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Zhou X, Zhang Y, Michal JJ, Qu L, Zhang S, Wildung MR, Du W, Pouchnik DJ, Zhao H, Xia Y, Shi H, Ji G, Davis JF, Smith GD, Griswold MD, Harland RM, Jiang Z. Alternative polyadenylation coordinates embryonic development, sexual dimorphism and longitudinal growth in Xenopus tropicalis. Cell Mol Life Sci 2019; 76:2185-2198. [PMID: 30729254 PMCID: PMC6597005 DOI: 10.1007/s00018-019-03036-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 01/09/2019] [Accepted: 01/30/2019] [Indexed: 12/27/2022]
Abstract
RNA alternative polyadenylation contributes to the complexity of information transfer from genome to phenome, thus amplifying gene function. Here, we report the first X. tropicalis resource with 127,914 alternative polyadenylation (APA) sites derived from embryos and adults. Overall, APA networks play central roles in coordinating the maternal-zygotic transition (MZT) in embryos, sexual dimorphism in adults and longitudinal growth from embryos to adults. APA sites coordinate reprogramming in embryos before the MZT, but developmental events after the MZT due to zygotic genome activation. The APA transcriptomes of young adults are more variable than growing adults and male frog APA transcriptomes are more divergent than females. The APA profiles of young females were similar to embryos before the MZT. Enriched pathways in developing embryos were distinct across the MZT and noticeably segregated from adults. Briefly, our results suggest that the minimal functional units in genomes are alternative transcripts as opposed to genes.
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Affiliation(s)
- Xiang Zhou
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, 99164-7620, USA
- College of Animal Sciences and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yangzi Zhang
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, 99164-7620, USA
| | - Jennifer J Michal
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, 99164-7620, USA
| | - Lujiang Qu
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, 99164-7620, USA
- College of Animal Sciences and Technology, China Agricultural University, Beijing, China
| | - Shuwen Zhang
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, 99164-7620, USA
| | - Mark R Wildung
- Laboratory for Biotechnology and Bioanalysis, Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Weiwei Du
- Laboratory for Biotechnology and Bioanalysis, Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Derek J Pouchnik
- Laboratory for Biotechnology and Bioanalysis, Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Hui Zhao
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Yin Xia
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Honghua Shi
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Guoli Ji
- Department of Automation, Xiamen University, Xiamen, China
| | - Jon F Davis
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA, USA
| | - Gary D Smith
- Departments of OB/GYN, Physiology, and Urology, University of Michigan, Ann Arbor, MI, USA
| | - Michael D Griswold
- Laboratory for Biotechnology and Bioanalysis, Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Richard M Harland
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Zhihua Jiang
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, 99164-7620, USA.
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Kerr NCH, Holmes FE, Wynick D. Novel isoforms of the sodium channels Nav1.8 and Nav1.5 are produced by a conserved mechanism in mouse and rat. J Biol Chem 2004; 279:24826-33. [PMID: 15047701 PMCID: PMC2726572 DOI: 10.1074/jbc.m401281200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The voltage-gated sodium channel Na(v)1.8 is only expressed in subsets of neurons in dorsal root ganglia (DRG) and trigeminal and nodose ganglia. We have isolated mouse partial length Na(v)1.8 cDNA clones spanning the exon 17 sequence, which have 17 nucleotide substitutions and 12 predicted amino acid differences from the published sequence. The absence of a mutually exclusive alternative exon 17 was confirmed by sequencing 4.1 kilobases of genomic DNA spanning exons 16-18 of Scn10a. A novel cDNA isoform was identified, designated Na(v)1.8c, which results from alternative 3'-splice site selection at a CAG/CAG motif to exclude the codon for glutamine 1031 within the interdomain cytoplasmic loop IDII/III. The ratio of Na(v)1.8c (CAG-skipped) to Na(v)1.8 (CAG-inclusive) mRNA in mouse is approximately 2:1 in adult DRG, trigeminal ganglion, and neonatal DRG. A Na(v)1.8c isoform also occurs in rat DRG, but is less common. Of the two other tetrodotoxin-resistant channels, no analogous alternative splicing of mouse Na(v)1.9 was detected, whereas rare alternative splicing of Na(v)1.5 at a CAG/CAG motif resulted in the introduction of a CAG trinucleotide. This isoform, designated Na(v)1.5c, is conserved in rat and encodes an additional glutamine residue that disrupts a putative CK2 phosphorylation site. In summary, novel isoforms of Na(v)1.8 and Na(v)1.5 are each generated by alternative splicing at CAG/CAG motifs, which result in the absence or presence of predicted glutamine residues within the interdomain cytoplasmic loop IDII/III. Mutations of sodium channels within this cytoplasmic loop have previously been demonstrated to alter electrophysiological properties and cause cardiac arrhythmias and epilepsy.
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Affiliation(s)
- Niall C. H. Kerr
- Laboratories for Integrated Neuroscience and Endocrinology (LINE), Dorothy Hodgkin Building, Whitson Street, Bristol BS1 3NY, United Kingdom
- NeuroTargets Ltd., Surrey Technology Centre, Occam Road, Surrey Research Park, Guilford, Surrey GU2 7YG, United Kingdom
| | - Fiona E. Holmes
- Laboratories for Integrated Neuroscience and Endocrinology (LINE), Dorothy Hodgkin Building, Whitson Street, Bristol BS1 3NY, United Kingdom
| | - David Wynick
- Laboratories for Integrated Neuroscience and Endocrinology (LINE), Dorothy Hodgkin Building, Whitson Street, Bristol BS1 3NY, United Kingdom
- NeuroTargets Ltd., Surrey Technology Centre, Occam Road, Surrey Research Park, Guilford, Surrey GU2 7YG, United Kingdom
- To whom correspondence should be addressed: LINE, Dorothy Hodgkin Building, Whitson St., Bristol BS1 3NY, UK. Tel.: 44-0-117-3313085; Fax: 44-0-117-3313084;
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Smith AJ, Ling Y, Morgan GT. Subnuclear localization and Cajal body targeting of transcription elongation factor TFIIS in amphibian oocytes. Mol Biol Cell 2003; 14:1255-67. [PMID: 12631738 PMCID: PMC151594 DOI: 10.1091/mbc.e02-09-0601] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
We have examined the localization and targeting of the RNA polymerase II (pol II) transcription elongation factor TFIIS in amphibian oocyte nuclei by immunofluorescence. Using a novel antibody against Xenopus TFIIS the major sites of immunostaining were found to be Cajal bodies, nuclear organelles that also contain pol II. Small granular structures attached to lampbrush chromosomes were also specifically stained but the transcriptionally active loops were not. Similar localization patterns were found for the newly synthesized myc-tagged TFIIS produced after injection of synthetic transcripts into the cytoplasm. The basis of the rapid and preferential targeting of TFIIS to Cajal bodies was investigated by examining the effects of deletion and site-specific mutations. Multiple regions of TFIIS contributed to efficient targeting including the domain required for its binding to pol II. The localization of TFIIS in Cajal bodies, and in particular the apparent involvement of pol II binding in achieving it, offer further support for a model in which Cajal bodies function in the preassembly of the transcriptional machinery. Although our findings are therefore consistent with TFIIS playing a role in early events of the transcription cycle, they also suggest that this elongation factor is not generally required during transcription in oocytes.
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Affiliation(s)
- Abigail J Smith
- Institute of Genetics, University of Nottingham, United Kingdom
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Fish RN, Kane CM. Promoting elongation with transcript cleavage stimulatory factors. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1577:287-307. [PMID: 12213659 DOI: 10.1016/s0167-4781(02)00459-1] [Citation(s) in RCA: 182] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Transcript elongation by RNA polymerase is a dynamic process, capable of responding to a number of intrinsic and extrinsic signals. A number of elongation factors have been identified that enhance the rate or efficiency of transcription. One such class of factors facilitates RNA polymerase transcription through blocks to elongation by stimulating the polymerase to cleave the nascent RNA transcript within the elongation complex. These cleavage factors are represented by the Gre factors from prokaryotes, and TFIIS and TFIIS-like factors found in archaea and eukaryotes. High-resolution structures of RNA polymerases and the cleavage factors in conjunction with biochemical investigations and genetic analyses have provided insights into the mechanism of action of these elongation factors. However, there are yet many unanswered questions regarding the regulation of these factors and their effects on target genes.
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Affiliation(s)
- Rachel N Fish
- Department of Molecular and Cell Biology, University of California-Berkeley, 401 Barker Hall, Berkeley, CA 94720-3202, USA
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Wilhelm V, Neckelman G, Allende JE, Allende CC. The genomic structure of two protein kinase CK2alpha genes of Xenopus laevis and features of the putative promoter region. Mol Cell Biochem 2001; 227:175-83. [PMID: 11827169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Protein kinase CK2 is an enzyme that is ubiquitous in eukaryotes. This enzyme, composed of catalytic (alpha and alpha') and regulatory (beta) subunits, is responsible for the phosphorylation of a large number of proteins and is implicated in cell division. Genomic clones coding for the CK2alpha subunit of Xenopus laevis have been isolated. Initial restriction enzyme profiles and subsequent PCR analysis and DNA sequencing indicated that these genomic clones correspond to two different genes. The two genes are highly homologous in the regions of the coding sequence (only 3 amino acid differences) but differ considerable in their intron sequences and lengths. Gene 1 corresponds to the cDNA of XlCK2alpha which had been previously isolated and described. The genomic clone for this gene was truncated. Gene 2 contains the entire coding region for CK2alpha subunit as well as a fragment of 6.4 kb of the 5' upstream region. The exon/intron boundaries of both genes obey the GT/AG rule with the exception of intron V where the less common GC/AG is seen. Comparison of the size of ten coding exons and sites where these are interrupted by introns shows strong conservation with respect to the human CK2alpha gene. RT-PCR analysis of mRNAs from X. laevis ovary, oocytes and early embryos using a specific primer for gene 2 demonstrated that this gene is expressed in these tissues and cells. Analysis of transcription start sites using 5'RACE and RNA from stage VI oocytes demonstrated that there are multiple start sites in the XlCK2alpha mRNA. It was also seen that a noncoding exon 1 is present 4 kb upstream of the translation start site and that alternate splicing occurs in gene 2 to give exon 1 of different lengths. Sequencing of the entire upstream genomic region of gene 2 revealed that there are regions of homology to the sequence of exon 1 of the human CK2alpha gene. Other sequences with consensus to transcription factor binding sites that are seen in the promoter region of human CK2alpha are also found in the X. laevis CK2alpha gene 2. These sites include Ets1, E2F, CCAAT and GC rich regions. No canonical TATA motif is observed.
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Affiliation(s)
- V Wilhelm
- Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago
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Oh Y, Lee S, Yoon J, Han K, Baek K. Promoter analysis of the Drosophila melanogaster gene encoding transcription elongation factor TFIIS. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1518:276-81. [PMID: 11311940 DOI: 10.1016/s0167-4781(01)00203-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The promoter region of the Drosophila melanogaster TFIIS gene was characterized by transient expression assay. Serial deletion analysis of the promoter region showed that the promoter region between -112 and +113 is required for the efficient expression of the D. melanogaster TFIIS gene. The results also suggest that the DNA fragments between -112 and -54 and between +94 and +113 contain the vital elements for the expression. The importance of these fragments was further substantiated by the findings that the sequences in these fragments of the D. melanogaster TFIIS gene are conserved in the 5'-flanking regions of the Drosophila virilis TFIIS gene. The comparison of the nucleotide sequences in the 5'-flanking region of the D. melanogaster and D. virilis TFIIS genes revealed that the three regions, -85--59, +76-+126, and the vicinity of the transcription initiation site of the D. melanogaster TFIIS gene, are conserved. It is very interesting that the long downstream DNA between +76 and +126 is highly conserved with 90% identities between the two species. The downstream promoter region between +94 and +113 of the D. melanogaster TFIIS gene was further analyzed by transient expression and band mobility shift assays. The results obtained suggest that the region between +94 and +113 is probably recognized by nuclear factors and that the sequence (+98)AGTAAACAACAT(+109) seems to make a great contribution to promoter activity of the D. melanogaster TFIIS gene.
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Affiliation(s)
- Y Oh
- Department and Institute of Genetic Engineering, Kyung Hee University, Yongin City 449-701, South Korea
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Taira Y, Kubo T, Natori S. Participation of transcription elongation factor XSII-K1 in mesoderm-derived tissue development in Xenopus laevis. J Biol Chem 2000; 275:32011-5. [PMID: 10900206 DOI: 10.1074/jbc.m003920200] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We isolated a cDNA clone for a novel member of the S-II family of transcription elongation factors from Xenopus laevis. This S-II, named XSII-K1, is assumed to be the Xenopus homologue of mouse SII-K1 that we reported previously (Taira, Y., Kubo, T., and Natori, S. (1998) Genes Cells 3, 289-296). Expression of the XSII-K1 gene was found to be restricted to mesoderm-derived tissues such as liver, kidney, and skeletal muscle. Contrary to the general S-II gene, expression of the XSII-K1 gene was not detected in embryos at stages earlier than 11. The animal cap assay revealed that activin A, but not basic fibroblast growth factor, induced expression of the XSII-K1 gene and that it participated in the expression of mesoderm-specific genes such as Xbra and Xalpha-actin. This is the first demonstration that the regulation at the level of transcription elongation is included in the development of mesoderm-derived tissues.
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Affiliation(s)
- Y Taira
- Graduate School of Pharmaceutical Sciences, University of Tokyo, Bunkyo-ku, Tokyo, Japan
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8
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Abstract
RNA chain elongation by RNA polymerase II (pol II) is a complex and regulated process which is coordinated with capping, splicing, and polyadenylation of the primary transcript. Numerous elongation factors that enable pol II to transcribe faster and/or more efficiently have been purified. SII is one such factor. It helps pol II bypass specific blocks to elongation that are encountered during transcript elongation. SII was first identified biochemically on the basis of its ability to enable pol II to synthesize long transcripts. ((1)) Both the high resolution structure of SII and the details of its novel mechanism of action have been refined through mutagenesis and sophisticated in vitro assays. SII engages transcribing pol II and assists it in bypassing blocks to elongation by stimulating a cryptic, nascent RNA cleavage activity intrinsic to RNA polymerase. The nuclease activity can also result in removal of misincorporated bases from RNA. Molecular genetic experiments in yeast suggest that SII is generally involved in mRNA synthesis in vivo and that it is one type of a growing collection of elongation factors that regulate pol II. In vertebrates, a family of related SII genes has been identified; some of its members are expressed in a tissue-specific manner. The principal challenge now is to understand the isoform-specific functional differences and the biology of regulation exerted by the SII family of proteins on target genes, particularly in multicellular organisms.
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Affiliation(s)
- Megan Wind
- Department of Biochemistry and Graduate Program in Genetics & Molecular Biology, Emory University School of Medicine, Atlanta, Georgia
| | - Daniel Reines
- Department of Biochemistry and Graduate Program in Genetics & Molecular Biology, Emory University School of Medicine, Atlanta, Georgia
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Ito T, Seldin MF, Taketo MM, Kubo T, Natori S. Gene structure and chromosome mapping of mouse transcription elongation factor S-II (Tcea1). Gene 2000; 244:55-63. [PMID: 10689187 DOI: 10.1016/s0378-1119(00)00007-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We report the organization and chromosome localization of the mouse transcription elongation factor S-II gene (Tcea1). This gene was found to be a single copy gene consisting of 10 exons spanning approximately 30kb. Its organization was the same as those of the mouse testis-specific S-II gene (Tcea2) and Xenopus general S-II gene (xTFIIS.oA), but different from that of the human S-II gene family. We also identified a processed pseudogene (Tcea1-ps1) with a sequence highly homologous to those of S-II cDNAs but containing a translation termination codon within its open reading frame. Linkage analysis showed that Tcea1 and Tcea1-ps1 are mapped on mouse chromosomes 1 and 15, respectively. Relationships between Tcea1 and S-II cDNAs isolated so far are discussed.
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Affiliation(s)
- T Ito
- Graduate School of Pharmaceutical Sciences, University of Tokyo, Bunkyo-ku, Tokyo, Japan
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10
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Brown LA, Yang SH, Hair A, Galanis A, Sharrocks AD. Molecular characterization of a zebrafish TCF ETS-domain transcription factor. Oncogene 1999; 18:7985-93. [PMID: 10637509 DOI: 10.1038/sj.onc.1203197] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The ternary complex factor (TCF) subfamily of ETS-transcription factors represent key nuclear targets of the MAP kinase pathways. Members of this subfamily are classified by the presence of several conserved domains for DNA binding, interaction with SRF, interaction with MAP kinases and transcriptional activation. In this study we have isolated a further member of this subfamily (TCF-1) from zebrafish. The protein product of zebrafish TCF-1 (zTCF-1), shares sequence similarity with the mammalian TCFs in all four conserved domains, with highest overall similarity to SAP-1. Zebrafish TCF-1 is expressed throughout zebrafish embryonic development and exhibits typical TCF DNA binding characteristics, with the B-box being required for interaction with SRF. Of the mammalian TCFs, its DNA binding specificity resembles Elk-1. zTCF-1 is a target for both the growth factor/mitogen-activated and stress-activated MAP kinase cascades in vitro and in vivo. However, differential targeting occurs, with the profile of its activation closely resembling that of mammalian SAP-1. Together, our results demonstrate that the TCFs have been functionally conserved during vertebrate development.
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Affiliation(s)
- L A Brown
- Department of Biochemistry and Genetics, The Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne, NE2 4HH, UK
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Wu Q, Krainer AR. AT-AC pre-mRNA splicing mechanisms and conservation of minor introns in voltage-gated ion channel genes. Mol Cell Biol 1999; 19:3225-36. [PMID: 10207048 PMCID: PMC84117 DOI: 10.1128/mcb.19.5.3225] [Citation(s) in RCA: 115] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Q Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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12
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Abstract
There is a family of genes encoding TFIIS-related proteins in human cells. We have focused upon the genomic organization of one family member expressed primarily in the testis. This gene encodes a transcription elongation factor similar to but distinct from that encoded by a previously reported TFIIS gene. Also in contrast to the previously reported TFIIS gene, the testis gene contains introns. All exon-intron junction sequences match the consensus GT/AG rule. The gene consists of seven exons and six introns with a total size of approximately 7 kb. The nucleotide sequence of the 5 flanking region of the testis TFIIS gene contains several potential regulatory factor-binding sites, not all of which are present in the TFIIS gene, whose expression is nearly ubiquitous. Elucidation of the full structure of the testis TFIIS gene should be useful for determining its chromosomal localization and its potential role in the regulation of gene expression in human tissues.
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Affiliation(s)
- Z A Weaver
- Department of Molecular and Cell Biology, University of California, Berkeley 94720-3202, USA.
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Labhart P. Transcript cleavage in an RNA polymerase I elongation complex. Evidence for a dissociable activity similar to but distinct from TFIIS. J Biol Chem 1997; 272:9055-61. [PMID: 9083031 DOI: 10.1074/jbc.272.14.9055] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Stalled Xenopus RNA polymerase I (pol I) elongation complexes bearing a 52-nucleotide RNA were prepared by promoter-initiated transcription in the absence of UTP. When such complexes were isolated and incubated in the presence of Mg2+, the associated RNA was shortened from the 3'-end, and mono- and dinucleotides were released. Shortened transcripts were still associated with the DNA and were quantitatively reelongated upon addition of NTPs. The cleavage activity could be removed from the pol I-ternary complex with buffers containing 0.25% Sarkosyl. These findings indicate that a factor with characteristics similar to elongation factor TFIIS is associated with the pol I elongation complex. However, addition of recombinant Xenopus TFIIS to Sarkosyl-washed pol I elongation complexes had no effect, whereas it showed the expected effects in control reactions with identically prepared pol II elongation complexes. The results thus suggest the existence of a pol I-specific cleavage/elongation factor. I also report the sequence of a novel type of Xenopus TFIIS. The predicted amino acid sequences of the present and previously identified Xenopus TFIIS are less than 65% conserved. Thus, like mammalian species, Xenopus has at least two highly divergent forms of TFIIS.
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Affiliation(s)
- P Labhart
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA.
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