part of this work.
2011: Jose AM, Garcia GA, Hunter CP. Two classes of silencing RNAs move between C. elegans tissues. Nature Structural and Molecular Biology. 18(11): 1184-8. Download pdf.
This study deduces the possible molecular identities of mobile RNAs. A news report on this work was published in the Harvard Gazette. The significance and commercial applicability of this work is highlighted at Harvard University's website.
2009: Jose AM, Smith JJ, Hunter CP. Export of RNA silencing from C. elegans tissues does not require the RNA channel SID-1. Proceedings of the National Academy of Sciences USA. 106(7): 2283-8. Download pdf.
This study establishes the generality of RNA transport between C. elegans cells and uncovers the existence of novel pathways that make and export mobile RNA. Description for the general public is available at Harvard University's website.