1
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Jin J, Nguyen LTG, Wassef A, Sadek R, Schmitt TM, Guo GL, Rasmussen TP, Zhong XB. Identification and Functional Characterization of Alternative Transcripts of LncRNA HNF1A-AS1 and Their Impacts on Cell Growth, Differentiation, Liver Diseases, and in Response to Drug Induction. Noncoding RNA 2024; 10:28. [PMID: 38668386 PMCID: PMC11053763 DOI: 10.3390/ncrna10020028] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 04/29/2024] Open
Abstract
The long non-coding RNA (lncRNA) hepatocyte nuclear factor-1 alpha (HNF1A) antisense RNA 1 (HNF1A-AS1) is an important lncRNA for liver growth, development, cell differentiation, and drug metabolism. Like many lncRNAs, HNF1A-AS1 has multiple annotated alternative transcripts in the human genome. Several fundamental biological questions are still not solved: (1) How many transcripts really exist in biological samples, such as liver samples and liver cell lines? (2) What are the expression patterns of different alternative HNF1A-AS1 transcripts at different conditions, including during cell growth and development, after exposure to xenobiotics (such as drugs), and in disease conditions, such as metabolic dysfunction-associated steatotic liver disease (MASLD), alcohol-associated liver disease (ALD) cirrhosis, and obesity? (3) Does the siRNA used in previous studies knock down one or multiple transcripts? (4) Do different transcripts have the same or different functions for gene regulation? The presented data confirm the existence of several annotated HNF1A-AS1 transcripts in liver samples and cell lines, but also identify some new transcripts, which are not annotated in the Ensembl genome database. Expression patterns of the identified HNF1A-AS1 transcripts are highly correlated with the cell differentiation of matured hepatocyte-like cells from human embryonic stem cells (hESC), growth and differentiation of HepaRG cells, in response to rifampicin induction, and in various liver disease conditions. The expression levels of the HNF1A-AS1 transcripts are also highly correlated to the expression of cytochrome P450 enzymes, such as CYP3A4, during HepaRG growth, differentiation, and in response to rifampicin induction.
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Affiliation(s)
- Jing Jin
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (J.J.); (L.T.G.N.); (T.P.R.)
| | - Le Tra Giang Nguyen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (J.J.); (L.T.G.N.); (T.P.R.)
| | - Andrew Wassef
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08901, USA;
- Center of Excellence for Pharmaceutical Translational Research and Education, Rutgers University, Piscataway, NJ 08901, USA
- Center of Excellence for Metabolic and Bariatric Surgery, Robert Wood Johnson Barnabas University Hospital, New Brunswick, NJ 08901, USA;
| | - Ragui Sadek
- Center of Excellence for Metabolic and Bariatric Surgery, Robert Wood Johnson Barnabas University Hospital, New Brunswick, NJ 08901, USA;
| | - Timothy M. Schmitt
- Department of General Surgery, University of Kansas Medical Center, Kansas City, KS 66160, USA;
| | - Grace L. Guo
- Department of Pharmacology and Toxicology, Ernst Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08901, USA;
| | - Theodore P. Rasmussen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (J.J.); (L.T.G.N.); (T.P.R.)
| | - Xiao-bo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (J.J.); (L.T.G.N.); (T.P.R.)
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Keehan L, Haviland I, Gofin Y, Swanson LC, El Achkar CM, Schreiber J, VanNoy GE, O’Heir E, O’Donnell-Luria A, Lewis RA, Magoulas P, Tran A, Azamian MS, Chao HT, Pham L, Samaco RC, Elsea S, Thorpe E, Kesari A, Perry D, Lee B, Lalani SR, Rosenfeld JA, Olson HE, Burrage LC. Wide range of phenotypic severity in individuals with late truncations unique to the predominant CDKL5 transcript in the brain. Am J Med Genet A 2022; 188:3516-3524. [PMID: 35934918 PMCID: PMC9669137 DOI: 10.1002/ajmg.a.62940] [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: 03/01/2022] [Revised: 05/10/2022] [Accepted: 06/19/2022] [Indexed: 01/31/2023]
Abstract
Cyclin-dependent kinase-like 5 (CDKL5) deficiency disorder (CDD) is caused by heterozygous or hemizygous variants in CDKL5 and is characterized by refractory epilepsy, cognitive and motor impairments, and cerebral visual impairment. CDKL5 has multiple transcripts, of which the longest transcripts, NM_003159 and NM_001037343, have been used historically in clinical laboratory testing. However, the transcript NM_001323289 is the most highly expressed in brain and contains 170 nucleotides at the 3' end of its last exon that are noncoding in other transcripts. Two truncating variants in this region have been reported in association with a CDD phenotype. To clarify the significance and range of phenotypes associated with late truncating variants in this region of the predominant transcript in the brain, we report detailed information on two individuals, updated clinical information on a third individual, and a summary of published and unpublished individuals reported in ClinVar. The two new individuals (one male and one female) each had a relatively mild clinical presentation including periods of pharmaco-responsive epilepsy, independent walking and limited purposeful communication skills. A previously reported male continued to have a severe phenotype. Overall, variants in this region demonstrate a range of clinical severity consistent with reports in CDD but with the potential for milder presentation.
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Affiliation(s)
- Laura Keehan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Isabel Haviland
- Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Yoel Gofin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Lindsay C. Swanson
- Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - Christelle Moufawad El Achkar
- Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
| | - John Schreiber
- Division of Epilepsy, Neurophysiology, and Critical Care Neurology, 8404 Children's National Hospital, Washington, DC, USA
| | - Grace E. VanNoy
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Emily O’Heir
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anne O’Donnell-Luria
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Richard A. Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Cullen Eye Institute, Department of Ophthalmology, Baylor College of Medicine, Houston, TX, USA
| | - Pilar Magoulas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Alyssa Tran
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Mahshid S. Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Hsiao-Tuan Chao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Departments of Neuroscience and Pediatrics, Division of Neurology and Developmental Neuroscience, BCM, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- McNair Medical Institute at the Robert and Janice McNair Foundation, Houston, TX, USA
| | - Lisa Pham
- The Meyer Center for Developmental Pediatrics, Texas Children’s Hospital, Houston, TX, USA
| | - Rodney C. Samaco
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Sarah Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | | | | | | | - Brendan Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Seema R. Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Heather E. Olson
- Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children’s Hospital, Boston, MA, USA
- Equal contributions
| | - Lindsay C. Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Equal contributions
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3
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Punzo P, Grillo S, Batelli G. Alternative splicing in plant abiotic stress responses. Biochem Soc Trans 2020; 48:2117-26. [PMID: 32869832 DOI: 10.1042/BST20200281] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/05/2020] [Accepted: 08/07/2020] [Indexed: 02/06/2023]
Abstract
Modifications of the cellular proteome pool upon stress allow plants to tolerate environmental changes. Alternative splicing is the most significant mechanism responsible for the production of multiple protein isoforms from a single gene. The spliceosome, a large ribonucleoprotein complex, together with several associated proteins, controls this pre-mRNA processing, adding an additional level of regulation to gene expression. Deep sequencing of transcriptomes revealed that this co- or post-transcriptional mechanism is highly induced by abiotic stress, and concerns vast numbers of stress-related genes. Confirming the importance of splicing in plant stress adaptation, key players of stress signaling have been shown to encode alternative transcripts, whereas mutants lacking splicing factors or associated components show a modified sensitivity and defective responses to abiotic stress. Here, we examine recent literature on alternative splicing and splicing alterations in response to environmental stresses, focusing on its role in stress adaptation and analyzing the future perspectives and directions for research.
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Li L, Pastor J, Zhang J, Davidson T, Hu MC, Moe OW. In search of alternatively spliced alpha-Klotho Kl1 protein in mouse brain. FASEB Bioadv 2021; 3:531-540. [PMID: 34258522 PMCID: PMC8255843 DOI: 10.1096/fba.2020-00066] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 01/01/2023] Open
Abstract
Alpha‐Klotho is a multi‐functional protein essential for maintenance of a myriad of cell functions. αKlotho is a single transmembrane protein with a large extracellular segment consisting of two domains (termed Kl1 and Kl2) which is shed into the extracellular fluid by proteolytic cleavage to furnish circulating soluble αKlotho. Based on cDNA sequence, an alternatively spliced mRNA is predicted to translate to a putative soluble αKlotho protein in mouse and human with only the Kl1 domain that represents a “spliced αKlotho Kl1” (spKl1) and is released from the cell without membrane targeting or cleavage. The existence of this protein remains in silico for two decades. We generated a novel antibody (anti‐spE15) against the 15 amino acid epitope (E15; VSPLTKPSVGLLLPH) which is not present in Kl1 or full‐length αKlotho and validated its specific reactivity against spKl1 in vitro. Using anti‐spE15 and two well‐established anti‐αKlotho monoclonal antibodies, we performed immunoblots, immunoprecipitation, and immunohistochemistry to investigate for expression of spKl1 in the mouse brain. We found anti‐spE15 labeling in mouse brain but were not able to see co‐labelling of Kl1 and spE15 epitopes on the same protein, which is the pre‐requisite for the existence of a spKl1 polypeptide, indicating that anti‐spE15 likely binds to another protein other than the putative spKl1. In isolated choroid plexus from mouse brain, we found strong staining with anti‐spE15, but did not find the spliced αKlotho transcript. We conclude that using reliable reagents and inclusion of proper controls, there is no evidence of the spKl1 protein in the mouse brain.
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Affiliation(s)
- Liping Li
- Charles and Jane Pak Center for Mineral Metabolism and Clinical Research Dallas TX USA
| | - Johanne Pastor
- Charles and Jane Pak Center for Mineral Metabolism and Clinical Research Dallas TX USA
| | - Jianning Zhang
- Division of Nephrology Department of Internal Medicine University of Texas Southwestern Medical Center Dallas TX USA
| | - Taylor Davidson
- Charles and Jane Pak Center for Mineral Metabolism and Clinical Research Dallas TX USA
| | - Ming-Chang Hu
- Charles and Jane Pak Center for Mineral Metabolism and Clinical Research Dallas TX USA
| | - Orson W Moe
- Charles and Jane Pak Center for Mineral Metabolism and Clinical Research Dallas TX USA.,Division of Nephrology Department of Internal Medicine University of Texas Southwestern Medical Center Dallas TX USA.,Department of Physiology University of Texas Southwestern Medical Center Dallas TX USA
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5
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Cruz-Garcia L, O’Brien G, Sipos B, Mayes S, Tichý A, Sirák I, Davídková M, Marková M, Turner DJ, Badie C. In Vivo Validation of Alternative FDXR Transcripts in Human Blood in Response to Ionizing Radiation. Int J Mol Sci 2020; 21:ijms21217851. [PMID: 33113898 PMCID: PMC7660203 DOI: 10.3390/ijms21217851] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 12/20/2022] Open
Abstract
Following cell stress such as ionising radiation (IR) exposure, multiple cellular pathways are activated. We recently demonstrated that ferredoxin reductase (FDXR) has a remarkable IR-induced transcriptional responsiveness in blood. Here, we provided a first comprehensive FDXR variant profile following DNA damage. First, specific quantitative real-time polymerase chain reaction (qPCR) primers were designed to establish dose-responses for eight curated FDXR variants, all up-regulated after IR in a dose-dependent manner. The potential role of gender on the expression of these variants was tested, and neither the variants response to IR nor the background level of expression was profoundly affected; moreover, in vitro induction of inflammation temporarily counteracted IR response early after exposure. Importantly, transcriptional up-regulation of these variants was further confirmed in vivo in blood of radiotherapy patients. Full-length nanopore sequencing was performed to identify other FDXR variants and revealed the high responsiveness of FDXR-201 and FDXR-208. Moreover, FDXR-218 and FDXR-219 showed no detectable endogenous expression, but a clear detection after IR. Overall, we characterised 14 FDXR transcript variants and identified for the first time their response to DNA damage in vivo. Future studies are required to unravel the function of these splicing variants, but they already represent a new class of radiation exposure biomarkers.
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Affiliation(s)
- Lourdes Cruz-Garcia
- Cancer Mechanisms and Biomarkers Group, Radiation Effects Department, Centre for Radiation, Chemical & Environmental Hazards, Public Health England, Chilton, Oxfordshire OX11 0RQ, UK; (L.C.-G.); (G.O.)
| | - Grainne O’Brien
- Cancer Mechanisms and Biomarkers Group, Radiation Effects Department, Centre for Radiation, Chemical & Environmental Hazards, Public Health England, Chilton, Oxfordshire OX11 0RQ, UK; (L.C.-G.); (G.O.)
| | - Botond Sipos
- Oxford Nanopore Technologies, Gosling Building, Edmund Halley Way, Oxford OX4 4DQ, UK; (B.S.); (S.M.); (D.J.T.)
| | - Simon Mayes
- Oxford Nanopore Technologies, Gosling Building, Edmund Halley Way, Oxford OX4 4DQ, UK; (B.S.); (S.M.); (D.J.T.)
| | - Aleš Tichý
- Department of Radiobiology, Faculty of Military Health Sciences in Hradec Králové, University of Defence in Brno, 500 01 Hradec Králové, Czech Republic;
- Biomedical Research Centre, Hradec Králové University Hospital, 500 01 Hradec Králové, Czech Republic
| | - Igor Sirák
- Department of Oncology and Radiotherapy and 4th Department of Internal Medicine—Hematology, University Hospital, 500 05 Hradec Králové, Czech Republic;
| | - Marie Davídková
- Department of Radiation Dosimetry, Nuclear Physics Institute of the Czech Academy of Sciences, 180 00 Prague 8, Czech Republic;
| | - Markéta Marková
- Institute of Hematology and Blood Transfusion, 128 00 Praha 2, Czech Republic;
| | - Daniel J. Turner
- Oxford Nanopore Technologies, Gosling Building, Edmund Halley Way, Oxford OX4 4DQ, UK; (B.S.); (S.M.); (D.J.T.)
| | - Christophe Badie
- Cancer Mechanisms and Biomarkers Group, Radiation Effects Department, Centre for Radiation, Chemical & Environmental Hazards, Public Health England, Chilton, Oxfordshire OX11 0RQ, UK; (L.C.-G.); (G.O.)
- Correspondence: ; Tel.: +44-(0)1235-825-088; Fax: +44-(0)1235-833-891
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6
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Shepelev MV, Saakian EK, Kalinichenko SV, Korobko IV. [Human Antithrombin III Minigene with an Optimized Splicing Pattern]. Mol Biol (Mosk) 2019; 53:411-420. [PMID: 31184606 DOI: 10.1134/s0026898419030170] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 12/11/2018] [Indexed: 11/23/2022]
Abstract
Antithrombin III (AT3) belongs to the superfamily of serine protease inhibitors (serpins) and is a major anticoagulant in physiological conditions. Based on SERPINC1 gene, a minigene coding for human AT3, which is valuable for medicine and biotechnology, was constructed by minimizing the size of lengthy introns and preserving the splicing site-flanking sequences. An analysis of the minigene splicing pattern identified one correct AT3 transcript and two alternatively spliced transcripts, which formed either due to minigene exons 2 and 3 skipping or an aberrant exon insertion via splicing at cryptic splicing sites in intron 1 of the minigene. Site-directed mutagenesis of the cryptic splicing sites successfully optimized the splicing pattern of the AT3 minigene to completely prevent the generation of the alternative transcripts. The presence of the cryptic splicing sites in intron 1 of the minigene was confirmed with Human Splicing Finder v. 3.1 software, thus demonstrating that putative alternative splicing sites are possible to identify in minimized or hybrid introns of minigenes and to eliminate via mutagenesis before experimentally testing the minigene splicing patterns. The approach to the design of minigenes together with the bioinformatical analysis of the nucleotide sequences of minigene introns can be used to construct minigenes in order to generate transgenic animals producing economically valuable proteins in the milk.
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Affiliation(s)
- M V Shepelev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia.,
| | - E K Saakian
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - S V Kalinichenko
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - I V Korobko
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
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7
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Haney RA, Matte T, Forsyth FS, Garb JE. Alternative Transcription at Venom Genes and Its Role as a Complementary Mechanism for the Generation of Venom Complexity in the Common House Spider. Front Ecol Evol 2019; 7. [PMID: 31431897 PMCID: PMC6700725 DOI: 10.3389/fevo.2019.00085] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The complex composition of venom, a proteinaceous secretion used by
diverse animal groups for predation or defense, is typically viewed as being
driven by gene duplication in conjunction with positive selection, leading to
large families of diversified toxins with selective venom gland expression. Yet,
the production of alternative transcripts at venom genes is often overlooked as
another potentially important process that could contribute proteins to venom,
and requires comprehensive datasets integrating genome and transcriptome
sequences together with proteomic characterization of venom to be fully
documented. In the common house spider, Parasteatoda
tepidariorum, we used RNA sequencing of four tissue types in
conjunction with the sequenced genome to provide a comprehensive transcriptome
annotation. We also used mass spectrometry to identify a minimum of 99 distinct
proteins in P tepidariorum venom, including at least 33
latrotoxins, pore-forming neurotoxins shared with the confamilial black widow.
We found that venom proteins are much more likely to come from multiple
transcript genes, whose transcripts produced distinct protein sequences. The
presence of multiple distinct proteins in venom from transcripts at individual
genes was confirmed for eight loci by mass spectrometry, and is possible at 21
others. Alternative transcripts from the same gene, whether encoding or not
encoding a protein found in venom, showed a range of expression patterns, but
were not necessarily restricted to the venom gland. However, approximately half
of venom protein encoding transcripts were found among the 1,318 transcripts
with strongly venom gland biased expression. Our findings revealed an important
role for alternative transcription in generating venom protein complexity and
expanded the traditional model of venom evolution.
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Affiliation(s)
- Robert A Haney
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, United States
| | - Taylor Matte
- Center for Regenerative Medicine, Boston University, Medical, Boston, MA, United States
| | - FitzAnthony S Forsyth
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, United States
| | - Jessica E Garb
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, United States
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8
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Fang C, Li J, Qi S, Lei Y, Zeng Y, Yu P, Hu Z, Zhou Y, Wang Y, Dai R, Li J, Huang S, Xu P, Chen K, Ding C, Yu FX. An alternatively transcribed TAZ variant negatively regulates JAK-STAT signaling. EMBO Rep 2019; 20:embr.201847227. [PMID: 30979708 DOI: 10.15252/embr.201847227] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 10/12/2018] [Revised: 03/25/2019] [Accepted: 03/25/2019] [Indexed: 12/11/2022] Open
Abstract
Type I interferon (IFN)-induced Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signaling drives the expression of IFN-stimulated genes (ISGs) to mediate antiviral response. The strength and duration of JAK-STAT signaling are tightly regulated to ensure effective antiviral defense while avoiding pathological inflammation and autoimmunity. Here, we report that cTAZ, an isoform of the Hippo pathway effector TAZ, is transcribed by an alternative promoter. Although majority of C-terminal sequences of TAZ is retained, cTAZ is not regulated by the Hippo signaling and does not mediate its growth-inhibitory functions. Instead, cTAZ negatively regulates JAK-STAT signaling by inhibiting STAT1/2 nuclear localization and ISG expression, and its expression is induced by type I IFN Thus, cTAZ functions as a modulator of JAK-STAT signaling and may play a role in fine-tuning cellular antiviral response.
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Affiliation(s)
- Chuantao Fang
- Children's Hospital and Institutes of Biomedical Sciences, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China
| | - Jian Li
- Children's Hospital and Institutes of Biomedical Sciences, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China
| | - Sixian Qi
- Children's Hospital and Institutes of Biomedical Sciences, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China
| | - Yubin Lei
- Children's Hospital and Institutes of Biomedical Sciences, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China
| | - Yan Zeng
- Children's Hospital and Institutes of Biomedical Sciences, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China
| | - Pengcheng Yu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhaolan Hu
- Department of Anesthesiology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yufeng Zhou
- Children's Hospital and Institutes of Biomedical Sciences, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China
| | - Yulong Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ruping Dai
- Department of Anesthesiology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jin Li
- Children's Hospital and Institutes of Biomedical Sciences, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China
| | - Shenglin Huang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Pinglong Xu
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Kang Chen
- Perinatology Research Branch, Eunice Kennedy Shriver NICHD, National Institutes of Health, Detroit, MI, USA.,Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA.,Jiangsu Province Hospital of TCM, The Affiliated Hospital of Nanjing University of TCM, Nanjing, China
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Institutes of Biomedical Sciences, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Fa-Xing Yu
- Children's Hospital and Institutes of Biomedical Sciences, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, China
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9
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Ten-Caten F, Vêncio RZN, Lorenzetti APR, Zaramela LS, Santana AC, Koide T. Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea. RNA Biol 2018; 15:1119-1132. [PMID: 30175688 PMCID: PMC6161675 DOI: 10.1080/15476286.2018.1509661] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Prokaryotic genomes show a high level of information compaction often with different molecules transcribed from the same locus. Although antisense RNAs have been relatively well studied, RNAs in the same strand, internal RNAs (intraRNAs), are still poorly understood. The question of how common is the translation of overlapping reading frames remains open. We address this question in the model archaeon Halobacterium salinarum. In the present work we used differential RNA-seq (dRNA-seq) in H. salinarum NRC-1 to locate intraRNA signals in subsets of internal transcription start sites (iTSS) and establish the open reading frames associated to them (intraORFs). Using C-terminally flagged proteins, we experimentally observed isoforms accurately predicted by intraRNA translation for kef1, acs3 and orc4 genes. We also recovered from the literature and mass spectrometry databases several instances of protein isoforms consistent with intraRNA translation such as the gas vesicle protein gene gvpC1. We found evidence for intraRNAs in horizontally transferred genes such as the chaperone dnaK and the aerobic respiration related cydA in both H. salinarum and Escherichia coli. Also, intraRNA translation evidence in H. salinarum, E. coli and yeast of a universal elongation factor (aEF-2, fusA and eEF-2) suggests that this is an ancient phenomenon present in all domains of life.
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Affiliation(s)
- Felipe Ten-Caten
- a Department of Biochemistry and Immunology , Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil
| | - Ricardo Z N Vêncio
- b Department of Computation and Mathematics, Faculdade de Filosofia , Ciências e Letras de Ribeirão Preto, University of São Paulo , Ribeirão Preto , Brazil
| | - Alan Péricles R Lorenzetti
- a Department of Biochemistry and Immunology , Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil
| | - Livia Soares Zaramela
- a Department of Biochemistry and Immunology , Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil
| | - Ana Carolina Santana
- c Department of Cell and Molecular Biology and Pathogenic Bioagents , Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil
| | - Tie Koide
- a Department of Biochemistry and Immunology , Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil
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Ishigami T, Kino T, Chen L, Minegishi S, Araki N, Umemura M, Abe K, Sasaki R, Yamana H, Umemura S. Identification of bona fide alternative renin transcripts expressed along cortical tubules and potential roles in promoting insulin resistance in vivo without significant plasma renin activity elevation. Hypertension 2014; 64:125-33. [PMID: 24777979 DOI: 10.1161/hypertensionaha.114.03394] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Renin belongs to a family of aspartyl proteases and is the rate-limiting enzyme in the synthesis of the potent vasoactive peptide angiotensin II. Processing of renal renin has been extensively investigated in juxtaglomerular granular cells, in which prorenin and active renin are present in secretory condensed granules. Previous studies demonstrated alternative renin transcription in rat adrenal glands. Different studies reported novel intracellular forms of renin deduced from novel 5' variants derived from renin mRNA in both mice and humans. Comprehensive detailed studies in genetically engineered mice showed that both a secreted and an intracellular form of renin plays divergent mechanism regulating fluid intake and metabolism by the brain renin-angiotensin system; however, the presence, regulation, and functions of these renin isoforms in kidney and adrenal gland are not fully understood in mice. To investigate the characteristics of renin isoforms in mice, we performed a systematic inventory of renin transcripts of mice with and without a duplication of the renin gene alternatively from previous studies. We discovered a novel isoform of renin of the Ren2 gene, which conserved functionally important residues of the prosegment and incomplete isoforms of the Ren1C/D gene lacking a pre-pro segment. In situ hybridization assays revealed alternative renin isoforms expressed along cortical tubules. Newly generated transgenic mice with systemic overexpression of alternative renin transcript showed enhanced local angiotensin II generation without elevation of plasma renin activity and systemic insulin resistance in vivo, providing new pathophysiological insights into insulin resistance exaggerated by bona fide renin isoform.
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Affiliation(s)
- Tomoaki Ishigami
- From the Department of Medical Science and Cardio-Renal Medicine, Yokohama City University, Graduate School of Medicine, Yokohama, Japan.
| | - Tabito Kino
- From the Department of Medical Science and Cardio-Renal Medicine, Yokohama City University, Graduate School of Medicine, Yokohama, Japan
| | - Lin Chen
- From the Department of Medical Science and Cardio-Renal Medicine, Yokohama City University, Graduate School of Medicine, Yokohama, Japan
| | - Shintaro Minegishi
- From the Department of Medical Science and Cardio-Renal Medicine, Yokohama City University, Graduate School of Medicine, Yokohama, Japan
| | - Naomi Araki
- From the Department of Medical Science and Cardio-Renal Medicine, Yokohama City University, Graduate School of Medicine, Yokohama, Japan
| | - Masanari Umemura
- From the Department of Medical Science and Cardio-Renal Medicine, Yokohama City University, Graduate School of Medicine, Yokohama, Japan
| | - Kaito Abe
- From the Department of Medical Science and Cardio-Renal Medicine, Yokohama City University, Graduate School of Medicine, Yokohama, Japan
| | - Rie Sasaki
- From the Department of Medical Science and Cardio-Renal Medicine, Yokohama City University, Graduate School of Medicine, Yokohama, Japan
| | - Hisako Yamana
- From the Department of Medical Science and Cardio-Renal Medicine, Yokohama City University, Graduate School of Medicine, Yokohama, Japan
| | - Satoshi Umemura
- From the Department of Medical Science and Cardio-Renal Medicine, Yokohama City University, Graduate School of Medicine, Yokohama, Japan
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Engstrom LD, Youkilis AS, Gorelick JL, Zheng D, Ackley V, Petroff CA, Benson LQ, Coon MR, Zhu X, Hanash SM, Wechsler DS. Mxi1-0, an alternatively transcribed Mxi1 isoform, is overexpressed in glioblastomas. Neoplasia 2004; 6:660-73. [PMID: 15548375 PMCID: PMC1531670 DOI: 10.1593/neo.04244] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [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: 03/19/2004] [Revised: 06/14/2004] [Indexed: 01/26/2023]
Abstract
The c-Myc transcription factor regulates expression of genes related to cell growth, division, and apoptosis. Mxi1, a member of the Mad family, represses transcription of c-Myc-regulated genes by mediating chromatin condensation via histone deacetylase and the Sin3 corepressor. Mxi1 is a c-Myc antagonist and suppresses cell proliferation in vitro. Here, we describe the identification of Mxi1-0, a novel Mxi1 isoform that is alternatively transcribed from an upstream exon. Mxi1-0 and Mxi1 have different amino-terminal sequences, but share identical Max- and DNA-binding domains. Both isoforms are able to bind Max, to recognize E-box binding sites, and to interact with Sin3. Despite these similarities and in contrast to Mxi1, Mxi1-0 is predominantly localized to the cytoplasm and fails to repress c-Myc-dependent transcription. Although Mxi1-0 and Mxi1 are coexpressed in both human and mouse cells, the relative levels of Mxi1-0 are higher in primary glioblastoma tumors than in normal brain tissue. This variation in the levels of Mxi1-0 and Mxi1 suggests that Mxi1-0 may modulate the Myc-inhibitory activity of Mxi1. The identification of Mxi1-0 as an alternatively transcribed Mxi1 isoform has significant implications for the interpretation of previous Mxi1 studies, particularly those related to the phenotype of the mxi1 knockout mouse.
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Affiliation(s)
- Lars D Engstrom
- Section of Pediatric Hematology-Oncology, Department of Pediatrics and Communicable Diseases, The University of Michigan School of Medicine, Ann Arbor, MI 48109-0936, USA
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