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Montano C, Flores-Arenas C, Carpenter S. LncRNAs, nuclear architecture and the immune response. Nucleus 2024; 15:2350182. [PMID: 38738760 PMCID: PMC11093052 DOI: 10.1080/19491034.2024.2350182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/22/2024] [Indexed: 05/14/2024] Open
Abstract
Long noncoding RNAs (LncRNAs) are key regulators of gene expression and can mediate their effects in both the nucleus and cytoplasm. Some of the best-characterized lncRNAs are localized within the nucleus, where they modulate the nuclear architecture and influence gene expression. In this review, we discuss the role of lncRNAs in nuclear architecture in the context of their gene regulatory functions in innate immunity. Here, we discuss various approaches to functionally characterize nuclear-localized lncRNAs and the challenges faced in the field.
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Affiliation(s)
- Christy Montano
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Cristina Flores-Arenas
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Susan Carpenter
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
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2
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Tang W, Wu S, Tang Y, Ma J, Ao Y, Liu L, Wei K. Microarray analysis identifies lncFirre as a potential regulator of obesity-related acute lung injury. Life Sci 2024; 340:122459. [PMID: 38307237 DOI: 10.1016/j.lfs.2024.122459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/04/2024]
Abstract
AIMS The inflammatory response in acute lung injury/acute respiratory distress syndrome (ALI/ARDS) is heightened in obesity. The aim of this study was to investigate whether lncRNAs are involved in the effects of obesity on acute lung injury and to find possible effector lncRNAs. MAIN METHODS Microarray analysis was used to assess the transcriptional profiles of lncRNAs and mRNAs in lung tissues from normal (CON), high-fat diet induced obese (DIO), and obese ALI mice (DIO-ALI). GO and KEGG analyses were employed to explore the biological functions of differentially expressed genes. A lncRNA-mRNA co-expression network was constructed to identify specific lncRNA. Lung tissues and peripheral blood samples from patients with obesity and healthy lean donors were utilized to confirm the expression characteristics of lncFirre through qRT-PCR. lncFirre was knocked down in MH-S macrophages to explore its function. ELISA and Griess reagent kit were used to detect PGE2 and NO. Flow cytometry was used to detect macrophages polarization. KEY FINDINGS There were 475 lncRNAs and 404 mRNAs differentially expressed between DIO and CON, while 1348 lncRNAs and 1349 mRNAs between DIO-ALI and DIO. Obesity increased lncFirre expression in both mice and patients, and PA elevated lncFirre in MH-S. PA exacerbated the inflammation and proinflammatory polarization of MH-S induced by LPS. LncFirre knockdown inhibited the secretion of PGE2 and NO, M1 differentiation while promoted the M2 differentiation in PA and LPS co-challenged MH-S. SIGNIFICANCE Interfering with lncFirre effectively inhibit inflammation in MH-S, lncFirre can serve as a promising target for treating obesity-related ALI.
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Affiliation(s)
- Wenjing Tang
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Siqi Wu
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yin Tang
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Jingyue Ma
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yichan Ao
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Ling Liu
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Ke Wei
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
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Al-Hawary SIS, Saleh RO, Taher SG, Ahmed SM, Hjazi A, Yumashev A, Ghildiyal P, Qasim MT, Alawadi A, Ihsan A. Tumor-derived lncRNAs: Behind-the-scenes mediators that modulate the immune system and play a role in cancer pathogenesis. Pathol Res Pract 2024; 254:155123. [PMID: 38277740 DOI: 10.1016/j.prp.2024.155123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/28/2024]
Abstract
Having been involved in complex cellular regulatory networks and cell-to-cell communications, non-coding RNAs (lncRNAs) have become functional carriers that transmit information between cells and tissues, modulate tumor microenvironments, encourage angiogenesis and invasion, and make tumor cells more resistant to drugs. Immune cells' exosomal lncRNAs may be introduced into tumor cells to influence the tumor's course and the treatment's effectiveness. Research has focused on determining if non-coding RNAs affect many target genes to mediate regulating recipient cells. The tumor microenvironment's immune and cancer cells are influenced by lncRNAs, which may impact a treatment's efficacy. The lncRNA-mediated interaction between cancer cells and immune cells invading the tumor microenvironment has been the subject of numerous recent studies. On the other hand, tumor-derived lncRNAs' control over the immune system has not gotten much attention and is still a relatively new area of study. Tumor-derived lncRNAs are recognized to contribute to tumor immunity, while the exact mechanism is unclear.
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Affiliation(s)
| | - Raed Obaid Saleh
- Department of Medical Laboratory Techniques, Al-Maarif University College, Al-Anbar, Iraq.
| | - Sada Gh Taher
- National University of Science and Technology, Dhi Qar, Iraq
| | | | - Ahmed Hjazi
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Alexey Yumashev
- Department of Prosthetic Dentistry, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Pallavi Ghildiyal
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Maytham T Qasim
- College of Health and Medical Technology, Al-Ayen University, Thi-Qar 64001, Iraq
| | - Ahmed Alawadi
- College of Health and Medical Technology, Al-Ayen University, Thi-Qar 64001, Iraq; College of Technical Engineering, the Islamic University, Najaf, Iraq; College of Technical Engineering, the Islamic University of Al Diwaniyah, Iraq
| | - Ali Ihsan
- College of Technical Engineering, the Islamic University of Babylon, Iraq; Department of Pediatrics, General Medicine Practice Program, Batterjee Medical College, Jeddah 21442, Saudi Arabia; Department of Medical Laboratory Technique, Imam Ja'afar Al-Sadiq University, Al-Muthanna 66002, Iraq
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Pan J, Zhan C, Yuan T, Gu W, Wang W, Sun Y, Chen L. Long noncoding RNA signatures in intrauterine infection/inflammation-induced lung injury: an integrative bioinformatics study. BMC Pulm Med 2023; 23:194. [PMID: 37280583 DOI: 10.1186/s12890-023-02505-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 05/31/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Intrauterine infection/inflammation can result in fetal and neonatal lung injury. However, the biological mechanisms of intrauterine infection/inflammation on fetal and neonatal lung injury and development are poorly known. To date, there are no reliable biomarkers for improving intrauterine infection/inflammation-induced lung injury. METHODS An animal model of intrauterine infection/inflammation-induced lung injury was established with pregnant Sprague-Dawley rats inoculated with Escherichia coli suspension. The intrauterine inflammatory status was assessed through the histological examination of the placenta and uterus. A serial of histological examinations of the fetal and neonatal rats lung tissues were performed. The fetal and neonatal rat lung tissues were harvested for next generation sequencing at embryonic day 17 and postnatal day 3, respectively. Differentially expressed mRNAs and lncRNAs were identified by conducting high-throughput sequencing technique. The target genes of identified differentially expressed lncRNAs were analyzed. Homology analyses for important differentially expressed lncRNAs were performed. RESULTS The histopathological results showed inflammatory infiltration, impaired alveolar vesicular structure, less alveolar numbers, and thickened alveolar septa in fetal and neonatal rat lung tissues. Transmission electron micrographs revealed inflammatory cellular swelling associated with diffuse alveolar damage and less surfactant-storing lamellar bodies in alveolar epithelial type II cells. As compared with the control group, there were 432 differentially expressed lncRNAs at embryonic day 17 and 125 differentially expressed lncRNAs at postnatal day 3 in the intrauterine infection group. The distribution, expression level, and function of these lncRNAs were shown in the rat genome. LncRNA TCONS_00009865, lncRNA TCONS_00030049, lncRNA TCONS_00081686, lncRNA TCONS_00091647, lncRNA TCONS_00175309, lncRNA TCONS_00255085, lncRNA TCONS_00277162, and lncRNA TCONS_00157962 may play an important role in intrauterine infection/inflammation-induced lung injury. Fifty homologous sequences in Homo sapiens were also identified. CONCLUSIONS This study provides genome-wide identification of novel lncRNAs which may serve as potential diagnostic biomarkers and therapeutic targets for intrauterine infection/inflammation-induced lung injury.
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Affiliation(s)
- Jiarong Pan
- Department of Neonatology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, Zhejiang, China
| | - Canyang Zhan
- Department of Neonatology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, Zhejiang, China
| | - Tianming Yuan
- Department of Neonatology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, Zhejiang, China.
| | - Weizhong Gu
- Zhejiang Key Laboratory for Diagnosis and Therapy of Neonatal Diseases, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, Zhejiang, China
| | - Weiyan Wang
- Department of Neonatology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, Zhejiang, China
| | - Yi Sun
- Department of Neonatology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, Zhejiang, China
| | - Lihua Chen
- Department of Neonatology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, Zhejiang, China
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Salih MM, Robinson EK, Malekos E, Perez E, Capili A, Kim K, Zhang WZ, Cloonan SM, Carpenter S. LincRNA-Cox2 Regulates Smoke-induced Inflammation in Murine Macrophages. Am J Respir Cell Mol Biol 2023; 68:511-522. [PMID: 36657060 DOI: 10.1165/rcmb.2022-0413oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/19/2023] [Indexed: 01/20/2023] Open
Abstract
Cigarette smoke (CS) exposure is a risk factor for many chronic diseases, including chronic obstructive pulmonary disease, but the mechanism by which smoke exposure can alter homeostasis and bring about chronic inflammation is poorly understood. Here, we showcase a novel role for smoke in regulating long noncoding RNAs, showing that it activates lincRNA-Cox2, which we previously characterized as functional in inflammatory regulation. Exposing lincRNA-Cox2 murine models to smoke in vivo confirmed lincRNA-Cox2 as a regulator of inflammatory gene expression in response to smoke both systemically and within the lung. We also report that lincRNA-Cox2 negatively regulates genes in smoked bone marrow-derived macrophages exposed to LPS stimulation. In addition to the effects on long noncoding RNAs, we also report dysregulated transcription and splicing of inflammatory protein-coding genes in the bone marrow niche after CS exposure in vivo. Collectively, this work provides insights into how innate immune signaling from gene expression to splicing is altered after in vivo exposure to CS and highlights an important new role for lincRNA-Cox2 in regulating immune genes after smoke exposure.
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Affiliation(s)
- Mays Mohammed Salih
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California
| | - Elektra Kantzari Robinson
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California
| | - Eric Malekos
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California
| | - Elizabeth Perez
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York; and
| | - Allyson Capili
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York; and
| | - Kihwan Kim
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York; and
| | - William Z Zhang
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York; and
| | - Suzanne M Cloonan
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York; and
- School of Medicine, Trinity Biomedical Sciences Institute, Trinity College, Dublin, Ireland
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California
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Yang H, Liang J, Li X, Yan L, Zhang Y. Inhibition of lincRNA-Cox2 alleviates apoptosis and inflammatory injury of lipopolysaccharide-stimulated human bronchial epithelial cells via the Nrf2/HO-1 axis. J Clin Biochem Nutr 2023; 72:234-241. [PMID: 37251964 PMCID: PMC10209602 DOI: 10.3164/jcbn.22-102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/28/2022] [Indexed: 05/31/2023] Open
Abstract
This study mainly explored the role and mechanism of lincRNA-Cox2 in inflammatory injury of human bronchial epithelial cells. BEAS-2B cells were stimulated with lipopolysaccharide to establish an in vitro inflammatory injury model. Real-time polymerase chain reaction was used to detect lincRNA-Cox2 expression in LPS-stimulated BEAS-2B. Cell viability and apoptosis of cells were assessed using CCK-8 and Annexin V-PI double staining. The contents of inflammatory factors were determined by enzyme-linked immunosorbent assay kits. The protein levels of nuclear factor erythrocyte 2-related factor 2 and haem oxygenase 1 protein levels were measured by Western blot. The results showed that lincRNA-Cox2 was upregulated in LPS-stimulated BEAS-2B cells. lincRNA-Cox2 knockdown inhibited apoptosis and the release of tumour necrosis factor alpha, interleukin 1beta (IL-1β), IL-4, IL-5, and IL-13 in BEAS-2B cells. lincRNA-Cox2 overexpression had the opposite effect. lincRNA-Cox2 knockdown also inhibited LPS-induced oxidative damage in BEAS-2B cells. Further mechanistic studies showed that inhibition of lincRNA-Cox2 upregulated the levels of Nrf2 and HO-1, and si-Nrf2 reversed the effects of si-lincRNA-Cox2. In conclusion, lincRNA-Cox2 knockdown inhibited BEAS-2B apoptosis and the level of inflammatory factors by activating the Nrf2/HO-1 pathway.
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Affiliation(s)
- Hua Yang
- Department of Pediatrics, Xi’an Children’s Hospital, Xi’an, Shaanxi 710003, China
| | - Jing Liang
- Department of Children Healthcare, Xi’an Fourth Hospital, Xi’an, Shaanxi 710004, China
| | - Xiangni Li
- Department of Pediatrics, Xi’an Children’s Hospital, Xi’an, Shaanxi 710003, China
| | - Liping Yan
- Department of Pediatrics, Xi’an Children’s Hospital, Xi’an, Shaanxi 710003, China
| | - Yi Zhang
- Department of Pediatrics, Xi’an Children’s Hospital, Xi’an, Shaanxi 710003, China
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Marangon D, Castro e Silva JH, Lecca D. Neuronal and Glial Communication via Non-Coding RNAs: Messages in Extracellular Vesicles. Int J Mol Sci 2022; 24:ijms24010470. [PMID: 36613914 PMCID: PMC9820657 DOI: 10.3390/ijms24010470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Extracellular vesicles (EVs) have been increasingly recognized as essential players in cell communication in many organs and systems, including the central nervous system (CNS). A proper interaction between neural cells is fundamental in the regulation of neurophysiological processes and its alteration could induce several pathological phenomena, such as neurodegeneration, neuroinflammation, and demyelination. EVs contain and transfer complex molecular cargoes typical of their cells of origin, such as proteins, lipids, carbohydrates, and metabolites to recipient cells. EVs are also enriched in non-coding RNAs (e.g., microRNAs, lncRNAs, and circRNA), which were formerly considered as cell-intrinsic regulators of CNS functions and pathologies, thus representing a new layer of regulation in the cell-to-cell communication. In this review, we summarize the most recent and advanced studies on the role of EV-derived ncRNAs in the CNS. First, we report the potential of neural stem cell-derived ncRNAs as new therapeutic tools for neurorepair. Then, we discuss the role of neuronal ncRNAs in regulating glia activation, and how alteration in glial ncRNAs influences neuronal survival and synaptic functions. We conclude that EV-derived ncRNAs can act as intercellular signals in the CNS to either propagate neuroinflammatory waves or promote reparative functions.
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Elsholtzia bodinieri Vaniot Ameliorated Acute Lung Injury by NQO1, BCL2 and PTGS2 In Silico and In Vitro Analyses. Int J Mol Sci 2022; 23:ijms232415651. [PMID: 36555290 PMCID: PMC9779453 DOI: 10.3390/ijms232415651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/29/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Acute lung injury (ALI) is a clinical respiratory disease caused by various factors, which lacks effective pharmacotherapy to reduce the mortality rate. Elsholtzia bodinieri Vaniot is an annual herbaceous plant used as a traditional herbal tea and folk medicine. Here we used bioinformatic databases and software to explore and analyze the potential key genes in ALI regulated by E. bodinieri Vaniot, including B cell leukemia/lymphoma 2 (Bcl2), prostaglandin-endoperoxide synthase 2 (Ptgs2) and NAD(P)H dehydrogenase, quinone 1 (Nqo1). In an inflammatory cells model, we verified bioinformatics results, and further mechanistic analysis showed that methanol extract of E. bodinieri Vaniot (EBE) could alleviate oxidative stress by upregulating the expression of NQO1, suppress pyroptosis by upregulating the expression of BCL2, and attenuate inflammation by downregulating the expression of PTGS2. In sum, our results demonstrated that EBE treatment could alleviate oxidative stress, suppress pyroptosis and attenuate inflammation by regulating NQO1, BCL2 and PTGS2 in a cells model, and E. bodinieri Vaniot might be a promising source for functional food or as a therapeutic agent.
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Malekos E, Carpenter S. Short open reading frame genes in innate immunity: from discovery to characterization. Trends Immunol 2022; 43:741-756. [PMID: 35965152 PMCID: PMC10118063 DOI: 10.1016/j.it.2022.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 12/27/2022]
Abstract
Next-generation sequencing (NGS) technologies have greatly expanded the size of the known transcriptome. Many newly discovered transcripts are classified as long noncoding RNAs (lncRNAs) which are assumed to affect phenotype through sequence and structure and not via translated protein products despite the vast majority of them harboring short open reading frames (sORFs). Recent advances have demonstrated that the noncoding designation is incorrect in many cases and that sORF-encoded peptides (SEPs) translated from these transcripts are important contributors to diverse biological processes. Interest in SEPs is at an early stage and there is evidence for the existence of thousands of SEPs that are yet unstudied. We hope to pique interest in investigating this unexplored proteome by providing a discussion of SEP characterization generally and describing specific discoveries in innate immunity.
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Affiliation(s)
- Eric Malekos
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA; Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Susan Carpenter
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA; Department of Molecular Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, USA.
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