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Recinos Y, Bao S, Wang X, Phillips BL, Yeh YT, Weyn-Vanhentenryck SM, Swanson MS, Zhang C. Lineage-specific splicing regulation of MAPT gene in the primate brain. CELL GENOMICS 2024; 4:100563. [PMID: 38772368 PMCID: PMC11228892 DOI: 10.1016/j.xgen.2024.100563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 01/22/2024] [Accepted: 04/23/2024] [Indexed: 05/23/2024]
Abstract
Divergence of precursor messenger RNA (pre-mRNA) alternative splicing (AS) is widespread in mammals, including primates, but the underlying mechanisms and functional impact are poorly understood. Here, we modeled cassette exon inclusion in primate brains as a quantitative trait and identified 1,170 (∼3%) exons with lineage-specific splicing shifts under stabilizing selection. Among them, microtubule-associated protein tau (MAPT) exons 2 and 10 underwent anticorrelated, two-step evolutionary shifts in the catarrhine and hominoid lineages, leading to their present inclusion levels in humans. The developmental-stage-specific divergence of exon 10 splicing, whose dysregulation can cause frontotemporal lobar degeneration (FTLD), is mediated by divergent distal intronic MBNL-binding sites. Competitive binding of these sites by CRISPR-dCas13d/gRNAs effectively reduces exon 10 inclusion, potentially providing a therapeutically compatible approach to modulate tau isoform expression. Our data suggest adaptation of MAPT function and, more generally, a role for AS in the evolutionary expansion of the primate brain.
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Affiliation(s)
- Yocelyn Recinos
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Suying Bao
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Xiaojian Wang
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Brittany L Phillips
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Yow-Tyng Yeh
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Sebastien M Weyn-Vanhentenryck
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Maurice S Swanson
- Department of Molecular Genetics and Microbiology, University of Florida, College of Medicine, Gainesville, FL 32610, USA; Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL 32610, USA
| | - Chaolin Zhang
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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2
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Bénitière F, Duret L, Necsulea A. GTDrift: a resource for exploring the interplay between genetic drift, genomic and transcriptomic characteristics in eukaryotes. NAR Genom Bioinform 2024; 6:lqae064. [PMID: 38867915 PMCID: PMC11167491 DOI: 10.1093/nargab/lqae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/22/2024] [Accepted: 05/27/2024] [Indexed: 06/14/2024] Open
Abstract
We present GTDrift, a comprehensive data resource that enables explorations of genomic and transcriptomic characteristics alongside proxies of the intensity of genetic drift in individual species. This resource encompasses data for 1506 eukaryotic species, including 1413 animals and 93 green plants, and is organized in three components. The first two components contain approximations of the effective population size, which serve as indicators of the extent of random genetic drift within each species. In the first component, we meticulously investigated public databases to assemble data on life history traits such as longevity, adult body length and body mass for a set of 979 species. The second component includes estimations of the ratio between the rate of non-synonymous substitutions and the rate of synonymous substitutions (dN/dS) in protein-coding sequences for 1324 species. This ratio provides an estimate of the efficiency of natural selection in purging deleterious substitutions. Additionally, we present polymorphism-derived N e estimates for 66 species. The third component encompasses various genomic and transcriptomic characteristics. With this component, we aim to facilitate comparative transcriptomics analyses across species, by providing easy-to-use processed data for more than 16 000 RNA-seq samples across 491 species. These data include intron-centered alternative splicing frequencies, gene expression levels and sequencing depth statistics for each species, obtained with a homogeneous analysis protocol. To enable cross-species comparisons, we provide orthology predictions for conserved single-copy genes based on BUSCO gene sets. To illustrate the possible uses of this database, we identify the most frequently used introns for each gene and we assess how the sequencing depth available for each species affects our power to identify major and minor splice variants.
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Affiliation(s)
- Florian Bénitière
- Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, UMR CNRS 5558, Villeurbanne, France
- Laboratoire d’Écologie des Hydrosystèmes Naturels et Anthropisés, Université Lyon 1, UMR CNRS 5023, Villeurbanne, France
| | - Laurent Duret
- Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, UMR CNRS 5558, Villeurbanne, France
| | - Anamaria Necsulea
- Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, UMR CNRS 5558, Villeurbanne, France
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3
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Long T, Mohapatra P, Ballou S, Menuz K. Odorant receptor co-receptors affect expression of tuning receptors in Drosophila. Front Cell Neurosci 2024; 18:1390557. [PMID: 38832356 PMCID: PMC11145718 DOI: 10.3389/fncel.2024.1390557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/01/2024] [Indexed: 06/05/2024] Open
Abstract
Insects detect odorants using two large families of heteromeric receptors, the Odorant Receptors (ORs) and Ionotropic Receptors (IRs). Most OR and IR genes encode odorant-binding "tuning" subunits, whereas four (Orco, Ir8a, Ir25a, and Ir76b) encode co-receptor subunits required for receptor function. Olfactory neurons are thought to degenerate in the absence of Orco in ants and bees, and limited data suggest this may happen to some olfactory neurons in Drosophila fruit flies as well. Here, we thoroughly examined the role of co-receptors on olfactory neuron survival in Drosophila. Leveraging knowledge that olfactory neuron classes are defined by the expression of different tuning receptors, we used tuning receptor expression in antennal transcriptomes as a proxy for the survival of distinct olfactory neuron classes. Consistent with olfactory neuron degeneration, expression of many OR-family tuning receptors is decreased in Orco mutants relative to controls, and transcript loss is progressive with age. The effects of Orco are highly receptor-dependent, with expression of some receptor transcripts nearly eliminated and others unaffected. Surprisingly, further studies revealed that olfactory neuron classes with reduced tuning receptor expression generally survive in Orco mutant flies. Furthermore, there is little apoptosis or neuronal loss in the antenna of these flies. We went on to investigate the effects of IR family co-receptor mutants using similar approaches and found that expression of IR tuning receptors is decreased in the absence of Ir8a and Ir25a, but not Ir76b. As in Orco mutants, Ir8a-dependent olfactory neurons mostly endure despite near-absent expression of associated tuning receptors. Finally, we used differential expression analysis to identify other antennal genes whose expression is changed in IR and OR co-receptor mutants. Taken together, our data indicate that odorant co-receptors are necessary for maintaining expression of many tuning receptors at the mRNA level. Further, most Drosophila olfactory neurons persist in OR and IR co-receptor mutants, suggesting that the impact of co-receptors on neuronal survival may vary across insect species.
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Affiliation(s)
- Teng Long
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, United States
| | - Pratyajit Mohapatra
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, United States
| | - Sydney Ballou
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, United States
| | - Karen Menuz
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT, United States
- Connecticut Institute for the Brain and Cognitive Sciences, University of Connecticut, Storrs, CT, United States
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, United States
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4
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Dogga SK, Rop JC, Cudini J, Farr E, Dara A, Ouologuem D, Djimdé AA, Talman AM, Lawniczak MKN. A single cell atlas of sexual development in Plasmodium falciparum. Science 2024; 384:eadj4088. [PMID: 38696552 DOI: 10.1126/science.adj4088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 03/14/2024] [Indexed: 05/04/2024]
Abstract
The developmental decision made by malaria parasites to become sexual underlies all malaria transmission. Here, we describe a rich atlas of short- and long-read single-cell transcriptomes of over 37,000 Plasmodium falciparum cells across intraerythrocytic asexual and sexual development. We used the atlas to explore transcriptional modules and exon usage along sexual development and expanded it to include malaria parasites collected from four Malian individuals naturally infected with multiple P. falciparum strains. We investigated genotypic and transcriptional heterogeneity within and among these wild strains at the single-cell level, finding differential expression between different strains even within the same host. These data are a key addition to the Malaria Cell Atlas interactive data resource, enabling a deeper understanding of the biology and diversity of transmission stages.
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Affiliation(s)
| | - Jesse C Rop
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | | | - Elias Farr
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Institute for Computational Biomedicine, University of Heidelberg, Im Neuenheimer Feld 130.3, 69120 Heidelberg, Germany
| | - Antoine Dara
- Malaria Research and Training Center (MRTC), Faculty of Pharmacy, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Point G, P.O. Box, 1805 Bamako, Mali
| | - Dinkorma Ouologuem
- Malaria Research and Training Center (MRTC), Faculty of Pharmacy, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Point G, P.O. Box, 1805 Bamako, Mali
| | - Abdoulaye A Djimdé
- Malaria Research and Training Center (MRTC), Faculty of Pharmacy, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Point G, P.O. Box, 1805 Bamako, Mali
| | - Arthur M Talman
- MIVEGEC, University of Montpellier, IRD, CNRS, Montpellier, France
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5
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Xi J, Snieckute G, Martínez JF, Arendrup FSW, Asthana A, Gaughan C, Lund AH, Bekker-Jensen S, Silverman RH. Initiation of a ZAKα-dependent ribotoxic stress response by the innate immunity endoribonuclease RNase L. Cell Rep 2024; 43:113998. [PMID: 38551960 PMCID: PMC11090160 DOI: 10.1016/j.celrep.2024.113998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/13/2024] [Accepted: 03/08/2024] [Indexed: 04/09/2024] Open
Abstract
RNase L is an endoribonuclease of higher vertebrates that functions in antiviral innate immunity. Interferons induce oligoadenylate synthetase enzymes that sense double-stranded RNA of viral origin leading to the synthesis of 2',5'-oligoadenylate (2-5A) activators of RNase L. However, it is unknown precisely how RNase L remodels the host cell transcriptome. To isolate effects of RNase L from other effects of double-stranded RNA or virus, 2-5A is directly introduced into cells. Here, we report that RNase L activation by 2-5A causes a ribotoxic stress response involving the MAP kinase kinase kinase (MAP3K) ZAKα, MAP2Ks, and the stress-activated protein kinases JNK and p38α. RNase L activation profoundly alters the transcriptome by widespread depletion of mRNAs associated with different cellular functions but also by JNK/p38α-stimulated induction of inflammatory genes. These results show that the 2-5A/RNase L system triggers a protein kinase cascade leading to proinflammatory signaling and apoptosis.
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Affiliation(s)
- Jiajia Xi
- Department Cancer Biology, Cleveland Clinic Foundation, Lerner Research Institute, Cleveland, OH 44195, USA.
| | - Goda Snieckute
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark; Center for Gene Expression, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - José Francisco Martínez
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark; Center for Gene Expression, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | | | - Abhishek Asthana
- Department Cancer Biology, Cleveland Clinic Foundation, Lerner Research Institute, Cleveland, OH 44195, USA
| | - Christina Gaughan
- Department Cancer Biology, Cleveland Clinic Foundation, Lerner Research Institute, Cleveland, OH 44195, USA
| | - Anders H Lund
- Biotech Research and Innovation Center, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Simon Bekker-Jensen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark; Center for Gene Expression, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
| | - Robert H Silverman
- Department Cancer Biology, Cleveland Clinic Foundation, Lerner Research Institute, Cleveland, OH 44195, USA.
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6
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Bénitière F, Necsulea A, Duret L. Random genetic drift sets an upper limit on mRNA splicing accuracy in metazoans. eLife 2024; 13:RP93629. [PMID: 38470242 DOI: 10.7554/elife.93629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024] Open
Abstract
Most eukaryotic genes undergo alternative splicing (AS), but the overall functional significance of this process remains a controversial issue. It has been noticed that the complexity of organisms (assayed by the number of distinct cell types) correlates positively with their genome-wide AS rate. This has been interpreted as evidence that AS plays an important role in adaptive evolution by increasing the functional repertoires of genomes. However, this observation also fits with a totally opposite interpretation: given that 'complex' organisms tend to have small effective population sizes (Ne), they are expected to be more affected by genetic drift, and hence more prone to accumulate deleterious mutations that decrease splicing accuracy. Thus, according to this 'drift barrier' theory, the elevated AS rate in complex organisms might simply result from a higher splicing error rate. To test this hypothesis, we analyzed 3496 transcriptome sequencing samples to quantify AS in 53 metazoan species spanning a wide range of Ne values. Our results show a negative correlation between Ne proxies and the genome-wide AS rates among species, consistent with the drift barrier hypothesis. This pattern is dominated by low abundance isoforms, which represent the vast majority of the splice variant repertoire. We show that these low abundance isoforms are depleted in functional AS events, and most likely correspond to errors. Conversely, the AS rate of abundant isoforms, which are relatively enriched in functional AS events, tends to be lower in more complex species. All these observations are consistent with the hypothesis that variation in AS rates across metazoans reflects the limits set by drift on the capacity of selection to prevent gene expression errors.
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Affiliation(s)
- Florian Bénitière
- Laboratoire de Biometrie et Biologie Evolutive, CNRS, Universite Lyon 1, Villeurbanne, France
| | - Anamaria Necsulea
- Laboratoire de Biometrie et Biologie Evolutive, CNRS, Universite Lyon 1, Villeurbanne, France
| | - Laurent Duret
- Laboratoire de Biometrie et Biologie Evolutive, CNRS, Universite Lyon 1, Villeurbanne, France
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7
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Greenberg ZF, Ali S, Schmittgen TD, Han S, Hughes SJ, Graim KS, He M. Peptide-based capture-and-release purification of extracellular vesicles and statistical algorithm enabled quality assessment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.578050. [PMID: 38370748 PMCID: PMC10871196 DOI: 10.1101/2024.02.06.578050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Circulating extracellular vesicles (EVs) have gained significant attention for discovering tumor biomarkers. However, isolating EVs with well-defined homogeneous populations from complex biological samples is challenging. Different isolation methods have been found to derive different EV populations carrying different molecular contents, which confounds current investigations and hinders subsequent clinical translation. Therefore, standardizing and building a rigorous assessment of isolated EV quality associated with downstream molecular analysis is essential. To address this need, we introduce a statistical algorithm (ExoQuality Index, EQI) by integrating multiple EV characterizations (size, particle concentration, zeta potential, total protein, and RNA), enabling direct EV quality assessment and comparisons between different isolation methods. We also introduced a novel capture-release isolation approach using a pH-responsive peptide conjugated with NanoPom magnetic beads (ExCy) for simple, fast, and homogeneous EV isolation from various biological fluids. Bioinformatic analysis of next-generation sequencing (NGS) data of EV total RNAs from pancreatic cancer patient plasma samples using our novel EV isolation approach and quality index strategy illuminates how this approach improves the identification of tumor associated molecular markers. Results showed higher human mRNA coverage compared to existing isolation approaches in terms of both pancreatic cancer pathways and EV cellular component pathways using gProfiler pathway analysis. This study provides a valuable resource for researchers, establishing a workflow to prepare and analyze EV samples carefully and contributing to the advancement of reliable and rigorous EV quality assessment and clinical translation.
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Affiliation(s)
- Zachary F. Greenberg
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Samantha Ali
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Thomas D. Schmittgen
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | - Song Han
- Department of Surgery, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Steven J. Hughes
- Department of Surgery, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Kiley S. Graim
- Department of Computer & Information Science & Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, Florida, 32610, USA
| | - Mei He
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
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8
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Theil AF, Pines A, Kalayci T, Heredia‐Genestar JM, Raams A, Rietveld MH, Sridharan S, Tanis SEJ, Mulder KW, Büyükbabani N, Karaman B, Uyguner ZO, Kayserili H, Hoeijmakers JHJ, Lans H, Demmers JAA, Pothof J, Altunoglu U, El Ghalbzouri A, Vermeulen W. Trichothiodystrophy-associated MPLKIP maintains DBR1 levels for proper lariat debranching and ectodermal differentiation. EMBO Mol Med 2023; 15:e17973. [PMID: 37800682 PMCID: PMC10630875 DOI: 10.15252/emmm.202317973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 10/07/2023] Open
Abstract
The brittle hair syndrome Trichothiodystrophy (TTD) is characterized by variable clinical features, including photosensitivity, ichthyosis, growth retardation, microcephaly, intellectual disability, hypogonadism, and anaemia. TTD-associated mutations typically cause unstable mutant proteins involved in various steps of gene expression, severely reducing steady-state mutant protein levels. However, to date, no such link to instability of gene-expression factors for TTD-associated mutations in MPLKIP/TTDN1 has been established. Here, we present seven additional TTD individuals with MPLKIP mutations from five consanguineous families, with a newly identified MPLKIP variant in one family. By mass spectrometry-based interaction proteomics, we demonstrate that MPLKIP interacts with core splicing factors and the lariat debranching protein DBR1. MPLKIP-deficient primary fibroblasts have reduced steady-state DBR1 protein levels. Using Human Skin Equivalents (HSEs), we observed impaired keratinocyte differentiation associated with compromised splicing and eventually, an imbalanced proteome affecting skin development and, interestingly, also the immune system. Our data show that MPLKIP, through its DBR1 stabilizing role, is implicated in mRNA splicing, which is of particular importance in highly differentiated tissue.
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Affiliation(s)
- Arjan F Theil
- Department of Molecular GeneticsErasmus MC Cancer InstituteRotterdamThe Netherlands
| | - Alex Pines
- Department of Molecular GeneticsErasmus MC Cancer InstituteRotterdamThe Netherlands
| | - Tuğba Kalayci
- Department of Medical Genetics, Istanbul Faculty of MedicineIstanbul UniversityIstanbulTurkey
| | | | - Anja Raams
- Department of Molecular GeneticsErasmus MC Cancer InstituteRotterdamThe Netherlands
| | - Marion H Rietveld
- Department of DermatologyLeiden University Medical Center (LUMC)LeidenThe Netherlands
| | - Sriram Sridharan
- Cancer Science Institute of SingaporeNational University of SingaporeSingaporeSingapore
| | - Sabine EJ Tanis
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life SciencesRadboud UniversityNijmegenThe Netherlands
| | - Klaas W Mulder
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life SciencesRadboud UniversityNijmegenThe Netherlands
| | - Nesimi Büyükbabani
- Department of Pathology, Istanbul Faculty of MedicineIstanbul UniversityIstanbulTurkey
- Department of Medical GeneticsKoc University HospitalIstanbulTurkey
| | - Birsen Karaman
- Department of Medical Genetics, Istanbul Faculty of MedicineIstanbul UniversityIstanbulTurkey
- Department of Pediatric Basic Sciences, Child Health InstituteIstanbul UniversityIstanbulTurkey
| | - Zehra O Uyguner
- Department of Medical Genetics, Istanbul Faculty of MedicineIstanbul UniversityIstanbulTurkey
| | - Hülya Kayserili
- Department of Medical Genetics, Istanbul Faculty of MedicineIstanbul UniversityIstanbulTurkey
- Department of Medical GeneticsKoc University School of Medicine (KUSOM)IstanbulTurkey
| | - Jan HJ Hoeijmakers
- Department of Molecular GeneticsErasmus MC Cancer InstituteRotterdamThe Netherlands
- Institute for Genome Stability in Aging and Disease, CECAD ForschungszentrumUniversity Hospital of CologneKölnGermany
- Princess Máxima Center for Pediatric OncologyONCODE InstituteUtrechtThe Netherlands
| | - Hannes Lans
- Department of Molecular GeneticsErasmus MC Cancer InstituteRotterdamThe Netherlands
| | | | - Joris Pothof
- Department of Molecular GeneticsErasmus MC Cancer InstituteRotterdamThe Netherlands
| | - Umut Altunoglu
- Department of Medical Genetics, Istanbul Faculty of MedicineIstanbul UniversityIstanbulTurkey
- Department of Medical GeneticsKoc University School of Medicine (KUSOM)IstanbulTurkey
| | | | - Wim Vermeulen
- Department of Molecular GeneticsErasmus MC Cancer InstituteRotterdamThe Netherlands
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9
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Dwivedi SL, Quiroz LF, Reddy ASN, Spillane C, Ortiz R. Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs. Int J Mol Sci 2023; 24:15205. [PMID: 37894886 PMCID: PMC10607462 DOI: 10.3390/ijms242015205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Alternative splicing (AS) is a gene regulatory mechanism modulating gene expression in multiple ways. AS is prevalent in all eukaryotes including plants. AS generates two or more mRNAs from the precursor mRNA (pre-mRNA) to regulate transcriptome complexity and proteome diversity. Advances in next-generation sequencing, omics technology, bioinformatics tools, and computational methods provide new opportunities to quantify and visualize AS-based quantitative trait variation associated with plant growth, development, reproduction, and stress tolerance. Domestication, polyploidization, and environmental perturbation may evolve novel splicing variants associated with agronomically beneficial traits. To date, pre-mRNAs from many genes are spliced into multiple transcripts that cause phenotypic variation for complex traits, both in model plant Arabidopsis and field crops. Cataloguing and exploiting such variation may provide new paths to enhance climate resilience, resource-use efficiency, productivity, and nutritional quality of staple food crops. This review provides insights into AS variation alongside a gene expression analysis to select for novel phenotypic diversity for use in breeding programs. AS contributes to heterosis, enhances plant symbiosis (mycorrhiza and rhizobium), and provides a mechanistic link between the core clock genes and diverse environmental clues.
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Affiliation(s)
| | - Luis Felipe Quiroz
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, H91 REW4 Galway, Ireland
| | - Anireddy S N Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Charles Spillane
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, H91 REW4 Galway, Ireland
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 23053 Alnarp, SE, Sweden
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10
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Uriostegui-Arcos M, Mick ST, Shi Z, Rahman R, Fiszbein A. Splicing activates transcription from weak promoters upstream of alternative exons. Nat Commun 2023; 14:3435. [PMID: 37301863 PMCID: PMC10256964 DOI: 10.1038/s41467-023-39200-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 06/02/2023] [Indexed: 06/12/2023] Open
Abstract
Transcription and splicing are intrinsically coupled. Alternative splicing of internal exons can fine-tune gene expression through a recently described phenomenon called exon-mediated activation of transcription starts (EMATS). However, the association of this phenomenon with human diseases remains unknown. Here, we develop a strategy to activate gene expression through EMATS and demonstrate its potential for treatment of genetic diseases caused by loss of expression of essential genes. We first identified a catalog of human EMATS genes and provide a list of their pathological variants. To test if EMATS can be used to activate gene expression, we constructed stable cell lines expressing a splicing reporter based on the alternative splicing of motor neuron 2 (SMN2) gene. Using small molecules and antisense oligonucleotides (ASOs) currently used for treatment of spinal muscular atrophy, we demonstrated that increase of inclusion of alternative exons can trigger an activation of gene expression up to 45-fold by enhancing transcription in EMATS-like genes. We observed the strongest effects in genes under the regulation of weak human promoters located proximal to highly included skipped exons.
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Affiliation(s)
| | - Steven T Mick
- Biology Department, Boston University, Boston, 02215, USA
| | - Zhuo Shi
- Biology Department, Massachusetts Institute of Technology, Cambridge, 02139, USA
| | - Rufuto Rahman
- Biology Department, Boston University, Boston, 02215, USA
| | - Ana Fiszbein
- Biology Department, Boston University, Boston, 02215, USA.
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11
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Insco ML, Abraham BJ, Dubbury SJ, Kaltheuner IH, Dust S, Wu C, Chen KY, Liu D, Bellaousov S, Cox AM, Martin BJ, Zhang T, Ludwig CG, Fabo T, Modhurima R, Esgdaille DE, Henriques T, Brown KM, Chanock SJ, Geyer M, Adelman K, Sharp PA, Young RA, Boutz PL, Zon LI. Oncogenic CDK13 mutations impede nuclear RNA surveillance. Science 2023; 380:eabn7625. [PMID: 37079685 PMCID: PMC10184553 DOI: 10.1126/science.abn7625] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/27/2023] [Indexed: 04/22/2023]
Abstract
RNA surveillance pathways detect and degrade defective transcripts to ensure RNA fidelity. We found that disrupted nuclear RNA surveillance is oncogenic. Cyclin-dependent kinase 13 (CDK13) is mutated in melanoma, and patient-mutated CDK13 accelerates zebrafish melanoma. CDK13 mutation causes aberrant RNA stabilization. CDK13 is required for ZC3H14 phosphorylation, which is necessary and sufficient to promote nuclear RNA degradation. Mutant CDK13 fails to activate nuclear RNA surveillance, causing aberrant protein-coding transcripts to be stabilized and translated. Forced aberrant RNA expression accelerates melanoma in zebrafish. We found recurrent mutations in genes encoding nuclear RNA surveillance components in many malignancies, establishing nuclear RNA surveillance as a tumor-suppressive pathway. Activating nuclear RNA surveillance is crucial to avoid accumulation of aberrant RNAs and their ensuing consequences in development and disease.
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Affiliation(s)
- Megan L. Insco
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Brian J. Abraham
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, 38105, USA
| | - Sara J. Dubbury
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Ines H. Kaltheuner
- Institute of Structural Biology, University of Bonn, Bonn, 53127, Germany
| | - Sofia Dust
- Institute of Structural Biology, University of Bonn, Bonn, 53127, Germany
| | - Constance Wu
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Kevin Y. Chen
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - David Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Stanislav Bellaousov
- University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Anna M. Cox
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Benjamin J.E. Martin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20850, USA
| | - Calvin G. Ludwig
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Tania Fabo
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Rodsy Modhurima
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Dakarai E. Esgdaille
- University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
| | - Telmo Henriques
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Kevin M. Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20850, USA
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20850, USA
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Bonn, 53127, Germany
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Phillip A. Sharp
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Richard A. Young
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Paul L. Boutz
- University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, NY, 14642, USA
- Center for Biomedical Informatics, University of Rochester, Rochester, NY, 14642, USA
| | - Leonard I. Zon
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital, Howard Hughes Medical Institute, Boston, MA, 02115, USA
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12
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Ernst MPT, Pronk E, van Dijk C, van Strien PMH, van Tienhoven TVD, Wevers MJW, Sanders MA, Bindels EMJ, Speck NA, Raaijmakers MHGP. Hematopoietic Cell Autonomous Disruption of Hematopoiesis in a Germline Loss-of-function Mouse Model of RUNX1-FPD. Hemasphere 2023; 7:e824. [PMID: 36741355 PMCID: PMC9891454 DOI: 10.1097/hs9.0000000000000824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/29/2022] [Indexed: 02/01/2023] Open
Abstract
RUNX1 familial platelet disorder (RUNX1-FPD) is a hematopoietic disorder caused by germline loss-of-function mutations in the RUNX1 gene and characterized by thrombocytopathy, thrombocytopenia, and an increased risk of developing hematologic malignancies, mostly of myeloid origin. Disease pathophysiology has remained incompletely understood, in part because of a shortage of in vivo models recapitulating the germline RUNX1 loss of function found in humans, precluding the study of potential contributions of non-hematopoietic cells to disease pathogenesis. Here, we studied mice harboring a germline hypomorphic mutation of one Runx1 allele with a loss-of-function mutation in the other Runx1 allele (Runx1 L148A/- mice), which display many hematologic characteristics found in human RUNX1-FPD patients. Runx1 L148A/- mice displayed robust and pronounced thrombocytopenia and myeloid-biased hematopoiesis, associated with an HSC intrinsic reconstitution defect in lymphopoiesis and expansion of myeloid progenitor cell pools. We demonstrate that specific deletion of Runx1 from bone marrow stromal cells in Prrx1-cre;Runx1 fl/fl mice did not recapitulate these abnormalities, indicating that the hematopoietic abnormalities are intrinsic to the hematopoietic lineage, and arguing against a driving role of the bone marrow microenvironment. In conclusion, we report a RUNX1-FPD mouse model faithfully recapitulating key characteristics of human disease. Findings do not support a driving role of ancillary, non-hematopoietic cells in the disruption of hematopoiesis under homeostatic conditions.
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Affiliation(s)
- Martijn P. T. Ernst
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Eline Pronk
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Claire van Dijk
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | | | | | - Michiel J. W. Wevers
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Mathijs A. Sanders
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Eric M. J. Bindels
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Nancy A. Speck
- Abramson Family Cancer Research Institute and Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
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13
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Klodová B, Potěšil D, Steinbachová L, Michailidis C, Lindner AC, Hackenberg D, Becker JD, Zdráhal Z, Twell D, Honys D. Regulatory dynamics of gene expression in the developing male gametophyte of Arabidopsis. PLANT REPRODUCTION 2022:10.1007/s00497-022-00452-5. [PMID: 36282332 PMCID: PMC10363097 DOI: 10.1007/s00497-022-00452-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Sexual reproduction in angiosperms requires the production and delivery of two male gametes by a three-celled haploid male gametophyte. This demands synchronized gene expression in a short developmental window to ensure double fertilization and seed set. While transcriptomic changes in developing pollen are known for Arabidopsis, no studies have integrated RNA and proteomic data in this model. Further, the role of alternative splicing has not been fully addressed, yet post-transcriptional and post-translational regulation may have a key role in gene expression dynamics during microgametogenesis. We have refined and substantially updated global transcriptomic and proteomic changes in developing pollen for two Arabidopsis accessions. Despite the superiority of RNA-seq over microarray-based platforms, we demonstrate high reproducibility and comparability. We identify thousands of long non-coding RNAs as potential regulators of pollen development, hundreds of changes in alternative splicing and provide insight into mRNA translation rate and storage in developing pollen. Our analysis delivers an integrated perspective of gene expression dynamics in developing Arabidopsis pollen and a foundation for studying the role of alternative splicing in this model.
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Affiliation(s)
- Božena Klodová
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, Praha 2, 128 00, Czech Republic
| | - David Potěšil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Lenka Steinbachová
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic
| | - Christos Michailidis
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic
| | - Ann-Cathrin Lindner
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Dieter Hackenberg
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
- KWS SAAT SE & Co. KGaA, Grimsehlstraße 31, 37574, Einbeck, Germany
| | - Jörg D Becker
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157, Oeiras, Portugal
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - David Twell
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.
| | - David Honys
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic.
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14
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Obermeyer S, Stöckl R, Schnekenburger T, Moehle C, Schwartz U, Grasser KD. Distinct role of subunits of the Arabidopsis RNA polymerase II elongation factor PAF1C in transcriptional reprogramming. FRONTIERS IN PLANT SCIENCE 2022; 13:974625. [PMID: 36247629 PMCID: PMC9558118 DOI: 10.3389/fpls.2022.974625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Abstract
Transcript elongation by RNA polymerase II (RNAPII) is dynamic and highly regulated, thereby contributing to the implementation of gene expression programs during plant development or in response to environmental cues. The heterohexameric polymerase-associated factor 1 complex (PAF1C) stabilizes the RNAPII elongation complex promoting efficient transcript synthesis. In addition, PAF1C links transcriptional elongation with various post-translational histone modifications at transcribed loci. We have exposed Arabidopsis mutants deficient in the PAF1C subunits ELF7 or CDC73 to elevated NaCl concentrations to provoke a transcriptional response. The growth of elf7 plants was reduced relative to that of wildtype under these challenging conditions, whereas cdc73 plants exhibited rather enhanced tolerance. Profiling of the transcriptional changes upon NaCl exposure revealed that cdc73 responded similar to wildtype. Relative to wildtype and cdc73, the transcriptional response of elf7 plants was severely reduced in accord with their greater susceptibility to NaCl. The data also imply that CDC73 is more relevant for the transcription of longer genes. Despite the fact that both ELF7 and CDC73 are part of PAF1C the strikingly different transcriptional response of the mutants upon NaCl exposure suggests that the subunits have (partially) specific functions.
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Affiliation(s)
- Simon Obermeyer
- Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Regensburg, Germany
| | - Richard Stöckl
- Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Regensburg, Germany
| | - Tobias Schnekenburger
- Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Regensburg, Germany
| | - Christoph Moehle
- Center of Excellence for Fluorescent Bioanalytics (KFB), University of Regensburg, Regensburg, Germany
| | - Uwe Schwartz
- NGS Analysis Centre, Biology and Pre-Clinical Medicine, University of Regensburg, Regensburg, Germany
| | - Klaus D. Grasser
- Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Regensburg, Germany
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15
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Zhu L, Choudhary K, Gonzalez-Teran B, Ang YS, Thomas R, Stone NR, Liu L, Zhou P, Zhu C, Ruan H, Huang Y, Jin S, Pelonero A, Koback F, Padmanabhan A, Sadagopan N, Hsu A, Costa MW, Gifford CA, van Bemmel J, Hüttenhain R, Vedantham V, Conklin BR, Black BL, Bruneau BG, Steinmetz L, Krogan NJ, Pollard KS, Srivastava D. Transcription Factor GATA4 Regulates Cell Type-Specific Splicing Through Direct Interaction With RNA in Human Induced Pluripotent Stem Cell-Derived Cardiac Progenitors. Circulation 2022; 146:770-787. [PMID: 35938400 PMCID: PMC9452483 DOI: 10.1161/circulationaha.121.057620] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
BACKGROUND GATA4 (GATA-binding protein 4), a zinc finger-containing, DNA-binding transcription factor, is essential for normal cardiac development and homeostasis in mice and humans, and mutations in this gene have been reported in human heart defects. Defects in alternative splicing are associated with many heart diseases, yet relatively little is known about how cell type- or cell state-specific alternative splicing is achieved in the heart. Here, we show that GATA4 regulates cell type-specific splicing through direct interaction with RNA and the spliceosome in human induced pluripotent stem cell-derived cardiac progenitors. METHODS We leveraged a combination of unbiased approaches including affinity purification of GATA4 and mass spectrometry, enhanced cross-linking with immunoprecipitation, electrophoretic mobility shift assays, in vitro splicing assays, and unbiased transcriptomic analysis to uncover GATA4's novel function as a splicing regulator in human induced pluripotent stem cell-derived cardiac progenitors. RESULTS We found that GATA4 interacts with many members of the spliceosome complex in human induced pluripotent stem cell-derived cardiac progenitors. Enhanced cross-linking with immunoprecipitation demonstrated that GATA4 also directly binds to a large number of mRNAs through defined RNA motifs in a sequence-specific manner. In vitro splicing assays indicated that GATA4 regulates alternative splicing through direct RNA binding, resulting in functionally distinct protein products. Correspondingly, knockdown of GATA4 in human induced pluripotent stem cell-derived cardiac progenitors resulted in differential alternative splicing of genes involved in cytoskeleton organization and calcium ion import, with functional consequences associated with the protein isoforms. CONCLUSIONS This study shows that in addition to its well described transcriptional function, GATA4 interacts with members of the spliceosome complex and regulates cell type-specific alternative splicing via sequence-specific interactions with RNA. Several genes that have splicing regulated by GATA4 have functional consequences and many are associated with dilated cardiomyopathy, suggesting a novel role for GATA4 in achieving the necessary cardiac proteome in normal and stress-responsive conditions.
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Affiliation(s)
- Lili Zhu
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | | | - Barbara Gonzalez-Teran
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Yen-Sin Ang
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | | | - Nicole R. Stone
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Lei Liu
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Ping Zhou
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Chenchen Zhu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Genome Technology Center, Palo Alto, CA, USA
| | - Hongmei Ruan
- Department of Medicine, University of California, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Yu Huang
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Shibo Jin
- Division of Cellular and Developmental Biology, Molecular and Cell Biology Department, University of California at Berkeley, Berkeley, CA, USA
| | - Angelo Pelonero
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Frances Koback
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Arun Padmanabhan
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Nandhini Sadagopan
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Austin Hsu
- Gladstone Institutes, San Francisco, CA, USA
| | - Mauro W. Costa
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Casey A. Gifford
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Joke van Bemmel
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
| | - Ruth Hüttenhain
- Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA
| | - Vasanth Vedantham
- Department of Medicine, University of California, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Bruce R. Conklin
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Brian L. Black
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
| | - Benoit G. Bruneau
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
- Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Lars Steinmetz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Genome Technology Center, Palo Alto, CA, USA
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Nevan J. Krogan
- Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA
| | - Katherine S. Pollard
- Gladstone Institutes, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Department of Epidemiology & Biostatistics, Institute for Computational Health Sciences, and Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Deepak Srivastava
- Gladstone Institutes, San Francisco, CA, USA
- Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA, USA
- Department of Pediatrics, University of California, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
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16
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Choi SH, Flamand MN, Liu B, Zhu H, Hu M, Wang M, Sewell J, Holley CL, Al-Hashimi HM, Meyer KD. RBM45 is an m 6A-binding protein that affects neuronal differentiation and the splicing of a subset of mRNAs. Cell Rep 2022; 40:111293. [PMID: 36044854 PMCID: PMC9472474 DOI: 10.1016/j.celrep.2022.111293] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 07/14/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
N6-methyladenosine (m6A) is deposited co-transcriptionally on thousands of cellular mRNAs and plays important roles in mRNA processing and cellular function. m6A is particularly abundant within the brain and is critical for neurodevelopment. However, the mechanisms through which m6A contributes to brain development are incompletely understood. RBM45 acts as an m6A-binding protein that is highly expressed during neurodevelopment. We find that RBM45 binds to thousands of cellular RNAs, predominantly within intronic regions. Rbm45 depletion disrupts the constitutive splicing of a subset of target pre-mRNAs, leading to altered mRNA and protein levels through both m6A-dependent and m6A-independent mechanisms. Finally, we find that RBM45 is necessary for neuroblastoma cell differentiation and that its depletion impacts the expression of genes involved in several neurodevelopmental signaling pathways. Altogether, our findings show a role for RBM45 in controlling mRNA processing and neuronal differentiation, mediated in part by the recognition of methylated RNA. Choi et al. identify RBM45 as an m6A-binding protein enriched in the developing brain. RBM45 binds to thousands of cellular RNAs, primarily within introns, and regulates constitutive splicing of target transcripts. Loss of RBM45 causes altered expression of neurodevelopmental genes and defects in the proliferation and differentiation of neuroblastoma cells.
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Affiliation(s)
- Seung H Choi
- Department of Biochemistry, Duke University School of Medicine, Durham NC 27710, USA
| | - Mathieu N Flamand
- Department of Biochemistry, Duke University School of Medicine, Durham NC 27710, USA
| | - Bei Liu
- Department of Biochemistry, Duke University School of Medicine, Durham NC 27710, USA
| | - Huanyu Zhu
- Department of Biochemistry, Duke University School of Medicine, Durham NC 27710, USA
| | - Meghan Hu
- Trinity College of Arts and Sciences, Duke University, Durham, NC 27710, USA
| | - Melanie Wang
- Trinity College of Arts and Sciences, Duke University, Durham, NC 27710, USA
| | - Jonathon Sewell
- Department of Biochemistry, Duke University School of Medicine, Durham NC 27710, USA
| | - Christopher L Holley
- Department of Medicine (Cardiology Division), Duke University School of Medicine, Durham, NC 27710, USA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Kate D Meyer
- Department of Biochemistry, Duke University School of Medicine, Durham NC 27710, USA; Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA.
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17
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Ma J, Wu JY, Zhu L. Detection of orthologous exons and isoforms using EGIO. Bioinformatics 2022; 38:4474-4480. [PMID: 35946527 PMCID: PMC9525004 DOI: 10.1093/bioinformatics/btac548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/15/2022] [Accepted: 08/05/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Alternative splicing is an important mechanism to generate transcriptomic and phenotypic diversity. Existing methods have limited power to detect orthologous isoforms. RESULTS We develop a new method, EGIO, to detect orthologous exons and orthologous isoforms from two species. EGIO uses unique exonic regions to construct exon groups, in which process dynamic programming strategy is used to do exon alignment. EGIO could cover all the coding exons within orthologous genes. A comparison between EGIO and ExTraMapper shows that EGIO could detect more orthologous isoforms with conserved sequence and exon structures. We apply EGIO to compare human and chimpanzee protein-coding isoforms expressed in the frontal cortex and identify 6912 genes that express human unique isoforms. Unexpectedly, more human unique isoforms are detected than those conserved between humans and chimpanzees. AVAILABILITY AND IMPLEMENTATION Source code and test data of EGIO are available at https://github.com/wu-lab-egio/EGIO. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jinfa Ma
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jane Y Wu
- To whom correspondence should be addressed. or
| | - Li Zhu
- To whom correspondence should be addressed. or
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18
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Wright CJ, Smith CWJ, Jiggins CD. Alternative splicing as a source of phenotypic diversity. Nat Rev Genet 2022; 23:697-710. [PMID: 35821097 DOI: 10.1038/s41576-022-00514-4] [Citation(s) in RCA: 102] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2022] [Indexed: 12/27/2022]
Abstract
A major goal of evolutionary genetics is to understand the genetic processes that give rise to phenotypic diversity in multicellular organisms. Alternative splicing generates multiple transcripts from a single gene, enriching the diversity of proteins and phenotypic traits. It is well established that alternative splicing contributes to key innovations over long evolutionary timescales, such as brain development in bilaterians. However, recent developments in long-read sequencing and the generation of high-quality genome assemblies for diverse organisms has facilitated comparisons of splicing profiles between closely related species, providing insights into how alternative splicing evolves over shorter timescales. Although most splicing variants are probably non-functional, alternative splicing is nonetheless emerging as a dynamic, evolutionarily labile process that can facilitate adaptation and contribute to species divergence.
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Affiliation(s)
- Charlotte J Wright
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK. .,Department of Zoology, University of Cambridge, Cambridge, UK.
| | | | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK.
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19
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Su S, Katopodi XL, Pita-Juarez YH, Maverakis E, Vlachos IS, Adamopoulos IE. Serine and arginine rich splicing factor 1 deficiency alters pathways involved in IL-17A expression and is implicated in human psoriasis. Clin Immunol 2022; 240:109041. [PMID: 35613697 PMCID: PMC10797199 DOI: 10.1016/j.clim.2022.109041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 12/25/2022]
Abstract
Serine and Arginine Rich Splicing Factor 1 (SRSF1) is a splicing factor that binds to exonic enhancers and stimulates splicing and is previously implicated with autoimmunity. Herein, we investigate the role of SRSF1 in regulating innate immune functions that are pertinent in the pathogenesis of auto-inflammatory diseases. Specifically, we show that conditional deletion of SRSF1 in mature lymphocytes resulted in higher expression of il-17a and il-17 f and an expansion of IL17A+ CD8 T cells. Mechanistically, the aberrant expression of IL-17A in SRSF1 cKO mice could not be attributed to alternative splicing of il-17a or il-17 f genes but possibly to defective CD11B+LY6C+ myeloid derived suppressor function in the spleen. Finally, meta-analysis of RNA-Seq collected from psoriasis patients demonstrate a clear correlation between SRSF1 and psoriasis that suggests a putative role of SRSF1 in IL-17A-induced psoriasis.
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Affiliation(s)
- Shi Su
- Department of Rheumatology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Xanthi-Lida Katopodi
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Yered H Pita-Juarez
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Emanual Maverakis
- Department of Dermatology, University of California, Davis, Sacramento, CA, USA
| | - Ioannis S Vlachos
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA; Harvard Medical School Initiative for RNA Medicine, Boston, MA, USA; Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Iannis E Adamopoulos
- Department of Rheumatology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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20
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Li H, Li X, Wang G, Zhang J, Wang G. Analysis of gene expression in early seed germination of rice: landscape and genetic regulation. BMC PLANT BIOLOGY 2022; 22:70. [PMID: 35176996 PMCID: PMC8851807 DOI: 10.1186/s12870-022-03458-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Seed germination is a crucial process, which determines the initiation of seed plant life cycle. The early events during this important life cycle transition that called early seed germination is defined as initially water uptake plus radicle growing out of the covering seed layers. However, a specific genome-wide analysis of early seed germination in rice is still obscure. RESULTS In this study, the physiological characteristics of rice seed during seed germination are determined to define key points of early seed germination. Transcriptome analyses of early phase of seed germination provided deeper insight into the genetic regulation landscape. Many genes involved in starch-to-sucrose transition were differentially expressed, especially alpha-amylase 1b and beta-amylase 2, which were predominantly expressed. Differential exon usage (DEU) genes were identified, which were significantly enriched in the pathway of starch and sucrose metabolism, indicating that DEU events were critical for starch-to-sucrose transition at early seed germination. Transcription factors (TFs) were also dramatic expressed, including the abscisic acid (ABA) responsive gene, OsABI5, and gibberellic acid (GA) responsive genes, GAI. Moreover, GAI transactivated GA responsive gene, GAMYB in vivo, indicating a potential pathway involved in early seed germination process. In addition, CBL-interacting protein kinase (CIPK) genes, such as CIPK13, CIPK14 and CIPK17 were potentially interacted with other proteins, indicating its pivotal role at early seed germination. CONCLUSION Taken together, gene regulation of early seed germination in rice was complex and protein-to-gene or protein-to-protein interactions were indispensable.
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Affiliation(s)
- Haoxuan Li
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong, China
| | - Xiaozheng Li
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Guanjie Wang
- College of Life Sciences, Jilin Agricultural University, Jilin, China
| | - Jianhua Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong, China.
| | - Guanqun Wang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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21
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Patient-specific MDS-RS iPSCs define the mis-spliced transcript repertoire and chromatin landscape of SF3B1-mutant HSPCs. Blood Adv 2022; 6:2992-3005. [PMID: 35042235 PMCID: PMC9131920 DOI: 10.1182/bloodadvances.2021006325] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/17/2021] [Indexed: 11/20/2022] Open
Abstract
Genetically matched MDS-RS and normal patient-specific iPSC-HSPCs are used to derive a mutant SF3B1 splicing signature. Integrated transcriptomics and chromatin accessibility nominate TEAD as a putative novel transcriptional regulator of SF3B1K700E cells.
SF3B1K700E is the most frequent mutation in myelodysplastic syndrome (MDS), but the mechanisms by which it drives MDS pathogenesis remain unclear. We derived a panel of 18 genetically matched SF3B1K700E- and SF3B1WT-induced pluripotent stem cell (iPSC) lines from patients with MDS with ring sideroblasts (MDS-RS) harboring isolated SF3B1K700E mutations and performed RNA and ATAC sequencing in purified CD34+/CD45+ hematopoietic stem/progenitor cells (HSPCs) derived from them. We developed a novel computational framework integrating splicing with transcript usage and gene expression analyses and derived a SF3B1K700E splicing signature consisting of 59 splicing events linked to 34 genes, which associates with the SF3B1 mutational status of primary MDS patient cells. The chromatin landscape of SF3B1K700E HSPCs showed increased priming toward the megakaryocyte- erythroid lineage. Transcription factor motifs enriched in chromatin regions more accessible in SF3B1K700E cells included, unexpectedly, motifs of the TEA domain (TEAD) transcription factor family. TEAD expression and transcriptional activity were upregulated in SF3B1-mutant iPSC-HSPCs, in support of a Hippo pathway-independent role of TEAD as a potential novel transcriptional regulator of SF3B1K700E cells. This study provides a comprehensive characterization of the transcriptional and chromatin landscape of SF3B1K700E HSPCs and nominates novel mis-spliced genes and transcriptional programs with putative roles in MDS-RS disease biology.
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22
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Zou X, Schaefke B, Li Y, Jia F, Sun W, Li G, Liang W, Reif T, Heyd F, Gao Q, Tian S, Li Y, Tang Y, Fang L, Hu Y, Chen W. Mammalian splicing divergence is shaped by drift, buffering in trans, and a scaling law. Life Sci Alliance 2022; 5:5/4/e202101333. [PMID: 34969779 PMCID: PMC8739531 DOI: 10.26508/lsa.202101333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 11/24/2022] Open
Abstract
This study globally investigates the allelic splicing pattern in multiple tissues of an F1 hybrid mouse and reveals the underlying driving forces shaping such tissue-dependent splicing divergence. Alternative splicing is ubiquitous, but the mechanisms underlying its pattern of evolutionary divergence across mammalian tissues are still underexplored. Here, we investigated the cis-regulatory divergences and their relationship with tissue-dependent trans-regulation in multiple tissues of an F1 hybrid between two mouse species. Large splicing changes between tissues are highly conserved and likely reflect functional tissue-dependent regulation. In particular, micro-exons frequently exhibit this pattern with high inclusion levels in the brain. Cis-divergence of splicing appears to be largely non-adaptive. Although divergence is in general associated with higher densities of sequence variants in regulatory regions, events with high usage of the dominant isoform apparently tolerate more mutations, explaining why their exon sequences are highly conserved but their intronic splicing site flanking regions are not. Moreover, we demonstrate that non-adaptive mutations are often masked in tissues where accurate splicing likely is more important, and experimentally attribute such buffering effect to trans-regulatory splicing efficiency.
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Affiliation(s)
- Xudong Zou
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Bernhard Schaefke
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
| | - Yisheng Li
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Fujian Jia
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wei Sun
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Guipeng Li
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
| | - Weizheng Liang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Tristan Reif
- Institute for Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Florian Heyd
- Institute for Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Qingsong Gao
- Laboratory for Systems Biology and Functional Genomics, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Shuye Tian
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yanping Li
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yisen Tang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Liang Fang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
| | - Yuhui Hu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wei Chen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China .,Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.,Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, China
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23
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Verta JP, Jacobs A. The role of alternative splicing in adaptation and evolution. Trends Ecol Evol 2021; 37:299-308. [PMID: 34920907 DOI: 10.1016/j.tree.2021.11.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/26/2021] [Accepted: 11/19/2021] [Indexed: 01/02/2023]
Abstract
Regulation of gene expression plays a central role in adaptive divergence and evolution. Although the role of gene regulation in microevolutionary processes is gaining wide acceptance, most studies have only investigated the evolution of transcript levels, ignoring the potentially significant role of transcript structures. We argue that variation in alternative splicing plays an important and widely unexplored role in adaptation (e.g., by increasing transcriptome and/or proteome diversity, or buffering potentially deleterious genetic variation). New studies increasingly highlight the potential for independent evolution in alternative splicing and transcript level, providing alternative paths for selection to act upon. We propose that alternative splicing and transcript levels can provide contrasting, nonredundant mechanisms of equal importance for adaptive diversification of gene function and regulation.
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Affiliation(s)
- Jukka-Pekka Verta
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Viikinkaari 9, 00790, Helsinki, Finland.
| | - Arne Jacobs
- Institute of Biodiversity, Animal Health, and Comparative Medicine, University of Glasgow, G12 8QQ, Glasgow, UK.
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24
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Santos-Rodriguez G, Voineagu I, Weatheritt RJ. Evolutionary dynamics of circular RNAs in primates. eLife 2021; 10:e69148. [PMID: 34542404 PMCID: PMC8516421 DOI: 10.7554/elife.69148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 09/06/2021] [Indexed: 12/13/2022] Open
Abstract
Many primate genes produce circular RNAs (circRNAs). However, the extent of circRNA conservation between closely related species remains unclear. By comparing tissue-specific transcriptomes across over 70 million years of primate evolution, we identify that within 3 million years circRNA expression profiles diverged such that they are more related to species identity than organ type. However, our analysis also revealed a subset of circRNAs with conserved neural expression across tens of millions of years of evolution. By comparing to species-specific circRNAs, we identified that the downstream intron of the conserved circRNAs display a dramatic lengthening during evolution due to the insertion of novel retrotransposons. Our work provides comparative analyses of the mechanisms promoting circRNAs to generate increased transcriptomic complexity in primates.
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Affiliation(s)
- Gabriela Santos-Rodriguez
- EMBL Australia, Garvan Institute of Medical ResearchDarlinghurstAustralia
- St. Vincent Clinical School, University of New South WalesDarlinghurstAustralia
| | - Irina Voineagu
- School of Biotechnology and Biomolecular Sciences, University of New South WalesSydneyAustralia
| | - Robert J Weatheritt
- EMBL Australia, Garvan Institute of Medical ResearchDarlinghurstAustralia
- St. Vincent Clinical School, University of New South WalesDarlinghurstAustralia
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25
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Márquez Y, Mantica F, Cozzuto L, Burguera D, Hermoso-Pulido A, Ponomarenko J, Roy SW, Irimia M. ExOrthist: a tool to infer exon orthologies at any evolutionary distance. Genome Biol 2021; 22:239. [PMID: 34416914 PMCID: PMC8379844 DOI: 10.1186/s13059-021-02441-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/26/2021] [Indexed: 12/14/2022] Open
Abstract
Several bioinformatic tools have been developed for genome-wide identification of orthologous and paralogous genes. However, no corresponding tool allows the detection of exon homology relationships. Here, we present ExOrthist, a fully reproducible Nextflow-based software enabling inference of exon homologs and orthogroups, visualization of evolution of exon-intron structures, and assessment of conservation of alternative splicing patterns. ExOrthist evaluates exon sequence conservation and considers the surrounding exon-intron context to derive genome-wide multi-species exon homologies at any evolutionary distance. We demonstrate its use in different evolutionary scenarios: whole genome duplication in frogs and convergence of Nova-regulated splicing networks (https://github.com/biocorecrg/ExOrthist).
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Affiliation(s)
- Yamile Márquez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain.
| | - Federica Mantica
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain
| | - Luca Cozzuto
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain
| | - Demian Burguera
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain.,Department of Zoology, Charles University, Vinicna 7, 12844, Prague, Czech Republic
| | - Antonio Hermoso-Pulido
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain
| | - Julia Ponomarenko
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Scott W Roy
- San Francisco State University, 1600 Holloway Ave, San Francisco, CA, 94132, USA
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003, Barcelona, Spain. .,Universitat Pompeu Fabra, Barcelona, Spain. .,ICREA, Barcelona, Spain.
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26
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Charton C, Youm DJ, Ko BJ, Seol D, Kim B, Chai HH, Lim D, Kim H. The transcriptomic blueprint of molt in rooster using various tissues from Ginkkoridak (Korean long-tailed chicken). BMC Genomics 2021; 22:594. [PMID: 34348642 PMCID: PMC8340483 DOI: 10.1186/s12864-021-07903-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/13/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Annual molt is a critical stage in the life cycle of birds. Although the most extensively documented aspects of molt are the renewing of plumage and the remodeling of the reproductive tract in laying hens, in chicken, molt deeply affects various tissues and physiological functions. However, with exception of the reproductive tract, the effect of molt on gene expression across the tissues known to be affected by molt has to date never been investigated. The present study aimed to decipher the transcriptomic effects of molt in Ginkkoridak, a Korean long-tailed chicken. Messenger RNA data available across 24 types of tissue samples (9 males) and a combination of mRNA and miRNA data on 10 males and 10 females blood were used. RESULTS The impact of molt on gene expression and gene transcript usage appeared to vary substantially across tissues types in terms of histological entities or physiological functions particularly related to nervous system. Blood was the tissue most affected by molt in terms of differentially expressed genes in both sexes, closely followed by meninges, bone marrow and heart. The effect of molt in blood appeared to differ between males and females, with a more than fivefold difference in the number of down-regulated genes between both sexes. The blueprint of molt in roosters appeared to be specific to tissues or group of tissues, with relatively few genes replicating extensively across tissues, excepted for the spliceosome genes (U1, U4) and the ribosomal proteins (RPL21, RPL23). By integrating miRNA and mRNA data, when chickens molt, potential roles of miRNA were discovered such as regulation of neurogenesis, regulation of immunity and development of various organs. Furthermore, reliable candidate biomarkers of molt were found, which are related to cell dynamics, nervous system or immunity, processes or functions that have been shown to be extensively modulated in response to molt. CONCLUSIONS Our results provide a comprehensive description at the scale of the whole organism deciphering the effects of molt on the transcriptome in chicken. Also, the conclusion of this study can be used as a valuable resource in transcriptome analyses of chicken in the future and provide new insights related to molt.
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Affiliation(s)
- Clémentine Charton
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Dong-Jae Youm
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Byung June Ko
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Donghyeok Seol
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- eGnome, Inc, Seoul, Republic of Korea
| | - Bongsang Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- eGnome, Inc, Seoul, Republic of Korea
| | - Han-Ha Chai
- Animal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA, 1500, Wanju, Republic of Korea
| | - Dajeong Lim
- Animal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA, 1500, Wanju, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
- eGnome, Inc, Seoul, Republic of Korea.
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27
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Lau CI, Rowell J, Yanez DC, Solanki A, Ross S, Ono M, Crompton T. The pioneer transcription factors Foxa1 and Foxa2 regulate alternative RNA splicing during thymocyte positive selection. Development 2021; 148:dev199754. [PMID: 34323272 PMCID: PMC8353164 DOI: 10.1242/dev.199754] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/28/2021] [Indexed: 02/02/2023]
Abstract
During positive selection at the transition from CD4+CD8+ double-positive (DP) to single-positive (SP) thymocyte, TCR signalling results in appropriate MHC restriction and signals for survival and progression. We show that the pioneer transcription factors Foxa1 and Foxa2 are required to regulate RNA splicing during positive selection of mouse T cells and that Foxa1 and Foxa2 have overlapping/compensatory roles. Conditional deletion of both Foxa1 and Foxa2 from DP thymocytes reduced positive selection and development of CD4SP, CD8SP and peripheral naïve CD4+ T cells. Foxa1 and Foxa2 regulated the expression of many genes encoding splicing factors and regulators, including Mbnl1, H1f0, Sf3b1, Hnrnpa1, Rnpc3, Prpf4b, Prpf40b and Snrpd3. Within the positively selecting CD69+DP cells, alternative RNA splicing was dysregulated in the double Foxa1/Foxa2 conditional knockout, leading to >850 differentially used exons. Many genes important for this stage of T-cell development (Ikzf1-3, Ptprc, Stat5a, Stat5b, Cd28, Tcf7) and splicing factors (Hnrnpab, Hnrnpa2b1, Hnrnpu, Hnrnpul1, Prpf8) showed multiple differentially used exons. Thus, Foxa1 and Foxa2 are required during positive selection to regulate alternative splicing of genes essential for T-cell development, and, by also regulating splicing of splicing factors, they exert widespread control of alternative splicing.
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Affiliation(s)
- Ching-In Lau
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
| | - Jasmine Rowell
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
| | - Diana C. Yanez
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
| | - Anisha Solanki
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
| | - Susan Ross
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
| | - Masahiro Ono
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Tessa Crompton
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
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28
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Dumont AA, Dumont L, Zhou D, Giguère H, Pileggi C, Harper ME, Blondin DP, Scott MS, Auger-Messier M. Cardiomyocyte-specific Srsf3 deletion reveals a mitochondrial regulatory role. FASEB J 2021; 35:e21544. [PMID: 33819356 DOI: 10.1096/fj.202002293rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 11/11/2022]
Abstract
Serine-rich splicing factor 3 (SRSF3) was recently reported as being necessary to preserve RNA stability via an mTOR mechanism in a cardiac mouse model in adulthood. Here, we demonstrate the link between Srsf3 and mitochondrial integrity in an embryonic cardiomyocyte-specific Srsf3 conditional knockout (cKO) mouse model. Fifteen-day-old Srsf3 cKO mice showed dramatically reduced (below 50%) survival and reduced the left ventricular systolic performance, and histological analysis of these hearts revealed a significant increase in cardiomyocyte size, confirming the severe remodeling induced by Srsf3 deletion. RNA-seq analysis of the hearts of 5-day-old Srsf3 cKO mice revealed early changes in expression levels and alternative splicing of several transcripts related to mitochondrial integrity and oxidative phosphorylation. Likewise, the levels of several protein complexes of the electron transport chain decreased, and mitochondrial complex I-driven respiration of permeabilized cardiac muscle fibers from the left ventricle was impaired. Furthermore, transmission electron microscopy analysis showed disordered mitochondrial length and cristae structure. Together with its indispensable role in the physiological maintenance of mouse hearts, these results highlight the previously unrecognized function of Srsf3 in regulating the mitochondrial integrity.
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Affiliation(s)
- Audrey-Ann Dumont
- Département de Médecine - Service de Cardiologie, Faculté de Médecine et des Sciences de la Santé, Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Lauralyne Dumont
- Département de Médecine - Service de Cardiologie, Faculté de Médecine et des Sciences de la Santé, Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Delong Zhou
- Département de microbiologie et d'infectiologie, Faculté de Médecine et des Sciences de la Santé, Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Hugo Giguère
- Département de Médecine - Service de Cardiologie, Faculté de Médecine et des Sciences de la Santé, Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Chantal Pileggi
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Mary-Ellen Harper
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Denis P Blondin
- Département de Médecine - Service de Cardiologie, Faculté de Médecine et des Sciences de la Santé, Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Michelle S Scott
- Département de Biochimie et Génomique Fonctionnelle, Faculté de Médecine et des Sciences de la Santé, Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Mannix Auger-Messier
- Département de Médecine - Service de Cardiologie, Faculté de Médecine et des Sciences de la Santé, Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
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29
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Identification of pathological transcription in autosomal dominant polycystic kidney disease epithelia. Sci Rep 2021; 11:15139. [PMID: 34301992 PMCID: PMC8302622 DOI: 10.1038/s41598-021-94442-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/08/2021] [Indexed: 11/09/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) affects more than 12 million people worldwide. Mutations in PKD1 and PKD2 cause cyst formation through unknown mechanisms. To unravel the pathogenic mechanisms in ADPKD, multiple studies have investigated transcriptional mis-regulation in cystic kidneys from patients and mouse models, and numerous dysregulated genes and pathways have been described. Yet, the concordance between studies has been rather limited. Furthermore, the cellular and genetic diversity in cystic kidneys has hampered the identification of mis-expressed genes in kidney epithelial cells with homozygous PKD mutations, which are critical to identify polycystin-dependent pathways. Here we performed transcriptomic analyses of Pkd1- and Pkd2-deficient mIMCD3 kidney epithelial cells followed by a meta-analysis to integrate all published ADPKD transcriptomic data sets. Based on the hypothesis that Pkd1 and Pkd2 operate in a common pathway, we first determined transcripts that are differentially regulated by both genes. RNA sequencing of genome-edited ADPKD kidney epithelial cells identified 178 genes that are concordantly regulated by Pkd1 and Pkd2. Subsequent integration of existing transcriptomic studies confirmed 31 previously described genes and identified 61 novel genes regulated by Pkd1 and Pkd2. Cluster analyses then linked Pkd1 and Pkd2 to mRNA splicing, specific factors of epithelial mesenchymal transition, post-translational protein modification and epithelial cell differentiation, including CD34, CDH2, CSF2RA, DLX5, HOXC9, PIK3R1, PLCB1 and TLR6. Taken together, this model-based integrative analysis of transcriptomic alterations in ADPKD annotated a conserved core transcriptomic profile and identified novel candidate genes for further experimental studies.
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Zhang Y, Cai Y, Roca X, Kwoh CK, Fullwood MJ. Chromatin loop anchors predict transcript and exon usage. Brief Bioinform 2021; 22:6319936. [PMID: 34263910 PMCID: PMC8575016 DOI: 10.1093/bib/bbab254] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/16/2021] [Accepted: 05/25/2021] [Indexed: 11/24/2022] Open
Abstract
Epigenomics and transcriptomics data from high-throughput sequencing techniques such as RNA-seq and ChIP-seq have been successfully applied in predicting gene transcript expression. However, the locations of chromatin loops in the genome identified by techniques such as Chromatin Interaction Analysis with Paired End Tag sequencing (ChIA-PET) have never been used for prediction tasks. Here, we developed machine learning models to investigate if ChIA-PET could contribute to transcript and exon usage prediction. In doing so, we used a large set of transcription factors as well as ChIA-PET data. We developed different Gradient Boosting Trees models according to the different tasks with the integrated datasets from three cell lines, including GM12878, HeLaS3 and K562. We validated the models via 10-fold cross validation, chromosome-split validation and cross-cell validation. Our results show that both transcript and splicing-derived exon usage can be effectively predicted with at least 0.7512 and 0.7459 of accuracy, respectively, on all cell lines from all kinds of validations. Examining the predictive features, we found that RNA Polymerase II ChIA-PET was one of the most important features in both transcript and exon usage prediction, suggesting that chromatin loop anchors are predictive of both transcript and exon usage.
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Affiliation(s)
- Yu Zhang
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Yichao Cai
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore 117599, Singapore
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Dr, Singapore 637551, Singapore
| | - Chee Keong Kwoh
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Melissa Jane Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore 117599, Singapore.,School of Biological Sciences, Nanyang Technological University, 637551, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Dr, Singapore 138673, Singapore
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MOCCASIN: a method for correcting for known and unknown confounders in RNA splicing analysis. Nat Commun 2021; 12:3353. [PMID: 34099673 PMCID: PMC8184769 DOI: 10.1038/s41467-021-23608-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 05/07/2021] [Indexed: 11/09/2022] Open
Abstract
The effects of confounding factors on gene expression analysis have been extensively studied following the introduction of high-throughput microarrays and subsequently RNA sequencing. In contrast, there is a lack of equivalent analysis and tools for RNA splicing. Here we first assess the effect of confounders on both expression and splicing quantifications in two large public RNA-Seq datasets (TARGET, ENCODE). We show quantification of splicing variations are affected at least as much as those of gene expression, revealing unwanted sources of variations in both datasets. Next, we develop MOCCASIN, a method to correct the effect of both known and unknown confounders on RNA splicing quantification and demonstrate MOCCASIN's effectiveness on both synthetic and real data. Code, synthetic and corrected datasets are all made available as resources.
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Parker MT, Knop K, Zacharaki V, Sherwood AV, Tomé D, Yu X, Martin PGP, Beynon J, Michaels SD, Barton GJ, Simpson GG. Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA. eLife 2021; 10:e65537. [PMID: 33904405 PMCID: PMC8116057 DOI: 10.7554/elife.65537] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/26/2021] [Indexed: 12/18/2022] Open
Abstract
Genes involved in disease resistance are some of the fastest evolving and most diverse components of genomes. Large numbers of nucleotide-binding, leucine-rich repeat (NLR) genes are found in plant genomes and are required for disease resistance. However, NLRs can trigger autoimmunity, disrupt beneficial microbiota or reduce fitness. It is therefore crucial to understand how NLRs are controlled. Here, we show that the RNA-binding protein FPA mediates widespread premature cleavage and polyadenylation of NLR transcripts, thereby controlling their functional expression and impacting immunity. Using long-read Nanopore direct RNA sequencing, we resolved the complexity of NLR transcript processing and gene annotation. Our results uncover a co-transcriptional layer of NLR control with implications for understanding the regulatory and evolutionary dynamics of NLRs in the immune responses of plants.
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Affiliation(s)
- Matthew T Parker
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Katarzyna Knop
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | | | - Anna V Sherwood
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Daniel Tomé
- School of Life Sciences, University of WarwickCoventryUnited Kingdom
| | - Xuhong Yu
- Department of Biology, Indiana UniversityBloomingtonUnited States
| | - Pascal GP Martin
- Department of Biology, Indiana UniversityBloomingtonUnited States
| | - Jim Beynon
- School of Life Sciences, University of WarwickCoventryUnited Kingdom
| | - Scott D Michaels
- Department of Biology, Indiana UniversityBloomingtonUnited States
| | | | - Gordon G Simpson
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
- The James Hutton InstituteInvergowrieUnited Kingdom
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Selective Activation of CNS and Reference PPARGC1A Promoters Is Associated with Distinct Gene Programs Relevant for Neurodegenerative Diseases. Int J Mol Sci 2021; 22:ijms22073296. [PMID: 33804860 PMCID: PMC8036390 DOI: 10.3390/ijms22073296] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/17/2021] [Accepted: 03/20/2021] [Indexed: 12/12/2022] Open
Abstract
The transcriptional regulator peroxisome proliferator activated receptor gamma coactivator 1A (PGC-1α), encoded by PPARGC1A, has been linked to neurodegenerative diseases. Recently discovered CNS-specific PPARGC1A transcripts are initiated far upstream of the reference promoter, spliced to exon 2 of the reference gene, and are more abundant than reference gene transcripts in post-mortem human brain samples. The proteins translated from the CNS and reference transcripts differ only at their N-terminal regions. To dissect functional differences between CNS-specific isoforms and reference proteins, we used clustered regularly interspaced short palindromic repeats transcriptional activation (CRISPRa) for selective endogenous activation of the CNS or the reference promoters in SH-SY5Y cells. Expression and/or exon usage of the targets was ascertained by RNA sequencing. Compared to controls, more differentially expressed genes were observed after activation of the CNS than the reference gene promoter, while the magnitude of alternative exon usage was comparable between activation of the two promoters. Promoter-selective associations were observed with canonical signaling pathways, mitochondrial and nervous system functions and neurological diseases. The distinct N-terminal as well as the shared downstream regions of PGC-1α isoforms affect the exon usage of numerous genes. Furthermore, associations of risk genes of amyotrophic lateral sclerosis and Parkinson's disease were noted with differentially expressed genes resulting from the activation of the CNS and reference gene promoter, respectively. Thus, CNS-specific isoforms markedly amplify the biological functions of PPARGC1A and CNS-specific isoforms and reference proteins have common, complementary and selective functions relevant for neurodegenerative diseases.
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Graim K, Gorenshteyn D, Robinson DG, Carriero NJ, Cahill JA, Chakrabarti R, Goldschmidt MH, Durham AC, Funk J, Storey JD, Kristensen VN, Theesfeld CL, Sorenmo KU, Troyanskaya OG. Modeling molecular development of breast cancer in canine mammary tumors. Genome Res 2021; 31:337-347. [PMID: 33361113 PMCID: PMC7849403 DOI: 10.1101/gr.256388.119] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 12/17/2020] [Indexed: 12/30/2022]
Abstract
Understanding the changes in diverse molecular pathways underlying the development of breast tumors is critical for improving diagnosis, treatment, and drug development. Here, we used RNA-profiling of canine mammary tumors (CMTs) coupled with a robust analysis framework to model molecular changes in human breast cancer. Our study leveraged a key advantage of the canine model, the frequent presence of multiple naturally occurring tumors at diagnosis, thus providing samples spanning normal tissue and benign and malignant tumors from each patient. We showed human breast cancer signals, at both expression and mutation level, are evident in CMTs. Profiling multiple tumors per patient enabled by the CMT model allowed us to resolve statistically robust transcription patterns and biological pathways specific to malignant tumors versus those arising in benign tumors or shared with normal tissues. We showed that multiple histological samples per patient is necessary to effectively capture these progression-related signatures, and that carcinoma-specific signatures are predictive of survival for human breast cancer patients. To catalyze and support similar analyses and use of the CMT model by other biomedical researchers, we provide FREYA, a robust data processing pipeline and statistical analyses framework.
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Affiliation(s)
- Kiley Graim
- Flatiron Institute, Simons Foundation, New York, New York 10010, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Dmitriy Gorenshteyn
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
- Graduate Program in Quantitative and Computational Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - David G Robinson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
- Graduate Program in Quantitative and Computational Biology, Princeton University, Princeton, New Jersey 08544, USA
| | | | - James A Cahill
- Laboratory of the Neurogenetics of Language, Rockefeller University, New York, New York 10065, USA
| | - Rumela Chakrabarti
- Department of Biomedical Sciences and the Penn Vet Cancer Center, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Michael H Goldschmidt
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Amy C Durham
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Julien Funk
- Flatiron Institute, Simons Foundation, New York, New York 10010, USA
| | - John D Storey
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
- Center for Statistics and Machine Learning, Princeton University, Princeton, New Jersey 08544, USA
| | - Vessela N Kristensen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, 0310 Oslo, Norway
| | - Chandra L Theesfeld
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
| | - Karin U Sorenmo
- Department of Biomedical Sciences and the Penn Vet Cancer Center, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Olga G Troyanskaya
- Flatiron Institute, Simons Foundation, New York, New York 10010, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
- Department of Computer Science, Princeton University, Princeton, New Jersey 08544, USA
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35
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Leal-Gutiérrez JD, Elzo MA, Carr C, Mateescu RG. RNA-seq analysis identifies cytoskeletal structural genes and pathways for meat quality in beef. PLoS One 2020; 15:e0240895. [PMID: 33175867 PMCID: PMC7657496 DOI: 10.1371/journal.pone.0240895] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 10/05/2020] [Indexed: 01/03/2023] Open
Abstract
RNA sequencing (RNA-seq) has allowed for transcriptional profiling of biological systems through the identification of differentially expressed (DE) genes and pathways. A total of 80 steers with extreme phenotypes were selected from the University of Florida multibreed Angus-Brahman herd. The average slaughter age was 12.91±8.69 months. Tenderness, juiciness and connective tissue assessed by sensory panel, along with marbling, Warner-Bratzler Shear Force (WBSF) and cooking loss, were measured in longissimus dorsi muscle. Total RNA was extracted from muscle and one RNA-seq library per sample was constructed, multiplexed, and sequenced based on protocols by Illumina HiSeq-3000 platform to generate 2×101 bp paired-end reads. The overall read mapping rate using the Btau_4.6.1 reference genome was 63%. A total of 8,799 genes were analyzed using two different methodologies, an expression association and a DE analysis. A gene and exon expression association analysis was carried out using a meat quality index on all 80 samples as a continuous response variable. The expression of 208 genes and 3,280 exons from 1,565 genes was associated with the meat quality index (p-value ≤ 0.05). A gene and isoform DE evaluation was performed analyzing two groups with extreme WBSF, tenderness and marbling. A total of 676 (adjusted p-value≤0.05), 70 (adjusted p-value≤0.1) and 198 (adjusted p-value≤0.1) genes were DE for WBSF, tenderness and marbling, respectively. A total of 106 isoforms from 98 genes for WBSF, 13 isoforms from 13 genes for tenderness and 43 isoforms from 42 genes for marbling (FDR≤0.1) were DE. Cytoskeletal and transmembrane anchoring genes and pathways were identified in the expression association, DE and the gene enrichment analyses; these proteins can have a direct effect on meat quality. Cytoskeletal proteins and transmembrane anchoring molecules can influence meat quality by allowing cytoskeletal interaction with myocyte and organelle membranes, contributing to cytoskeletal structure and architecture maintenance postmortem.
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Affiliation(s)
- Joel D. Leal-Gutiérrez
- Department of Animal Sciences, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
| | - Mauricio A. Elzo
- Department of Animal Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Chad Carr
- Department of Animal Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Raluca G. Mateescu
- Department of Animal Sciences, University of Florida, Gainesville, Florida, United States of America
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Glycyrrhizin Blocks the Detrimental Effects of HMGB1 on Cortical Neurogenesis After Traumatic Neuronal Injury. Brain Sci 2020; 10:brainsci10100760. [PMID: 33096930 PMCID: PMC7593920 DOI: 10.3390/brainsci10100760] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 12/20/2022] Open
Abstract
Despite medical advances, neurological recovery after severe traumatic brain injury (TBI) remains poor. Elevated levels of high mobility group box protein-1 (HMGB1) are associated with poor outcomes; likely via interaction with receptors for advanced-glycation-end-products (RAGE). We examined the hypothesis that HMGB1 post-TBI is anti-neurogenic and whether this is pharmacologically reversible. Post-natal rat cortical mixed neuro-glial cell cultures were subjected to needle-scratch injury and examined for HMGB1-activation/neuroinflammation. HMGB1-related genes/networks were examined using genome-wide RNA-seq studies in cortical perilesional tissue samples from adult mice. Post-natal rat cortical neural stem/progenitor cell cultures were generated to quantify effects of injury-condition medium (ICM) on neurogenesis with/without RAGE antagonist glycyrrhizin. Needle-injury upregulated TNF-α/NOS-2 mRNA-expressions at 6 h, increased proportions of activated microglia, and caused neuronal loss at 24 h. Transcriptome analysis revealed activation of HMGB1 pathway genes/canonical pathways in vivo at 24 h. A 50% increase in HMGB1 protein expression, and nuclear-to-cytoplasmic translocation of HMGB1 in neurons and microglia at 24 h post-injury was demonstrated in vitro. ICM reduced total numbers/proportions of neuronal cells, but reversed by 0.5 μM glycyrrhizin. HMGB1 is activated following in vivo post mechanical injury, and glycyrrhizin alleviates detrimental effects of ICM on cortical neurogenesis. Our findings highlight glycyrrhizin as a potential therapeutic agent post-TBI.
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Solanki A, Yánez DC, Lau CI, Rowell J, Barbarulo A, Ross S, Sahni H, Crompton T. The transcriptional repressor Bcl6 promotes pre-TCR-induced thymocyte differentiation and attenuates Notch1 activation. Development 2020; 147:dev.192203. [PMID: 32907850 DOI: 10.1242/dev.192203] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022]
Abstract
Pre-T-cell receptor (TCR) signal transduction is required for developing thymocytes to differentiate from CD4-CD8- double-negative (DN) cell to CD4+CD8+ double-positive (DP) cell. Notch signalling is required for T-cell fate specification and must be maintained throughout β-selection, but inappropriate Notch activation in DN4 and DP cells is oncogenic. Here, we show that pre-TCR signalling leads to increased expression of the transcriptional repressor Bcl6 and that Bcl6 is required for differentiation to DP. Conditional deletion of Bcl6 from thymocytes reduced pre-TCR-induced differentiation to DP cells, disrupted expansion and enrichment of intracellular TCRβ+ cells within the DN population and increased DN4 cell death. Deletion also increased Notch1 activation and Notch-mediated transcription in the DP population. Thus, Bcl6 is required in thymocyte development for efficient differentiation from DN3 to DP and to attenuate Notch1 activation in DP cells. Given the importance of inappropriate NOTCH1 signalling in T-cell acute lymphoblastic leukaemia (T-ALL), and the involvement of BCL6 in other types of leukaemia, this study is important to our understanding of T-ALL.
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Affiliation(s)
- Anisha Solanki
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
| | - Diana C Yánez
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
| | - Ching-In Lau
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
| | - Jasmine Rowell
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
| | - Alessandro Barbarulo
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
| | - Susan Ross
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
| | - Hemant Sahni
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
| | - Tessa Crompton
- UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK
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Rodriguez JM, Pozo F, di Domenico T, Vazquez J, Tress ML. An analysis of tissue-specific alternative splicing at the protein level. PLoS Comput Biol 2020; 16:e1008287. [PMID: 33017396 PMCID: PMC7561204 DOI: 10.1371/journal.pcbi.1008287] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 10/15/2020] [Accepted: 08/25/2020] [Indexed: 01/09/2023] Open
Abstract
The role of alternative splicing is one of the great unanswered questions in cellular biology. There is strong evidence for alternative splicing at the transcript level, and transcriptomics experiments show that many splice events are tissue specific. It has been suggested that alternative splicing evolved in order to remodel tissue-specific protein-protein networks. Here we investigated the evidence for tissue-specific splicing among splice isoforms detected in a large-scale proteomics analysis. Although the data supporting alternative splicing is limited at the protein level, clear patterns emerged among the small numbers of alternative splice events that we could detect in the proteomics data. More than a third of these splice events were tissue-specific and most were ancient: over 95% of splice events that were tissue-specific in both proteomics and RNAseq analyses evolved prior to the ancestors of lobe-finned fish, at least 400 million years ago. By way of contrast, three in four alternative exons in the human gene set arose in the primate lineage, so our results cannot be extrapolated to the whole genome. Tissue-specific alternative protein forms in the proteomics analysis were particularly abundant in nervous and muscle tissues and their genes had roles related to the cytoskeleton and either the structure of muscle fibres or cell-cell connections. Our results suggest that this conserved tissue-specific alternative splicing may have played a role in the development of the vertebrate brain and heart. We manually curated a set of 255 splice events detected in a large-scale tissue-based proteomics experiment and found that more than a third had evidence of significant tissue-specific differences. Events that were significantly tissue-specific at the protein level were highly conserved; almost 75% evolved over 400 million years ago. The tissues in which we found most evidence for tissue-specific splicing were nervous tissues and cardiac tissues. Genes with tissue-specific events in these two tissues had functions related to important cellular structures in brain and heart tissues. These splice events may have been essential for the development of vertebrate heart and muscle. However, our data set may not be representative of alternative exons as a whole. We found that most tissue specific splicing was strongly conserved, but just 5% of annotated alternative exons in the human gene set are ancient. More than three quarters of alternative exons are primate-derived. Although the analysis does not provide a definitive answer to the question of the functional role of alternative splicing, our results do indicate that alternative splice variants may have played a significant part in the evolution of brain and heart tissues in vertebrates.
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Affiliation(s)
- Jose Manuel Rodriguez
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Calle Melchor Fernandez, Madrid, Spain
| | - Fernando Pozo
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez, Madrid, Spain
| | - Tomas di Domenico
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez, Madrid, Spain
| | - Jesus Vazquez
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Calle Melchor Fernandez, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Michael L. Tress
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Calle Melchor Fernandez, Madrid, Spain
- * E-mail:
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DiMSum: an error model and pipeline for analyzing deep mutational scanning data and diagnosing common experimental pathologies. Genome Biol 2020; 21:207. [PMID: 32799905 PMCID: PMC7429474 DOI: 10.1186/s13059-020-02091-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 07/05/2020] [Indexed: 12/30/2022] Open
Abstract
Deep mutational scanning (DMS) enables multiplexed measurement of the effects of thousands of variants of proteins, RNAs, and regulatory elements. Here, we present a customizable pipeline, DiMSum, that represents an end-to-end solution for obtaining variant fitness and error estimates from raw sequencing data. A key innovation of DiMSum is the use of an interpretable error model that captures the main sources of variability arising in DMS workflows, outperforming previous methods. DiMSum is available as an R/Bioconda package and provides summary reports to help researchers diagnose common DMS pathologies and take remedial steps in their analyses.
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40
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Adar RNA editing-dependent and -independent effects are required for brain and innate immune functions in Drosophila. Nat Commun 2020; 11:1580. [PMID: 32221286 PMCID: PMC7101428 DOI: 10.1038/s41467-020-15435-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 02/24/2020] [Indexed: 12/31/2022] Open
Abstract
ADAR RNA editing enzymes are high-affinity dsRNA-binding proteins that deaminate adenosines to inosines in pre-mRNA hairpins and also exert editing-independent effects. We generated a Drosophila AdarE374A mutant strain encoding a catalytically inactive Adar with CRISPR/Cas9. We demonstrate that Adar adenosine deamination activity is necessary for normal locomotion and prevents age-dependent neurodegeneration. The catalytically inactive protein, when expressed at a higher than physiological level, can rescue neurodegeneration in Adar mutants, suggesting also editing-independent effects. Furthermore, loss of Adar RNA editing activity leads to innate immune induction, indicating that Drosophila Adar, despite being the homolog of mammalian ADAR2, also has functions similar to mammalian ADAR1. The innate immune induction in fly Adar mutants is suppressed by silencing of Dicer-2, which has a RNA helicase domain similar to MDA5 that senses unedited dsRNAs in mammalian Adar1 mutants. Our work demonstrates that the single Adar enzyme in Drosophila unexpectedly has dual functions.
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Ait-Hamlat A, Zea DJ, Labeeuw A, Polit L, Richard H, Laine E. Transcripts' Evolutionary History and Structural Dynamics Give Mechanistic Insights into the Functional Diversity of the JNK Family. J Mol Biol 2020; 432:2121-2140. [PMID: 32067951 DOI: 10.1016/j.jmb.2020.01.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/03/2020] [Accepted: 01/28/2020] [Indexed: 12/14/2022]
Abstract
Alternative splicing and alternative initiation/termination transcription sites have the potential to greatly expand the proteome in eukaryotes by producing several transcript isoforms from the same gene. Although these mechanisms are well described at the genomic level, little is known about their contribution to protein evolution and their impact at the protein structure level. Here, we address both issues by reconstructing the evolutionary history of transcripts and by modeling the tertiary structures of the corresponding protein isoforms. We reconstruct phylogenetic forests relating 60 protein-coding transcripts from the c-Jun N-terminal kinase (JNK) family observed in seven species. We identify two alternative splicing events of ancient origin and show that they induce subtle changes in the protein's structural dynamics. We highlight a previously uncharacterized transcript whose predicted structure seems stable in solution. We further demonstrate that orphan transcripts, for which no phylogeny could be reconstructed, display peculiar sequence and structural properties. Our approach is implemented in PhyloSofS (Phylogenies of Splicing Isoforms Structures), a fully automated computational tool freely available at https://github.com/PhyloSofS-Team/PhyloSofS.
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Affiliation(s)
- Adel Ait-Hamlat
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Paris, 75005, France
| | - Diego Javier Zea
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Paris, 75005, France
| | - Antoine Labeeuw
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Paris, 75005, France
| | - Lélia Polit
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Paris, 75005, France
| | - Hugues Richard
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Paris, 75005, France.
| | - Elodie Laine
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Paris, 75005, France.
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42
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Frumkin I, Yofe I, Bar-Ziv R, Gurvich Y, Lu YY, Voichek Y, Towers R, Schirman D, Krebber H, Pilpel Y. Evolution of intron splicing towards optimized gene expression is based on various Cis- and Trans-molecular mechanisms. PLoS Biol 2019; 17:e3000423. [PMID: 31442222 PMCID: PMC6728054 DOI: 10.1371/journal.pbio.3000423] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 09/05/2019] [Accepted: 08/08/2019] [Indexed: 01/09/2023] Open
Abstract
Splicing expands, reshapes, and regulates the transcriptome of eukaryotic organisms. Despite its importance, key questions remain unanswered, including the following: Can splicing evolve when organisms adapt to new challenges? How does evolution optimize inefficiency of introns’ splicing and of the splicing machinery? To explore these questions, we evolved yeast cells that were engineered to contain an inefficiently spliced intron inside a gene whose protein product was under selection for an increased expression level. We identified a combination of mutations in Cis (within the gene of interest) and in Trans (in mRNA-maturation machinery). Surprisingly, the mutations in Cis resided outside of known intronic functional sites and improved the intron’s splicing efficiency potentially by easing tight mRNA structures. One of these mutations hampered a protein’s domain that was not under selection, demonstrating the evolutionary flexibility of multi-domain proteins as one domain functionality was improved at the expense of the other domain. The Trans adaptations resided in two proteins, Npl3 and Gbp2, that bind pre-mRNAs and are central to their maturation. Interestingly, these mutations either increased or decreased the affinity of these proteins to mRNA, presumably allowing faster spliceosome recruitment or increased time before degradation of the pre-mRNAs, respectively. Altogether, our work reveals various mechanistic pathways toward optimizations of intron splicing to ultimately adapt gene expression patterns to novel demands. An experimental evolution study involving an inefficiently spliced intron reveals that the splicing machinery, introns, and RNA quality control factors evolve in Cis and in Trans when cells optimize their transcriptome to new challenges.
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Affiliation(s)
- Idan Frumkin
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- * E-mail: (IF); (YP)
| | - Ido Yofe
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Raz Bar-Ziv
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yonat Gurvich
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yen-Yun Lu
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Göttingen, Germany
| | - Yoav Voichek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ruth Towers
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Dvir Schirman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Heike Krebber
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Göttingen, Germany
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- * E-mail: (IF); (YP)
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43
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Uncovering the signaling landscape controlling breast cancer cell migration identifies novel metastasis driver genes. Nat Commun 2019; 10:2983. [PMID: 31278301 PMCID: PMC6611796 DOI: 10.1038/s41467-019-11020-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/06/2019] [Indexed: 12/18/2022] Open
Abstract
Ttriple-negative breast cancer (TNBC) is an aggressive and highly metastatic breast cancer subtype. Enhanced TNBC cell motility is a prerequisite of TNBC cell dissemination. Here, we apply an imaging-based RNAi phenotypic cell migration screen using two highly motile TNBC cell lines (Hs578T and MDA-MB-231) to provide a repository of signaling determinants that functionally drive TNBC cell motility. We have screened ~4,200 target genes individually and discovered 133 and 113 migratory modulators of Hs578T and MDA-MB-231, respectively, which are linked to signaling networks predictive for breast cancer progression. The splicing factors PRPF4B and BUD31 and the transcription factor BPTF are essential for cancer cell migration, amplified in human primary breast tumors and associated with metastasis-free survival. Depletion of PRPF4B, BUD31 and BPTF causes primarily down regulation of genes involved in focal adhesion and ECM-interaction pathways. PRPF4B is essential for TNBC metastasis formation in vivo, making PRPF4B a candidate for further drug development. Triple-negative breast cancers (TNBC) have enhanced migratory behaviour. Here, the authors perform a phenotypic imaging-based RNAi screen to identify several genes associated with regulation of migratory phenotypes and show that one of the regulators, PRPF4B, mediates metastasis in TNBC in mice.
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44
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Biallelic variants in POLR3GL cause endosteal hyperostosis and oligodontia. Eur J Hum Genet 2019; 28:31-39. [PMID: 31089205 DOI: 10.1038/s41431-019-0427-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 04/03/2019] [Accepted: 04/16/2019] [Indexed: 11/08/2022] Open
Abstract
RNA polymerase III (Pol III) is an essential 17-subunit complex responsible for the transcription of small housekeeping RNAs such as transfer RNAs and 5S ribosomal RNA. Biallelic variants in four genes (POLR3A, POLR3B, and POLR1C and POLR3K) encoding Pol III subunits have previously been found in individuals with (neuro-) developmental disorders. In this report, we describe three individuals with biallelic variants in POLR3GL, a gene encoding a Pol III subunit that has not been associated with disease before. Using whole exome sequencing in a monozygotic twin and an unrelated individual, we detected homozygous and compound heterozygous POLR3GL splice acceptor site variants. RNA sequencing confirmed the loss of full-length POLR3GL RNA transcripts in blood samples of the individuals. The phenotypes of the described individuals are mainly characterized by axial endosteal hyperostosis, oligodontia, short stature, and mild facial dysmorphisms. These features largely fit within the spectrum of phenotypes caused by previously described biallelic variants in POLR3A, POLR3B, POLR1C, and POLR3K. These findings further expand the spectrum of POLR3-related disorders and implicate that POLR3GL should be included in genetic testing if such disorders are suspected.
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45
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Differential gene expression in the mesocorticolimbic system of innately high- and low-impulsive rats. Behav Brain Res 2019; 364:193-204. [DOI: 10.1016/j.bbr.2019.01.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 12/12/2018] [Accepted: 01/12/2019] [Indexed: 02/02/2023]
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46
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Colgan TJ, Fletcher IK, Arce AN, Gill RJ, Ramos Rodrigues A, Stolle E, Chittka L, Wurm Y. Caste- and pesticide-specific effects of neonicotinoid pesticide exposure on gene expression in bumblebees. Mol Ecol 2019; 28:1964-1974. [PMID: 30843300 PMCID: PMC6563198 DOI: 10.1111/mec.15047] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 01/31/2019] [Accepted: 02/05/2019] [Indexed: 01/10/2023]
Abstract
Social bees are important insect pollinators of wildflowers and agricultural crops, making their reported declines a global concern. A major factor implicated in these declines is the widespread use of neonicotinoid pesticides. Indeed, recent research has demonstrated that exposure to low doses of these neurotoxic pesticides impairs bee behaviours important for colony function and survival. However, our understanding of the molecular-genetic pathways that lead to such effects is limited, as is our knowledge of how effects may differ between colony members. To understand what genes and pathways are affected by exposure of bumblebee workers and queens to neonicotinoid pesticides, we implemented a transcriptome-wide gene expression study. We chronically exposed Bombus terrestriscolonies to either clothianidin or imidacloprid at field-realistic concentrations while controlling for factors including colony social environment and worker age. We reveal that genes involved in important biological processes including mitochondrial function are differentially expressed in response to neonicotinoid exposure. Additionally, clothianidin exposure had stronger effects on gene expression amplitude and alternative splicing than imidacloprid. Finally, exposure affected workers more strongly than queens. Our work demonstrates how RNA-Seq transcriptome profiling can provide detailed novel insight on the mechanisms mediating pesticide toxicity to a key insect pollinator.
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Affiliation(s)
- Thomas J Colgan
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.,School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Isabel K Fletcher
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Andres N Arce
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Richard J Gill
- Department of Life Sciences, Imperial College London, Ascot, UK
| | | | - Eckart Stolle
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Lars Chittka
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Yannick Wurm
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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47
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Xiong J, Jiang X, Ditsiou A, Gao Y, Sun J, Lowenstein ED, Huang S, Khaitovich P. Predominant patterns of splicing evolution on human, chimpanzee and macaque evolutionary lineages. Hum Mol Genet 2019; 27:1474-1485. [PMID: 29452398 DOI: 10.1093/hmg/ddy058] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 02/12/2018] [Indexed: 11/14/2022] Open
Abstract
Although splicing is widespread and evolves rapidly among species, the mechanisms driving this evolution, as well as its functional implications, are not yet fully understood. We analyzed the evolution of splicing patterns based on transcriptome data from five tissues of humans, chimpanzees, rhesus macaques and mice. In total, 1526 exons and exon sets from 1236 genes showed significant splicing differences among primates. More than 60% of these differences represent constitutive-to-alternative exon transitions while an additional 25% represent changes in exon inclusion frequency. These two dominant evolutionary patterns have contrasting conservation, regulation and functional features. The sum of these features indicates that, despite their prevalence, constitutive-to-alternative exon transitions do not substantially contribute to long-term functional transcriptome changes. Conversely, changes in exon inclusion frequency appear to be functionally relevant, especially for changes taking place in the brain on the human evolutionary lineage.
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Affiliation(s)
- Jieyi Xiong
- Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Xi Jiang
- Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China
| | - Angeliki Ditsiou
- JBC/WTB Biocentre, University of Dundee, DD1 5EH Scotland, UK.,JMS Building, University of Sussex, BN1 9QG Brighton, UK
| | - Yang Gao
- Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China
| | - Jing Sun
- Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China
| | - Elijah D Lowenstein
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.,Freie Universität Berlin, 14195 Berlin, Germany
| | - Shuyun Huang
- Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Philipp Khaitovich
- Skolkovo Institute of Science and Technology, 143025 Skolkovo, Russia.,Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031 Shanghai, China
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48
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Chabbert CD, Eberhart T, Guccini I, Krek W, Kovacs WJ. Correction of gene model annotations improves isoform abundance estimates: the example of ketohexokinase ( Khk). F1000Res 2018; 7:1956. [PMID: 31001414 PMCID: PMC6464065 DOI: 10.12688/f1000research.17082.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/20/2019] [Indexed: 12/13/2022] Open
Abstract
Next generation sequencing protocols such as RNA-seq have made the genome-wide characterization of the transcriptome a crucial part of many research projects in biology. Analyses of the resulting data provide key information on gene expression and in certain cases on exon or isoform usage. The emergence of transcript quantification software such as Salmon has enabled researchers to efficiently estimate isoform and gene expressions across the genome while tremendously reducing the necessary computational power. Although overall gene expression estimations were shown to be accurate, isoform expression quantifications appear to be a more challenging task. Low expression levels and uneven or insufficient coverage were reported as potential explanations for inconsistent estimates. Here, through the example of the ketohexokinase (
Khk) gene in mouse, we demonstrate that the use of an incorrect gene annotation can also result in erroneous isoform quantification results. Manual correction of the input
Khk gene model provided a much more accurate estimation of relative
Khk isoform expression when compared to quantitative PCR (qPCR measurements). In particular, removal of an unexpressed retained intron and a proper adjustment of the 5’ and 3’ untranslated regions both had a strong impact on the correction of erroneous estimates. Finally, we observed a better concordance in isoform quantification between datasets and sequencing strategies when relying on the newly generated
Khk annotations. These results highlight the importance of accurate gene models and annotations for correct isoform quantification and reassert the need for orthogonal methods of estimation of isoform expression to confirm important findings.
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Affiliation(s)
| | - Tanja Eberhart
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, 8093, Switzerland
| | - Ilaria Guccini
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, 8093, Switzerland
| | - Wilhelm Krek
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, 8093, Switzerland
| | - Werner J Kovacs
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, 8093, Switzerland
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49
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Zhu Y, Sousa AMM, Gao T, Skarica M, Li M, Santpere G, Esteller-Cucala P, Juan D, Ferrández-Peral L, Gulden FO, Yang M, Miller DJ, Marques-Bonet T, Imamura Kawasawa Y, Zhao H, Sestan N. Spatiotemporal transcriptomic divergence across human and macaque brain development. Science 2018; 362:362/6420/eaat8077. [PMID: 30545855 DOI: 10.1126/science.aat8077] [Citation(s) in RCA: 223] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 11/08/2018] [Indexed: 12/12/2022]
Abstract
Human nervous system development is an intricate and protracted process that requires precise spatiotemporal transcriptional regulation. We generated tissue-level and single-cell transcriptomic data from up to 16 brain regions covering prenatal and postnatal rhesus macaque development. Integrative analysis with complementary human data revealed that global intraspecies (ontogenetic) and interspecies (phylogenetic) regional transcriptomic differences exhibit concerted cup-shaped patterns, with a late fetal-to-infancy (perinatal) convergence. Prenatal neocortical transcriptomic patterns revealed transient topographic gradients, whereas postnatal patterns largely reflected functional hierarchy. Genes exhibiting heterotopic and heterochronic divergence included those transiently enriched in the prenatal prefrontal cortex or linked to autism spectrum disorder and schizophrenia. Our findings shed light on transcriptomic programs underlying the evolution of human brain development and the pathogenesis of neuropsychiatric disorders.
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Affiliation(s)
- Ying Zhu
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA.,Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - André M M Sousa
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Tianliuyun Gao
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Mario Skarica
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Mingfeng Li
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Gabriel Santpere
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | | | - David Juan
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
| | | | - Forrest O Gulden
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Mo Yang
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Daniel J Miller
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Yuka Imamura Kawasawa
- Departments of Pharmacology and Biochemistry and Molecular Biology, Institute for Personalized Medicine, Penn State University College of Medicine, Hershey, PA, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Nenad Sestan
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA. .,Departments of Genetics, Psychiatry, and Comparative Medicine, Program in Cellular Neuroscience, Neurodegeneration and Repair, and Yale Child Study Center, Yale School of Medicine, New Haven, CT, USA
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50
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Wolfe SA, Farris SP, Mayfield JE, Heaney CF, Erickson EK, Harris RA, Mayfield RD, Raab-Graham KF. Ethanol and a rapid-acting antidepressant produce overlapping changes in exon expression in the synaptic transcriptome. Neuropharmacology 2018; 146:289-299. [PMID: 30419244 DOI: 10.1016/j.neuropharm.2018.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 10/03/2018] [Accepted: 11/07/2018] [Indexed: 01/02/2023]
Abstract
Alcohol use disorder (AUD) and major depressive disorder (MDD) are prevalent, debilitating, and highly comorbid disorders. The molecular changes that underlie their comorbidity are beginning to emerge. For example, recent evidence showed that acute ethanol exposure produces rapid antidepressant-like biochemical and behavioral responses. Both ethanol and fast-acting antidepressants block N-methyl-D-aspartate receptor (NMDAR) activity, leading to synaptic changes and long-lasting antidepressant-like behavioral effects. We used RNA sequencing to analyze changes in the synaptic transcriptome after acute treatment with ethanol or the NMDAR antagonist, Ro 25-6981. Ethanol and Ro 25-6981 induced differential, independent changes in gene expression. In contrast with gene-level expression, ethanol and Ro 25-6981 produced overlapping changes in exons, as measured by analysis of differentially expressed exons (DEEs). A prominent overlap in genes with DEEs indicated that changes in exon usage were important for both ethanol and Ro 25-6981 action. Structural modeling provided evidence that ethanol-induced exon expression in the NMDAR1 amino-terminal domain could induce conformational changes and thus alter NMDAR function. These findings suggest that the rapid antidepressant effects of ethanol and NMDAR antagonists reported previously may depend on synaptic exon usage rather than gene expression.
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Affiliation(s)
- Sarah A Wolfe
- Committee on the Neurobiology of Addictive Disorders, The Scripps Research Institute, La Jolla, CA, 92037, United States
| | - Sean P Farris
- Waggoner Center for Alcohol and Addiction Research, Department of Neuroscience, University of Texas at Austin, 2500 Speedway, Austin, TX, 78712, United States
| | - Joshua E Mayfield
- Department of Molecular Biosciences, University of Texas at Austin, 2500 Speedway, Austin, TX, 78712, United States
| | - Chelcie F Heaney
- Department of Physiology and Pharmacology, Wake Forest University Health Sciences, Medical Center Boulevard, Winston-Salem, NC, 27157-1083, United States
| | - Emma K Erickson
- Waggoner Center for Alcohol and Addiction Research, Department of Neuroscience, University of Texas at Austin, 2500 Speedway, Austin, TX, 78712, United States
| | - R Adron Harris
- Waggoner Center for Alcohol and Addiction Research, Department of Neuroscience, University of Texas at Austin, 2500 Speedway, Austin, TX, 78712, United States
| | - R Dayne Mayfield
- Waggoner Center for Alcohol and Addiction Research, Department of Neuroscience, University of Texas at Austin, 2500 Speedway, Austin, TX, 78712, United States
| | - Kimberly F Raab-Graham
- Department of Physiology and Pharmacology, Wake Forest University Health Sciences, Medical Center Boulevard, Winston-Salem, NC, 27157-1083, United States.
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