1
|
Ranum JN, Ledwith MP, Alnaji FG, Diefenbacher M, Orton R, Sloan E, Güereca M, Feltman E, Smollett K, da Silva Filipe A, Conley M, Russell A, Brooke C, Hutchinson E, Mehle A. Cryptic proteins translated from deletion-containing viral genomes dramatically expand the influenza virus proteome. Nucleic Acids Res 2024; 52:3199-3212. [PMID: 38407436 PMCID: PMC11014358 DOI: 10.1093/nar/gkae133] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 12/06/2023] [Revised: 02/06/2024] [Accepted: 02/15/2024] [Indexed: 02/27/2024] Open
Abstract
Productive infections by RNA viruses require faithful replication of the entire genome. Yet many RNA viruses also produce deletion-containing viral genomes (DelVGs), aberrant replication products with large internal deletions. DelVGs interfere with the replication of wild-type virus and their presence in patients is associated with better clinical outcomes. The DelVG RNA itself is hypothesized to confer this interfering activity. DelVGs antagonize replication by out-competing the full-length genome and triggering innate immune responses. Here, we identify an additionally inhibitory mechanism mediated by a new class of viral proteins encoded by DelVGs. We identified hundreds of cryptic viral proteins translated from DelVGs. These DelVG-encoded proteins (DPRs) include canonical viral proteins with large internal deletions, as well as proteins with novel C-termini translated from alternative reading frames. Many DPRs retain functional domains shared with their full-length counterparts, suggesting they may have activity during infection. Mechanistic studies of DPRs derived from the influenza virus protein PB2 showed that they poison replication of wild-type virus by acting as dominant-negative inhibitors of the viral polymerase. These findings reveal that DelVGs have a dual inhibitory mechanism, acting at both the RNA and protein level. They further show that DPRs have the potential to dramatically expand the functional proteomes of diverse RNA viruses.
Collapse
Affiliation(s)
- Jordan N Ranum
- Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Mitchell P Ledwith
- Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Fadi G Alnaji
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Meghan Diefenbacher
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Richard Orton
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Elizabeth Sloan
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Melissa Güereca
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Elizabeth M Feltman
- Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Katherine Smollett
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | | | - Michaela Conley
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Alistair B Russell
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Christopher B Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Edward Hutchinson
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Andrew Mehle
- Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| |
Collapse
|
2
|
Ward G, Wurster JI, Lamb PS, DeCost G, Belenky P, Monnig MA. Alcohol consumption and oral microbiome composition in a sample of healthy young adults. Alcohol Alcohol 2023; 58:573-577. [PMID: 37501505 PMCID: PMC10642607 DOI: 10.1093/alcalc/agad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/06/2023] [Accepted: 07/03/2023] [Indexed: 07/29/2023] Open
Abstract
The oral microbiomes of 24 healthy adults (50% female; mean age = 24.3) were examined using 16 s ribosomal RNA sequencing and compared between light and heavy drinkers. Beta diversity was related at the trend level to drinking group, and light drinkers had significantly higher abundances of key oral taxa such as Lactobacillales. These preliminary results may offer insight into early effects of heavy drinking on the composition of the oral microbiome.
Collapse
Affiliation(s)
- Gyles Ward
- New York University Langone Health, New York, NY 10016, United States
| | - Jenna I Wurster
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, United States
| | - Philip S Lamb
- Institute of Child Development, University of Minnesota, Minneapolis, MN 55455, United States
| | - Grace DeCost
- Center for Alcohol and Addiction Studies, Brown University School of Public Health, Providence, RI 02912, United States
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI 02912, United States
| | - Mollie A Monnig
- Center for Alcohol and Addiction Studies, Brown University School of Public Health, Providence, RI 02912, United States
| |
Collapse
|
3
|
Chernoff MB, Delgado D, Tong L, Chen L, Oliva M, Tamayo LI, Best LG, Cole S, Jasmine F, Kibriya MG, Nelson H, Huang L, Haack K, Kent J, Umans JG, Graziano J, Navas-Acien A, Karagas MR, Ahsan H, Pierce BL. Sequencing-based fine-mapping and in silico functional characterization of the 10q24.32 arsenic metabolism efficiency locus across multiple arsenic-exposed populations. PLoS Genet 2023; 19:e1010588. [PMID: 36668670 PMCID: PMC9891528 DOI: 10.1371/journal.pgen.1010588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 02/01/2023] [Accepted: 12/20/2022] [Indexed: 01/22/2023] Open
Abstract
Inorganic arsenic is highly toxic and carcinogenic to humans. Exposed individuals vary in their ability to metabolize arsenic, and variability in arsenic metabolism efficiency (AME) is associated with risks of arsenic-related toxicities. Inherited genetic variation in the 10q24.32 region, near the arsenic methyltransferase (AS3MT) gene, is associated with urine-based measures of AME in multiple arsenic-exposed populations. To identify potential causal variants in this region, we applied fine mapping approaches to targeted sequencing data generated for exposed individuals from Bangladeshi, American Indian, and European American populations (n = 2,357, 557, and 648 respectively). We identified three independent association signals for Bangladeshis, two for American Indians, and one for European Americans. The size of the confidence sets for each signal varied from 4 to 85 variants. There was one signal shared across all three populations, represented by the same SNP in American Indians and European Americans (rs191177668) and in strong linkage disequilibrium (LD) with a lead SNP in Bangladesh (rs145537350). Beyond this shared signal, differences in LD patterns, minor allele frequency (MAF) (e.g., rs12573221 ~13% in Bangladesh ~0.2% among American Indians), and/or heterogeneity in effect sizes across populations likely contributed to the apparent population specificity of the additional identified signals. One of our potential causal variants influences AS3MT expression and nearby DNA methylation in numerous GTEx tissue types (with rs4919690 as a likely causal variant). Several SNPs in our confidence sets overlap transcription factor binding sites and cis-regulatory elements (from ENCODE). Taken together, our analyses reveal multiple potential causal variants in the 10q24.32 region influencing AME, including a variant shared across populations, and elucidate potential biological mechanisms underlying the impact of genetic variation on AME.
Collapse
Affiliation(s)
- Meytal Batya Chernoff
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois, United States of America
- Interdisciplinary Scientist Training Program, University of Chicago, Chicago, Illinois, United States of America
- University of Chicago Pritzker School of Medicine, Chicago, Illinois, United States of America
| | - Dayana Delgado
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois, United States of America
| | - Lin Tong
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois, United States of America
| | - Lin Chen
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois, United States of America
| | - Meritxell Oliva
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois, United States of America
| | - Lizeth I. Tamayo
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois, United States of America
| | - Lyle G. Best
- Missouri Breaks Industries Research Inc, Eagle Butte, South Dakota, United States of America
| | - Shelley Cole
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Farzana Jasmine
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois, United States of America
| | - Muhammad G. Kibriya
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois, United States of America
| | - Heather Nelson
- School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Lei Huang
- Center for Research Informatics, University of Chicago, Chicago, Illinois, United States of America
| | - Karin Haack
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Jack Kent
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Jason G. Umans
- MedStar Health Research Institute, Hyattsville, Maryland, United States of America
- Georgetown-Howard Universities Center for Clinical and Translational Science, Georgetown University, Washington, District of Columbia, United States of America
| | - Joseph Graziano
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
- Department of Pharmacology, Columbia University, New York City, New York, United States of America
| | - Ana Navas-Acien
- Mailman School of Public Health, Columbia University, New York City, New York, United States of America
| | - Margaret R. Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Habib Ahsan
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois, United States of America
- Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, United States of America
- Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Brandon L. Pierce
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois, United States of America
- Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, United States of America
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| |
Collapse
|
4
|
de Castro RO, Previato de Almeida L, Carbajal A, Gryniuk I, Pezza RJ. PBAF chromatin remodeler complexes that mediate meiotic transitions in mouse. Development 2022; 149:dev199967. [PMID: 36111709 PMCID: PMC9573785 DOI: 10.1242/dev.199967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/18/2022] [Indexed: 09/18/2023]
Abstract
Gametogenesis in mammals encompasses highly regulated developmental transitions. These are associated with changes in transcription that cause characteristic patterns of gene expression observed during distinct stages of gamete development, which include specific activities with critical meiotic functions. SWI/SNF chromatin remodelers are recognized regulators of gene transcription and DNA repair, but their composition and functions in meiosis are poorly understood. We have generated gamete-specific conditional knockout mice for ARID2, a specific regulatory subunit of PBAF, and have compared its phenotype with BRG1 knockouts, the catalytic subunit of PBAF/BAF complexes. While Brg1Δ/Δ knockout acts at an early stage of meiosis and causes cell arrest at pachynema, ARID2 activity is apparently required at the end of prophase I. Striking defects in spindle assembly and chromosome-spindle attachment observed in Arid2Δ/Δ knockouts are attributed to an increase in aurora B kinase, a master regulator of chromosome segregation, at centromeres. Further genetic and biochemical analyses suggest the formation of a canonical PBAF and a BRG1-independent complex containing ARID2 and PBRM1 as core components. The data support a model in which different PBAF complexes regulate different stages of meiosis and gametogenesis.
Collapse
Affiliation(s)
- Rodrigo O. de Castro
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Luciana Previato de Almeida
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Agustin Carbajal
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Irma Gryniuk
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Roberto J. Pezza
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
- Department of Cell Biology, University of Oklahoma Health Science Center, Oklahoma City, OK 73104, USA
| |
Collapse
|
5
|
Nicholson-Shaw AL, Kofman ER, Yeo GW, Pasquinelli A. Nuclear and cytoplasmic poly(A) binding proteins (PABPs) favor distinct transcripts and isoforms. Nucleic Acids Res 2022; 50:4685-4702. [PMID: 35438785 PMCID: PMC9071453 DOI: 10.1093/nar/gkac263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 02/11/2022] [Revised: 03/23/2022] [Accepted: 04/04/2022] [Indexed: 11/14/2022] Open
Abstract
The poly(A)-tail appended to the 3'-end of most eukaryotic transcripts plays a key role in their stability, nuclear transport, and translation. These roles are largely mediated by Poly(A) Binding Proteins (PABPs) that coat poly(A)-tails and interact with various proteins involved in the biogenesis and function of RNA. While it is well-established that the nuclear PABP (PABPN) binds newly synthesized poly(A)-tails and is replaced by the cytoplasmic PABP (PABPC) on transcripts exported to the cytoplasm, the distribution of transcripts for different genes or isoforms of the same gene on these PABPs has not been investigated on a genome-wide scale. Here, we analyzed the identity, splicing status, poly(A)-tail size, and translation status of RNAs co-immunoprecipitated with endogenous PABPN or PABPC in human cells. At steady state, many protein-coding and non-coding RNAs exhibit strong bias for association with PABPN or PABPC. While PABPN-enriched transcripts more often were incompletely spliced and harbored longer poly(A)-tails and PABPC-enriched RNAs had longer half-lives and higher translation efficiency, there are curious outliers. Overall, our study reveals the landscape of RNAs bound by PABPN and PABPC, providing new details that support and advance the current understanding of the roles these proteins play in poly(A)-tail synthesis, maintenance, and function.
Collapse
Affiliation(s)
| | - Eric R Kofman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- UCSD Stem Cell Program, Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- UCSD Stem Cell Program, Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Amy E Pasquinelli
- Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA
| |
Collapse
|
6
|
Williams AE, Watt J, Robertson LW, Gadupudi G, Osborn ML, Soares MJ, Iqbal K, Pedersen KB, Shankar K, Littleton S, Maimone C, Eti NA, Suva LJ, Ronis MJJ. Skeletal Toxicity of Coplanar Polychlorinated Biphenyl Congener 126 in the Rat Is Aryl Hydrocarbon Receptor Dependent. Toxicol Sci 2020; 175:113-125. [PMID: 32119087 PMCID: PMC7197949 DOI: 10.1093/toxsci/kfaa030] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Epidemiological evidence links polychlorinated biphenyls (PCBs) to skeletal toxicity, however mechanisms whereby PCBs affect bone are poorly studied. In this study, coplanar PCB 126 (5 μmol/kg) or corn oil vehicle was administered to N = 5 and 6 male and female, wild type (WT) or AhR -/- rats via intraperitoneal injection. Animals were sacrificed after 4 weeks. Bone length was measured; bone morphology was assessed by microcomputed tomography and dynamic histomorphometry. Reduced bone length was the only genotype-specific effect and only observed in males (p < .05). WT rats exposed to PCB 126 had reduced serum calcium, and smaller bones with reduced tibial length, cortical area, and medullary area relative to vehicle controls (p < .05). Reduced bone formation rate observed in dynamic histomorphometry was consistent with inhibition of endosteal and periosteal bone growth. The effects of PCB 126 were abolished in AhR -/- rats. Gene expression in bone marrow and shaft were assessed by RNA sequencing. Approximately 75% of the PCB-regulated genes appeared AhR dependent with 89 genes significantly (p < .05) regulated by both PCB 126 and knockout of the AhR gene. Novel targets significantly induced by PCB 126 included Indian hedgehog (Ihh) and connective tissue growth factor (Ctgf/Ccn2), which regulate chondrocyte proliferation and differentiation in the bone growth plate and cell-matrix interactions. These data suggest the toxic effects of PCB 126 on bone are mediated by AhR, which has direct effects on the growth plate and indirect actions related to endocrine disruption. These studies clarify important mechanisms underlying skeletal toxicity of dioxin-like PCBs and highlight potential therapeutic targets.
Collapse
Affiliation(s)
- Ashlee E Williams
- Department of Pharmacology & Experimental Therapeutics, Louisiana State University Health Sciences Center New Orleans, New Orleans, Louisiana 70112
| | - James Watt
- Department of Pharmacology & Experimental Therapeutics, Louisiana State University Health Sciences Center New Orleans, New Orleans, Louisiana 70112
| | - Larry W Robertson
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, Iowa
| | - Gopi Gadupudi
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, Iowa
| | - Michele L Osborn
- Department of Comparative Biomedical Sciences, LSU School of Veterinary Medicine, Baton Rouge, Louisiana
| | - Michael J Soares
- Department of Pathology, University of Kansas Medical Center, Kansas City, Missouri
| | - Khursheed Iqbal
- Department of Pathology, University of Kansas Medical Center, Kansas City, Missouri
| | - Kim B Pedersen
- Department of Pharmacology & Experimental Therapeutics, Louisiana State University Health Sciences Center New Orleans, New Orleans, Louisiana 70112
| | - Kartik Shankar
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado
| | - Shana Littleton
- Department of Pharmacology & Experimental Therapeutics, Louisiana State University Health Sciences Center New Orleans, New Orleans, Louisiana 70112
| | - Cole Maimone
- Department of Pharmacology & Experimental Therapeutics, Louisiana State University Health Sciences Center New Orleans, New Orleans, Louisiana 70112
| | - Nazmin A Eti
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, Iowa
| | - Larry J Suva
- Department of Veterinary Physiology & Pharmacology, Texas A&M University, College Station, Texas
| | - Martin J J Ronis
- Department of Pharmacology & Experimental Therapeutics, Louisiana State University Health Sciences Center New Orleans, New Orleans, Louisiana 70112
| |
Collapse
|
7
|
Ronis MJ, Watt J, Pulliam CF, Williams AE, Alund AW, Haque E, Gadupudi GS, Robertson LW. Skeletal toxicity resulting from exposure of growing male rats to coplanar PCB 126 is associated with disruption of calcium homeostasis and the GH-IGF-1 axis and direct effects on bone formation. Arch Toxicol 2019; 94:389-399. [PMID: 31820026 DOI: 10.1007/s00204-019-02645-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/04/2019] [Indexed: 12/13/2022]
Abstract
Skeletal toxicity has been reported following exposure to polychlorinated biphenyl (PCB) mixtures. However, molecular mechanisms remain poorly understood. We exposed groups of male 4-5-week-old Sprague-Dawley rats to 3,3', 4, 4', 5-pentachlorobiphenyl (PCB 126), a dioxin-like coplanar PCB congener by a single i.p. injection of 5 µmol/kg in soy oil vehicle or vehicle alone. After 4 weeks, rats were euthanized. PCB exposure resulted in hypocalcemia (P < 0.05) and significant increases in serum PTH without changes in serum phosphorous. Hyperparathyroidism was accompanied by increased expression of mRNAs of vitamin D3 metabolizing cytochrome P450 enzymes CYP27B1 and CYP24 in the kidney (P < 0.05). PCB exposure also reduced body weight, serum IGF-1, and hepatic expression of mRNAs encoding the male-specific GH-pattern-regulated CYP2C11 and CYP3A2 relative to controls (P < 0.05). PCB exposure reduced long bone length, diameter, and surface area, but increased trabecular thickness and volume (P < 0.05). Serum osteocalcin (P < 0.05), a marker and a regulator of bone formation, was reduced, but PCB exposure had no effect on the bone resorption marker RatLaps. Exposure of human intestinal Caco-2 cells to 10-100 nM PCB 126 in the presence of vitamin D3 resulted in inhibition of mRNAs for the calcium transporters TRPV6 and PMCA1b (P < 0.05). In addition, PCB 126 suppressed osteoblastogenesis in primary bone marrow mesenchymal stem cell cultures which was blunted by the AhR antagonist CH-223191. These data provide novel evidence that skeletal toxicity after exposure to PCB 126 is a result of disruption of calcium homeostasis and the GH-IGF-1 axis, and involves direct AhR-mediated effects on bone formation.
Collapse
Affiliation(s)
- Martin J Ronis
- Department of Pharmacology and Experimental Therapeutics, Louisiana State University Health Sciences Center-New Orleans, 1901 Perdido Str., New Orleans, LA, 70112, USA.
| | - James Watt
- Department of Pharmacology and Experimental Therapeutics, Louisiana State University Health Sciences Center-New Orleans, 1901 Perdido Str., New Orleans, LA, 70112, USA
| | - Casey F Pulliam
- Department of Pharmacology and Experimental Therapeutics, Louisiana State University Health Sciences Center-New Orleans, 1901 Perdido Str., New Orleans, LA, 70112, USA
| | - Ashlee E Williams
- Department of Pharmacology and Experimental Therapeutics, Louisiana State University Health Sciences Center-New Orleans, 1901 Perdido Str., New Orleans, LA, 70112, USA
| | - Alexander W Alund
- Department of Pharmacology and Toxicology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ezazul Haque
- IDGP in Human Toxicology and Department of Occupational and Environmental Health, University of Iowa, Iowa City, IA, USA
| | - Gopi S Gadupudi
- IDGP in Human Toxicology and Department of Occupational and Environmental Health, University of Iowa, Iowa City, IA, USA
| | - Larry W Robertson
- IDGP in Human Toxicology and Department of Occupational and Environmental Health, University of Iowa, Iowa City, IA, USA
| |
Collapse
|
8
|
Abstract
XIST RNA triggers the transformation of an active X chromosome into a condensed, inactive Barr body and therefore provides a unique window into transitions of higher-order chromosome architecture. Despite recent progress, how XIST RNA localizes and interacts with the X chromosome remains poorly understood. Genetic engineering of XIST into a trisomic autosome demonstrates remarkable capacity of XIST RNA to localize and comprehensively silence that autosome. Thus, XIST does not require X chromosome-specific sequences but operates on mechanisms available genome-wide. Prior results suggested XIST localization is controlled by attachment to the insoluble nuclear scaffold. Our recent work affirms that scaffold attachment factor A (SAF-A) is involved in anchoring XIST, but argues against the view that SAF-A provides a unimolecular bridge between RNA and the chromosome. Rather, we suggest that a complex meshwork of architectural proteins interact with XIST RNA. Parallel work studying the territory of actively transcribed chromosomes suggests that repeat-rich RNA 'coats' euchromatin and may impact chromosome architecture in a manner opposite of XIST A model is discussed whereby RNA may not just recruit histone modifications, but more directly impact higher-order chromatin condensation via interaction with architectural proteins of the nucleus.This article is part of the themed issue 'X-chromosome inactivation: a tribute to Mary Lyon'.
Collapse
Affiliation(s)
- K M Creamer
- Department of Neurology and Pediatrics, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - J B Lawrence
- Department of Neurology and Pediatrics, University of Massachusetts Medical School, Worcester, MA 01655, USA
| |
Collapse
|