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REVIEW COMMUNICATIONS
GENETICS
Organ-specific transcripts as a source of gene multifunctionality: lessons learned from
the Drosophila melanogaster sbr (Dm nxfl) gene
Ludmila Mamon1, Viktoria Ginanova1, Sergey Kliver2, Mariya Toropko1, and Elena Golubkova1
1Department of Genetics and Biotechnology, Faculty of Biology,
Saint Petersburg State University, Universitetskaya nab., 7-9, Saint Petersburg,
199034, Russian Federation
2Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, Sredniy Pr., 41, Saint Petersburg, 199004, Russian Federation
Address correspondence and requests for materials to Elena Golubkova, elena_golubkova@mail.ru, e.golubkova@spbu.ru
Abstract
Citation: Mamon, L., Ginanova, V., Kliver, S., Toropko, M., and Golubkova, E. 2019. Organ-specific transcripts as a source of gene multifunctionality: lessons learned from the Drosophila melanogaster sbr (Dm nxfl) gene. Bio. Comm. 64(2): 146-157. https://doi.org/10.21638/spbu03.2019.206
Author's information: Ludmila Mamon, Dr. of Sci. in Biology, Professor, orcid. org/0000-0001-5338-0703; Viktoria Ginanova, PhD, Junior Researcher, orcid. org/0000-0002-8404-9893; Sergey Kliver, MSc, Junior Researcher, orcid.org/0000-0002-2965-3617; Mariya Toropko, student; Elena Golubkova, PhD, Associate Professor, orcid.org/0000-0002-9528-5760
Manuscript Editor: Anton Nizhnikov, Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
Received: May 6, 2019;
Revised: June 17, 2019;
Accepted: June 20, 2019;
Copyright: © 2019 Mamon et al. This is an open-access article distributed under the terms of the License Agreement with Saint Petersburg State University, which permits to the authors unrestricted distribution, and self-archiving free of charge.
Funding: This work was supported by the Russian Foundation for Basic Research (19-04-01255 а).
Competing interests: The authors have declared that no competing interests exist.
Analysis of the transcriptomes of different organisms has demonstrated that a single gene can have multiple transcripts. The sources of transcriptional variability are the alternative promoters, polyadenylation sites, splicing, and RNA editing. A comparison of the organisms of different taxa has demonstrated that the complexity of organization during evolution arises not due to an increase in the number of protein-coding genes. The greatest variability of transcripts is specific to the nervous and germinal systems. A variety of mechanisms providing for the complexity of the transcriptome ensures a precise and coordinated regulation of organ-specific functions through a combination of cis-acting elements and trans-acting factors. The D. melanogaster sbr (Dm nxfl) gene has proven to be an excellent model for investigating mechanisms potentially leading to the emergence of multiple products with various functions. Keywords: nxf (nuclear export factor), D. melanogaster, alternative splicing, in-tron retention, transcriptional variability, alternative polyadenylation.
Contributors to Transcriptome Complexity
Analysis of the transcriptomes of different organisms has demonstrated that a single gene can have multiple transcripts. In Drosophila melanogaster, 47 genes can potentially code for more than 1000 transcript isoforms each (Brown et al., 2014). The sources of transcriptional variability are the alternative promoters, polyadenylation sites, splicing, and RNA editing. The same DNA sequence can encode both protein coding transcripts and non-coding RNAs, including regulatory antisense transcripts. The so-called nested genes provide an additional opportunity for an increased variability of transcripts that are products of the same genome locus. These can be separate genes located either on the same strand or on opposite strands within the host gene (Kumar, 2009). Such "nested" genes are located in intron 3 of the D. melanogaster sbr (small bristles) gene (Fig. 1). Ten exons and nine introns of the sbr gene with a length of 14341 bp are located in genomic region X:10,832,752..10,847,092 (FlyBase, 2019). Intron 3 (8892 nt) comprises 62 % of this gene sequence. Within this intron, there exist three genes: CG32669, CG15209, and CG15210. Initially they were predicted to be ORFs; their transcriptional activity was demonstrated later. The expression pattern and functions of these genes have been poorly investigated so far. One of them, CG32669, has the same orientation as the sbr gene, and the other two genes — CG15209 and CG15210 — are transcribed in the opposite direction.
CG15209
Fig. 1. The structure of the sbr (Dm nxfl) gene. The CG15210, CG15209 and CG32669 genes in intron 3 of the sbr gene.
Antisense transcripts that are complementary to the coding part of the gene are a common feature of tran-scriptomes. They include both long non-coding RNAs (lncRNAs) and short RNAs. Comprehensive analysis of the Drosophila transcriptome (Brown et al., 2014) has found both sense and antisense transcripts to be present in the same cell type at the same time. Sometimes antisense lncRNAs overlap with the 3' and 5' UTRs of adjacent genes, forming gene chains across contiguously transcribed regions. Antisense transcripts may overlap with both non-coding and coding sequences (CDSs). Moreover, orthologous genes have comparable antisense transcripts, which suggests a conserved regulation of gene expression with antisense transcripts (Brown et al., 2014).
The presence of paralogous genes with specific functions as a result of duplication followed by subsequent functional divergence may increase the flexibility of the gene expression network and, subsequently, adaptive reaction. The Nxf gene family is a good example of the research of the evolution of paralogous genes. Inside this family, only the Nxfl gene is homologous for all the species; other genes, even those sharing the same name, may be non-homologous in distant species. For example, the nxf3 of Drosophila is not homologous to the mammalian Nxf3 (Herold et al., 2001; Mamon et al, 2013), and the mouse Nxf3 is not orthologous to the human Nxf3 (Sasaki et al., 2005).
In mammals, the Nxf family includes genes with testis-specific and brain-specific expression (Jun et al., 2001; Tretyakova et al., 2005; Zhou et al., 2011). However, in D. melanogaster, the presence of organ-specific transcripts generated by different alternative events (such as the use of alternative promoters, alternative splicing, and polyadenylation) has been demonstrated only for the sbr (Dm nxf1) gene (Ivankova et al., 2010; Ginanova et al., 2016; Ginanova, 2017). An organ-specific pool of significantly different transcripts serves as the basis for the multifunctionality of the sbr gene. It is possible that certain tissue-specific functions are scattered throughout different paralogous genes in mammals.
Alternative sources of transcriptome complexity
DIFFERENTIAL PROMOTER USAGE
Core promoters consist of a variety of sequence elements, such as the TATA box, the Initiator (INR), and the downstream promoter element (DPE), recognized by the TATA-binding protein (TBP) and TBP-associated factors of the TFIID complex (Xu et al., 2016). No universal elements have been discovered in all core promoters, and the TATA box is found only in about 10 to 20 % of the metazoan core promoters (Kadonaga, 2012). The canonical basal transcription machinery, including RNA polymerase II (RNA-PII), interacts with the core promoter, typically located within -40 to +40 of the transcription start site (Kadonaga, 2002). The activity of the basal transcription machinery itself is quite low. Additional factors, such as activators or repressors with a variety of co-regulators (co-activators or co-repressors), are necessary for an effective transcription initiation by the RNAPII basal transcription machinery at the core promoter (Xu et al., 2016). These sequence-specific regulators of transcription are bound to regulatory DNA sequences, located at promoter-proximal or more distal regions. Transcription initiation efficiency of the RNAPII transcription machinery depends on the core promoter elements, combinatorial assortments of a variety of transcriptional activators or repressors, and chromatin modifications that can be navigated by RNAs, including miRNAs (Kadonaga, 2002, 2012).
Alternative promoter usage is yet another mechanism responsible for the complexity of the transcriptome and proteome (Vacik and Raska, 2017). If alternative promoters are located downstream of the canonical transcription start site, usually in one of the introns, they drive the expression of alternative RNA isoforms without upstream exons. As a result, some important functional domains coded for by the upstream exons will be lost in proteins coded for by alternative mRNA isoforms. Such shortened protein isoforms can be functionally distinct from the full-length protein, coded for by the canonical mRNA isoform.
ALTERNATIVE SPLICING
Alternative splicing (AS) is a common mechanism for increasing protein variety in eukaryotes (Black, 2000; Graveley, 2001; Nilsen and Graveley, 2010). Approximately 95 % of human genes are characterized by alternative pre-mRNA splicing (Wang et al., 2008). The major types of alternative splicing are exon "skipping" the use of exon cassettes that are sets of several adjacent exons with only a single exon from each cassette being chosen during the splicing of pre-mRNA, and the use of different 5' and 3' splice sites in exons or introns. A complex interplay of cis- and trans-acting factors promotes or represses the assembly of a splicing complex called a spliceosome at the splice site, and carries out the selection of canonic or an alternative 5' or 3' splice site. The spliceosome is a multi-protein-RNA complex, responsible for the precise excision of introns or intron/ exon blocks from the pre-mRNA and the fusion of the remaining exons together.
If the pre-mRNA of a gene undergoes alternative splicing of different types, the number of protein iso-forms may exceed the number of coding genes of the respective organism. The Drosophila Dscam (Down syndrome cell adhesion molecule) gene encoding axon guidance receptors are a great example thereof. This gene includes four exon cassettes of varying exon numbers, and can potentially generate over 38000 mRNA splice-isoforms. Different Dscam mRNAs probably label cell types or even single cells in the Drosophila brain (Schmucker, 2000; Graveley, 2005).
INTRON RETENTION
Intron retention (IR) is one of the variants of AS common in mammals. IR is considered to be a mechanism of gene expression regulation (Braunschweig et al., 2014; Jacob and Smith, 2017; Schmitz et al., 2017). IR enhances the complexity of the transcriptome (Schmitz et al., 2017). Within the main open reading frame, IR may result in the emergence of premature termination codons (PTCs), leading to the nonsense-mediated decay of mRNA with a retained intron, or, possibly, to the production of truncated proteins. mRNAs with retained introns give rise to alternative protein isoforms, and are therefore a source for the functional diversity of gene products. The existence of mRNA with an intron is a conservative feature of nxf1 genes in different organisms (Mamon et al., 2013, 2014; Wang et al., 2015). The retained intron may be part of the protein coding sequence, as in the Ce nxf1 mRNA, or it may only code for either the 17 C-terminus amino acids of the mammalian short NXF1 protein (Li et al., 2006) or the 5 C-terminus of the Drosophila short SBR (Mamon et al., 2013, 2014). The use of the PTC in the retained intron leads to the production of truncated proteins. In all cases, IR leads
to the emergence of mRNAs with an extended 3' UTR, including the canonical sequence of the Nxf1 mRNAs downstream of the retained intron. This suggests the presence of special regulatory functions related to the control of the spatial-temporal properties of mRNAs with a retained intron (Schmitz et al., 2017).
ALTERNATIVE POLYADENYLATION
The 3' end mRNA processing is a necessary step of mRNA maturation in eukaryotes, including endonucleolytic cleavage and untemplated polyadenylation. The cleavage and polyadenylation (CPA) machinery is composed of macromolecular complexes, such as the cleavage and polyadenylation stimulatory factor (CPSF), cleavage stimulatory factor (CStF), cleavage factor complexes — Im (CFIm) and IIm (CFIIm), and others (Proudfoot, 2011; Erson-Bensan, 2016). CPSF recognizes the polyadenylation signal (PAS), located ~10-30 nt upstream of the cleavage site. Most eukaryotic genes have multiple PASs used in alternative cleavage and polyadenylation (APA). There are two major PAS hexamers: AAUAAA and AUUAAA. Other weaker signal variants were later detected in different species: UAUAAA, AGUAAA, AA-GAAA, AAUAUA, AAUACA, CAUAAA, GAUAAA, AAUGAA, UUUAAA, ACUAAA, AAUAGA, AAAUAA, AUAAAA, AUAAAU, AUAAAG, CAAUAA, UAAUAA, AUAAAC, AAAAUA, AAAAAA, AAAAAG, AACAAA, UUAUAU, AAAAAU, and UUUAUU (Beaudoing et al., 2000; Tian et al., 2005; Derti et al., 2012; Sanfilippo et al., 2017). Such noncanonical PASs may be recognized by specific trans-acting factors and serve for alternative polyadenylation. The choice of the cleavage and polyad-enylation site is determined not only by PAS but also by the two motifs adjacent to it: U-rich/UGUA upstream elements (USEs) and the U-/GU-rich downstream element (DSE) (Colgan and Manley, 1997; Neve et al., 2017). The CstF complex interacts with DSE and mediates mRNA cleavage at the polyadenylation (pA) site (Neilson and Sandberg, 2010; Erson-Bensan, 2016). The CFIm complex binds to USE and mediates the cleavage reaction. The CFIIm complex promotes the termination of the RNA polymerase II-mediated transcription, and poly(A) polymerases (PAPs) catalyze the addition of untemplated adenosines downstream of the pA site (Proudfoot, 2011). The assembly process of the core factors of the cleavage and polyadenylation complex, including CPSF, CStF, CFIm, CFIIm, PAP, and others, is complicated by the interconnection between the 3' end processing with 5' capping, pre-mRNA splicing, and the transcription in the nucleus (Perales and Bentley, 2009; Szostak and Gebauer, 2012; Neve et al., 2017).
Depending on the location of the cleavage and polyadenylation (pA) site, APA events can be classified into two major groups: coding region APA (CR-APA) and UTR-
APA. CR-APA uses pA sites that are located within either CDS or the introns between CDS segments. As a result, alternative mRNA isoforms differ in their coding potential. UTR-APA uses the different pA sites that are located in the 3' UTR, and the resulting coding potential of alternative mRNA isoforms does not change (Neve et al., 2017).
The majority of genes contain multiple PASs in their 3' UTRs (Elkon et al., 2012); therefore, 3' UTR-APA may be a very common event, increasing the variability of transcripts at a transcriptome level. mRNA is usually a part of the ribonucleoprotein (RNP) complex of RNAs and RNA-binding proteins attracted by a combination of cis-acting elements in the 3' UTR or in another part of mRNA. The longer 3' UTRs may contain additional regulatory cis-acting elements that can regulate mRNA localization and protein abundance, or create conditions and act a scaffolding for recruiting a protein complex containing RNA-binding proteins (Berkovits and Mayr, 2015; Mitra et al., 2015).
The use of the proximal PAS in the 3' UTR may lead to a loss of cis-elements for binding with microRNAs and/or RNA-binding proteins (RBPs) (López de Salines et al., 2004; Flynt and Lai, 2008; Szostak and Gebauer, 2012; White et al., 2012). RBPs can recognize not only certain sequences, but also a specific secondary structure of the 3' UTR. RBP target sites in 3' UTR can overlap and form targets for miRNAs, and vice versa. In each case, mRNA's fate is determined by the combination of cis-elements in 3' UTR and the combination of transacting factors (RBP and miRNA). A different length of 3' UTR can serve as a mechanism for differential regulation of subcellular functions of the same proteins (An et al., 2008). There are two types of mRNA BDNF (brain-derived neurotrophic factor) with long 3' UTR and short 3' UTR in mice. It was shown that only the long 3' UTR provides the targeting mRNA BDNF to dendrites, controlling the abundance of the dendritic BDNF protein and the pruning and enlargement of dendritic spines. miRNAs binding sites in the 3' UTRs are cis-acting elements, which mediate mRNA decay and translational repression in animals (Iwakawa and Tomari, 2015). So, despite no changes in the protein-coding capacity difference in 3' UTR, it may be functionally significant and can influence the transport, stability, translation efficiency, and subcellular localization of mRNAs (Colgan and Manley, 1997; Hilger et al., 2011).
The length of 3' UTRs can change by increasing or decreasing the poly(A)-tail in the cytoplasm allowing for the regulation of the stability of mRNA and the efficiency of its translation (Richter, 1996). The cytoplasmic polyadenylation element (CPE) in 3' UTR is the binding site for the CPE-binding protein (CPEB) that promotes polyadenylation-induced translation. CPE (UUUUUAU) is located upstream of the nuclear PAS (AAUAAA). In Xenopus laevis, CPEB associates with Maskin, binding
the translation initiation factor 4E (Barnard et al., 2005). The interaction of Maskin with eIF4E excludes eIF4G and prevents the formation of the eIF4F initiation complex. Phosphorylation events within the CPE-binding protein complex disrupt its connection with the eIF4F initiation complex and allow the cytoplasmic poly(A) polymerase to elongate the poly(A) tail of mRNA. The elongated poly(A) tail is bound by the poly(A)-binding protein, which in turn binds eIF4G, disrupting the Maskin and eIF4E interaction, thereby initiating translation (Barnard et al., 2005; Richter and Sonenberg, 2005). Such strategy of translation regulation allows for the storage of mRNAs in a state of temporary unavailability for translation and for the activation of mRNA translation with the corresponding signal. This mechanism of translation regulation of specific mRNAs in cell cycle regulation (Barnard et al., 2005; Richter and Sonenberg, 2005) and the synapto-dendritic compartment of neurons (Wells et al., 2000; Du and Richter, 2005) has been found.
During the process of CR-APA, the use of an alternative PAS in an intron leads to the formation of a protein isoform without the C-terminus of a full-length protein. The U1snRNP actively suppresses PASs in introns. These PASs are called cryptic (Neve et al., 2017). However, these intronic PASs can become available during increased proliferation (Elkon et al., 2012). mRNAs with APA in the intron are a source of truncated proteins that are incapable of performing the functions of full-length proteins that are coded by the same gene. Identification of trans-acting APA regulators and cis-acting regulatory elements may promote understanding of the mechanisms of APA (White et al., 2012).
The majority of the sources of transcriptome complexity is the cornerstone of the origin of the sbr organ-specific transcripts.
ORGAN-SPECIFIC TRANSCRIPTS
The analysis of transcriptomes has made it possible to conclude that the greatest variability of transcripts is specific to the nervous and germinal systems. Genes expressed in the testes, brain, and ovaries have properties that promote the variability of transcriptomes.
BRAIN-SPECIFIC TRANSCRIPTS
The presence of mRNAs with an extended 3' UTR is a conserved feature of the nervous system in contrast to the testis transcripts (Miura et al., 2013, 2014; Hilger et al., 2011; Smibert et al., 2012). In the nervous system, hundreds of genes have mRNAs being processed with the use of increasingly distant PASs, and their 3' UTRs reach tens of kb in length (Hilgers, 2015). Specific RNA-binding proteins inhibit cleavage and polyadenylation (CPA) at proximal sites. In Drosophila, the ELAV (embryonic-lethal abnormal visual system) protein is known to play
I
Poly(U)-Tract
CCGCCUGAGGCUUUUAUGAAGUAAAUCGCAUAGGAGUUUCCGUAGGACAGAGCCGCGUGCCACAUCCACAUAAUCGAAUGCUGUUUUUUUUUUUUUGGUU major PAS
UUGUAAUUAAAUUUUAAAAUUAUUAGAGAAACCUCUAUAUAAUAAUAAUAAUUAAUAUUAUUAAGCUGCGAAGUUGUGUGCACAUUCGGGCAGUAGCAAU
UAUUAUCCCAGCACUGCGGGCAAUGUGCAUCAACGAUCACAGUUCUUCGAUAGAUUAGUUUAGCUCUCUUUAAGUUCCGUCCGCAGAUCCGCUGGUCUAC
miR-281-2-5p miR-184-3p
AUUGAGGCCAGGACGAGUCUGCGAACGGUAGUCCCUUUAGAGUUAAAGUUGUUUUAGAUUCCUAAGCCAAACACCUUCAAACACACACAACACGACAACA
major PAS CPE
CUAUUAAACGUAAUGCAACAAUGUUGUCGAAUCGAAAGAAACCCAAUUUUUAUUUUAAUAUAUACGACGAUACCGAAACCAAGGCGAUGGUCGAAAAGCA
miR-33-5p miR-iab-4-5p major PAS
UGGAUCGCGCCAAUAAUUCUAUAUUCCCCGCUUUCCCAGAUCCUCGACUCGCCUUACAUUUUGUAUACAAAUACCAUAGAAUAAAAAGAAACAUUUUGAC miR-1011-3p
CACUGUAAAAAUUUUGUAACGCUCGGAAACCAAAAUUACCUUUAUUUCUUAAUAGAAAAAAAUUAGUGUAAGAUUCGAUUUACAAUACACGCUUA
miR-965-3p
GCCG UAAAU UCAAU UG AAU U UAAUAUAUAAAAAU UAUAUACAU U AAG ACAAAAG UGUAGAU UCAUAAAUAAAU U U U UCAGAAUAGAAUG A miR-1006/10-3p
Fig. 2. Exon 10 sequence of the sbr gene. The end of the coding region is shown in bold. Arrows mark the ends of testis-specific transcripts detected by 3' RACE-PCR. Arrow head marks the 3' ends of the head and/or ovary transcripts. Important polyadenylation elements are depicted as poly(U)-tract, major PAS — major polyadenylation signal, CPE — cytoplasmic polyadenylation element. The sequences corresponding to predicted poorly conserved sites for conserved miRNA families are underlined.
Fig. 3. The testis-specific sbr mRNAs are detected by 5' and 3' RACE-PCR. Boxes indicate exons included in the sbr mRNAs. Exon numbers are signed under each box. RBD — RNA-Binding Domain; LRR — Leucine-Rich Domain; NTF2L — Nuclear Transport Factor 2 Like; UBA — Ubiquitin-Associated domain; NLS — Nuclear Localization Signal. In testes, all sbr mRNAs have the shortened 3' UTR. In all transcripts, length of the 3' UTR varies from 44 to 124 nucleotides. Two sbr mRNAs, using the alternative promoters in intron 3, give rise the shortened protein isoform without NLS and the part of RBD, which are present in the canonical full-length SBR.
the role of APA regulators. However, no binding sites for ELAV have been identified in the extended 3' UTRs (Hilger et al., 2012; Smibert et al., 2012). It was suggested that the distant APA depends on specific sequences in the promoters of genes producing mRNAs with an extended 3' UTR (Hilgers et al., 2012; Hilgers, 2015; Oktaba et al., 2015). A search of such sequences by means of computational analysis has revealed that the GAGA element is frequently found in the promoter regions of the genes producing mRNAs with extended 3' UTR (Li and Gilmour, 2013; Oktaba et al., 2015). The GAGA element signals pausing to the RNA Polymerase II (Pol II). This confirms the hypothesis that there exists interrelation between the processes of transcription initiation and CPA.
CStF-64 is a brain-specific CStF. CStF-64 is a splice variant of CStF and is found in all regions of the brain and the peripheral nervous system (MacDonald and McMahon, 2010). CStF-64 may play a role in determining the polyadenylation site in brain-specific mRNAs.
Interestingly, the hippocampus exhibits the largest number of 3' UTR extensions in comparison with all other tissues (Miura et al., 2013). 3' UTR lengthening may increase the number of cis-acting elements used as target sites for neural-specific miRNAs.
There are transcripts that undergo post-transcrip-tional cleavage to release specific fragments, which then function independently (Tuck and Tollervey, 2011), and 3' UTR extensions may be a source of ncRNAs after post-transcriptional cleavage (Miura et al., 2013). A significant increase in the 3' UTR length is observed in the sbr mRNA with retained intron 5. This intron was dubbed a cassette intron because it is part of the evolutionarily conserved cassette exon — 110 bp — intron — exon — 37 bp, which is found in the Nxfl genes in different organisms. mRNAs with a cassette intron are also found in organisms of different taxa (Mamon et al., 2013, 2014; Wang et al., 2015). Cassette introns contain evolutionarily conserved motifs. In Drosophilidae they are evident in the form of
Fig. 4. The sbr mRNAs are detected by 5' and 3' RACE-PCR in the head RNA probe. The symbols are the same as in Fig. 3. Horizontal arrows show the alternative transcription start sites, arrow heads show the alternative site of cleavage and polyadenylation. The sbr mRNAs isoforms are listed in order of decrease of their quantity.
Fig. 5. The sbr mRNA isoforms are detected by 5' and 3' RACE-PCR in the ovary RNA probe. The symbols are the same as in Fig. 3. Horizontal arrows show the alternative transcription start sites, arrow heads show the alternative site of cleavage and polyadenylation. The sbr mRNAs isoforms are listed in order of decrease of their quantity. The ovary-specific sbr mRNA isoforms are marked by asterisk.
two extended poly(A) sequences. Such poly(A)-tracts are known to facilitate the inclusion of corresponding introns into the processed RNA (Jacob and Smith, 2017).
It should be noted that the sbr gene's intron containing mRNA is the most abundant among the sbr transcripts in adult fly heads (Fig. 4). This is also supported by the results of a northern blot analysis, and suggests neurospecificity of the mRNAs with the retained intron (Ivankova et al., 2010). The sbr mRNA with the retained intron gives rise to a truncated protein (unpublished). The investigation of the role of the truncated SBR protein in the formation and function of the nervous system is currently underway.
TESTIS-SPECIFIC TRANSCRIPTS
Translational regulation is a fundamental characteristic of gene expression in mammalian testes (Kleene, 2001, 2003). Long-living mRNAs that are synthesized long
before translation have been found. They are stored in a translationally inactive state for several days, and are then translated in transcriptionally inactive elongated spermatids during the formation of spermatozoa from spermatids (Hawthorne et al., 2006). The widespread use of the alternative promoter, upstream PAS, and alternative splicing are features of gene expression in sper-matogenic cells (Kleene, 2001, 2003). In spermatogenic cells, the transcripts of some housekeeping genes encode truncated proteins that cannot have the same functions as the full-length products of the same genes in somatic cells (Kleene, 2001). Alternative promoter usage forms an alternative 5' UTR determining the efficiency of mRNA translation. Translation is repressed with the upstream reading frames (uORFs) in the 5' UTR before the start co-don (AUG) of the reading frame encoding the "functional" protein in the mRNA (Child et al., 1999). The presence of uORFs in mRNA's 5' UTR is an additional mechanism of the translation regulation in spermatogenesis (Kleene,
2003). Paralogous genes within gene families with only testes-specific expression are yet another feature of spermatogenesis. In mice, round spermatids express a testis-specific isoform of poly(A) polymerase, which is localized in the cytoplasm in contrast to the somatic isoform with the nuclear localization (Kashiwabara et al., 2000, 2002). Thus, cytoplasmic polyadenylation is an additional way of translation regulation of mRNAs during spermatogenesis (Kashiwabara et al., 2002; Kleene, 2003). There are testis-specific translation repressors, such as Y-box proteins and the testis-brain RNA binding protein (TB-RBP) in mammals (Kleene, 2003). It is an additional source allowing each mRNA to use its own mechanism of translational regulation. The specifics of a testis-specific transcrip-tome consist of transcripts of many genes, which are expressed in both somatic and spermatogenic cells, and are modified by alternative transcription start sites, splicing, and upstream polyadenylation sites, that form the atypical patterns of gene expression in spermatogenical cells (Kleene, 2001, 2003).
Mammalian and invertebrate testes use many mRNAs with shorter 3' UTRs compared to other tissues (Liu et al., 2007; Smibert et al., 2012; Neve et al., 2017). 3' UTR shortening promotes mRNA stability and transla-tional effectivity. It has been demonstrated that in mice, shortening the 3' UTR eliminates destabilizing elements, such as AU-rich elements and transposable elements located downstream of testis-specific APA (tsAPA) in 3' UTR (Li W. et al., 2016).
Since tsAPA is not used efficiently in somatic cells, it has been suggested that there are testis-specific factors involved in the cleavage and polyadenylation process in non-canonical proximal APAs, such as the testis-specif-ic form of CStF-64 (Wallace et al., 1999). The 64-kDa subunit of the CStF polyadenylation factor binds to pre-mRNAs downstream of the cleavage site and influences the cleavage site choice (MacDonald et al., 1994; MacDonald and McMahon, 2010). Somatic and testis-specific forms of CStF-64 have been found (Wallace et al., 1999). The CStF-64 gene for the somatic form is encoded on the X chromosome in both mice and humans. This suggests that the somatic form of CStF-64 is absent in meiotic cells because of the X chromosome in-activation, whereas the autosomal CStf2t gene encodes the testis-specific form xCStF-64 (Das et al., 2007). The xCStF-64 is found in spermatocytes and early spermatids (Wallace et al., 1999).
Alternative promoters in the intron 3 of the Dro-sophila melanogaster sbr (Dm nxf1) gene drive the expression of two testis-specific mRNA isoforms without exons 1, 2, and 3. 5' UTRs of these mRNAs isoforms contain either uORFs, or a small intron (Ginanova et al., 2016). Both features of the 5' UTR are known to control translation efficiency of the corresponding mRNAs in mammals (Mededbach et al., 2011; Bicknell et al., 2012);
their functionality in Drosophila is unknown. The testis-specific sbr mRNAs initiate the synthesis of the testis-specific short protein (tSBR), which excludes nuclear localization signals (NLS) present in the canonical SBR protein (Fig. 3). This suggests that tSBR is unable to get into the nucleus by itself and carries out some functions in the cytoplasm, likely participating in the biogenesis of long-living mRNAs during meiosis and spermiogenesis (Ginanova et al., 2016).
All sbr (Dm nxfl) mRNAs have a shortened 3' UTR in testes (Ginanova et al., 2016) (Fig. 2). The 3' UTR of the full-length sbr mRNAs has several cis-acting elements, such as AU-rich, alternative PASs, CPE, and the predicted target-sites for miRNAs. All of them are located downstream of the cleavage and polyadenylation sites, which are used during the processing of the testis-specific sbr mRNAs. The poly(U)-tract is among the cis-elements in the 3' UTR of sbr (Dm nxf1) mRNAs, and remains in the shortened 3' UTR of sbr (Dm nxf1) mRNAs. The polypyrimidine-tract-binding (PTB) protein 2 regulates meiotic male germ cell mRNAs in mice (Iguchi et al., 2006). The dmPTB plays an important role during spermatogenesis in Drosophila (Sridharan et al., 2016).
Testis-specific transcripts are unknown for the mammalian Nxf1 gene. There are testis-specific paralo-gous genes among Nxf gene family in mice (Sasaki et al., 2005) and humans (Yang et al., 2001).
TRANSCRIPTS IN OOGENESIS
A subset of maternal mRNAs and proteins are synthesized during oogenesis and are retained in the oocyte to direct the first mitotic divisions and specify the patterning of the embryo. Early embryogenesis passes through a stage when developmental control is handed from maternally provided gene products to those synthesized from (by) the zygotic genome (Tadros and Lipshitz, 2009). The oocyte-to-embryo transition (OET) can be subdivided into two interrelated processes: first, a subset of maternal mRNAs and proteins is eliminated; then the transcription of the zygotic genome begins.
There are several pathways of maternal mRNA degradation. One of them is the ARE (AU-rich element)-mediated pathway known in Xenopus laevis (Voeltz and Steitz, 1998). The Embryonic Deadenylation Element Binding Protein (EDEN-BP) triggers the deadenylation of maternal transcripts upon fertilization via the recognition of AU-rich cis-elements. The activity of EDEN-BP is regulated by phosphorylation (Detivaud et al., 2003). This may explain the different activity of EDEN-BP in oocytes and early embryos. Another way to mediate the maternal mRNA degradation is accomplished through the binding of a miRNA (Guo et al., 2008; Lund et al., 2009).
Yet another way of post-transcriptional regulation of the maternal mRNAs in early embryogenesis is the
CPE-dependent mRNA polyadenylation and its consequent translation. CPEB-mediated mRNA silencing/ re-activation is essential to oogenesis (Tay and Richter, 2001) and in developing hippocampal neurons (Kundel et al. 2009) in mice. Cytoplasmic polyadenylation is a major mRNA regulator during oogenesis and embryogenesis in Drosophila (Coll et al., 2010; Cui et al., 2013).
The sequence motifs in the 3' UTRs are the "combinatorial code" allowing for a precise spatial-temporal regulation of mRNA translation during OET (Evsikov et al. 2006), and the keys to a specific code combination are provided by a combination and/or modifications of the corresponding trans-acting factors with protective or destructive functions (Svoboda et al., 2015; Schultz et al., 2018).
The greatest variety of the sbr mRNAs is found in the ovaries (Fig. 5). Moreover, the canonical isoform is not the most numerous. Several different promoters are used as transcription starts for different mRNAs sbr. Alternative promoters are located in exons 2, 3, and 4 in addition to the canonical one. The sbr expression patterns in early embryos (0-2 h) and in the ovaries are similar, according to the northern blot analysis (Ivankova et al., 2010). One may hypothesize that the majority of sbr mRNA isoforms are transcribed during oogenesis, and the maternal products of the sbr gene are necessary during early development of the embryo. The mutations of the sbr gene have a maternal effect on early development. The SBR protein is abundant in early embryos and marks the spindles of nuclear divisions (Golubkova et al., 2015). The fraction of the shorter sbr mRNAs that is present in embryos 1-2 h of age disappears when zygotic transcription begins (Ivankova et al., 2010). These results imply an essential role of the sbr gene in the early embryogenesis of D. melanogaster. Since the early embryogenesis of D. melanogaster occurs in the absence of a transcription, the functions of SBR (Dm NXF1) as a factor of nuclear export of mRNAs are unnecessary. Nuclear division in syncytial embryos of D. melanogaster is characterized by semiclosed mitosis within the nuclear membranes, which are only disrupted at the poles adjacent to the centrioles (Stafstrom and Staehelin, 1984). The NPC (nuclear pore complex) assembly and disassembly at the site of fusion between the mitotic nuclear envelope and the overlying spindle membrane are detected during early synchronous mitosis in D. melanogaster embryos (Kiseleva et al., 2001). The predicted truncated products of the sbr gene during oogenesis can have alternative functions. The sbr gene products participate in complicated processes that can be relatively independent from transcription. These processes are provided by the cyclic translation of mRNAs of factors that are involved in DNA replication, nuclear divisions, and cytoskeleton dynamics.
A variety of SBR isoforms allow each of them to be part of a particular RNP complex that includes mRNAs for nuclear divisions in early embryos. mRNAs with dif-
ferent functional and regulatory capabilities require specialized RBPs. SBR (Dm NXF1) interacts with the sub-units of the origin recognition complex, which associates with replication origins and initiates the pre-replication complex assembly (Kopitova et al., 2016). The sbr gene is essential for nuclear divisions (Golubkova and Mamon, 2012) and the cytoskeleton (Mamon et al., 2017). Since the RNA-binding protein SBR is found not only in the nucleus or nuclear envelope but also in the cytoplasm, it may be part of RNP complexes storing organ-specific long-living mRNAs. The nucleoporin-binding domains in the truncated SBR isoforms allow for the localization of the corresponding RNP complexes in the nuclear envelope (Mamon et al., 2017).
The sbr mRNA diversity in ovaries reflects the specificity of the early embryonic development of D. melano-gaster. Various maternal mRNAs are involved in control of the synchronous nuclear divisions. The specific RNA-binding proteins are needed for functioning of different mRNA. This also applies to the SBR proteins.
Conclusion
A comparison of the organisms of different taxa has demonstrated that the complexity of organization during evolution arises not due to an increase in the number of protein-coding genes. One of the reasons is alternative transcript processing, which generates functional diversity from the same or similar number of genes. A variety of mechanisms providing for the complexity of the transcriptome ensures a precise and coordinated regulation of organ-specific functions through a combination of cis-acting elements and trans-acting factors. The D. melanogaster sbr (Dm nxf1) gene has proven to be an excellent model for investigating these mechanisms, potentially leading to the emergence of multiple products with various functions.
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