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Rosikiewicz W, Sikora J, Skrzypczak T, Kubiak MR, Makałowska I. Promoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5' ends. Sci Rep 2021; 11:8984. [PMID: 33903630 PMCID: PMC8076222 DOI: 10.1038/s41598-021-87970-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/07/2021] [Indexed: 11/09/2022] Open
Abstract
Despite the number of studies focused on sense-antisense transcription, the key question of whether such organization evolved as a regulator of gene expression or if this is only a byproduct of other regulatory processes has not been elucidated to date. In this study, protein-coding sense-antisense gene pairs were analyzed with a particular focus on pairs overlapping at their 5' ends. Analyses were performed in 73 human transcription start site libraries. The results of our studies showed that the overlap between genes is not a stable feature and depends on which TSSs are utilized in a given cell type. An analysis of gene expression did not confirm that overlap between genes causes downregulation of their expression. This observation contradicts earlier findings. In addition, we showed that the switch from one promoter to another, leading to genes overlap, may occur in response to changing environment of a cell or tissue. We also demonstrated that in transfected and cancerous cells genes overlap is observed more often in comparison with normal tissues. Moreover, utilization of overlapping promoters depends on particular state of a cell and, at least in some groups of genes, is not merely coincidental.
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Affiliation(s)
- Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jarosław Sikora
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Tomasz Skrzypczak
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
- Center for Advanced Technology, Adam Mickiewicz University, Poznań, Poland
| | - Magdalena R Kubiak
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Izabela Makałowska
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland.
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2
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Identification of Dominant Transcripts in Oxidative Stress Response by a Full-Length Transcriptome Analysis. Mol Cell Biol 2021; 41:MCB.00472-20. [PMID: 33168698 DOI: 10.1128/mcb.00472-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 11/02/2020] [Indexed: 12/30/2022] Open
Abstract
Our body responds to environmental stress by changing the expression levels of a series of cytoprotective enzymes/proteins through multilayered regulatory mechanisms, including the KEAP1-NRF2 system. While NRF2 upregulates the expression of many cytoprotective genes, there are fundamental limitations in short-read RNA sequencing (RNA-Seq), resulting in confusion regarding interpreting the effectiveness of cytoprotective gene induction at the transcript level. To precisely delineate isoform usage in the stress response, we conducted independent full-length transcriptome profiling (isoform sequencing; Iso-Seq) analyses of lymphoblastoid cells from three volunteers under normal and electrophilic stress-induced conditions. We first determined the first exon usage in KEAP1 and NFE2L2 (encoding NRF2) and found the presence of transcript diversity. We then examined changes in isoform usage of NRF2 target genes under stress conditions and identified a few isoforms dominantly expressed in the majority of NRF2 target genes. The expression levels of isoforms determined by Iso-Seq analyses showed striking differences from those determined by short-read RNA-Seq; the latter could be misleading concerning the abundance of transcripts. These results support that transcript usage is tightly regulated to produce functional proteins under electrophilic stress. Our present study strongly argues that there are important benefits that can be achieved by long-read transcriptome sequencing.
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3
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Russo R, Marra R, Rosato BE, Iolascon A, Andolfo I. Genetics and Genomics Approaches for Diagnosis and Research Into Hereditary Anemias. Front Physiol 2020; 11:613559. [PMID: 33414725 PMCID: PMC7783452 DOI: 10.3389/fphys.2020.613559] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/03/2020] [Indexed: 01/19/2023] Open
Abstract
The hereditary anemias are a relatively heterogeneous set of disorders that can show wide clinical and genetic heterogeneity, which often hampers correct clinical diagnosis. The classical diagnostic workflow for these conditions generally used to start with analysis of the family and personal histories, followed by biochemical and morphological evaluations, and ending with genetic testing. However, the diagnostic framework has changed more recently, and genetic testing is now a suitable approach for differential diagnosis of these patients. There are several approaches to this genetic testing, the choice of which depends on phenotyping, genetic heterogeneity, and gene size. For patients who show complete phenotyping, single-gene testing remains recommended. However, genetic analysis now includes next-generation sequencing, which is generally based on custom-designed targeting panels and whole-exome sequencing. The use of next-generation sequencing also allows the identification of new causative genes, and of polygenic conditions and genetic factors that modify disease severity of hereditary anemias. In the research field, whole-genome sequencing is useful for the identification of non-coding causative mutations, which might account for the disruption of transcriptional factor occupancy sites and cis-regulatory elements. Moreover, advances in high-throughput sequencing techniques have now resulted in the identification of genome-wide profiling of the chromatin structures known as the topologically associating domains. These represent a recurrent disease mechanism that exposes genes to inappropriate regulatory elements, causing errors in gene expression. This review focuses on the challenges of diagnosis and research into hereditary anemias, with indications of both the advantages and disadvantages. Finally, we consider the future perspectives for the use of next-generation sequencing technologies in this era of precision medicine.
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Affiliation(s)
- Roberta Russo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Roberta Marra
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Barbara Eleni Rosato
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Achille Iolascon
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Immacolata Andolfo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy
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4
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Ubaida-Mohien C, Lyashkov A, Gonzalez-Freire M, Tharakan R, Shardell M, Moaddel R, Semba RD, Chia CW, Gorospe M, Sen R, Ferrucci L. Discovery proteomics in aging human skeletal muscle finds change in spliceosome, immunity, proteostasis and mitochondria. eLife 2019; 8:49874. [PMID: 31642809 PMCID: PMC6810669 DOI: 10.7554/elife.49874] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 09/16/2019] [Indexed: 12/19/2022] Open
Abstract
A decline of skeletal muscle strength with aging is a primary cause of mobility loss and frailty in older persons, but the molecular mechanisms of such decline are not understood. Here, we performed quantitative proteomic analysis from skeletal muscle collected from 58 healthy persons aged 20 to 87 years. In muscle from older persons, ribosomal proteins and proteins related to energetic metabolism, including those related to the TCA cycle, mitochondria respiration, and glycolysis, were underrepresented, while proteins implicated in innate and adaptive immunity, proteostasis, and alternative splicing were overrepresented. Consistent with reports in animal models, older human muscle was characterized by deranged energetic metabolism, a pro-inflammatory environment and increased proteolysis. Changes in alternative splicing with aging were confirmed by RNA-seq analysis. We propose that changes in the splicing machinery enables muscle cells to respond to a rise in damage with aging. As humans age, their muscles become weaker, making it increasingly harder for them to move, a condition known as sarcopenia. Analyzing old muscles in other animals revealed that they produce energy inefficiently, they destroy more proteins than younger muscles, and they have high levels of molecules that cause inflammation. These characteristics may be involved in causing muscle weakness. Proteomics is the study of proteins, the molecules that play many roles in keeping the body working: for example, they accelerate chemical reactions, participate in copying DNA and help cells respond to stimuli. Using proteomics, it is possible to examine a large number of the different proteins in a tissue, which can provide information about the state of that tissue. Ubaida-Mohien et al. used this approach to answer the question of why muscles become weaker with age. First, they analyzed the levels of all the proteins found in skeletal muscle collected from 58 healthy volunteers between 20 and 87 years of age. This revealed that the muscles of older people have fewer copies of the proteins that make up ribosomes – the cellular machines that produce new proteins – and fewer proteins involved in providing the cell with chemical energy. In contrast, proteins implicated in the immune system, in the maintenance of existing proteins, and in processing other molecules called RNAs were more abundant in older muscles. Ubaida-Mohien et al. then looked more closely at changes involving RNA processing. Cells make proteins by copying DNA sequences into an RNA template and using this template to instruct the ribosomes on how to make the specific protein. Before the RNA can be ‘read’ by a ribosome, however, some parts must be cut out and others added, which can lead to different versions of the final RNA, also known as alternative transcripts. In order to check whether the difference in the levels of proteins that process RNAs was affecting the RNAs being produced, Ubaida-Mohien et al. extracted the RNAs from older and younger muscles and compared them. This showed that the RNA in older people had more alternative transcripts, confirming that the change in protein levels was having downstream effects. Currently, it is not possible to prevent or delay the loss of muscle strength associated with aging. Understanding how the protein make-up of muscles changes as humans grow older may help find new ways to prevent and perhaps even reverse this decline.
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Affiliation(s)
- Ceereena Ubaida-Mohien
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, United States
| | - Alexey Lyashkov
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, United States
| | - Marta Gonzalez-Freire
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, United States
| | - Ravi Tharakan
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, United States
| | - Michelle Shardell
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, United States
| | - Ruin Moaddel
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, United States
| | | | - Chee W Chia
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, United States
| | - Myriam Gorospe
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, United States
| | - Ranjan Sen
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, United States
| | - Luigi Ferrucci
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, United States
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Moore KS, von Lindern M. RNA Binding Proteins and Regulation of mRNA Translation in Erythropoiesis. Front Physiol 2018; 9:910. [PMID: 30087616 PMCID: PMC6066521 DOI: 10.3389/fphys.2018.00910] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/21/2018] [Indexed: 12/12/2022] Open
Abstract
Control of gene expression in erythropoiesis has to respond to signals that may emerge from intracellular processes or environmental factors. Control of mRNA translation allows for relatively rapid modulation of protein synthesis from the existing transcriptome. For instance, the protein synthesis rate needs to be reduced when reactive oxygen species or unfolded proteins accumulate in the cells, but also when iron supply is low or when growth factors are lacking in the environment. In addition, regulation of mRNA translation can be important as an additional layer of control on top of gene transcription, in which RNA binding proteins (RBPs) can modify translation of a set of transcripts to the cell’s actual protein requirement. The 5′ and 3′ untranslated regions of mRNA (5′UTR, 3′UTR) contain binding sites for general and sequence specific translation factors. They also contain secondary structures that may hamper scanning of the 5′UTR by translation complexes or may help to recruit translation factors. In addition, the term 5′UTR is not fully correct because many transcripts contain small open reading frames in their 5′UTR that are translated and contribute to regulation of mRNA translation. It is becoming increasingly clear that the transcriptome only partly predicts the proteome. The aim of this review is (i) to summarize how the availability of general translation initiation factors can selectively regulate transcripts because the 5′UTR contains secondary structures or short translated sequences, (ii) to discuss mechanisms that control the length of the mRNA poly(A) tail in relation to mRNA translation, and (iii) to give examples of sequence specific RBPs and their targets. We focused on transcripts and RBPs required for erythropoiesis. Whereas differentiation of erythroblasts to erythrocytes is orchestrated by erythroid transcription factors, the production of erythrocytes needs to respond to the availability of growth factors and nutrients, particularly the availability of iron.
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Affiliation(s)
- Kat S Moore
- Department of Hematopoiesis, Sanquin Research, and Landsteiner Laboratory, Amsterdam UMC, Amsterdam, Netherlands
| | - Marieke von Lindern
- Department of Hematopoiesis, Sanquin Research, and Landsteiner Laboratory, Amsterdam UMC, Amsterdam, Netherlands
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Impact of spliceosome mutations on RNA splicing in myelodysplasia: dysregulated genes/pathways and clinical associations. Blood 2018; 132:1225-1240. [PMID: 29930011 DOI: 10.1182/blood-2018-04-843771] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/11/2018] [Indexed: 12/14/2022] Open
Abstract
SF3B1, SRSF2, and U2AF1 are the most frequently mutated splicing factor genes in the myelodysplastic syndromes (MDS). We have performed a comprehensive and systematic analysis to determine the effect of these commonly mutated splicing factors on pre-mRNA splicing in the bone marrow stem/progenitor cells and in the erythroid and myeloid precursors in splicing factor mutant MDS. Using RNA-seq, we determined the aberrantly spliced genes and dysregulated pathways in CD34+ cells of 84 patients with MDS. Splicing factor mutations result in different alterations in splicing and largely affect different genes, but these converge in common dysregulated pathways and cellular processes, focused on RNA splicing, protein synthesis, and mitochondrial dysfunction, suggesting common mechanisms of action in MDS. Many of these dysregulated pathways and cellular processes can be linked to the known disease pathophysiology associated with splicing factor mutations in MDS, whereas several others have not been previously associated with MDS, such as sirtuin signaling. We identified aberrantly spliced events associated with clinical variables, and isoforms that independently predict survival in MDS and implicate dysregulation of focal adhesion and extracellular exosomes as drivers of poor survival. Aberrantly spliced genes and dysregulated pathways were identified in the MDS-affected lineages in splicing factor mutant MDS. Functional studies demonstrated that knockdown of the mitosis regulators SEPT2 and AKAP8, aberrantly spliced target genes of SF3B1 and SRSF2 mutations, respectively, led to impaired erythroid cell growth and differentiation. This study illuminates the effect of the common spliceosome mutations on the MDS phenotype and provides novel insights into disease pathophysiology.
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7
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Relatively frequent switching of transcription start sites during cerebellar development. BMC Genomics 2017; 18:461. [PMID: 28610618 PMCID: PMC5470264 DOI: 10.1186/s12864-017-3834-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 05/31/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alternative transcription start site (TSS) usage plays important roles in transcriptional control of mammalian gene expression. The growing interest in alternative TSSs and their role in genome diversification spawned many single-gene studies on differential usages of tissue-specific or temporal-specific alternative TSSs. However, exploration of the switching usage of alternative TSS usage on a genomic level, especially in the central nervous system, is largely lacking. RESULTS In this study, We have prepared a unique set of time-course data for the developing cerebellum, as part of the FANTOM5 consortium ( http://fantom.gsc.riken.jp/5/ ) that uses their innovative capturing of 5' ends of all transcripts followed by Helicos next generation sequencing. We analyzed the usage of all transcription start sites (TSSs) at each time point during cerebellar development that provided information on multiple RNA isoforms that emerged from the same gene. We developed a mathematical method that systematically compares the expression of different TSSs of a gene to identify temporal crossover and non-crossover switching events. We identified 48,489 novel TSS switching events in 5433 genes during cerebellar development. This includes 9767 crossover TSS switching events in 1511 genes, where the dominant TSS shifts over time. CONCLUSIONS We observed a relatively high prevalence of TSS switching in cerebellar development where the resulting temporally-specific gene transcripts and protein products can play important regulatory and functional roles.
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Schrankel CS, Solek CM, Buckley KM, Anderson MK, Rast JP. A conserved alternative form of the purple sea urchin HEB/E2-2/E2A transcription factor mediates a switch in E-protein regulatory state in differentiating immune cells. Dev Biol 2016; 416:149-161. [PMID: 27265865 DOI: 10.1016/j.ydbio.2016.05.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/26/2016] [Accepted: 05/27/2016] [Indexed: 12/11/2022]
Abstract
E-proteins are basic helix-loop-helix (bHLH) transcription factors with essential roles in animal development. In mammals, these are encoded by three loci: E2-2 (ITF-2/ME2/SEF2/TCF4), E2A (TCF3), and HEB (ME1/REB/TCF12). The HEB and E2-2 paralogs are expressed as alternative (Alt) isoforms with distinct N-terminal sequences encoded by unique exons under separate regulatory control. Expression of these alternative transcripts is restricted relative to the longer (Can) forms, suggesting distinct regulatory roles, although the functions of the Alt proteins remain poorly understood. Here, we characterize the single sea urchin E-protein ortholog (SpE-protein). The organization of the SpE-protein gene closely resembles that of the extended HEB/E2-2 vertebrate loci, including a transcript that initiates at a homologous alternative transcription start site (SpE-Alt). The existence of an Alt form in the sea urchin indicates that this feature predates the emergence of the vertebrates. We present additional evidence indicating that this transcript was present in the common bilaterian ancestor. In contrast to the widely expressed canonical form (SpE-Can), SpE-Alt expression is tightly restricted. SpE-Alt is expressed in two phases: first in aboral non-skeletogenic mesenchyme (NSM) cells and then in oral NSM cells preceding their differentiation and ingression into the blastocoel. Derivatives of these cells mediate immune response in the larval stage. Inhibition of SpE-Alt activity interferes with these events. Notably, although the two isoforms are initially co-expressed, as these cells differentiate, SpE-Can is excluded from the SpE-Alt(+) cell population. This mutually exclusive expression is dependent on SpE-Alt function, which reveals a previously undescribed negative regulatory linkage between the two E-protein forms. Collectively, these findings reorient our understanding of the evolution of this transcription factor family and highlight fundamental properties of E-protein biology.
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Affiliation(s)
- Catherine S Schrankel
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Cynthia M Solek
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Katherine M Buckley
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Michele K Anderson
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Jonathan P Rast
- Biological Sciences, Sunnybrook Research Institute, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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9
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Histones to the cytosol: exportin 7 is essential for normal terminal erythroid nuclear maturation. Blood 2015; 124:1931-40. [PMID: 25092175 DOI: 10.1182/blood-2013-11-537761] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Global nuclear condensation, culminating in enucleation during terminal erythropoiesis, is poorly understood. Proteomic examination of extruded erythroid nuclei from fetal liver revealed a striking depletion of most nuclear proteins, suggesting that nuclear protein export had occurred. Expression of the nuclear export protein, Exportin 7 (Xpo7), is highly erythroid-specific, induced during erythropoiesis, and abundant in very late erythroblasts. Knockdown of Xpo7 in primary mouse fetal liver erythroblasts resulted in severe inhibition of chromatin condensation and enucleation but otherwise had little effect on erythroid differentiation, including hemoglobin accumulation. Nuclei in Xpo7-knockdown cells were larger and less dense than normal and accumulated most nuclear proteins as measured by mass spectrometry. Strikingly,many DNA binding proteins such as histones H2A and H3 were found to have migrated into the cytoplasm of normal late erythroblasts prior to and during enucleation, but not in Xpo7-knockdown cells. Thus, terminal erythroid maturation involves migration of histones into the cytoplasm via a process likely facilitated by Xpo7.
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Dolatshad H, Pellagatti A, Fernandez-Mercado M, Yip BH, Malcovati L, Attwood M, Przychodzen B, Sahgal N, Kanapin AA, Lockstone H, Scifo L, Vandenberghe P, Papaemmanuil E, Smith CWJ, Campbell PJ, Ogawa S, Maciejewski JP, Cazzola M, Savage KI, Boultwood J. Disruption of SF3B1 results in deregulated expression and splicing of key genes and pathways in myelodysplastic syndrome hematopoietic stem and progenitor cells. Leukemia 2015; 29:1092-103. [PMID: 25428262 PMCID: PMC4430703 DOI: 10.1038/leu.2014.331] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 10/30/2014] [Accepted: 11/19/2014] [Indexed: 02/06/2023]
Abstract
The splicing factor SF3B1 is the most commonly mutated gene in the myelodysplastic syndrome (MDS), particularly in patients with refractory anemia with ring sideroblasts (RARS). We investigated the functional effects of SF3B1 disruption in myeloid cell lines: SF3B1 knockdown resulted in growth inhibition, cell cycle arrest and impaired erythroid differentiation and deregulation of many genes and pathways, including cell cycle regulation and RNA processing. MDS is a disorder of the hematopoietic stem cell and we thus studied the transcriptome of CD34(+) cells from MDS patients with SF3B1 mutations using RNA sequencing. Genes significantly differentially expressed at the transcript and/or exon level in SF3B1 mutant compared with wild-type cases include genes that are involved in MDS pathogenesis (ASXL1 and CBL), iron homeostasis and mitochondrial metabolism (ALAS2, ABCB7 and SLC25A37) and RNA splicing/processing (PRPF8 and HNRNPD). Many genes regulated by a DNA damage-induced BRCA1-BCLAF1-SF3B1 protein complex showed differential expression/splicing in SF3B1 mutant cases. This is the first study to determine the target genes of SF3B1 mutation in MDS CD34(+) cells. Our data indicate that SF3B1 has a critical role in MDS by affecting the expression and splicing of genes involved in specific cellular processes/pathways, many of which are relevant to the known RARS pathophysiology, suggesting a causal link.
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Affiliation(s)
- H Dolatshad
- LLR Molecular Haematology Unit, NDCLS, RDM, University of Oxford, Oxford, UK
| | - A Pellagatti
- LLR Molecular Haematology Unit, NDCLS, RDM, University of Oxford, Oxford, UK
| | - M Fernandez-Mercado
- LLR Molecular Haematology Unit, NDCLS, RDM, University of Oxford, Oxford, UK
| | - B H Yip
- LLR Molecular Haematology Unit, NDCLS, RDM, University of Oxford, Oxford, UK
| | - L Malcovati
- Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Molecular Medicine and Medical Therapy, University of Pavia, Pavia, Italy
| | - M Attwood
- LLR Molecular Haematology Unit, NDCLS, RDM, University of Oxford, Oxford, UK
| | - B Przychodzen
- Department of Translational Haematology and Oncology Research, Taussig Cancer Institute, Cleveland, OH, USA
| | - N Sahgal
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - A A Kanapin
- Department of Oncology, University of Oxford, Oxford, UK
| | - H Lockstone
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - L Scifo
- LLR Molecular Haematology Unit, NDCLS, RDM, University of Oxford, Oxford, UK
| | - P Vandenberghe
- Center for Human Genetics, Katholieke Universiteit Leuven/University Hospital Leuven, Leuven, Belgium
| | - E Papaemmanuil
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - C W J Smith
- Department of Biochemistry, Downing Site, University of Cambridge, Cambridge, UK
| | - P J Campbell
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - S Ogawa
- Cancer Genomics Projects, Graduate School of Medicine, Tokyo, Japan
| | - J P Maciejewski
- Department of Translational Haematology and Oncology Research, Taussig Cancer Institute, Cleveland, OH, USA
| | - M Cazzola
- Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Molecular Medicine and Medical Therapy, University of Pavia, Pavia, Italy
| | - K I Savage
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - J Boultwood
- LLR Molecular Haematology Unit, NDCLS, RDM, University of Oxford, Oxford, UK
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11
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Shi L, Lin YH, Sierant MC, Zhu F, Cui S, Guan Y, Sartor MA, Tanabe O, Lim KC, Engel JD. Developmental transcriptome analysis of human erythropoiesis. Hum Mol Genet 2014; 23:4528-42. [PMID: 24781209 DOI: 10.1093/hmg/ddu167] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To globally survey the changes in transcriptional landscape during terminal erythroid differentiation, we performed RNA sequencing (RNA-seq) on primary human CD34(+) cells after ex vivo differentiation from the earliest into the most mature erythroid cell stages. This analysis identified thousands of novel intergenic and intronic transcripts as well as novel alternative transcript isoforms. After rigorous data filtering, 51 (presumptive) novel protein-coding transcripts, 5326 long and 679 small non-coding RNA candidates remained. The analysis also revealed two clear transcriptional trends during terminal erythroid differentiation: first, the complexity of transcript diversity was predominantly achieved by alternative splicing, and second, splicing junctional diversity diminished during erythroid differentiation. Finally, 404 genes that were not known previously to be differentially expressed in erythroid cells were annotated. Analysis of the most extremely differentially expressed transcripts revealed that these gene products were all closely associated with hematopoietic lineage differentiation. Taken together, this study will serve as a comprehensive platform for future in-depth investigation of human erythroid development that, in turn, may reveal new insights into multiple layers of the transcriptional regulatory hierarchy that controls erythropoiesis.
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Affiliation(s)
- Lihong Shi
- Department of Cell and Developmental Biology and
| | - Yu-Hsuan Lin
- Department of Cell and Developmental Biology and Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - M C Sierant
- Department of Cell and Developmental Biology and
| | - Fan Zhu
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Osamu Tanabe
- Department of Cell and Developmental Biology and Department of Integrative Genomics, Tohoku Medical Megabank, Tohoku University, 2-1 Seiryo-machi, Sendai 980-8573, Japan
| | - Kim-Chew Lim
- Department of Cell and Developmental Biology and
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12
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Tzou WS, Chu Y, Lin TY, Hu CH, Pai TW, Liu HF, Lin HJ, Cases I, Rojas A, Sanchez M, You ZY, Hsu MW. Molecular evolution of multiple-level control of heme biosynthesis pathway in animal kingdom. PLoS One 2014; 9:e86718. [PMID: 24489775 PMCID: PMC3904948 DOI: 10.1371/journal.pone.0086718] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 12/12/2013] [Indexed: 01/23/2023] Open
Abstract
Adaptation of enzymes in a metabolic pathway can occur not only through changes in amino acid sequences but also through variations in transcriptional activation, mRNA splicing and mRNA translation. The heme biosynthesis pathway, a linear pathway comprised of eight consecutive enzymes in animals, provides researchers with ample information for multiple types of evolutionary analyses performed with respect to the position of each enzyme in the pathway. Through bioinformatics analysis, we found that the protein-coding sequences of all enzymes in this pathway are under strong purifying selection, from cnidarians to mammals. However, loose evolutionary constraints are observed for enzymes in which self-catalysis occurs. Through comparative genomics, we found that in animals, the first intron of the enzyme-encoding genes has been co-opted for transcriptional activation of the genes in this pathway. Organisms sense the cellular content of iron, and through iron-responsive elements in the 5′ untranslated regions of mRNAs and the intron-exon boundary regions of pathway genes, translational inhibition and exon choice in enzymes may be enabled, respectively. Pathway product (heme)-mediated negative feedback control can affect the transport of pathway enzymes into the mitochondria as well as the ubiquitin-mediated stability of enzymes. Remarkably, the positions of these controls on pathway activity are not ubiquitous but are biased towards the enzymes in the upstream portion of the pathway. We revealed that multiple-level controls on the activity of the heme biosynthesis pathway depend on the linear depth of the enzymes in the pathway, indicating a new strategy for discovering the molecular constraints that shape the evolution of a metabolic pathway.
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Affiliation(s)
- Wen-Shyong Tzou
- Department of Life Sciences, National Taiwan Ocean University, Keelung, Taiwan
- * E-mail:
| | - Ying Chu
- Department of Life Sciences, National Taiwan Ocean University, Keelung, Taiwan
| | - Tzung-Yi Lin
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Chin-Hwa Hu
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Tun-Wen Pai
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan
| | - Hsin-Fu Liu
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan
| | - Han-Jia Lin
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Ildeofonso Cases
- Computational Cell Biology Group, Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Barcelona, Spain
| | - Ana Rojas
- Computational Cell Biology Group, Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Barcelona, Spain
| | - Mayka Sanchez
- Cancer and Iron Group, Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Barcelona, Spain
| | - Zong-Ye You
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Ming-Wei Hsu
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
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13
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Grech G, Pollacco J, Portelli M, Sacco K, Baldacchino S, Grixti J, Saliba C. Expression of different functional isoforms in haematopoiesis. Int J Hematol 2013; 99:4-11. [PMID: 24293279 DOI: 10.1007/s12185-013-1477-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 11/18/2013] [Accepted: 11/18/2013] [Indexed: 12/26/2022]
Abstract
Haematopoiesis is a complex process regulated at various levels facilitating rapid responses to external factors including stress, modulation of lineage commitment and terminal differentiation of progenitors. Although the transcription program determines the RNA pool of a cell, various mRNA strands can be obtained from the same template, giving rise to multiple protein isoforms. The majority of variants and isoforms co-occur in normal haematopoietic cells or are differentially expressed at various maturity stages of progenitor maturation and cellular differentiation within the same lineage or across lineages. Genetic aberrations or specific cellular states result in the predominant expression of abnormal isoforms leading to deregulation and disease. The presence of upstream open reading frames (uORF) in 5' untranslated regions (UTRs) of a transcript, couples the utilization of start codons with the cellular status and availability of translation initiation factors (eIFs). In addition, tissue-specific and cell lineage-specific alternative promoter use, regulates several transcription factors producing transcript variants with variable 5' exons. In this review, we propose to give a detailed account of the differential isoform formation, causing haematological malignancies.
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Affiliation(s)
- Godfrey Grech
- Department of Pathology, Medical School, University of Malta, Msida, MSD2090, Malta,
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14
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Abstract
The human ankyrin-1 gene (ANK1) contains 3 tissue-specific alternative promoters. We have shown previously that the erythroid-specific ankyrin 1 (ANK1E) core promoter contains a 5' DNase I hypersensitive site (HS) with barrier insulator function that prevents gene silencing in vitro and in vivo. Mutations in the ANK1E barrier region lead to decreased ANK1 mRNA levels and hereditary spherocytosis. In this report, we demonstrate a second ANK1E regulatory element located in an adjacent pair of DNase I HS located 5.6 kb 3' of the ANK1E promoter at the 3' boundary of an erythroid-specific DNase I-sensitive chromatin domain. The 3' regulatory element exhibits enhancer activity in vitro and in transgenic mice, and it has the histone modifications associated with an enhancer element. One of the ANK1E 3'HS contains an NF-E2 binding site that is required for enhancer function. We show that a chromatin loop brings the 3' enhancer and NF-E2 into proximity with the 5' barrier region including the ANK1E core promoter. These observations demonstrate a model for the tissue-specific activation of alternative promoters that may be applicable to the ∼ 30% of mammalian genes with alternative promoters that exhibit distinct expression patterns.
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15
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Ho MR, Tsai KW, Lin WC. A unified framework of overlapping genes: towards the origination and endogenic regulation. Genomics 2012; 100:231-9. [PMID: 22766524 DOI: 10.1016/j.ygeno.2012.06.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 06/21/2012] [Accepted: 06/25/2012] [Indexed: 11/27/2022]
Abstract
Overlapping genes are pairs of adjacent genes whose genomic regions partially overlap. They are notable by their potential intricate regulation, such as cis-regulation of nested gene-promoter configurations, and post-transcriptional regulation of natural antisense transcripts. The originations and consequent detailed regulation remain obscure. Herein, we propose a unified framework comprising biological classification rules followed by extensive analyses, namely, exon-sharing analysis, a human-mouse conservation study, and transcriptome analysis of hundreds of microarrays and transcriptome sequencing data (mRNA-Seq). We demonstrate that the tail-to-tail architecture would result from sharing functional elements in 3'-untranslated regions (3'-UTRs) of pre-existing genes. Dissimilarly, we illustrate that the other gene overlaps would originate from a new gene arising in a pre-existing gene locus. Interestingly, these types of coupled overlapping genes may influence each other synergistically or competitively during transcription, depending on the promoter configurations. This framework discloses distinctive characteristics of overlapping genes to be a foundation for a further comprehensive understanding of them.
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Affiliation(s)
- Meng-Ru Ho
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan
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16
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Identification of a novel A4GALT exon reveals the genetic basis of the P1/P2 histo-blood groups. Blood 2011; 117:678-87. [DOI: 10.1182/blood-2010-08-301333] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
The A4GALT locus encodes a glycosyltransferase that synthesizes the terminal Galα1-4Gal of the Pk (Gb3/CD77) glycosphingolipid, important in transfusion medicine, obstetrics, and pathogen susceptibility. Critical nucleotide changes in A4GALT not only abolish Pk formation but also another Galα1-4Gal–defined antigen, P1, which belongs to the only blood group system for which the responsible locus remains undefined. Since known A4GALT polymorphisms do not explain the P1−Pk+ phenotype, P2, we set out to elucidate the genetic basis of P1/P2. Despite marked differences (P1 > P2) in A4GALT transcript levels in blood, luciferase experiments showed no difference between P1/P2-related promoter sequences. Investigation of A4GALT mRNA in cultured human bone marrow cells revealed novel transcripts containing only the noncoding exon 1 and a sequence (here termed exon 2a) from intron 1. These 5′-capped transcripts include poly-A tails and 3 polymorphic sites, one of which was P1/P2-specific among > 200 donors and opens a short reading frame in P2 alleles. We exploited these data to devise the first genotyping assays to predict P1 status. P1/P2 genotypes correlated with both transcript levels and P1/Pk expression on red cells. Thus, P1 zygosity partially explains the well-known interindividual variation in P1 strength. Future investigations need to focus on regulatory mechanisms underlying P1 synthesis.
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17
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Ferroportin and erythroid cells: an update. Adv Hematol 2010; 2010. [PMID: 20827391 PMCID: PMC2935194 DOI: 10.1155/2010/404173] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2009] [Revised: 04/08/2010] [Accepted: 06/23/2010] [Indexed: 12/21/2022] Open
Abstract
In recent years there have been major advances in our knowledge of the regulation of iron metabolism that have had implications for understanding the pathophysiology of some human disorders like beta-thalassemia and other iron overload diseases. However, little is known about the relationship among ineffective erythropoiesis, the role of iron-regulatory genes, and tissue iron distribution in beta-thalassemia. The principal aim of this paper is an update about the role of Ferroportin during human normal and pathological erythroid differentiation. Particular attention will be given to beta-thalassemia and other diseases with iron overload. Recent discoveries indicate that there is a potential for therapeutic intervention in beta-thalassemia by means of manipulating iron metabolism.
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18
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Coupled transcription-splicing regulation of mutually exclusive splicing events at the 5' exons of protein 4.1R gene. Blood 2009; 114:4233-42. [PMID: 19729518 DOI: 10.1182/blood-2009-02-206219] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The tightly regulated production of distinct erythrocyte protein 4.1R isoforms involves differential splicing of 3 mutually exclusive first exons (1A, 1B, 1C) to the alternative 3' splice sites (ss) of exon 2'/2. Here, we demonstrate that exon 1 and 2'/2 splicing diversity is regulated by a transcription-coupled splicing mechanism. We also implicate distinctive regulatory elements that promote the splicing of exon 1A to the distal 3' ss and exon 1B to the proximal 3' ss in murine erythroleukemia cells. A hybrid minigene driven by cytomegalovirus promoter mimicked 1B-promoter-driven splicing patterns but differed from 1A-promoter-driven splicing patterns, suggesting that promoter identity affects exon 2'/2 splicing. Furthermore, splicing factor SF2/ASF ultraviolet (UV) cross-linked to the exon 2'/2 junction CAGAGAA, a sequence that overlaps the distal U2AF(35)-binding 3' ss. Consequently, depletion of SF2/ASF allowed exon 1B to splice to the distal 3' ss but had no effect on exon 1A splicing. These findings identify for the first time that an SF2/ASF binding site also can serve as a 3' ss in a transcript-dependent manner. Taken together, our results suggest that 4.1R gene expression involves transcriptional regulation coupled with a complex splicing regulatory network.
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19
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Abstract
Erythropoietic and megakaryocytic programs are directed by the transcription factor GATA1. Friend of GATA1 (FOG1), a protein interaction partner of GATA1, is critical for GATA1 function in multiple contexts. Previous work has shown that FOG1 recruits two multi-protein complexes, the nucleosome remodeling domain (NuRD) complex and a C-terminal binding protein (CTBP)-containing complex, into association with GATA1 to mediate activation and repression of target genes. To elucidate mechanisms that might differentially regulate the association of FOG1, as well as GATA1, with these two complexes, we characterized a previously unrecognized translational isoform of FOG1. We found that an N-terminally truncated version of FOG1 is produced from an internal ATG and that this isoform, designated FOG1S, lacks the nucleosome remodeling domain-binding domain, altering the complexes with which it interacts. Both isoforms interact with the C-terminal binding protein complex, which we show also contains lysine-specific demethylase 1 (LSD1). FOG1S is preferentially excluded from the nucleus by unknown mechanisms. These data reveal two novel mechanisms for the regulation of GATA1 interaction with FOG1-dependent protein complexes through the production of two translational isoforms with differential interaction profiles and independent nuclear localization controls.
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Affiliation(s)
- Jonathan W Snow
- Division of Hematology/Oncology, Children's Hospital, Boston, Massachusetts 02115, USA
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20
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Pinós T, Barbosa-Desongles A, Hurtado A, Santamaria-Martínez A, de Torres I, Morote J, Reventós J, Munell F. Identification, characterization and expression of novel Sex Hormone Binding Globulin alternative first exons in the human prostate. BMC Mol Biol 2009; 10:59. [PMID: 19534810 PMCID: PMC2706245 DOI: 10.1186/1471-2199-10-59] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Accepted: 06/17/2009] [Indexed: 11/21/2022] Open
Abstract
Background The human Sex Hormone Binding Globulin (SHBG) gene, located at 17p13.1, comprises, at least, two different transcription units regulated by two different promoters. The first transcription unit begins with the exon 1 sequence and is responsible for the production of plasma SHBG by the hepatocytes, while the second begins with an alternative exon 1 sequence, which replaces the exon 1 present in liver transcripts. Alternative exon 1 transcription and translation has only been demonstrated in the testis of transgenic mice containing an 11-kb human SHBG transgene and in the human testis. Our goal has been to further characterize the 5' end of the SHBG gene and analyze the presence of the SHBG alternative transcripts in human prostate tissue and derived cell lines. Results Using a combination of in silico and in vitro studies, we have demonstrated that the SHBG gene, along with exon 1 and alternative exon 1 (renamed here exon 1A), contains four additional alternative first exons: the novel exons 1B, 1C, and 1E, and a previously identified exon 1N, which has been further characterized and renamed as exon 1D. We have shown that these four alternative first exons are all spliced to the same 3' splice site of SHBG exon 2, and that exon 1A and the novel exon 1B can be spliced to exon 1. We have also demonstrated the presence of SHBG transcripts beginning with exons 1B, 1C and 1D in prostate tissues and cell lines, as well as in several non-prostatic cell lines. Finally, the alignment of the SHBG mammalian sequences revealed that, while exons 1C, 1D and 1E are very well conserved phylogenetically through non-primate mammal species, exon 1B probably aroused in apes due to a single nucleotide change that generated a new 5' splice site in exon 1B. Conclusion The identification of multiple transcription start sites (TSS) upstream of the annotated first exon of human SHBG, and the detection of the alternative transcripts in human prostate, concur with the prediction of the ENCODE (ENCyclopedia of DNA Elements) project, and suggest that the regulation of SHBG is much more complex than previously reported.
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Affiliation(s)
- Tomàs Pinós
- Institut de Recerca Hospital Universitari Vall d'Hebrón, Barcelona, Spain.
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21
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Al-Fageeh MB, Smales CM. Cold-inducible RNA binding protein (CIRP) expression is modulated by alternative mRNAs. RNA (NEW YORK, N.Y.) 2009; 15:1164-1176. [PMID: 19398494 PMCID: PMC2685524 DOI: 10.1261/rna.1179109] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2008] [Accepted: 03/11/2009] [Indexed: 05/27/2023]
Abstract
Cold-inducible RNA binding protein (CIRP) is a mammalian protein whose expression is up-regulated in response to mild hypothermia. Although the exact function of this protein is currently unknown, it is thought to function as an RNA chaperone, facilitating mRNA translation upon the perception of cold stress. In this study we have identified and characterized the major CIRP 5'-untranslated region (5'-UTR) transcripts in mouse embryonic fibroblast NIH-3T3 cells. We show that the 5'-UTR of CIRP, a protein highly homologous to the cold-shock protein Rbm3, is much shorter than the previously published 5' leader sequence of Rbm3. In addition, three major CIRP transcripts with different transcription start sites are generated, with the levels of each of these transcripts being regulated in response to time and temperature. The major transcript generated at 37 degrees C does not encode for the full-length CIRP open reading frame, while the two major transcripts at 32 degrees C do. Further, the longest transcript detected at 32 degrees C shows a discrete expression and stability profile under mild hypothermic conditions and exhibits internal ribosome entry segment (IRES)-like activity. The IRES-like activity is not responsive to conditions of mild hypothermia or hypoxia, but the levels and stability of the transcript harboring the putative IRES are increased at 32 degrees C. We discuss the emerging transcriptional and translational mechanisms by which CIRP expression appears to be controlled and the role that the 5'-UTR plays in the modulation of CIRP expression.
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Affiliation(s)
- Mohamed B Al-Fageeh
- Protein Science Group, Department of Biosciences, University of Kent, Canterbury, Kent CT27NJ, United Kingdom
- National Centre for Biotechnology, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - C Mark Smales
- Protein Science Group, Department of Biosciences, University of Kent, Canterbury, Kent CT27NJ, United Kingdom
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22
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Yamamoto ML, Clark TA, Gee SL, Kang JA, Schweitzer AC, Wickrema A, Conboy JG. Alternative pre-mRNA splicing switches modulate gene expression in late erythropoiesis. Blood 2009; 113:3363-70. [PMID: 19196664 PMCID: PMC2665901 DOI: 10.1182/blood-2008-05-160325] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Accepted: 12/02/2008] [Indexed: 12/19/2022] Open
Abstract
Differentiating erythroid cells execute a unique gene expression program that insures synthesis of the appropriate proteome at each stage of maturation. Standard expression microarrays provide important insight into erythroid gene expression but cannot detect qualitative changes in transcript structure, mediated by RNA processing, that alter structure and function of encoded proteins. We analyzed stage-specific changes in the late erythroid transcriptome via use of high-resolution microarrays that detect altered expression of individual exons. Ten differentiation-associated changes in erythroblast splicing patterns were identified, including the previously known activation of protein 4.1R exon 16 splicing. Six new alternative splicing switches involving enhanced inclusion of internal cassette exons were discovered, as well as 3 changes in use of alternative first exons. All of these erythroid stage-specific splicing events represent activated inclusion of authentic annotated exons, suggesting they represent an active regulatory process rather than a general loss of splicing fidelity. The observation that 3 of the regulated transcripts encode RNA binding proteins (SNRP70, HNRPLL, MBNL2) may indicate significant changes in the RNA processing machinery of late erythroblasts. Together, these results support the existence of a regulated alternative pre-mRNA splicing program that is critical for late erythroid differentiation.
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Affiliation(s)
- Miki L Yamamoto
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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23
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Davuluri RV, Suzuki Y, Sugano S, Plass C, Huang THM. The functional consequences of alternative promoter use in mammalian genomes. Trends Genet 2008; 24:167-77. [PMID: 18329129 DOI: 10.1016/j.tig.2008.01.008] [Citation(s) in RCA: 238] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2007] [Revised: 01/17/2008] [Accepted: 01/18/2008] [Indexed: 12/19/2022]
Abstract
We are beginning to appreciate the increasing complexity of mammalian gene structure. A phenomenon that adds an important dimension to this complexity is the use of alternative gene promoters that drive widespread cell type, tissue type or developmental gene regulation. Recent annotations of the human genome suggest that almost one half of the protein-coding genes contain alternative promoters, including those of many disease-associated genes. Aberrant use of one promoter over another has been found to be associated with various diseases, including cancer. Here we discuss the functional consequences of use and misuse of alternative promoters in normal and disease genomes and review the molecular mechanisms regulating alternative promoter use in mammalian genomes.
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Affiliation(s)
- Ramana V Davuluri
- Human Cancer Genetics Program, Comprehensive Cancer Center, Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH 43210, USA.
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24
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Intrasplicing coordinates alternative first exons with alternative splicing in the protein 4.1R gene. EMBO J 2007; 27:122-31. [PMID: 18079699 DOI: 10.1038/sj.emboj.7601957] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2007] [Accepted: 11/19/2007] [Indexed: 11/08/2022] Open
Abstract
In the protein 4.1R gene, alternative first exons splice differentially to alternative 3' splice sites far downstream in exon 2'/2 (E2'/2). We describe a novel intrasplicing mechanism by which exon 1A (E1A) splices exclusively to the distal E2'/2 acceptor via two nested splicing reactions regulated by novel properties of exon 1B (E1B). E1B behaves as an exon in the first step, using its consensus 5' donor to splice to the proximal E2'/2 acceptor. A long region of downstream intron is excised, juxtaposing E1B with E2'/2 to generate a new composite acceptor containing the E1B branchpoint/pyrimidine tract and E2 distal 3' AG-dinucleotide. Next, the upstream E1A splices over E1B to this distal acceptor, excising the remaining intron plus E1B and E2' to form mature E1A/E2 product. We mapped branchpoints for both intrasplicing reactions and demonstrated that mutation of the E1B 5' splice site or branchpoint abrogates intrasplicing. In the 4.1R gene, intrasplicing ultimately determines N-terminal protein structure and function. More generally, intrasplicing represents a new mechanism by which alternative promoters can be coordinated with downstream alternative splicing.
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25
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Thuresson B, Chester MA, Storry JR, Olsson ML. ABO transcript levels in peripheral blood and erythropoietic culture show different allele-related patterns independent of the CBF/NF-Y enhancer motif and multiple novel allele-specific variations in the 5'- and 3'-noncoding regions. Transfusion 2007; 48:493-504. [PMID: 18067502 DOI: 10.1111/j.1537-2995.2007.01554.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Mechanisms regulating the ABO gene are unclear, especially in the hematopoietic compartment. The number of 43-bp repeats in the CBF/NF-Y-binding enhancer region is considered to have a major influence on transcription. STUDY DESIGN AND METHODS Transcript levels in peripheral blood and in erythropoietic culture of CD34+ cells from marrow donors were measured with TaqMan assays. The 5'-regulatory region and 3'-downstream sequences were investigated to determine if allelic variations occur. RESULTS Surprisingly, transcripts from A(1) and A(2) alleles could not be detected in peripheral blood, although transcripts from B/O(1)/O(1v)/O(2) alleles were readily observed. Sequencing of approximately 4 kb upstream and 1.8 kb downstream of the coding region showed multiple novel allele-specific and allele-related motifs. No correlation between these sequence variations and transcript levels was found, however. Contradictory to the results with peripheral blood, in erythropoietic culture of CD34+ cells from healthy marrow donors transcripts from A(1) and A(2) alleles were found at higher levels than transcripts from B/O(1)/O(1v) alleles. CONCLUSION These data do not support previous suggestions that nonsense-mutated O(1)/O(1v) transcripts are eliminated first. Furthermore, our results contradict the notion that the number of repeats in the upstream CBF/NF-Y-binding enhancer region, which contains four 43-bp repeats in A(2)/B/O(1)/O(1v) but only one 43-bp unit in A(1)/O(2) alleles, determines the transcription rate. The reason for the remarkable discrepancy between blood and marrow remains to be elucidated.
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Affiliation(s)
- Britt Thuresson
- Department of Laboratory Medicine, Lund University & Blood Center, Lund University Hospital, Lund, Sweden
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26
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Funnell APW, Maloney CA, Thompson LJ, Keys J, Tallack M, Perkins AC, Crossley M. Erythroid Krüppel-like factor directly activates the basic Krüppel-like factor gene in erythroid cells. Mol Cell Biol 2007; 27:2777-90. [PMID: 17283065 PMCID: PMC1899893 DOI: 10.1128/mcb.01658-06] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The Sp/Krüppel-like factor (Sp/Klf) family is comprised of around 25 zinc finger transcription factors that recognize CACCC boxes and GC-rich elements. We have investigated basic Krüppel-like factor (Bklf/Klf3) and show that in erythroid tissues its expression is highly dependent on another family member, erythroid Krüppel-like factor (Eklf/Klf1). We observe that Bklf mRNA is significantly reduced in erythroid tissues from Eklf-null murine embryos. We find that Bklf is driven primarily by two promoters, a ubiquitously active GC-rich upstream promoter, 1a, and an erythroid downstream promoter, 1b. Transcripts from the two promoters encode identical proteins. Interestingly, both the ubiquitous and the erythroid promoter are dependent on Eklf in erythroid cells. Eklf also activates both promoters in transient assays. Experiments utilizing an inducible form of Eklf demonstrate activation of the endogenous Bklf gene in the presence of an inhibitor of protein synthesis. The kinetics of activation are also consistent with Bklf being a direct Eklf target. Chromatin immunoprecipitation assays confirm that Eklf associates with both Bklf promoters. Eklf is typically an activator of transcription, whereas Bklf is noted as a repressor. Our results support the hypothesis that feedback cross-regulation occurs within the Sp/Klf family in vivo.
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Affiliation(s)
- Alister P W Funnell
- School of Molecular and Microbial Biosciences, G08, University of Sydney, Sydney, NSW 2006, Australia
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27
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Bickel KS, Morris DR. Silencing the transcriptome's dark matter: mechanisms for suppressing translation of intergenic transcripts. Mol Cell 2006; 22:309-16. [PMID: 16678103 DOI: 10.1016/j.molcel.2006.04.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Large portions of the genomes of higher eukaryotes are transcribed into RNA molecules that are never destined for translation into proteins. Although some of these transcripts have clearly defined biological roles other than protein coding, most arise from genomic regions devoid of functional genes and many are antisense to regions containing annotated genes. A variety of mechanisms exist to prevent adventitious production of proteins from these transcripts, ranging from degradation within the nucleus to translational silencing in the cytosol.
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Affiliation(s)
- Kellie S Bickel
- Department of Biochemistry, University of Washington, Box 357350, Seattle, 98133, USA
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