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Lai JH, Keum JW, Lee HG, Molaei M, Blair EJ, Li S, Soliman JW, Raol VK, Barker CL, Fodor SPA, Fan HC, Shum EY. New realm of precision multiplexing enabled by massively-parallel single molecule UltraPCR. bioRxiv 2023:2023.10.09.561546. [PMID: 37873291 PMCID: PMC10592712 DOI: 10.1101/2023.10.09.561546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
PCR has been a reliable and inexpensive method for nucleic acid detection in the past several decades. In particular, multiplex PCR is a powerful tool to analyze many biomarkers in the same reaction, thus maximizing detection sensitivity and reducing sample usage. However, balancing the amplification kinetics between amplicons and distinguishing them can be challenging, diminishing the broad adoption of high order multiplex PCR panels. Here, we present a new paradigm in PCR amplification and multiplexed detection using UltraPCR. UltraPCR utilizes a simple centrifugation workflow to split a PCR reaction into ∼34 million partitions, forming an optically clear pellet of spatially separated reaction compartments in a PCR tube. After in situ thermocycling, light sheet scanning is used to produce a 3D reconstruction of the fluorescent positive compartments within the pellet. At typical sample DNA concentrations, the magnitude of partitions offered by UltraPCR dictate that the vast majority of target molecules occupy a compartment uniquely. This single molecule realm allows for isolated amplification events, thereby eliminating competition between different targets and generating unambiguous optical signals for detection. Using a 4-color optical setup, we demonstrate that we can incorporate 10 different fluorescent dyes in the same UltraPCR reaction. We further push multiplexing to an unprecedented level by combinatorial labeling with fluorescent dyes - referred to as "comboplex" technology. Using the same 4-color optical setup, we developed a 22-target comboplex panel that can detect all targets simultaneously at high precision. Collectively, UltraPCR has the potential to push PCR applications beyond what is currently available, enabling a new class of precision genomics assays.
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2
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Shum EY, Lai JH, Li S, Lee HG, Soliman J, Raol VK, Lee CK, Fodor SP, Fan HC. Next-Generation Digital Polymerase Chain Reaction: High-Dynamic-Range Single-Molecule DNA Counting via Ultrapartitioning. Anal Chem 2022; 94:17868-17876. [PMID: 36508568 PMCID: PMC9798378 DOI: 10.1021/acs.analchem.2c03649] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Digital PCR (dPCR) was first conceived for single-molecule quantitation. However, current dPCR systems often require DNA templates to share partitions due to limited partitioning capacities. Here, we introduce UltraPCR, a next-generation dPCR system where DNA counting is performed in a single-molecule regimen through a 6-log dynamic range using a swift and parallelized workflow. Each UltraPCR reaction is divided into >30 million partitions without microfluidics to achieve single template occupancy. Combined with a unique emulsion chemistry, partitions are optically clear, enabling the use of a three-dimensional imaging technique to rapidly detect DNA-positive partitions. Single-molecule occupancy also allows for more straightforward multiplex assay development due to the absence of partition-specific competition. As a proof of concept, we developed a 222-plex UltraPCR assay and demonstrated its potential use as a rapid, low-cost screening assay for noninvasive prenatal testing for as low as 4% trisomy fraction samples with high precision, accuracy, and reproducibility.
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3
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Tan K, Jones SH, Lake BB, Chousal JN, Shum EY, Zhang L, Chen S, Sohni A, Pandya S, Gallo RL, Zhang K, Cook-Andersen H, Wilkinson MF. The role of the NMD factor UPF3B in olfactory sensory neurons. eLife 2020; 9:e57525. [PMID: 32773035 PMCID: PMC7452722 DOI: 10.7554/elife.57525] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/09/2020] [Indexed: 12/13/2022] Open
Abstract
The UPF3B-dependent branch of the nonsense-mediated RNA decay (NMD) pathway is critical for human cognition. Here, we examined the role of UPF3B in the olfactory system. Single-cell RNA-sequencing (scRNA-seq) analysis demonstrated considerable heterogeneity of olfactory sensory neuron (OSN) cell populations in wild-type (WT) mice, and revealed that UPF3B loss influences specific subsets of these cell populations. UPF3B also regulates the expression of a large cadre of antimicrobial genes in OSNs, and promotes the selection of specific olfactory receptor (Olfr) genes for expression in mature OSNs (mOSNs). RNA-seq and Ribotag analyses identified classes of mRNAs expressed and translated at different levels in WT and Upf3b-null mOSNs. Integrating multiple computational approaches, UPF3B-dependent NMD target transcripts that are candidates to mediate the functions of NMD in mOSNs were identified in vivo. Together, our data provides a valuable resource for the olfactory field and insights into the roles of NMD in vivo.
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Affiliation(s)
- Kun Tan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine University of California, San DiegoSan DiegoUnited States
| | - Samantha H Jones
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine University of California, San DiegoSan DiegoUnited States
| | - Blue B Lake
- Department of Bioengineering, University of California, San DiegoSan DiegoUnited States
| | - Jennifer N Chousal
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine University of California, San DiegoSan DiegoUnited States
| | - Eleen Y Shum
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine University of California, San DiegoSan DiegoUnited States
| | - Lingjuan Zhang
- Department of Dermatology, University of California, San DiegoSan DiegoUnited States
| | - Song Chen
- Department of Bioengineering, University of California, San DiegoSan DiegoUnited States
| | - Abhishek Sohni
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine University of California, San DiegoSan DiegoUnited States
| | - Shivam Pandya
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine University of California, San DiegoSan DiegoUnited States
| | - Richard L Gallo
- Department of Dermatology, University of California, San DiegoSan DiegoUnited States
| | - Kun Zhang
- Department of Bioengineering, University of California, San DiegoSan DiegoUnited States
| | - Heidi Cook-Andersen
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine University of California, San DiegoSan DiegoUnited States
- Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | - Miles F Wilkinson
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine University of California, San DiegoSan DiegoUnited States
- Institute of Genomic Medicine, University of California, San DiegoSan DiegoUnited States
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Ramaiah M, Tan K, Plank TM, Song H, Chousal JN, Jones S, Shum EY, Sheridan SD, Peterson KJ, Gromoll J, Haggarty SJ, Cook‐Andersen H, Wilkinson MF. Response to: X-linked miR-506 family miRNAs promote FMRP expression in mouse spermatogonia. EMBO Rep 2020; 21:e49354. [PMID: 31808609 PMCID: PMC6944912 DOI: 10.15252/embr.201949354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Madhuvanthi Ramaiah
- Department of Obstetrics, Gynecology, and Reproductive SciencesUniversity of CaliforniaSan DiegoLa JollaCAUSA
| | - Kun Tan
- Department of Obstetrics, Gynecology, and Reproductive SciencesUniversity of CaliforniaSan DiegoLa JollaCAUSA
| | - Terra‐Dawn M Plank
- Department of Obstetrics, Gynecology, and Reproductive SciencesUniversity of CaliforniaSan DiegoLa JollaCAUSA
| | - Hye‐Won Song
- Department of Obstetrics, Gynecology, and Reproductive SciencesUniversity of CaliforniaSan DiegoLa JollaCAUSA
| | - Jennifer N Chousal
- Department of Obstetrics, Gynecology, and Reproductive SciencesUniversity of CaliforniaSan DiegoLa JollaCAUSA
| | - Samantha Jones
- Department of Obstetrics, Gynecology, and Reproductive SciencesUniversity of CaliforniaSan DiegoLa JollaCAUSA
| | - Eleen Y Shum
- Department of Obstetrics, Gynecology, and Reproductive SciencesUniversity of CaliforniaSan DiegoLa JollaCAUSA
| | - Steven D Sheridan
- Chemical Neurobiology LaboratoryCenter for Genomic MedicineBostonMAUSA
- Departments of Neurology and PsychiatryMassachusetts General HospitalBostonMAUSA
| | | | - Jörg Gromoll
- Center for Reproductive Medicine and AndrologyUniversity of MünsterMünsterGermany
| | - Stephen J Haggarty
- Chemical Neurobiology LaboratoryCenter for Genomic MedicineBostonMAUSA
- Departments of Neurology and PsychiatryMassachusetts General HospitalBostonMAUSA
| | - Heidi Cook‐Andersen
- Department of Obstetrics, Gynecology, and Reproductive SciencesUniversity of CaliforniaSan DiegoLa JollaCAUSA
- Division of Biological SciencesUniversity of CaliforniaSan DiegoLa JollaCAUSA
| | - Miles F Wilkinson
- Department of Obstetrics, Gynecology, and Reproductive SciencesUniversity of CaliforniaSan DiegoLa JollaCAUSA
- Institute of Genomic MedicineUniversity of CaliforniaSan DiegoLa JollaCAUSA
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5
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Ramaiah M, Tan K, Plank TDM, Song HW, Chousal JN, Jones S, Shum EY, Sheridan SD, Peterson KJ, Gromoll J, Haggarty SJ, Cook-Andersen H, Wilkinson MF. A microRNA cluster in the Fragile-X region expressed during spermatogenesis targets FMR1. EMBO Rep 2019; 20:e46566. [PMID: 30573526 PMCID: PMC6362356 DOI: 10.15252/embr.201846566] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 11/12/2018] [Accepted: 11/21/2018] [Indexed: 01/08/2023] Open
Abstract
Testis-expressed X-linked genes typically evolve rapidly. Here, we report on a testis-expressed X-linked microRNA (miRNA) cluster that despite rapid alterations in sequence has retained its position in the Fragile-X region of the X chromosome in placental mammals. Surprisingly, the miRNAs encoded by this cluster (Fx-mir) have a predilection for targeting the immediately adjacent gene, Fmr1, an unexpected finding given that miRNAs usually act in trans, not in cis Robust repression of Fmr1 is conferred by combinations of Fx-mir miRNAs induced in Sertoli cells (SCs) during postnatal development when they terminate proliferation. Physiological significance is suggested by the finding that FMRP, the protein product of Fmr1, is downregulated when Fx-mir miRNAs are induced, and that FMRP loss causes SC hyperproliferation and spermatogenic defects. Fx-mir miRNAs not only regulate the expression of FMRP, but also regulate the expression of eIF4E and CYFIP1, which together with FMRP form a translational regulatory complex. Our results support a model in which Fx-mir family members act cooperatively to regulate the translation of batteries of mRNAs in a developmentally regulated manner in SCs.
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Affiliation(s)
- Madhuvanthi Ramaiah
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Kun Tan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Terra-Dawn M Plank
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Hye-Won Song
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Jennifer N Chousal
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Samantha Jones
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Eleen Y Shum
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Steven D Sheridan
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Boston, MA, USA
- Departments of Neurology and Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Jörg Gromoll
- Center for Reproductive Medicine and Andrology, University of Münster, Münster, Germany
| | - Stephen J Haggarty
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Boston, MA, USA
- Departments of Neurology and Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Heidi Cook-Andersen
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Miles F Wilkinson
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
- Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
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6
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Shum EY, Walczak EM, Chang C, Christina Fan H. Quantitation of mRNA Transcripts and Proteins Using the BD Rhapsody™ Single-Cell Analysis System. Adv Exp Med Biol 2019; 1129:63-79. [PMID: 30968361 DOI: 10.1007/978-981-13-6037-4_5] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this review, we describe the BD Rhapsody™ Single-Cell Analysis System, a platform that allows high-throughput capture of nucleic acids from single cells using a simple cartridge workflow and a multitier barcoding system. The resulting captured information can be used to generate various types of next-generation sequencing (NGS) libraries, including whole transcriptome analysis for discovery biology and targeted RNA analysis for high sensitivity transcript detection. The BD Rhapsody system can be used with emerging applications, such as BD™ AbSeq assays, to profile gene expression in both mRNA and protein level to provide ultra-high resolution analysis of single cells.
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7
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Huang L, Shum EY, Jones SH, Lou CH, Chousal J, Kim H, Roberts AJ, Jolly LA, Espinoza JL, Skarbrevik DM, Phan MH, Cook-Andersen H, Swerdlow NR, Gecz J, Wilkinson MF. A Upf3b-mutant mouse model with behavioral and neurogenesis defects. Mol Psychiatry 2018; 23:1773-1786. [PMID: 28948974 PMCID: PMC5869067 DOI: 10.1038/mp.2017.173] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/05/2017] [Accepted: 06/21/2017] [Indexed: 02/07/2023]
Abstract
Nonsense-mediated RNA decay (NMD) is a highly conserved and selective RNA degradation pathway that acts on RNAs terminating their reading frames in specific contexts. NMD is regulated in a tissue-specific and developmentally controlled manner, raising the possibility that it influences developmental events. Indeed, loss or depletion of NMD factors have been shown to disrupt developmental events in organisms spanning the phylogenetic scale. In humans, mutations in the NMD factor gene, UPF3B, cause intellectual disability (ID) and are strongly associated with autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD) and schizophrenia (SCZ). Here, we report the generation and characterization of mice harboring a null Upf3b allele. These Upf3b-null mice exhibit deficits in fear-conditioned learning, but not spatial learning. Upf3b-null mice also have a profound defect in prepulse inhibition (PPI), a measure of sensorimotor gating commonly deficient in individuals with SCZ and other brain disorders. Consistent with both their PPI and learning defects, cortical pyramidal neurons from Upf3b-null mice display deficient dendritic spine maturation in vivo. In addition, neural stem cells from Upf3b-null mice have impaired ability to undergo differentiation and require prolonged culture to give rise to functional neurons with electrical activity. RNA sequencing (RNAseq) analysis of the frontal cortex identified UPF3B-regulated RNAs, including direct NMD target transcripts encoding proteins with known functions in neural differentiation, maturation and disease. We suggest Upf3b-null mice serve as a novel model system to decipher cellular and molecular defects underlying ID and neurodevelopmental disorders.
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Affiliation(s)
- L Huang
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - E Y Shum
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - S H Jones
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - C-H Lou
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - J Chousal
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - H Kim
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - A J Roberts
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, CA, USA
| | - L A Jolly
- Adelaide Medical School and Robison Research Institute, University of Adelaide, Adelaide, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - J L Espinoza
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - D M Skarbrevik
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - M H Phan
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - H Cook-Andersen
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - N R Swerdlow
- Department of Psychiatry, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - J Gecz
- Adelaide Medical School and Robison Research Institute, University of Adelaide, Adelaide, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - M F Wilkinson
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA.
- Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
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8
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Bansal N, Chang C, Liang Y, Shum EY, Martin JC, Ghadiali J, Jensen D, Hu J, Rosenfeld D, Zheng Y, Fan HC. Sample multiplexing of peripheral immune populations for high throughput single-cell RNA-sequencing. The Journal of Immunology 2018. [DOI: 10.4049/jimmunol.200.supp.120.11] [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] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Diverse immune populations reside in non-lymphoid organs and contribute to immune defense and tissue homeostasis. However, these cells are often hard to study due to low cell abundance and high heterogeneity. Recent advancements in single-cell sequencing technology provides a powerful high parameter tool to study these peripheral immune populations. But current single cell experiments are costly and limited by sample throughput. To address these limitations, we have developed a novel sample multiplexing approach for high throughput single-cell sequencing.
In this study, we performed single-cell sequencing analysis of thousands of immune cells isolated from peripheral tissues in mice, and utilized a DNA barcoded universal antibody to sample multiplex up to 12 samples in a single experiment. This allowed us to combine samples from different mice and tissue types into a single pooled sample, significantly reducing experimental scale and cost, while eliminating potential batch effects. The sample pool was captured on the BD Rhapsody™ system and a targeted assay was performed to measure gene expression of ~400 genes. We were able to de-multiplex the pooled samples with high specificity after sequencing. The targeted gene panel provided robust clustering of the major immune cell types, enabling us to perform immuno-profiling and compare gene expression of major cell populations across different tissues. We observed distinct tissue-specific expression profiles of major immune populations, and further investigation of the differentially expressed genes may provide better understanding of the interactions between these tissue immune populations and their local environment.
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9
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Lou CH, Chousal J, Goetz A, Shum EY, Brafman D, Liao X, Mora-Castilla S, Ramaiah M, Cook-Andersen H, Laurent L, Wilkinson MF. Nonsense-Mediated RNA Decay Influences Human Embryonic Stem Cell Fate. Stem Cell Reports 2017; 6:844-857. [PMID: 27304915 PMCID: PMC4912386 DOI: 10.1016/j.stemcr.2016.05.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/13/2016] [Accepted: 05/16/2016] [Indexed: 11/18/2022] Open
Abstract
Nonsense-mediated RNA decay (NMD) is a highly conserved pathway that selectively degrades specific subsets of RNA transcripts. Here, we provide evidence that NMD regulates early human developmental cell fate. We found that NMD factors tend to be expressed at higher levels in human pluripotent cells than in differentiated cells, raising the possibility that NMD must be downregulated to permit differentiation. Loss- and gain-of-function experiments in human embryonic stem cells (hESCs) demonstrated that, indeed, NMD downregulation is essential for efficient generation of definitive endoderm. RNA-seq analysis identified NMD target transcripts induced when NMD is suppressed in hESCs, including many encoding signaling components. This led us to test the role of TGF-β and BMP signaling, which we found NMD acts through to influence definitive endoderm versus mesoderm fate. Our results suggest that selective RNA decay is critical for specifying the developmental fate of specific human embryonic cell lineages. The NMD RNA degradation pathway is highly active in pluripotent cells RNA-seq analysis identifies mRNA targets of NMD in human embryonic stem cells NMD degrades mRNAs encoding TGF-β/BMP, WNT, and FGF signaling components NMD acts through signaling pathways to influence endoderm versus mesoderm cell fate
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Affiliation(s)
- Chih-Hong Lou
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jennifer Chousal
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Alexandra Goetz
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Eleen Y Shum
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - David Brafman
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
| | - Xiaoyan Liao
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Sergio Mora-Castilla
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Madhuvanthi Ramaiah
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Heidi Cook-Andersen
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Louise Laurent
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Miles F Wilkinson
- Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA.
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10
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Song HW, Bettegowda A, Lake BB, Zhao AH, Skarbrevik D, Babajanian E, Sukhwani M, Shum EY, Phan MH, Plank TDM, Richardson ME, Ramaiah M, Sridhar V, de Rooij DG, Orwig KE, Zhang K, Wilkinson MF. The Homeobox Transcription Factor RHOX10 Drives Mouse Spermatogonial Stem Cell Establishment. Cell Rep 2017; 17:149-164. [PMID: 27681428 DOI: 10.1016/j.celrep.2016.08.090] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [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: 11/25/2015] [Revised: 07/19/2016] [Accepted: 08/27/2016] [Indexed: 12/31/2022] Open
Abstract
The developmental origins of most adult stem cells are poorly understood. Here, we report the identification of a transcription factor-RHOX10-critical for the initial establishment of spermatogonial stem cells (SSCs). Conditional loss of the entire 33-gene X-linked homeobox gene cluster that includes Rhox10 causes progressive spermatogenic decline, a phenotype indistinguishable from that caused by loss of only Rhox10. We demonstrate that this phenotype results from dramatically reduced SSC generation. By using a battery of approaches, including single-cell-RNA sequencing (scRNA-seq) analysis, we show that Rhox10 drives SSC generation by promoting pro-spermatogonia differentiation. Rhox10 also regulates batteries of migration genes and promotes the migration of pro-spermatogonia into the SSC niche. The identification of an X-linked homeobox gene that drives the initial generation of SSCs has implications for the evolution of X-linked gene clusters and sheds light on regulatory mechanisms influencing adult stem cell generation in general.
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Affiliation(s)
- Hye-Won Song
- School of Medicine, Department of Reproductive Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Anilkumar Bettegowda
- School of Medicine, Department of Reproductive Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Blue B Lake
- Department of Bioengineering, University of California at San Diego, La Jolla, CA 92093, USA
| | - Adrienne H Zhao
- School of Medicine, Department of Reproductive Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - David Skarbrevik
- School of Medicine, Department of Reproductive Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Eric Babajanian
- School of Medicine, Department of Reproductive Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Meena Sukhwani
- Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Magee-Womens Research Institute, Pittsburgh, PA 15213, USA
| | - Eleen Y Shum
- School of Medicine, Department of Reproductive Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Mimi H Phan
- School of Medicine, Department of Reproductive Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Terra-Dawn M Plank
- School of Medicine, Department of Reproductive Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Marcy E Richardson
- School of Medicine, Department of Reproductive Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Madhuvanthi Ramaiah
- School of Medicine, Department of Reproductive Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Vaishnavi Sridhar
- School of Medicine, Department of Reproductive Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Dirk G de Rooij
- Reproductive Biology Group, Division of Developmental Biology, Faculty of Science, Department of Biology, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Kyle E Orwig
- Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Magee-Womens Research Institute, Pittsburgh, PA 15213, USA
| | - Kun Zhang
- Department of Bioengineering, University of California at San Diego, La Jolla, CA 92093, USA
| | - Miles F Wilkinson
- School of Medicine, Department of Reproductive Medicine, University of California at San Diego, La Jolla, CA 92093, USA; Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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11
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Chang C, Shum EY, Bansal N, Dreux J, Lam G, Fan J, Fan HC. High throughput single cell analysis of human T cell differentiation dynamics by multiplexed PCR. The Journal of Immunology 2017. [DOI: 10.4049/jimmunol.198.supp.157.15] [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] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Abstract
CD4 T cells are critical components of the adaptive immune system and can differentiate into specialized effector subsets to mediate immune response against a wide host of pathogens. Studying the transcriptional profile of distinct T helper subsets has illuminated important pathways and mechanisms for effector cell function and lineage. Recently, single cell whole transcriptome analysis (WTA) provides a high resolution view of the complex and highly heterogeneous transcriptional dynamics of immune cell populations. However, such methods are often labor and cost prohibiting for high throughput analysis. Moreover, a significant portion of sequencing reads consist of high expressing housekeeping genes that make meaningful cluster analysis difficult.
In this study we explored a targeted approach to single cell sequencing of in vitro differentiated human Th1 and Th17 cells, by way of highly multiplexed PCR, and compared the results to WTA of the same samples. Using the BD Resolve Targeted T cell assay, we surveyed more than 300 genes in thousands of cells. We were able to distinguish between T cells that were cultured in different polarizing conditions using cluster analysis, and identify cells in different activation and differentiation states. In addition, the targeted assay produced better sensitivity for T cell critical genes with less than one tenth of the sequencing reads needed in WTA to achieve similar sequencing depths, and allowed us to detect low abundance T cell markers that are difficult to capture in WTA. Our results show that single cell analysis by multiplexed PCR is a powerful and cost effective way to study the functional states of T cells.
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Shum EY, Jones SH, Shao A, Chousal JN, Krause MD, Chan WK, Lou CH, Espinoza JL, Song HW, Phan MH, Ramaiah M, Huang L, McCarrey JR, Peterson KJ, De Rooij DG, Cook-Andersen H, Wilkinson MF. The Antagonistic Gene Paralogs Upf3a and Upf3b Govern Nonsense-Mediated RNA Decay. Cell 2016; 165:382-95. [PMID: 27040500 PMCID: PMC4826573 DOI: 10.1016/j.cell.2016.02.046] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/02/2016] [Accepted: 02/20/2016] [Indexed: 01/11/2023]
Abstract
Gene duplication is a major evolutionary force driving adaptation and speciation, as it allows for the acquisition of new functions and can augment or diversify existing functions. Here, we report a gene duplication event that yielded another outcome--the generation of antagonistic functions. One product of this duplication event--UPF3B--is critical for the nonsense-mediated RNA decay (NMD) pathway, while its autosomal counterpart--UPF3A--encodes an enigmatic protein previously shown to have trace NMD activity. Using loss-of-function approaches in vitro and in vivo, we discovered that UPF3A acts primarily as a potent NMD inhibitor that stabilizes hundreds of transcripts. Evidence suggests that UPF3A acquired repressor activity through simple impairment of a critical domain, a rapid mechanism that may have been widely used in evolution. Mice conditionally lacking UPF3A exhibit "hyper" NMD and display defects in embryogenesis and gametogenesis. Our results support a model in which UPF3A serves as a molecular rheostat that directs developmental events.
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Affiliation(s)
- Eleen Y. Shum
- Department of Reproductive Medicine, School of Medicine, University
of California, San Diego, La Jolla, California, USA
| | - Samantha H. Jones
- Department of Reproductive Medicine, School of Medicine, University
of California, San Diego, La Jolla, California, USA
| | - Ada Shao
- Department of Reproductive Medicine, School of Medicine, University
of California, San Diego, La Jolla, California, USA
| | - Jennifer N. Chousal
- Department of Reproductive Medicine, School of Medicine, University
of California, San Diego, La Jolla, California, USA
| | - Matthew D. Krause
- Department of Reproductive Medicine, School of Medicine, University
of California, San Diego, La Jolla, California, USA
| | - Wai-Kin Chan
- Department of Bioinformatics and Computational Biology, University
of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Chih-Hong Lou
- Department of Reproductive Medicine, School of Medicine, University
of California, San Diego, La Jolla, California, USA
| | - Josh L. Espinoza
- Department of Reproductive Medicine, School of Medicine, University
of California, San Diego, La Jolla, California, USA
| | - Hye-Won Song
- Department of Reproductive Medicine, School of Medicine, University
of California, San Diego, La Jolla, California, USA
| | - Mimi H. Phan
- Department of Reproductive Medicine, School of Medicine, University
of California, San Diego, La Jolla, California, USA
| | - Madhuvanthi Ramaiah
- Department of Reproductive Medicine, School of Medicine, University
of California, San Diego, La Jolla, California, USA
| | - Lulu Huang
- Department of Reproductive Medicine, School of Medicine, University
of California, San Diego, La Jolla, California, USA
| | - John R. McCarrey
- Department of Biology, University of Texas at San Antonio, San
Antonio, Texas, USA
| | - Kevin J. Peterson
- Department of Biology, Dartmouth College, Hanover, New Hampshire,
USA
| | - Dirk G. De Rooij
- Reproductive Biology Group, Division of Developmental Biology,
Department of Biology, Faculty of Science, Utrecht University, Utrecht, The
Netherlands
| | - Heidi Cook-Andersen
- Department of Reproductive Medicine, School of Medicine, University
of California, San Diego, La Jolla, California, USA
| | - Miles F. Wilkinson
- Department of Reproductive Medicine, School of Medicine, University
of California, San Diego, La Jolla, California, USA,Institute of Genomic Medicine, University of California, San Diego,
La Jolla, California, USA
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Shum EY, Espinoza JL, Ramaiah M, Wilkinson MF. Identification of novel post-transcriptional features in olfactory receptor family mRNAs. Nucleic Acids Res 2015; 43:9314-26. [PMID: 25908788 PMCID: PMC4627058 DOI: 10.1093/nar/gkv324] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 03/30/2015] [Indexed: 01/23/2023] Open
Abstract
Olfactory receptor (Olfr) genes comprise the largest gene family in mice. Despite their importance in olfaction, how most Olfr mRNAs are regulated remains unexplored. Using RNA-seq analysis coupled with analysis of pre-existing databases, we found that Olfr mRNAs have several atypical features suggesting that post-transcriptional regulation impacts their expression. First, Olfr mRNAs, as a group, have dramatically higher average AU-content and lower predicted secondary structure than do control mRNAs. Second, Olfr mRNAs have a higher density of AU-rich elements (AREs) in their 3'UTR and upstream open reading frames (uORFs) in their 5 UTR than do control mRNAs. Third, Olfr mRNAs have shorter 3' UTR regions and with fewer predicted miRNA-binding sites. All of these novel properties correlated with higher Olfr expression. We also identified striking differences in the post-transcriptional features of the mRNAs from the two major classes of Olfr genes, a finding consistent with their independent evolutionary origin. Together, our results suggest that the Olfr gene family has encountered unusual selective forces in neural cells that have driven them to acquire unique post-transcriptional regulatory features. In support of this possibility, we found that while Olfr mRNAs are degraded by a deadenylation-dependent mechanism, they are largely protected from this decay in neural lineage cells.
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Affiliation(s)
- Eleen Y Shum
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0695, USA
| | - Josh L Espinoza
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0695, USA
| | - Madhuvanthi Ramaiah
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0695, USA
| | - Miles F Wilkinson
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0695, USA Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
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Affiliation(s)
- Chih-Hong Lou
- Department of Reproductive Medicine, University of California San Diego, La Jolla, CA, USA
| | - Eleen Y Shum
- Department of Reproductive Medicine, University of California San Diego, La Jolla, CA, USA
| | - Miles F Wilkinson
- Department of Reproductive Medicine, University of California San Diego, La Jolla, CA, USA Institute of Genomic Medicine University of California San Diego, La Jolla, CA, USA
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15
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Lou CH, Shao A, Shum EY, Espinoza JL, Huang L, Karam R, Wilkinson MF. Posttranscriptional control of the stem cell and neurogenic programs by the nonsense-mediated RNA decay pathway. Cell Rep 2014; 6:748-64. [PMID: 24529710 DOI: 10.1016/j.celrep.2014.01.028] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [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: 05/02/2013] [Revised: 12/11/2013] [Accepted: 01/21/2014] [Indexed: 11/19/2022] Open
Abstract
The mechanisms dictating whether a cell proliferates or differentiates have undergone intense scrutiny, but they remain poorly understood. Here, we report that UPF1, a central component in the nonsense-mediated RNA decay (NMD) pathway, plays a key role in this decision by promoting the proliferative, undifferentiated cell state. UPF1 acts, in part, by destabilizing the NMD substrate encoding the TGF-β inhibitor SMAD7 and stimulating TGF-β signaling. UPF1 also promotes the decay of mRNAs encoding many other proteins that oppose the proliferative, undifferentiated cell state. Neural differentiation is triggered when NMD is downregulated by neurally expressed microRNAs (miRNAs). This UPF1-miRNA circuitry is highly conserved and harbors negative feedback loops that act as a molecular switch. Our results suggest that the NMD pathway collaborates with the TGF-β signaling pathway to lock in the stem-like state, a cellular state that is stably reversed when neural differentiation signals that induce NMD-repressive miRNAs are received.
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Affiliation(s)
- Chih H Lou
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0695, USA
| | - Ada Shao
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0695, USA
| | - Eleen Y Shum
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0695, USA
| | - Josh L Espinoza
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0695, USA
| | - Lulu Huang
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0695, USA
| | - Rachid Karam
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0695, USA
| | - Miles F Wilkinson
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0695, USA; Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA 92093-0695, USA.
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Abstract
Capped and polyadenylated long noncoding RNAs (lncRNAs) are shown to be degraded by a DCP2-mediated turnover mechanism by Geisler et al. (2012); this provides a new level of regulatory control for inducible genes by lncRNAs.
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Affiliation(s)
- Madhuvanthi Ramaiah
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093-0695, USA
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Huang L, Shum EY, Karam R, Nguyen LS, Gecz J, Wilkinson MF. NMD‐deficient Upf3b‐null mice display behavioral and neuropathological defects. FASEB J 2012. [DOI: 10.1096/fasebj.26.1_supplement.747.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Lulu Huang
- Department of Reproductive MedicineUniversity of CaliforniaSan Diego, La JollaCA
| | - Eleen Y. Shum
- Department of Reproductive MedicineUniversity of CaliforniaSan Diego, La JollaCA
| | - Rachid Karam
- Department of Reproductive MedicineUniversity of CaliforniaSan Diego, La JollaCA
| | - Lam Son Nguyen
- Department of Genetic MedicineWomen's and Children's HospitalAdelaideAustralia
| | - Jozef Gecz
- Department of Genetic MedicineWomen's and Children's HospitalAdelaideAustralia
| | - Miles F Wilkinson
- Department of Reproductive MedicineUniversity of CaliforniaSan Diego, La JollaCA
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Ramaiah M, Shum EY, Wilkinson MF. Rapidly Evolving MicroRNAs Retain Their Targets by a Co‐Evolution Mechanism. FASEB J 2012. [DOI: 10.1096/fasebj.26.1_supplement.952.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Madhuvanthi Ramaiah
- Department of Reproductive MedicineUniversity of CaliforniaSan Diego, La JollaCA
| | - Eleen Y. Shum
- Department of Reproductive MedicineUniversity of CaliforniaSan Diego, La JollaCA
| | - Miles F. Wilkinson
- Department of Reproductive MedicineUniversity of CaliforniaSan Diego, La JollaCA
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Shum EY, Lou CH, Wilkinson MF. Convergence of the MicroRNA and NMD Pathways in Neurons. FASEB J 2012. [DOI: 10.1096/fasebj.26.1_supplement.733.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Eleen Y Shum
- Department of Reproductive MedicineUniversity of CaliforniaSan Diego, La JollaCA
| | - Chih H Lou
- Department of Reproductive MedicineUniversity of CaliforniaSan Diego, La JollaCA
| | - Miles F Wilkinson
- Department of Reproductive MedicineUniversity of CaliforniaSan Diego, La JollaCA
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Huang L, Lou CH, Chan W, Shum EY, Shao A, Stone E, Karam R, Song HW, Wilkinson MF. RNA homeostasis governed by cell type-specific and branched feedback loops acting on NMD. Mol Cell 2011; 43:950-61. [PMID: 21925383 DOI: 10.1016/j.molcel.2011.06.031] [Citation(s) in RCA: 158] [Impact Index Per Article: 12.2] [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: 09/10/2010] [Revised: 03/28/2011] [Accepted: 06/22/2011] [Indexed: 11/17/2022]
Abstract
Nonsense-mediated mRNA decay (NMD) is a conserved RNA decay pathway that degrades aberrant mRNAs and directly regulates many normal mRNAs. This dual role for NMD raises the possibility that its magnitude is buffered to prevent the potentially catastrophic alterations in gene expression that would otherwise occur if NMD were perturbed by environmental or genetic insults. In support of this, here we report the existence of a negative feedback regulatory network that directly acts on seven NMD factors. Feedback regulation is conferred by different branches of the NMD pathway in a cell type-specific and developmentally regulated manner. We identify feedback-regulated NMD factors that are rate limiting for NMD and demonstrate that reversal of feedback regulation in response to NMD perturbation is crucial for maintaining NMD. Together, our results suggest the existence of an intricate feedback network that maintains both RNA surveillance and the homeostasis of normal gene expression in mammalian cells.
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Affiliation(s)
- Lulu Huang
- Department of Reproductive Medicine, School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
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Bruno IG, Karam R, Huang L, Bhardwaj A, Lou CH, Shum EY, Song HW, Corbett MA, Gifford WD, Gecz J, Pfaff SL, Wilkinson MF. Identification of a microRNA that activates gene expression by repressing nonsense-mediated RNA decay. Mol Cell 2011; 42:500-10. [PMID: 21596314 DOI: 10.1016/j.molcel.2011.04.018] [Citation(s) in RCA: 225] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 03/09/2011] [Accepted: 04/27/2011] [Indexed: 12/24/2022]
Abstract
Nonsense-mediated decay (NMD) degrades both normal and aberrant transcripts harboring stop codons in particular contexts. Mutations that perturb NMD cause neurological disorders in humans, suggesting that NMD has roles in the brain. Here, we identify a brain-specific microRNA-miR-128-that represses NMD and thereby controls batteries of transcripts in neural cells. miR-128 represses NMD by targeting the RNA helicase UPF1 and the exon-junction complex core component MLN51. The ability of miR-128 to regulate NMD is a conserved response occurring in frogs, chickens, and mammals. miR-128 levels are dramatically increased in differentiating neuronal cells and during brain development, leading to repressed NMD and upregulation of mRNAs normally targeted for decay by NMD; overrepresented are those encoding proteins controlling neuron development and function. Together, these results suggest the existence of a conserved RNA circuit linking the microRNA and NMD pathways that induces cell type-specific transcripts during development.
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Affiliation(s)
- Ivone G Bruno
- Department of Biochemistry and Molecular Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77033, USA
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