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Paukszto Ł, Wiśniewska J, Liszewska E, Majewska M, Jastrzębski J, Jankowski J, Ciereszko A, Słowińska M. Specific expression of alternatively spliced genes in the turkey (Meleagris gallopavo) reproductive tract revealed their function in spermatogenesis and post-testicular sperm maturation. Poult Sci 2023; 102:102484. [PMID: 36709584 PMCID: PMC9922982 DOI: 10.1016/j.psj.2023.102484] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/22/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023] Open
Abstract
The tissue-specific profile of alternatively spliced genes (ASGs) and their involvement in reproduction processes characteristic of turkey testis, epididymis, and ductus deferens were investigated for the first time in birds. Deep sequencing of male turkey reproductive tissue RNA samples (n = 6) was performed using Illumina RNA-Seq with 2 independent methods, rMATs and SUPPA2, for differential alternative splicing (DAS) event prediction. The expression of selected ASGs was validated using quantitative real-time reverse transcriptase-polymerase chain reaction. The testis was found to be the site of the highest number of posttranscriptional splicing events within the reproductive tract, and skipping exons were the most frequently occurring class of alternative splicing (AS) among the reproductive tract. Statistical analysis revealed 86, 229, and 6 DAS events in the testis/epididymis, testis/ductus deferens, and epididymis/ductus deferens comparison, respectively. Alternative splicing was found to be a mechanism of gene expression regulation within the turkey reproduction tract. In testis, modification was observed for spermatogenesis specific genes; the changes in 5' UTR could act as regulator of MEIG1 expression (a player during spermatocytes meiosis), and modification of 3' UTR led to diversification of CREM mRNA (modulator of gene expression related to the structuring of mature spermatozoa). Sperm tail formation can be regulated by changes in the 5' UTR of testicular SLC9A3R1 and gene silencing by producing dysfunctional variants of ODF2 in the testis and ATP1B3 in the epididymis. Predicted differentially ASGs in the turkey reproductive tract seem to be involved in the regulation of spermatogenesis, including acrosome formation and sperm tail formation and binding of sperm to the zona pellucida. Several ASGs were classified as cilia by actin and microtubule cytoskeleton organization. Such genes may play a role in the organization of sperm flagellum and post-testicular motility development. To our knowledge, this is the first functional investigation of alternatively spliced genes associated with tissue-specific processes in the turkey reproductive tract.
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Affiliation(s)
- Łukasz Paukszto
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology; University of Warmia and Mazury in Olsztyn, 10-719, Olsztyn, Poland
| | - Joanna Wiśniewska
- Department of Biological Function of Food, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences in Olsztyn, 10-748, Olsztyn, Poland
| | - Ewa Liszewska
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences in Olsztyn, 10-748, Olsztyn, Poland
| | - Marta Majewska
- Department of Human Physiology and Pathophysiology, School of Medicine, Collegium Medicum; University of Warmia and Mazury in Olsztyn, 10-561 Olsztyn, Poland
| | - Jan Jastrzębski
- Department of Plant Physiology, Genetics, and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719, Olsztyn, Poland
| | - Jan Jankowski
- Department of Poultry Science, University of Warmia and Mazury in Olsztyn, 10-719, Olsztyn, Poland
| | - Andrzej Ciereszko
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences in Olsztyn, 10-748, Olsztyn, Poland
| | - Mariola Słowińska
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences in Olsztyn, 10-748, Olsztyn, Poland.
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Linder J, Koplik SE, Kundaje A, Seelig G. Deciphering the impact of genetic variation on human polyadenylation using APARENT2. Genome Biol 2022; 23:232. [PMID: 36335397 PMCID: PMC9636789 DOI: 10.1186/s13059-022-02799-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 10/19/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND 3'-end processing by cleavage and polyadenylation is an important and finely tuned regulatory process during mRNA maturation. Numerous genetic variants are known to cause or contribute to human disorders by disrupting the cis-regulatory code of polyadenylation signals. Yet, due to the complexity of this code, variant interpretation remains challenging. RESULTS We introduce a residual neural network model, APARENT2, that can infer 3'-cleavage and polyadenylation from DNA sequence more accurately than any previous model. This model generalizes to the case of alternative polyadenylation (APA) for a variable number of polyadenylation signals. We demonstrate APARENT2's performance on several variant datasets, including functional reporter data and human 3' aQTLs from GTEx. We apply neural network interpretation methods to gain insights into disrupted or protective higher-order features of polyadenylation. We fine-tune APARENT2 on human tissue-resolved transcriptomic data to elucidate tissue-specific variant effects. By combining APARENT2 with models of mRNA stability, we extend aQTL effect size predictions to the entire 3' untranslated region. Finally, we perform in silico saturation mutagenesis of all human polyadenylation signals and compare the predicted effects of [Formula: see text] million variants against gnomAD. While loss-of-function variants were generally selected against, we also find specific clinical conditions linked to gain-of-function mutations. For example, we detect an association between gain-of-function mutations in the 3'-end and autism spectrum disorder. To experimentally validate APARENT2's predictions, we assayed clinically relevant variants in multiple cell lines, including microglia-derived cells. CONCLUSIONS A sequence-to-function model based on deep residual learning enables accurate functional interpretation of genetic variants in polyadenylation signals and, when coupled with large human variation databases, elucidates the link between functional 3'-end mutations and human health.
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Affiliation(s)
| | | | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, USA
- Department of Computer Science, Stanford University, Stanford, USA
| | - Georg Seelig
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, USA
- Department of Electrical and Computer Engineering, University of Washington, Seattle, USA
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Mohanan NK, Shaji F, Koshre GR, Laishram RS. Alternative polyadenylation: An enigma of transcript length variation in health and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1692. [PMID: 34581021 DOI: 10.1002/wrna.1692] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/16/2021] [Accepted: 08/24/2021] [Indexed: 12/19/2022]
Abstract
Alternative polyadenylation (APA) is a molecular mechanism during a pre-mRNA processing that involves usage of more than one polyadenylation site (PA-site) generating transcripts of varying length from a single gene. The location of a PA-site affects transcript length and coding potential of an mRNA contributing to both mRNA and protein diversification. This variation in the transcript length affects mRNA stability and translation, mRNA subcellular and tissue localization, and protein function. APA is now considered as an important regulatory mechanism in the pathophysiology of human diseases. An important consequence of the changes in the length of 3'-untranslated region (UTR) from disease-induced APA is altered protein expression. Yet, the relationship between 3'-UTR length and protein expression remains a paradox in a majority of diseases. Here, we review occurrence of APA, mechanism of PA-site selection, and consequences of transcript length variation in different diseases. Emerging evidence reveals coordinated involvement of core RNA processing factors including poly(A) polymerases in the PA-site selection in diseases-associated APAs. Targeting such APA regulators will be therapeutically significant in combating drug resistance in cancer and other complex diseases. This article is categorized under: RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Disease Translation > Regulation.
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Affiliation(s)
- Neeraja K Mohanan
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Manipal Academy of Higher Education, Manipal, India
| | - Feba Shaji
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Ganesh R Koshre
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Manipal Academy of Higher Education, Manipal, India
| | - Rakesh S Laishram
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
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4
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Gorukmez O, Gorukmez O. First Infertile Case with CSTF2TGene Mutation. Mol Syndromol 2020; 11:228-231. [PMID: 33224017 DOI: 10.1159/000509686] [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: 04/15/2020] [Accepted: 06/11/2020] [Indexed: 12/13/2022] Open
Abstract
Male infertility is multifactorial and presents with heterogeneous phenotypic features. Genetic factors are responsible for up to 15% of the male infertility cases. Loss of the Cstf2t gene in male mice results in infertility. No disease-associated mutations have been described for this gene in infertile men. Here, we report a patient diagnosed with infertility in whom a homozygous nonsense mutation in the CSTF2T gene was detected by clinical exome sequencing. This case is the first description of an infertile patient who has a homozygous CSTF2T mutation.
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Affiliation(s)
- Ozlem Gorukmez
- Department of Medical Genetics, Bursa Yüksek İhtisas Training and Research Hospital, Bursa, Turkey
| | - Orhan Gorukmez
- Department of Medical Genetics, Bursa Yüksek İhtisas Training and Research Hospital, Bursa, Turkey
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Grozdanov PN, Masoumzadeh E, Kalscheuer VM, Bienvenu T, Billuart P, Delrue MA, Latham MP, MacDonald CC. A missense mutation in the CSTF2 gene that impairs the function of the RNA recognition motif and causes defects in 3' end processing is associated with intellectual disability in humans. Nucleic Acids Res 2020; 48:9804-9821. [PMID: 32816001 PMCID: PMC7515730 DOI: 10.1093/nar/gkaa689] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 08/03/2020] [Accepted: 08/18/2020] [Indexed: 11/25/2022] Open
Abstract
CSTF2 encodes an RNA-binding protein that is essential for mRNA cleavage and polyadenylation (C/P). No disease-associated mutations have been described for this gene. Here, we report a mutation in the RNA recognition motif (RRM) of CSTF2 that changes an aspartic acid at position 50 to alanine (p.D50A), resulting in intellectual disability in male patients. In mice, this mutation was sufficient to alter polyadenylation sites in over 1300 genes critical for brain development. Using a reporter gene assay, we demonstrated that C/P efficiency of CSTF2D50A was lower than wild type. To account for this, we determined that p.D50A changed locations of amino acid side chains altering RNA binding sites in the RRM. The changes modified the electrostatic potential of the RRM leading to a greater affinity for RNA. These results highlight the significance of 3′ end mRNA processing in expression of genes important for brain plasticity and neuronal development.
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Affiliation(s)
- Petar N Grozdanov
- Department of Cell Biology & Biochemistry, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430-6540, USA
| | - Elahe Masoumzadeh
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Vera M Kalscheuer
- Max Planck Institute for Molecular Genetics, Research Group Development and Disease, Ihnestr. 63-73, D-14195 Berlin, Germany
| | - Thierry Bienvenu
- Institut de Psychiatrie et de Neurosciences de Paris, Inserm U1266, 102 rue de la Santé, 75014 Paris, France
| | - Pierre Billuart
- Institut de Psychiatrie et de Neurosciences de Paris, Inserm U1266, 102 rue de la Santé, 75014 Paris, France
| | - Marie-Ange Delrue
- Département de Génétique Médicale, CHU Sainte Justine, Montréal, Canada
| | - Michael P Latham
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Clinton C MacDonald
- Department of Cell Biology & Biochemistry, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430-6540, USA
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MacDonald CC. Tissue-specific mechanisms of alternative polyadenylation: Testis, brain, and beyond (2018 update). WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1526. [PMID: 30816016 PMCID: PMC6617714 DOI: 10.1002/wrna.1526] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/05/2018] [Accepted: 01/14/2019] [Indexed: 12/21/2022]
Abstract
Alternative polyadenylation (APA) is how genes choose different sites for 3′ end formation for mRNAs during transcription. APA often occurs in a tissue‐ or developmental stage‐specific manner that can significantly affect gene activity by changing the protein product generated, the stability of the transcript, its localization within the cell, or its translatability. Despite the important regulatory effects that APA has on tissue‐specific gene expression, only a few examples have been characterized mechanistically. In this 2018 update to our 2010 review, we examine mechanisms for the control of APA and update our understanding of the older mechanisms since 2010. We once postulated the existence of tissue‐specific factors in APA. However, while a few tissue‐specific polyadenylation factors are known, the emerging conclusion is that the majority of APA is accomplished by altering levels of core polyadenylation proteins. Examples of those core proteins include CSTF2, CPSF1, and subunits of mammalian cleavage factor I. But despite support for these mechanisms, no one has yet documented any of these proteins changing in either a tissue‐specific or developmental manner. Given the profound effect that APA can have on gene expression and human health, improved understanding of tissue‐specific APA could lead to numerous advances in gene activity control. This article is categorized under:RNA Processing > 3′ End Processing RNA in Disease and Development > RNA in Development
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Affiliation(s)
- Clinton C MacDonald
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas
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7
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Grozdanov PN, Masoumzadeh E, Latham MP, MacDonald CC. The structural basis of CstF-77 modulation of cleavage and polyadenylation through stimulation of CstF-64 activity. Nucleic Acids Res 2018; 46:12022-12039. [PMID: 30257008 PMCID: PMC6294498 DOI: 10.1093/nar/gky862] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 08/31/2018] [Accepted: 09/12/2018] [Indexed: 01/14/2023] Open
Abstract
Cleavage and polyadenylation (C/P) of mRNA is an important cellular process that promotes increased diversity of mRNA isoforms and could change their stability in different cell types. The cleavage stimulation factor (CstF) complex, part of the C/P machinery, binds to U- and GU-rich sequences located downstream from the cleavage site through its RNA-binding subunit, CstF-64. Less is known about the function of the other two subunits of CstF, CstF-77 and CstF-50. Here, we show that the carboxy-terminus of CstF-77 plays a previously unrecognized role in enhancing C/P by altering how the RNA recognition motif (RRM) of CstF-64 binds RNA. In support of this finding, we also show that CstF-64 relies on CstF-77 to be transported to the nucleus; excess CstF-64 localizes to the cytoplasm, possibly via interaction with cytoplasmic RNAs. Reverse genetics and nuclear magnetic resonance studies of recombinant CstF-64 (RRM-Hinge) and CstF-77 (monkeytail-carboxy-terminal domain) indicate that the last 30 amino acids of CstF-77 increases the stability of the RRM, thus altering the affinity of the complex for RNA. These results provide new insights into the mechanism by which CstF regulates the location of the RNA cleavage site during C/P.
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Affiliation(s)
- Petar N Grozdanov
- Department of Cell Biology & Biochemistry, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430-6540, USA
| | - Elahe Masoumzadeh
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Michael P Latham
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Clinton C MacDonald
- Department of Cell Biology & Biochemistry, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430-6540, USA
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8
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MacDonald CC, Grozdanov PN. Nonsense in the testis: multiple roles for nonsense-mediated decay revealed in male reproduction. Biol Reprod 2018; 96:939-947. [PMID: 28444146 PMCID: PMC5803779 DOI: 10.1093/biolre/iox033] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/20/2017] [Indexed: 01/23/2023] Open
Abstract
Nonsense-mediated mRNA decay, or NMD, is a quality control mechanism that identifies cytoplasmic mRNAs containing translational termination (stop) codons in specific contexts—either premature termination codons or unusually long 3΄ untranslated regions (UTRs)—and targets them for degradation. In recent studies, researchers in different labs have knocked out important genes involved in NMD, the up-frameshift genes Upf2 and Upf3a, and one component of chromatoid bodies, the Tudor domain-containing protein Tdrd6, and examined the consequences for spermatogenesis. Disruption of Upf2 during early stages of spermatogenesis resulted in disappearance of nearly all spermatogenic cells through loss of NMD. However, disruption of Upf2 during postmeiotic stages resulted in decreased long 3΄ UTR-mediated NMD but no interruption of exon junction-associated NMD. This difference in NMD targeting is possibly due to increased expression of Upf3a in postmeiotic germ cells that antagonizes the functions of Upf3b and somehow favors long 3΄ UTR-mediated NMD. Tying these all together, loss of Tdrd6, a structural component of the germ cell-specific cytoplasmic structures called chromatoid bodies, also resulted in loss of long 3΄ UTR-mediated NMD by interfering with UPF1/UPF2 interactions, delocalizing UPF1, and destroying chromatoid body integrity. These results suggest that chromatoid bodies play a specialized role in modulating the NMD machinery in postmeiotic spermatids.
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Affiliation(s)
- Clinton C. MacDonald
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas
- Correspondence: Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430-6540, USA. Tel: +1-806-743-2524; Fax: +1-806-743-2990; E-mail:
| | - Petar N. Grozdanov
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas
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9
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Grozdanov PN, Li J, Yu P, Yan W, MacDonald CC. Cstf2t Regulates expression of histones and histone-like proteins in male germ cells. Andrology 2018; 6:605-615. [PMID: 29673127 DOI: 10.1111/andr.12488] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/02/2018] [Accepted: 03/05/2018] [Indexed: 12/18/2022]
Abstract
Formation of the 3' ends of mature mRNAs requires recognition of the correct site within the last exon, cleavage of the nascent pre-mRNA, and, for most mRNAs, addition of a poly(A) tail. Several factors are involved in recognition of the correct 3'-end site. The cleavage stimulation factor (CstF) has three subunits, CstF-50 (gene symbol Cstf1), CstF-64 (Cstf2), and CstF-77 (Cstf3). Of these, CstF-64 is the RNA-binding subunit that interacts with the pre-mRNA downstream of the cleavage site. In male germ cells where CstF-64 is not expressed, a paralog, τCstF-64 (gene symbol Cstf2t) assumes its functions. Accordingly, Cstf2t knockout (Cstf2t-/- ) mice exhibit male infertility due to defective development of spermatocytes and spermatids. To discover differentially expressed genes responsive to τCstF-64, we performed RNA-Seq in seminiferous tubules from wild-type and Cstf2t-/- mice, and found that several histone and histone-like mRNAs were reduced in Cstf2t-/- mice. We further observed delayed accumulation of the testis-specific histone, H1fnt (formerly, H1t2 or Hanp1) in Cstf2t-/- mice. High-throughput sequence analysis of polyadenylation sites (A-seq) indicated reduced use of polyadenylation sites within a cluster downstream of H1fnt in knockout mice. However, high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP) was not consistent with a direct role of τCstF-64 in polyadenylation of H1fnt. These findings together suggest that the τCstF-64 may control other reproductive functions that are not directly linked to the formation of 3' ends of mature polyadenylated mRNAs during male germ cell formation.
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Affiliation(s)
- P N Grozdanov
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - J Li
- Department of Electrical and Computer Engineering & TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX, USA
| | - P Yu
- Department of Electrical and Computer Engineering & TEES-AgriLife Center for Bioinformatics and Genomic Systems Engineering, Texas A&M University, College Station, TX, USA
| | - W Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - C C MacDonald
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX, USA
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10
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The Cstf2t Polyadenylation Gene Plays a Sex-Specific Role in Learning Behaviors in Mice. PLoS One 2016; 11:e0165976. [PMID: 27812195 PMCID: PMC5094787 DOI: 10.1371/journal.pone.0165976] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/20/2016] [Indexed: 11/19/2022] Open
Abstract
Polyadenylation is an essential mechanism for the processing of mRNA 3′ ends. CstF-64 (the 64,000 Mr subunit of the cleavage stimulation factor; gene symbol Cstf2) is an RNA-binding protein that regulates mRNA polyadenylation site usage. We discovered a paralogous form of CstF-64 called τCstF-64 (Cstf2t). The Cstf2t gene is conserved in all eutherian mammals including mice and humans, but the τCstF-64 protein is expressed only in a subset of mammalian tissues, mostly testis and brain. Male mice that lack Cstf2t (Cstf2t-/- mice) experience disruption of spermatogenesis and are infertile, although female fertility is unaffected. However, a role for τCstF-64 in the brain has not yet been determined. Given the importance of RNA polyadenylation and splicing in neuronal gene expression, we chose to test the hypothesis that τCstF-64 is important for brain function. Male and female 185-day old wild type and Cstf2t-/- mice were examined for motor function, general activity, learning, and memory using rotarod, open field activity, 8-arm radial arm maze, and Morris water maze tasks. Male wild type and Cstf2t-/- mice did not show differences in learning and memory. However, female Cstf2t-/- mice showed significantly better retention of learned maze tasks than did female wild type mice. These results suggest that τCstf-64 is important in memory function in female mice. Interestingly, male Cstf2t-/- mice displayed less thigmotactic behavior than did wild type mice, suggesting that Cstf2t may play a role in anxiety in males. Taken together, our studies highlight the importance of mRNA processing in cognition and behavior as well as their established functions in reproduction.
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11
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Li W, Park JY, Zheng D, Hoque M, Yehia G, Tian B. Alternative cleavage and polyadenylation in spermatogenesis connects chromatin regulation with post-transcriptional control. BMC Biol 2016; 14:6. [PMID: 26801249 PMCID: PMC4724118 DOI: 10.1186/s12915-016-0229-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 01/12/2016] [Indexed: 11/10/2022] Open
Abstract
Background Most mammalian genes display alternative cleavage and polyadenylation (APA). Previous studies have indicated preferential expression of APA isoforms with short 3’ untranslated regions (3’UTRs) in testes. Results By deep sequencing of the 3’ end region of poly(A) + transcripts, we report widespread shortening of 3’UTR through APA during the first wave of spermatogenesis in mouse, with 3’UTR size being the shortest in spermatids. Using genes without APA as a control, we show that shortening of 3’UTR eliminates destabilizing elements, such as U-rich elements and transposable elements, which appear highly potent during spermatogenesis. We additionally found widespread regulation of APA events in introns and exons that can affect the coding sequence of transcripts and global activation of antisense transcripts upstream of the transcription start site, suggesting modulation of splicing and initiation of transcription during spermatogenesis. Importantly, genes that display significant 3’UTR shortening tend to have functions critical for further sperm maturation, and testis-specific genes display greater 3’UTR shortening than ubiquitously expressed ones, indicating functional relevance of APA to spermatogenesis. Interestingly, genes with shortened 3’UTRs tend to have higher RNA polymerase II and H3K4me3 levels in spermatids as compared to spermatocytes, features previously known to be associated with open chromatin state. Conclusions Our data suggest that open chromatin may create a favorable cis environment for 3’ end processing, leading to global shortening of 3’UTR during spermatogenesis. mRNAs with shortened 3’UTRs are relatively stable thanks to evasion of powerful mRNA degradation mechanisms acting on 3’UTR elements. Stable mRNAs generated in spermatids may be important for protein production at later stages of sperm maturation, when transcription is globally halted. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0229-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wencheng Li
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Ji Yeon Park
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Dinghai Zheng
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Mainul Hoque
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Ghassan Yehia
- Transgenic Core Facility, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA. .,Rutgers Cancer Institute of New Jersey, Newark, NJ, USA.
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12
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Huang Y, Xiong Y, Lin Z, Feng X, Jiang X, Songyang Z, Huang J. Specific Tandem 3'UTR Patterns and Gene Expression Profiles in Mouse Thy1+ Germline Stem Cells. PLoS One 2015; 10:e0145417. [PMID: 26713853 PMCID: PMC4699828 DOI: 10.1371/journal.pone.0145417] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 12/03/2015] [Indexed: 12/14/2022] Open
Abstract
A recently developed strategy of sequencing alternative polyadenylation (APA) sites (SAPAS) with second-generation sequencing technology can be used to explore complete genome-wide patterns of tandem APA sites and global gene expression profiles. spermatogonial stem cells (SSCs) maintain long-term reproductive abilities in male mammals. The detailed mechanisms by which SSCs self-renew and generate mature spermatozoa are not clear. To understand the specific alternative polyadenylation pattern and global gene expression profile of male germline stem cells (GSCs, mainly referred to SSCs here), we isolated and purified mouse Thy1+ cells from testis by magnetic-activated cell sorting (MACS) and then used the SAPAS method for analysis, using pluripotent embryonic stem cells (ESCs) and differentiated mouse embryonic fibroblast cells (MEFs) as controls. As a result, we obtained 99,944 poly(A) sites, approximately 40% of which were newly detected in our experiments. These poly(A) sites originated from three mouse cell types and covered 17,499 genes, including 831 long non-coding RNA (lncRNA) genes. We observed that GSCs tend to have shorter 3'UTR lengths while MEFs tend towards longer 3'UTR lengths. We also identified 1337 genes that were highly expressed in GSCs, and these genes were highly consistent with the functional characteristics of GSCs. Our detailed bioinformatics analysis identified APA site-switching events at 3'UTRs and many new specifically expressed genes in GSCs, which we experimentally confirmed. Furthermore, qRT-PCR was performed to validate several events of the 334 genes with distal-to-proximal poly(A) switch in GSCs. Consistently APA reporter assay confirmed the total 3'UTR shortening in GSCs compared to MEFs. We also analyzed the cis elements around the proximal poly(A) site preferentially used in GSCs and found C-rich elements may contribute to this regulation. Overall, our results identified the expression level and polyadenylation site profiles and these data provide new insights into the processes potentially involved in the GSC life cycle and spermatogenesis.
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Affiliation(s)
- Yan Huang
- Key Laboratory of Reproductive Medicine of Guangdong Province, the First Affiliated Hospital and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, 51000, China
| | - Yuanyan Xiong
- Key Laboratory of Reproductive Medicine of Guangdong Province, the First Affiliated Hospital and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, 51000, China
- SYSU-CMU Shunde International Joint Research Institute, Shunde, China
| | - Zhuoheng Lin
- Key Laboratory of Reproductive Medicine of Guangdong Province, the First Affiliated Hospital and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, 51000, China
| | - Xuyang Feng
- Key Laboratory of Reproductive Medicine of Guangdong Province, the First Affiliated Hospital and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, 51000, China
| | - Xue Jiang
- Key Laboratory of Reproductive Medicine of Guangdong Province, the First Affiliated Hospital and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, 51000, China
| | - Zhou Songyang
- Key Laboratory of Reproductive Medicine of Guangdong Province, the First Affiliated Hospital and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, 51000, China
| | - Junjiu Huang
- Key Laboratory of Reproductive Medicine of Guangdong Province, the First Affiliated Hospital and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, 51000, China
- * E-mail:
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13
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Grozdanov PN, Amatullah A, Graber JH, MacDonald CC. TauCstF-64 Mediates Correct mRNA Polyadenylation and Splicing of Activator and Repressor Isoforms of the Cyclic AMP-Responsive Element Modulator (CREM) in Mouse Testis. Biol Reprod 2015; 94:34. [PMID: 26700942 PMCID: PMC4787626 DOI: 10.1095/biolreprod.115.134684] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 12/17/2015] [Indexed: 12/12/2022] Open
Abstract
Spermatogenesis is coordinated by the spatial and temporal expression of many transcriptional and posttranscriptional factors. The cyclic AMP-responsive element modulator (CREM) gene encodes both activator and repressor isoforms that act as transcription factors to regulate spermiogenesis. We found that the testis-expressed paralog of CstF-64, tauCstF-64 (gene symbol Cstf2t), is involved in a polyadenylation site choice switch of Crem mRNA and leads to an overall decrease of the Crem mRNAs that are generated from internal promoters in Cstf2t(-/-) mice. More surprisingly, loss of tauCstF-64 also leads to alternative splicing of Crem exon 4, which contains an important activation domain. Thus, testis-specific CREMtau2 isoform protein levels are reduced in Cstf2t(-/-) mice. Consequently, expression of 15 CREM-regulated genes is decreased in testes of Cstf2t(-/-) mice at 25 days postpartum. These effects might further contribute to the infertility phenotype of these animals. This demonstrates that tauCstF-64 is an important stage-specific regulator of Crem mRNA processing that modulates the spatial and temporal expression of downstream stage-specific genes necessary for the proper development of sperm in mice.
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Affiliation(s)
- Petar N Grozdanov
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas
| | - Atia Amatullah
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas
| | - Joel H Graber
- Center for Genome Dynamics, The Jackson Laboratory, Bar Harbor, Maine
| | - Clinton C MacDonald
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas
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14
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Li W, You B, Hoque M, Zheng D, Luo W, Ji Z, Park JY, Gunderson SI, Kalsotra A, Manley JL, Tian B. Systematic profiling of poly(A)+ transcripts modulated by core 3' end processing and splicing factors reveals regulatory rules of alternative cleavage and polyadenylation. PLoS Genet 2015; 11:e1005166. [PMID: 25906188 PMCID: PMC4407891 DOI: 10.1371/journal.pgen.1005166] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 03/20/2015] [Indexed: 12/18/2022] Open
Abstract
Alternative cleavage and polyadenylation (APA) results in mRNA isoforms containing different 3’ untranslated regions (3’UTRs) and/or coding sequences. How core cleavage/polyadenylation (C/P) factors regulate APA is not well understood. Using siRNA knockdown coupled with deep sequencing, we found that several C/P factors can play significant roles in 3’UTR-APA. Whereas Pcf11 and Fip1 enhance usage of proximal poly(A) sites (pAs), CFI-25/68, PABPN1 and PABPC1 promote usage of distal pAs. Strong cis element biases were found for pAs regulated by CFI-25/68 or Fip1, and the distance between pAs plays an important role in APA regulation. In addition, intronic pAs are substantially regulated by splicing factors, with U1 mostly inhibiting C/P events in introns near the 5’ end of gene and U2 suppressing those in introns with features for efficient splicing. Furthermore, PABPN1 inhibits expression of transcripts with pAs near the transcription start site (TSS), a property possibly related to its role in RNA degradation. Finally, we found that groups of APA events regulated by C/P factors are also modulated in cell differentiation and development with distinct trends. Together, our results support an APA code where an APA event in a given cellular context is regulated by a number of parameters, including relative location to the TSS, splicing context, distance between competing pAs, surrounding cis elements and concentrations of core C/P factors. A gene can express multiple isoforms varying in the 3’ end, a phenomenon called alternative cleavage and polyadenylation, or APA. Previous studies have indicated that most eukaryotic genes display APA and the APA profile changes under different physiological and pathological conditions. However, how APA is regulated in the cell is unclear. Here using gene knockdown and high throughput sequencing we examine how APA is regulated by factors in the machinery responsible for cleavage and polyadenylation as well as factors that play essential roles in splicing. We identify several factors that play significant roles in APA in the last exon, including CFI-25/68, PABPN1, PABPC1, Fip1 and Pcf11. We also elucidate how cleavage and polyadenylation events are regulated in introns and near the transcription start site. We uncover a group of APA events that are highly regulated by core factors as well as in cell differentiation and development. We present an APA code where an APA event in a given cellular context is regulated by a number of parameters, including relative location to the transcription start site, splicing context, distance between competing pAs, surrounding cis elements and concentrations of core cleavage and polyadenylation factors.
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Affiliation(s)
- Wencheng Li
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey, United States of America
| | - Bei You
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America
| | - Mainul Hoque
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America
| | - Dinghai Zheng
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey, United States of America
| | - Wenting Luo
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America
- Rutgers Graduate School of Biomedical Sciences, Newark, New Jersey, United States of America
| | - Zhe Ji
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America
- Rutgers Graduate School of Biomedical Sciences, Newark, New Jersey, United States of America
| | - Ji Yeon Park
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America
| | - Samuel I. Gunderson
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America
| | - Auinash Kalsotra
- Departments of Biochemistry and Medical Biochemistry, University of Illinois, Urbana, Illinois, United States of America
| | - James L. Manley
- Department of Biological Sciences, Columbia University, New York, New York, United Staes of America
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey, United States of America
- Rutgers Graduate School of Biomedical Sciences, Newark, New Jersey, United States of America
- * E-mail:
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15
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Grozdanov PN, Macdonald CC. High-throughput sequencing of RNA isolated by cross-linking and immunoprecipitation (HITS-CLIP) to determine sites of binding of CstF-64 on nascent RNAs. Methods Mol Biol 2014; 1125:187-208. [PMID: 24590791 DOI: 10.1007/978-1-62703-971-0_17] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Genome-wide analysis of gene expression has changed the RNA world. Recent techniques leading to this revolution have been the use of cross-linking and immunoprecipitation (CLIP) combined with high-throughput sequencing (HITS-CLIP) to determine sites on nascent mRNAs to which RNA-binding proteins bind. Several researchers (including us) have been examining the role of RNA-binding proteins in polyadenylation, including the role of the 64,000 Mr component of the cleavage stimulation factor, CstF-64. In this chapter, we present our optimizations of the CLIP procedure for examination of CstF-64 binding to nascent pre-mRNAs expressed in testis. For CstF-64 CLIP, we use a well-characterized monoclonal antibody (3A7) that recognizes CstF-64. Rather than optimizing tricky but essential RNA fragment cloning schemes, we illustrate the use of the proprietary Illumina TruSeq Small RNA Sample Preparation kit for this step. Other techniques such as SDS-PAGE and the transfer to the nitrocellulose membrane techniques follow the original Illumina protocol (though we point out potential pitfalls). Finally, we discuss the options for high-throughput sequencing and some general suggestions for bioinformatic analysis of the data.
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Affiliation(s)
- Petar N Grozdanov
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, 3601 Fourth Street, STOP 6540, Lubbock, TX, 79430, USA
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16
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Youngblood BA, MacDonald CC. CstF-64 is necessary for endoderm differentiation resulting in cardiomyocyte defects. Stem Cell Res 2014; 13:413-21. [PMID: 25460602 DOI: 10.1016/j.scr.2014.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/06/2014] [Accepted: 09/16/2014] [Indexed: 12/23/2022] Open
Abstract
Although adult cardiomyocytes have the capacity for cellular regeneration, they are unable to fully repair severely injured hearts. The use of embryonic stem cell (ESC)-derived cardiomyocytes as transplantable heart muscle cells has been proposed as a solution, but is limited by the lack of understanding of the developmental pathways leading to specification of cardiac progenitors. Identification of these pathways will enhance the ability to differentiate cardiomyocytes into a clinical source of transplantable cells. Here, we show that the mRNA 3' end processing protein, CstF-64, is essential for cardiomyocyte differentiation in mouse ESCs. Loss of CstF-64 in mouse ESCs results in loss of differentiation potential toward the endodermal lineage. However, CstF-64 knockout (Cstf2(E6)) cells were able to differentiate into neuronal progenitors, demonstrating that some differentiation pathways were still intact. Markers for mesodermal differentiation were also present, although Cstf2(E6) cells were defective in forming beating cardiomyocytes and expressing cardiac specific markers. Since the extraembryonic endoderm is needed for cardiomyocyte differentiation and endodermal markers were decreased, we hypothesized that endodermal factors were required for efficient cardiomyocyte formation in the Cstf2(E6) cells. Using conditioned medium from the extraembryonic endodermal (XEN) stem cell line we were able to restore cardiomyocyte differentiation in Cstf2(E6) cells, suggesting that CstF-64 has a role in regulating endoderm differentiation that is necessary for cardiac specification and that extraembryonic endoderm signaling is essential for cardiomyocyte development.
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Affiliation(s)
- Bradford A Youngblood
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430-6540, USA
| | - Clinton C MacDonald
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430-6540, USA.
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17
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Di Giammartino DC, Manley JL. New links between mRNA polyadenylation and diverse nuclear pathways. Mol Cells 2014; 37:644-9. [PMID: 25081038 PMCID: PMC4179132 DOI: 10.14348/molcells.2014.0177] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 06/28/2014] [Indexed: 11/27/2022] Open
Abstract
The 3' ends of most eukaryotic messenger RNAs must undergo a maturation step that includes an endonuc-leolytic cleavage followed by addition of a polyadenylate tail. While this reaction is catalyzed by the action of only two enzymes it is supported by an unexpectedly large number of proteins. This complexity reflects the necessity of coordinating this process with other nuclear events, and growing evidence indicates that even more factors than previously thought are necessary to connect 3' processing to additional cellular pathways. In this review we summarize the current understanding of the molecular machinery involved in this step of mRNA maturation, focusing on new core and auxiliary proteins that connect polyadenylation to splicing, DNA damage, transcription and cancer.
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Affiliation(s)
| | - James L Manley
- Columbia University, Department of Biological Sciences, New York NY, 10027, USA
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18
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Hollerer I, Grund K, Hentze MW, Kulozik AE. mRNA 3'end processing: A tale of the tail reaches the clinic. EMBO Mol Med 2014; 6:16-26. [PMID: 24408965 PMCID: PMC3936486 DOI: 10.1002/emmm.201303300] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Recent advances reveal mRNA 3′end processing as a highly regulated process that fine-tunes posttranscriptional gene expression. This process can affect the site and/or the efficiency of 3′end processing, controlling the quality and the quantity of substrate mRNAs. The regulation of 3′end processing plays a central role in fundamental physiology such as blood coagulation and innate immunity. In addition, errors in mRNA 3′end processing have been associated with a broad spectrum of human diseases, including cancer. We summarize and discuss the paradigmatic shift in the understanding of 3′end processing as a mechanism of posttranscriptional gene regulation that has reached clinical medicine.
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Affiliation(s)
- Ina Hollerer
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
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19
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Youngblood BA, Grozdanov PN, MacDonald CC. CstF-64 supports pluripotency and regulates cell cycle progression in embryonic stem cells through histone 3' end processing. Nucleic Acids Res 2014; 42:8330-42. [PMID: 24957598 PMCID: PMC4117776 DOI: 10.1093/nar/gku551] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Embryonic stem cells (ESCs) exhibit a unique cell cycle with a shortened G1 phase that supports their pluripotency, while apparently buffering them against pro-differentiation stimuli. In ESCs, expression of replication-dependent histones is a main component of this abbreviated G1 phase, although the details of this mechanism are not well understood. Similarly, the role of 3' end processing in regulation of ESC pluripotency and cell cycle is poorly understood. To better understand these processes, we examined mouse ESCs that lack the 3' end-processing factor CstF-64. These ESCs display slower growth, loss of pluripotency and a lengthened G1 phase, correlating with increased polyadenylation of histone mRNAs. Interestingly, these ESCs also express the τCstF-64 paralog of CstF-64. However, τCstF-64 only partially compensates for lost CstF-64 function, despite being recruited to the histone mRNA 3' end-processing complex. Reduction of τCstF-64 in CstF-64-deficient ESCs results in even greater levels of histone mRNA polyadenylation, suggesting that both CstF-64 and τCstF-64 function to inhibit polyadenylation of histone mRNAs. These results suggest that CstF-64 plays a key role in modulating the cell cycle in ESCs while simultaneously controlling histone mRNA 3' end processing.
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Affiliation(s)
- Bradford A Youngblood
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430-6540, USA
| | - Petar N Grozdanov
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430-6540, USA
| | - Clinton C MacDonald
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430-6540, USA
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20
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Delineating the structural blueprint of the pre-mRNA 3'-end processing machinery. Mol Cell Biol 2014; 34:1894-910. [PMID: 24591651 DOI: 10.1128/mcb.00084-14] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Processing of mRNA precursors (pre-mRNAs) by polyadenylation is an essential step in gene expression. Polyadenylation consists of two steps, cleavage and poly(A) synthesis, and requires multiple cis elements in the pre-mRNA and a megadalton protein complex bearing the two essential enzymatic activities. While genetic and biochemical studies remain the major approaches in characterizing these factors, structural biology has emerged during the past decade to help understand the molecular assembly and mechanistic details of the process. With structural information about more proteins and higher-order complexes becoming available, we are coming closer to obtaining a structural blueprint of the polyadenylation machinery that explains both how this complex functions and how it is regulated and connected to other cellular processes.
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21
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Yao C, Choi EA, Weng L, Xie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, Shi Y. Overlapping and distinct functions of CstF64 and CstF64τ in mammalian mRNA 3' processing. RNA (NEW YORK, N.Y.) 2013; 19:1781-1790. [PMID: 24149845 PMCID: PMC3884657 DOI: 10.1261/rna.042317.113] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 09/12/2013] [Indexed: 06/02/2023]
Abstract
mRNA 3' processing is dynamically regulated spatially and temporally. However, the underlying mechanisms remain poorly understood. CstF64τ is a paralog of the general mRNA 3' processing factor, CstF64, and has been implicated in mediating testis-specific mRNA alternative polyadenylation (APA). However, the functions of CstF64τ in mRNA 3' processing have not been systematically investigated. We carried out a comprehensive characterization of CstF64τ and compared its properties to those of CstF64. In contrast to previous reports, we found that both CstF64 and CstF64τ are widely expressed in mammalian tissues, and their protein levels display tissue-specific variations. We further demonstrated that CstF64 and CstF64τ have highly similar RNA-binding specificities both in vitro and in vivo. CstF64 and CstF64τ modulate one another's expression and play overlapping as well as distinct roles in regulating global APA profiles. Interestingly, protein interactome analyses revealed key differences between CstF64 and CstF64τ, including their interactions with another mRNA 3' processing factor, symplekin. Together, our study of CstF64 and CstF64τ revealed both functional overlap and specificity of these two important mRNA 3' processing factors and provided new insights into the regulatory mechanisms of mRNA 3' processing.
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Affiliation(s)
- Chengguo Yao
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
| | - Eun-A Choi
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
| | - Lingjie Weng
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California 92697, USA
- Department of Computer Science, University of California, Irvine, Irvine, California 92697, USA
| | - Xiaohui Xie
- Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California 92697, USA
- Department of Computer Science, University of California, Irvine, Irvine, California 92697, USA
| | - Ji Wan
- Interdepartmental Graduate Program in Genetics, University of Iowa, Iowa City, Iowa 52242, USA
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Yi Xing
- Interdepartmental Graduate Program in Genetics, University of Iowa, Iowa City, Iowa 52242, USA
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa 52242, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - James J. Moresco
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Patricia G. Tu
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Yongsheng Shi
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
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22
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Shankarling GS, MacDonald CC. Polyadenylation site-specific differences in the activity of the neuronal βCstF-64 protein in PC-12 cells. Gene 2013; 529:220-7. [PMID: 23948079 DOI: 10.1016/j.gene.2013.08.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 07/23/2013] [Accepted: 08/02/2013] [Indexed: 12/13/2022]
Abstract
Recent genome-wide analyses have implicated alternative polyadenylation - the process of regulated mRNA 3' end formation - as a critical mechanism that influences multiple steps of mRNA metabolism in addition to increasing the protein-coding capacity of the genome. Although the functional consequences of alternative polyadenylation are well known, protein factors that regulate this process are poorly characterized. Previously, we described an evolutionarily conserved family of neuronal splice variants of the CstF-64 mRNA, βCstF-64, that we hypothesized to function in alternative polyadenylation in the nervous system. In the present study, we show that βCstF-64 mRNA and protein expression increase in response to nerve growth factor (NGF), concomitant with differentiation of adrenal PC-12 cells into a neuronal phenotype, suggesting a role for βCstF-64 in neuronal gene expression. Using PC-12 cells as model, we show that βCstF-64 is a bona fide polyadenylation protein, as evidenced by its association with the CstF complex, and by its ability to stimulate polyadenylation of luciferase reporter mRNA. Using luciferase assays, we show that βCstF-64 stimulates polyadenylation equivalently at the two weak poly(A) sites of the β-adducin mRNA. Notably, we demonstrate that the activity of βCstF-64 is less than CstF-64 on a strong polyadenylation signal, suggesting polyadenylation site-specific differences in the activity of the βCstF-64 protein. Our data address the polyadenylation functions of βCstF-64 for the first time, and provide initial insights into the mechanism of alternative poly(A) site selection in the nervous system.
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Affiliation(s)
- Ganesh S Shankarling
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430-6540, USA
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23
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Rehfeld A, Plass M, Krogh A, Friis-Hansen L. Alterations in polyadenylation and its implications for endocrine disease. Front Endocrinol (Lausanne) 2013; 4:53. [PMID: 23658553 PMCID: PMC3647115 DOI: 10.3389/fendo.2013.00053] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 04/22/2013] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION Polyadenylation is the process in which the pre-mRNA is cleaved at the poly(A) site and a poly(A) tail is added - a process necessary for normal mRNA formation. Genes with multiple poly(A) sites can undergo alternative polyadenylation (APA), producing distinct mRNA isoforms with different 3' untranslated regions (3' UTRs) and in some cases different coding regions. Two thirds of all human genes undergo APA. The efficiency of the polyadenylation process regulates gene expression and APA plays an important part in post-transcriptional regulation, as the 3' UTR contains various cis-elements associated with post-transcriptional regulation, such as target sites for micro-RNAs and RNA-binding proteins. Implications of alterations in polyadenylation for endocrine disease: Alterations in polyadenylation have been found to be causative of neonatal diabetes and IPEX (immune dysfunction, polyendocrinopathy, enteropathy, X-linked) and to be associated with type I and II diabetes, pre-eclampsia, fragile X-associated premature ovarian insufficiency, ectopic Cushing syndrome, and many cancer diseases, including several types of endocrine tumor diseases. PERSPECTIVES Recent developments in high-throughput sequencing have made it possible to characterize polyadenylation genome-wide. Antisense elements inhibiting or enhancing specific poly(A) site usage can induce desired alterations in polyadenylation, and thus hold the promise of new therapeutic approaches. SUMMARY This review gives a detailed description of alterations in polyadenylation in endocrine disease, an overview of the current literature on polyadenylation and summarizes the clinical implications of the current state of research in this field.
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Affiliation(s)
- Anders Rehfeld
- Genomic Medicine, Rigshospitalet, Copenhagen University HospitalCopenhagen, Denmark
| | - Mireya Plass
- Department of Biology, The Bioinformatics Centre, University of CopenhagenCopenhagen, Denmark
| | - Anders Krogh
- Department of Biology, The Bioinformatics Centre, University of CopenhagenCopenhagen, Denmark
| | - Lennart Friis-Hansen
- Genomic Medicine, Rigshospitalet, Copenhagen University HospitalCopenhagen, Denmark
- *Correspondence: Lennart Friis-Hansen, Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, 4113, Blegdamsvej 9, DK2100 Copenhagen, Denmark. e-mail:
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