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Gibbons M, Hong JM, Foster M, Chavarha M, Shao S, Ching L, Church VA, Schiff L, Ahadi S, Berndl M, Jess P, Pawlosky A. Million spot binding array platform for exploring and optimizing multiple simultaneous detection events. STAR Protoc 2022; 3:101829. [DOI: 10.1016/j.xpro.2022.101829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Oh YM, Lee SW, Kim WK, Chen S, Church VA, Cates K, Li T, Zhang B, Dolle RE, Dahiya S, Pak SC, Silverman GA, Perlmutter DH, Yoo AS. Age-related Huntington's disease progression modeled in directly reprogrammed patient-derived striatal neurons highlights impaired autophagy. Nat Neurosci 2022; 25:1420-1433. [PMID: 36303071 PMCID: PMC10162007 DOI: 10.1038/s41593-022-01185-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 09/19/2022] [Indexed: 01/13/2023]
Abstract
Huntington's disease (HD) is an inherited neurodegenerative disorder with adult-onset clinical symptoms, but the mechanism by which aging drives the onset of neurodegeneration in patients with HD remains unclear. In this study we examined striatal medium spiny neurons (MSNs) directly reprogrammed from fibroblasts of patients with HD to model the age-dependent onset of pathology. We found that pronounced neuronal death occurred selectively in reprogrammed MSNs from symptomatic patients with HD (HD-MSNs) compared to MSNs derived from younger, pre-symptomatic patients (pre-HD-MSNs) and control MSNs from age-matched healthy individuals. We observed age-associated alterations in chromatin accessibility between HD-MSNs and pre-HD-MSNs and identified miR-29b-3p, whose age-associated upregulation promotes HD-MSN degeneration by impairing autophagic function through human-specific targeting of the STAT3 3' untranslated region. Reducing miR-29b-3p or chemically promoting autophagy increased the resilience of HD-MSNs against neurodegeneration. Our results demonstrate miRNA upregulation with aging in HD as a detrimental process driving MSN degeneration and potential approaches for enhancing autophagy and resilience of HD-MSNs.
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Affiliation(s)
- Young Mi Oh
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Seong Won Lee
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Woo Kyung Kim
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Shawei Chen
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Victoria A Church
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kitra Cates
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Tiandao Li
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Bo Zhang
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Roland E Dolle
- Department of Biochemistry, Washington University School of Medicine, St. Louis, MO, USA
| | - Sonika Dahiya
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Stephen C Pak
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Gary A Silverman
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - David H Perlmutter
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrew S Yoo
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, USA.
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Hong JM, Gibbons M, Bashir A, Wu D, Shao S, Cutts Z, Chavarha M, Chen Y, Schiff L, Foster M, Church VA, Ching L, Ahadi S, Hieu-Thao Le A, Tran A, Dimon M, Coram M, Williams B, Jess P, Berndl M, Pawlosky A. ProtSeq: Toward high-throughput, single-molecule protein sequencing via amino acid conversion into DNA barcodes. iScience 2022; 25:103586. [PMID: 35005536 PMCID: PMC8717419 DOI: 10.1016/j.isci.2021.103586] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 10/06/2021] [Accepted: 12/07/2021] [Indexed: 12/13/2022] Open
Abstract
We demonstrate early progress toward constructing a high-throughput, single-molecule protein sequencing technology utilizing barcoded DNA aptamers (binders) to recognize terminal amino acids of peptides (targets) tethered on a next-generation sequencing chip. DNA binders deposit unique, amino acid-identifying barcodes on the chip. The end goal is that, over multiple binding cycles, a sequential chain of DNA barcodes will identify the amino acid sequence of a peptide. Toward this, we demonstrate successful target identification with two sets of target-binder pairs: DNA-DNA and Peptide-Protein. For DNA-DNA binding, we show assembly and sequencing of DNA barcodes over six consecutive binding cycles. Intriguingly, our computational simulation predicts that a small set of semi-selective DNA binders offers significant coverage of the human proteome. Toward this end, we introduce a binder discovery pipeline that ultimately could merge with the chip assay into a technology called ProtSeq, for future high-throughput, single-molecule protein sequencing. Designed ProtSeq protein sequencing method compatible with widely used NGS technology Built Target-Switch SELEX to isolate aptamers specific to N-terminal amino acids (AAs) Showed binding, ligation, cleavage, and NGS of six DNA binders in ordered barcode chain Developed pipeline to deconvolve AAs from DNA barcodes to identify putative proteins
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Affiliation(s)
| | | | - Ali Bashir
- Google, LLC, Mountain View, CA 94043, USA
| | - Diana Wu
- Google, LLC, Mountain View, CA 94043, USA
| | | | | | | | - Ye Chen
- Google, LLC, Mountain View, CA 94043, USA
| | | | | | | | | | - Sara Ahadi
- Google, LLC, Mountain View, CA 94043, USA
| | | | | | | | - Marc Coram
- Google, LLC, Mountain View, CA 94043, USA
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Church VA, Yoo AS. MiR-218 steps down to a threshold of motor impairment. Neuron 2021; 109:3233-3235. [PMID: 34672981 DOI: 10.1016/j.neuron.2021.09.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this issue of Neuron, Amin et al. (2021) generate genetic tools to titrate down levels of miR-218, a motor neuron-enriched microRNA, in vivo. Varying miR-218 dose alters target selection, results in distinct dose-response curves reflecting 3' UTR features, and reveals a miR-218 threshold below which motor neuron deficits emerge.
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Affiliation(s)
- Victoria A Church
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrew S Yoo
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Church VA, Pressman S, Isaji M, Truscott M, Cizmecioglu NT, Buratowski S, Frolov MV, Carthew RW. Microprocessor Recruitment to Elongating RNA Polymerase II Is Required for Differential Expression of MicroRNAs. Cell Rep 2018; 20:3123-3134. [PMID: 28954229 DOI: 10.1016/j.celrep.2017.09.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 08/18/2017] [Accepted: 09/04/2017] [Indexed: 01/24/2023] Open
Abstract
The cellular abundance of mature microRNAs (miRNAs) is dictated by the efficiency of nuclear processing of primary miRNA transcripts (pri-miRNAs) into pre-miRNA intermediates. The Microprocessor complex of Drosha and DGCR8 carries this out, but it has been unclear what controls Microprocessor's differential processing of various pri-miRNAs. Here, we show that Drosophila DGCR8 (Pasha) directly associates with the C-terminal domain of the RNA polymerase II elongation complex when it is phosphorylated by the Cdk9 kinase (pTEFb). When association is blocked by loss of Cdk9 activity, a global change in pri-miRNA processing is detected. Processing of pri-miRNAs with a UGU sequence motif in their apical junction domain increases, while processing of pri-miRNAs lacking this motif decreases. Therefore, phosphorylation of RNA polymerase II recruits Microprocessor for co-transcriptional processing of non-UGU pri-miRNAs that would otherwise be poorly processed. In contrast, UGU-positive pri-miRNAs are robustly processed by Microprocessor independent of RNA polymerase association.
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Affiliation(s)
- Victoria A Church
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Sigal Pressman
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Mamiko Isaji
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Mary Truscott
- Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, IL 60607, USA
| | - Nihal Terzi Cizmecioglu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Middle East Technical University, Department of Biological Sciences, 06800, Ankara, Turkey
| | - Stephen Buratowski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Maxim V Frolov
- Department of Biochemistry and Molecular Genetics, University of Illinois, Chicago, IL 60607, USA
| | - Richard W Carthew
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
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