However, each of these methods alone captures an incomplete picture of gene expression. These reports demonstrate that each level of gene regulation could be captured from specific cell types with negligible effect of the methods themselves on gene expression. Transgenic techniques based on this concept have been applied in laboratory mice to purify translating mRNA, mature miRNA, pulse-labeled total RNA, and chromatin and nuclear RNA. These methods often employ a recombinase system, providing access to a wide spectrum of cell types based on cell identity, developmental stage, or neuronal activity, for example. Several strategies were developed that share the common theme of using cell type–specific genetically engineered handles or tags to purify the target nucleic acids. An innovative solution to tackle this challenge is the purification of nucleic acids from a related subset of cells after tissue sample lysis. ![]() Typical assays, when applied to such tissues, provide information on general regulatory trends but give little to no information about the cellular source of the observed changes, or about the specific level(s) of gene expression regulation that directed them. Our understanding of how gene expression is coordinated at the cellular level of mammalian tissues has been impeded by their heterogenous nature. This landscape is complemented by various classes of long noncoding RNAs (lncRNAs), RNA species incompletely understood but thought to have a role in many aspects of gene expression regulation. The latter can stall translation or target mRNAs for degradation. Translation is controlled at both the level of ribosome subunits binding to mRNAs and through the actions of the RNA-induced silencing complex (RISC) guided by microRNAs (miRNAs). Some transcripts are then processed into mature mRNAs and shuttled to the cytoplasm, where the encoded information is translated by ribosomes into protein. A coordinated action of activators and repressors, as well as of chromatin-modifying enzymes, govern which information is converted into RNA transcripts and which remains silent. In the nucleus, chemical and conformational modifications to chromatin modulate the access of transcriptional machineries to gene regulatory elements in DNA. Gene expression, a compilation of processes actuating information encoded in the genome, is exquisitely controlled at multiple levels. Woodchuck Hepatitis Virus Postranscriptional Response Element WT, Variance stabilizing transformation WPRE, Translating ribosomes affinity purification tRFP, Uracil phosphoribosyltransferase from Toxoplasma gondii TK, Stable isotope labeling with amino acids in cell culture TES, Special AT-rich sequence-binding protein 2 scRNAseq, Large subunit ribosomal protein 22-hemagglutinin (Ribo-Tag protein) RPM, Large subunit ribosomal protein 22 RPL22-HA, Principal cell layer of the hippocampus PGDB, Methylated DNA immunoprecipitation miRAP, ![]() Isolation of nuclei tagged in specific cell types IP, ![]() The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ĭompeting interests: The authors have declared that no competing interests exist.Ĭytomegalovirus:chicken actin fusion promoter CaMKIIα,Ĭalcium/calmodulin dependent protein kinase II Cre,įluorescence activated cell sorting FDR, VB, AR, RR, and SB were supported by DFG and BMBF (BO4221, IDSN, SFB 1286 Z2), Helmholtz iMed, and VW German-Israeli grants. ![]() Additionally, MF was supported by grants from the German Research Foundation (SFB 1089, C01, B06) and ERA-NET NEURON (MicroSynDep, MicroSchiz). This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.ĭata Availability: The accession number for all the raw NGS data generated in this study is GSE123422.įunding: This work was generously supported by internal funding from the Knut and Alice Wallenberg Foundation and the German Center for Neurodegenerative Diseases. Received: Accepted: JPublished: August 8, 2019Ĭopyright: © 2019 Kaczmarczyk et al. PLoS Biol 17(8):Īcademic Editor: Wendy V. (2019) Tagger-A Swiss army knife for multiomics to dissect cell type–specific mechanisms of gene expression in mice. Citation: Kaczmarczyk L, Bansal V, Rajput A, Rahman R-u, Krzyżak W, Degen J, et al.
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