Alternative Splicing, RNA Editing, and the Current Limits of Next Generation Sequencing
Abstract
:1. Introduction
2. RNA Modifications
3. mRNA Splicing and Alternative Splicing
3.1. Serine/Arginine-Rich Splicing Factors (SRSFs)
3.2. Heterogeneous Nuclear Ribonucleoproteins (hnRNPs)
3.3. Consequences of Alternative Splicing and Measures to Address the Issue
4. RNA Editing and RNA Editing Enzymes
4.1. Adenosine Deaminases
4.2. Cytidine Deaminases
4.3. Consequences of RNA Editing and Measures to Address the Issue
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Protein (UniProt ID) | Gene | Location | Function/Role | Localization | 1 Alternant Transcripts/Isoforms | 2 PTMs |
---|---|---|---|---|---|---|
* SREK1 (Q8WXA9) | SREK1 | Ch.5q12.3 | Regulates alternative splicing by influencing the activity of other splicing factors. Inhibits the splicing activity of SFRS1, SFRS2, and SFRS6, but augments the splicing activity of SFRS3. | Nuc | 3 trscpts/2 isoforms | 18 (uc) |
* SRRM1 (Q8IYB3) | SRRM1 | Ch.1p36.11 | Part of the pre- and post-splicing mRNP complex. Promotes constitutive ESE-dependent splicing by bridging sequence-specific SRSFs, TRA2B, and basal snRNP factors. Ubiquitously expressed. | Nuc matrix, Speckles | 1 trscpt/2 isoforms # | 166 (uc) |
* SRRM2 (Q9UQ35) | SRRM2 | Ch.16p13.3 | A required component of the pre-mRNA spliceosome. Mainly expressed in liver placenta and leukocytes. Associates with SRRM1, SRSF3, SRSF4, and SRSF5. | Nuc, Speckles | 3 trscpts/3 isoforms | 736 (uc) |
SRSF1 (Q07955) | SRSF1 | Ch.17q22 | Prevents exon skipping to ensure the accuracy of splicing and alternative splicing by forming a bridge between the 5′- and 3′-splice site binding components, U1 snRNP, and U2AF. Isoform 1 acts as a splicing enhancer. Isoforms 2 and 3 act as splicing repressors. | Speckles, Cyto (shuttles) | 2 trscpts/3 isoforms | 65 (muc) |
SRSF2 (Q01130) | SRSF2 | Ch.17q25.1 | Central to pre-mRNA splicing. Required for the formation of the ATP-dependent splicing complex. Forms a bridge between the 5′- and 3′-splice site binding components, U1 snRNP, and U2AF. | Nuc, Nucleoplasm, Speckles | 3 trscpts/2 isoforms | 45 (muc) |
SRSF3 (P84103) | SRSF3 | Ch.6p21.31-21.2 | Specifically promotes exon inclusion during alternative splicing. Recruitment of SFRS3 to mRNA binding elements near N6-meythyladenosine (m6A) sites, leads to exon inclusion. | Nuc, Cyto, Speckles | 2 trscpts/2 isoforms* | 33 (muc) |
SRSF4 (Q08170) | SRSF4 | Ch.1p35.3 | Plays a role in alternative splice site selection during pre-mRNA splicing. | Speckles | 1 trscpt/1 isoform | 67 (uc) |
SRSF5 (Q13243) | SRSF5 | Ch.14q24.1 | Plays a role in constitutive splicing and can influence alternative splice site selection. | Nuc | 4 trscpts/2 isoforms # | 39 (uc) |
SRSF6 (Q13247) | SRSF6 | Ch.20q13.11 | Plays a role in constitutive splicing and can influence alternative splice site selection. | Nuc, Speckles | 1 trscpt/3 isoforms # | 56 (uc) |
SRSF7 (Q16629) | SRSF7 | Ch.2p22.1 | Required for pre-mRNA splicing. Can modulate alternative splicing in vitro. Prevalent in brain, kidneys, and lungs. | Nuc, Cyto | 5 trscpts/4 isoforms # | 53 (uc) |
SRSF8 (Q9BRL6) | SRSF8 | Ch.11q21 | Involved in pre-mRNA alternative splicing. Highly expressed in pancreas, spleen, and prostate; poorly expressed in lungs, liver, and thymus. | Nuc | 1 trscpt/2 isoforms # | 44 (uc) |
SRSF9 (Q13242) | SRSF9 | Ch.12q24.31 | Plays a role in constitutive splicing and can influence alternative splice site selection. Highly expressed in heart, kidneys, pancreas, and placenta; poorly expressed in brain, liver, lungs, and skeletal muscle. | Nuc | 1 trscpt/1 isoform | 49 (uc) |
SRS10 (O75494) | SRSF10 | Ch.1p36.11 | Acts as a general repressor of pre-mRNA splicing when in its dephosphorylated form by interfering with the U1 snRNP 5′ splice recognition of SNRNP70. Required for splicing repression in M-phase cells and after heat shock. Promotes exon skipping during alternative splicing. May be involved in the regulation of alternative splicing in neurons, with Isoform 1 acting to promote alternative splicing and Isoform 3 acting to suppress alternative splicing. | Speckles, Cyto | 7 trscpts/6 isoforms | 46 (muc) |
SRS11 (Q05519) | SRSF11 | Ch.1p31.1 | May function in pre-mRNA splicing. | Nuc | 4 trscpts/3 isoforms | 58 (uc) |
SRS12 (Q8WXF0) | SRSF12 | Ch.6q15 | Acts as an antagonist to SR proteins in pre-mRNA splicing regulation. Mainly expressed in testis. | Nuc | 1 trscpt/1 isoform | 21 (uc) |
* TIA1 (P31483) | TIA1 | Ch.2p13.3 | Regulates alternative pre-RNA splicing by binding U-rich sequences immediately downstream of 5′ splice sites in a U snRNP-dependent manner. Can promote atypical 5′ splice site selection by promoting splicing of exons with weak 5′ splice sites. Isoform 2 demonstrates enhanced splicing regulatory activity as compared to Isoform 1. Most prominently expressed in heart, small intestine, kidneys, liver, lungs, skeletal muscle, pancreas, ovary, and testis. Disease associated. | Nuc, Cyto, Stress granule | 5 trscpts/5 isoforms | 11 (uc) |
* TRA2A (Q13595) | TRA2A | Ch.7p15.3 | Associates with pre-mRNA in a sequence-specific manner to regulate pre-mRNA splicing. Expression is ubiquitous. Associates with SR30, SRSF3, SRSF4, SRSF5, and SRSF6. | Nuc | 3 trscpts/3 isoforms | 63 (uc) |
* TRA2B (P62995) | TRA2B | Ch.3q27.2 | Associates with pre-mRNA in a sequence-specific manner to promote or inhibit exon inclusion. Works by antagonizing splicing regulators belonging to the hnRNP class of proteins. Ubiquitously expressed with highest expression in heart, skeletal muscle, and pancreas; lowest expression in kidneys and liver. | Nuc | 2 trscpts/2 isoforms | 67 (uc) |
Protein (UniProt ID) | Gene | Location | Function/Role | Localization | 1 Alternant Transcripts/Isoforms | 2 PTMs |
---|---|---|---|---|---|---|
FUS (P35637) | FUS | Ch.16p11.2 | Also referred to as hnRNP P2. DNA/RNA-binding protein that plays a role in transcription regulation, RNA splicing, RNA transport, and DNA damage response. Acts as a molecular mediator between RNA polymerase II and U1 small nuclear ribonucleoprotein, thus coupling transcription and splicing. Autoregulates its own expression through nonsense mediated decay. Disease associated. | Nuc | 2 trscpts/2 isoforms | 98 (46 wc) |
ROA0 (Q13151) | HNRNPA0 | Ch.5q31.2 | Specifically binds AU-rich element (ARE)-containing mRNAs and is involved in post-transcriptional stability of diverse cytokine mRNAs. | Nuc | 1 trscpt/1 isoform | 62 (muc) |
ROA1 (P09651) | HNRNPA1 | Ch.12q13.13 | Involved in the packaging of pre-mRNA into hnRNP particles, nucleo-cytoplasmic transport of poly(A) mRNA, and modulation of splice site selection. Disease associated. | Nuc, Cyto (shuttles) | 5 trscpts/3 isoforms | 91 (ssc) |
RA1L2 (Q32P51) | HNRNPA1L2 | Ch.13q14.3 | Involved in the packaging of pre-mRNA into hnRNP particles, nucleo-cytoplasmic transport of poly(A) mRNA, and modulation of splice site selection. | Nuc, Cyto | 1 trscpt/1 isoform | 37 (uc) |
ROAA (Q99729) | HNRNPAB | Ch.5q35.3 | Has high affinity for G-rich and U-rich regions of ss hnRNA. Binds to APOB transcripts around the APOBEC C-to-U RNA editing site. | Nuc, Cyto | 4 trscpts/4 isoforms | 43 (uc) |
ROA2 (P22626) | HNRNPA2B1 | Ch.7p15.2 | Associates with pre-mRNAs in a sequence-dependent fashion to package the transcripts. Packaging plays a role in transcription, pre-mRNA processing, RNA nuclear export, subcellular location, mRNA translation, and stability of mature mRNAs. Promotes pri-miRNA processing and sorting. Involved in innate immune response activation. Disease associated. | Nuc, Cyto, Nucleoplasm, Cyto granules, secreted | 7 trscpts/2 isoforms | 107 (muc) |
ROA3 (P51991) | HNRNPA3 | Ch.2q31.2 | Has a role in cytoplasmic trafficking of RNA. May be involved in pre-mRNA splicing. | Nuc | 5 trscpts/2 isoforms | 94 (muc) |
HNRPC (P07910) | HNRNPC | Ch.14q11.2 | Nucleates assembly of 40S hnRNP particles by binding pre-mRNA. May play a role in the early steps of spliceosome assembly and pre-mRNA splicing. N6-methyladenosine (m6A) has been shown to influence mRNA splicing by enhancing HNRNPC binding. | Nuc | 9 trscpts/4 isoforms | 82 (ssc) |
HNRC1 (O60812) | HNRNPCL1 | Ch.1p36.21 | May play a role in nucleosome assembly. Specifically found in skeletal muscle tissue. | Nuc | 1 trscpt/1 isoform | 23 (uc) |
HNRC2 (B2RXH8) | HNRNPCL2 | Ch.1p36.21 | May play a role in nucleosome assembly. Tissue expression is unclear. | Nuc | 1 trscpt/1 isoform | 4 (uc) |
HNRC3 (B7ZW38) | HNRNPCL3 | Ch.1p36.21 | Role unknown. Expressed mainly in the cortical plate, blood, and hindlimb stylopod muscle. | Nuc | 1 trscpt/1 isoform | 11 (uc) |
HNRPD (Q14103) | HNRNPD | Ch.4q21.22 | Binds with high affinity to AU-rich elements (AREs) found within the 3′-UTR of many proto-oncogenes and cytokine mRNAs. Also functions as a transcription factor. May be involved in translationally coupled mRNA turnover. | Nuc, Cyto (shuttles with circadian clock) | 5 trscpts/4 isoforms | 76 (muc) |
HNRDL (O14979) | HNRNPDL | Ch.4q21.22 | Promotes transcriptional activation or repression in a context-dependent manner. Binds AU-rich elements (AREs) found within the 3′-UTR of many proto-oncogenes and cytokine mRNAs with high affinity. Preferentially expressed in heart, brain, placenta, lungs, liver, skeletal muscle, kidneys, pancreas, spleen, thymus, prostate, testis, ovary, small intestine, colon, and leukocytes. Disease associated. Elevated expression observed in diverse cancers. | Nuc, Cyto (shuttles) | 6 trscpts/3 isoforms | 61 (uc) |
HNRPF (P52597) | HNRNPF | Ch.10q11.21 | Component of the heterogeneous nuclear ribonucleoprotein (hnRNP) complexes. Plays a role in regulating alternative splicing events. Maintains target RNA in an unfolded state. | Nuc, Nucleoplasm | 6 trscpts/1 isoform | 65 (muc) |
HNRH1 (P31943) | HNRNPH1 | Ch.5q35.3 | Component of the heterogeneous nuclear ribonucleoprotein (hnRNP) complexes. Regulates pre-mRNA alternative splicing. Disease associated. | Nuc, Nucleoplasm | 4 trscpts/2 isoforms | 64 (muc) |
HNRH2 (P55795) | HNRNPH2 | Ch.Xq22.1 | Component of the heterogeneous nuclear ribonucleoprotein (hnRNP) complexes. Disease associated. | Nuc, Nucleoplasm | 1 trscpt/1 isoform | 48 (muc) |
HNRH3 (P31942) | HNRNPH3 | Ch.10q21.3 | Participates in early heat shock-induced splicing arrest. Different isoforms suspected of possessing distinct functions in splicing. | Nuc | 2 trscpts/6 isoforms | 60 (uc) |
HNRPK (P61978) | HNRNPK | Ch.9q21.32 | A major pre-mRNA-binding protein that binds to poly(C) sequences. Plays a vital role in the p53/TP53 response to DNA damage. Disease associated. | Nuc, Cyto, Nucleoplasm, Cellular Projections | 15 trscpts/3 isoforms | 132 (23 wc) |
HNRPL (P14866) | HNRNPL | Ch.19p13.2 | Component of heterogeneous nuclear ribonucleoprotein (hnRNP) complexes. Binds to exonic or intronic sites to function as an activator or repressor of exon inclusion. Regulates its own expression through the inclusion of a "poison" exon. | Nuc, Cyto, Nucleoplasm | 2 trscpts/2 isoforms | 90 (ssc) |
HNRPM (P52272) | HNRNPM | Ch.19p13.2 | Pre-mRNA binding protein involved in splicing. Acts as a receptor for carcinoembryonic antigen in Kupffer cells to initiate signaling events, leading to the induction of IL-1 alpha, IL-6, IL-10, and TNFα. | Nuc, Nucleolus | 3 trscpts/2 isoforms | 125 (muc) |
HNRPR (O43390) | HNRNPR | Ch.1q36.12 | Component of ribonucleosomes. Role unknown. Disease associated. | Nuc, Cyto, Nucleoplasm, Microsome | 6 trscpts/5 isoforms | 76 (uc) |
HNRPU (Q00839) | HNRNPU | Ch.1q44 | DNA-/RNA-binding protein involved in nuclear chromatin organization, telomere-length regulation, transcription, mRNA alternative splicing and stability, transcriptional silencing, and mitotic cell progression. Required for embryonic development. Disease associated. | Nuc, Cyto, Nuc Matrix, Speckles, cytoskeleton | 3 trscpts/3 isoforms | 185 (ssc) |
PCBP1 (Q15365) | PCBP1 | Ch.2p13.3 | Also referred to as hnRNP E1. Binds ssRNA and ssDNA. Together with PCBP2, may regulate erythropoiesis through mRNA splicing. Predominantly expressed in skeletal muscle, thymus, and peripheral blood leukocytes; lower expression observed in prostate, spleen, testis, ovary, small intestine, heart, liver, and adrenal and thyroid glands. | Nuc, Cyto (shuttles) | 1 trscpt/1 isoform | 49 (muc) |
PCBP2 (Q15366) | PCBP2 | Ch.12q13.13 | Also referred to as hnRNP E2. Binds ssRNA and ssDNA. Negatively regulates innate immune antiviral responses mediated by MAVS, and the cGAS-STING pathway. Together with PCBP1, may regulate erythropoiesis through mRNA splicing. | Nuc, Cyto (shuttles) | 9 trscpts/8 isoforms | 42 (ssc) |
PTBP1 (P26599) | PTBP1 | Ch.19p13.3 | Polypyrimidine tract binding protein (PTBP)-1 (also known as hnRNP I) interacts with polypyrimidine (PP) stretches at the branch point region. Plays a role in pre-mRNA splicing, alternative splicing, and alternate 5′-3′ splice site usage. Promotes exon skipping of its own pre-mRNA during muscle cell differentiation. Can sequester miRNAs. | Nuc | 4 trscpts/4 isoforms | 65 (uc) |
RBMX (P38159) | RBMX | Ch.Xq26.3 | Also referred to as hnRNP G. Involved in the regulation of pre- and post-transcriptional processes. A component of the supraspliceosome complex that regulates pre-mRNA alternative splice site selection. Can activate or suppress exon inclusion. Ubiquitously expressed. Disease associated. | Nuc | 3 trscpts/3 isoforms | 118 (uc) |
HNRPQ (O60506) | SYNCRIP | Ch.6q14.3 | Component of the CRD-mediated complex. Isoform 1 binds to APOB mRNA AU-rich sequences and is a regulatory part of the APOB mRNA editosome complex. May be involved in translationally coupled mRNA turnover. Isoform 3 is a component of the GAIT (gamma interferon-activated inhibitor of translation) complex, which mediates interferon-gamma-induced transcript-selective translation inhibition in inflammation processes. The GAIT complex binds GAIT elements in the 3′-UTR of diverse inflammatory mRNAs to suppress their translation. | Nuc, Cyto, Microsome, ER (Isoforms 1-3 preferentially localize in the nucleoplasm) | 9 trscpts/4 isoforms | 87 (uc) |
Protein (UniProt ID) | Gene | Location | 1 Substrate | Function/Role | Localization | 2 Alternant Transcripts/Isoforms | 3 PTMs |
---|---|---|---|---|---|---|---|
ADAR Family of Adenosine Deaminases | |||||||
DSRAD (P55265) | ADAR | Ch.1q21.3 | dsRNA, Z-DNA | Catalyzes the deamination of A-to-I in RNA of complex secondary structure. May affect gene expression by altering protein coding, pre-mRNA splicing, RNA stability, RNA transport, miRNA targeting, and RNA–protein interactions. Edits both host and foreign RNAs. May have a role in DNA strand break repair. Isoform 1 is interferon-inducible, primarily localizes to the cytoplasm, and demonstrates elevated activity toward foreign (viral) RNAs. Suppresses PKR activation and the induction of the integrated stress response. Can associate with Z-DNA or Z-RNA. Isoform 5 is constitutively expressed and localizes primarily to the nucleus. Ubiquitously expressed with highest expression in brain and lungs. Disease associated. Overexpressed in many cancers; expression associated with cancer aggressiveness. | Nuc, Nucleolus, Cyto (shuttles) | 12
trscpts/5 isoforms # These numbers may double due to alternate exon 1 usage. | 125 (ssc) |
RED1 (P78563) | ADARB1 | Ch.22q22.3 | dsRNA | Catalyzes the deamination of A-to-I in RNA of complex secondary structure. May affect gene expression by altering protein coding, pre-mRNA splicing, RNA stability, RNA transport, miRNA targeting, and RNA–protein interactions. Edits both host and foreign RNAs. Suppresses PKR activation and the induction of the integrated stress response. Involved in the RNA editing of RNA/DNA hybrids during DNA double-strand break repair. Disease associated. Ubiquitously expressed. Highly expressed in brain, heart, lower placenta; moderately expressed in lungs, liver, and kidneys. Isoform 5 is seen in hippocampus and colon. Decreased activity in astrocytomas correlated with disease severity. | Nuc | 5 trscpts/6 isoforms # | 23 (ssc) |
RED2 (Q9NS39) | ADARB2 | Ch.10q15.3 | dsRNA | ADAR family member that lacks editing activity. Likely alters/regulates ADAR1 and ADAR2. Binds both ss and dsRNA. Expression is brain-specific. | Nuc | 2 trscpts/2 isoforms | 13 (uc) |
Cytidine Deaminases: APOBEC Family and AID | |||||||
ABEC1 (P41238) | APOBEC1 | Ch.12p13.31 | ssRNA, ssDNA (h) | Catalyzes the C-to-U post-transcriptional editing of several mRNAs, including APOB and NF1. Acts as a homodimer. May play a role in the epigenetic regulation of gene expression. Expressed exclusively in small intestine. | Nuc, Cyto | 1 trscpt/1 isoform # | 2 (wc) |
ABEC2 (Q9Y235) | APOBEC2 | Ch.6p21.1 | ss/dsDNA (h) (binding only) | A potential C-to-U editing enzyme with no known substrate and poor deaminase activity. May have a role in epigenetic regulation of gene expression. Exclusively expressed in heart and skeletal muscle. | Nuc, Cyto | 1 trscpt/1 isoform | 2 (uc) |
ABC3A (P31941) | APOBEC3A | Ch.22q13.1 | ssRNA, ssDNA | Demonstrates C-to-U editing activity toward ssRNA and ssDNA. Best effectiveness against ssDNAs of foreign origin (viral). Deaminates both C and meC and can hyper-edit nuclear and mitochondrial DNA. May have a role in epigenetic regulation of gene expression. Expressed in peripheral leukocytes and CD14+ phagocytic cells. Highly expressed in keratinocytes and peripheral blood monocytes. Present at detectable levels in other lymphoid tissue, lungs, bladder, urinary tract, and adipose tissue. Enhanced expression observed in diverse tumor tissues. Induced by interferon and CpG ssDNA. | Nuc, Cyto | 3 trscpts/2 isoforms # | 4 (uc) |
ABC3B (Q9UH17) | APOBEC3B | Ch.22q13.1 | ssDNA | Demonstrates C-to-U editing activity. Selectively targets ssDNAs of foreign origin (viral). Has the ability to hyper-edit nuclear and mitochondrial DNA. Acts as a homodimer. Interacts with APOBEC3G. Expressed in peripheral blood leukocytes, bone marrow, spleen, kidneys, bladder, urinary tract, testes, prostate, heart, thymus, ovary, and gastrointestinal tract. Expression is induced by interferon. | Nuc | 3 trscpts/3 isoforms | 10 (muc) |
ABC3C (Q9NRW3) | APOBEC3C | Ch.22q13.1 | ssDNA (v) | Demonstrates C-to-U editing activity. Selectively targets ssDNAs of foreign origin (viral). May play a role in epigenetic regulation of gene expression. Expressed in peripheral blood mononuclear cells, bone marrow, spleen, thymus, respiratory tract, kidneys, bladder, urinary tract, testes, prostate, skin, muscle, heart, ovary, endocrine tissues, liver, and gastrointestinal tract. Expression is induced by interferon. | Nuc, Cyto | 1 trscpt/1 isoform | 5 (uc) |
ABC3D (Q96AK3) | APOBEC3D | Ch.22q13.1 | ssDNA (v) | Demonstrates C-to-U editing activity. Selectively targets ssDNAs of foreign origin (viral). Antiviral activity occurs through both deaminase-dependent and -independent mechanisms. Can homodimerize or form heterodimers with APOBEC3F and APOBEC3G. Expressed in peripheral blood mononuclear cells, bone marrow, lymphoid tissues, gastrointestinal tract, and female reproductive system. | Cyto, P-bodies | 2 trscpts/2 isoforms | 4 (uc) |
ABC3F (Q8UX4) | APOBEC3F | Ch.22q13.1 | ssDNA (v) | Demonstrates C-to-U editing activity. Selectively targets ssDNAs of foreign origin (viral). Exhibits antiviral activity toward wide spectrum of viruses through both deaminase-dependent and -independent mechanisms. Has not been shown to target nuclear or mitochondrial DNA. May play a role in epigenetic regulation of gene expression. Widely expressed with highest expression observed in ovary. Interacts with APOBEC3G. Expression is induced by interferon. | Cyto, P-bodies | 2 trscpts/3 isoforms # | 3 (muc) |
ABC3G (Q9HC16) | APOBEC3G | Ch.22q13.1 | ssRNA, ssDNA (v) | Demonstrates C-to-U editing activity. Selectively targets ssDNAs of foreign origin (viral). Antiviral activity occurs through both deaminase-dependent and -independent mechanisms. Acts as a homodimer or homo-oligomer. Can bind RNA and form inactive high molecular weight (HMM) or active low molecular weight (LMM) ribonucleoprotein complexes. Expressed in peripheral blood mononuclear cells, bone marrow, lymphoid tissue, ovary, testis, bladder, urinary tract, gastrointestinal tract, and liver respiratory tract. Interacts with APOBEC3B, APOBEC3F, MOV10, AGO2, EIF4E, EIF4ENIF1, DCP2, and DDX6 in an RNA-dependent manner. Expression is induced by interferon. Upregulated in certain tumors. | Nuc, Cyto, P-bodies | 1 trscpt/2 isoforms # | 11 (ssc) |
ABC3H (Q6NTF7) | APOBEC3H | Ch.22q13.1 | ssDNA (v) | Demonstrates C-to-U editing activity. Selectively targets ssDNAs of foreign origin (viral). Antiviral activity occurs through both deaminase-dependent and -independent mechanisms. Expressed in peripheral blood mononuclear cells, bone marrow, lymphoid tissue, lungs, testis, ovary, and skin. | Nuc, Cyto, P-bodies | 6 trscpts/4 isoforms | 1 (uc) |
ABEC4 (Q8WW27) | APOBEC4 | Ch.1q25.3 | ND | Possible C-to-U editing enzyme with no known substrate. Expression is restricted to testis. | Nuc (predicted) | 1 trscpt/1 isoform | 1 (uc) |
AICDA (Q9GZX7) | AICDA | 12p13.31 | ssRNA (binding only), ssDNA (h), RNA/DNA hybrid | Demonstrates C-to-U editing activity. Involved in somatic hyper-editing, gene conversion, and class-switch recombination in B-lymphocytes. Necessary for B-cell differentiation and antibody maturation. Hyper-edits other sites in the genome in several pathologies. May have a role in epigenetic regulation of gene expression. Disease associated. Highly expressed in lymphoid tissues and germinal center B-cells. | Nuc, Cyto (predominant) | 4 trscpts/4 isoforms | 7 (2 wc) |
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Piazzi, M.; Bavelloni, A.; Salucci, S.; Faenza, I.; Blalock, W.L. Alternative Splicing, RNA Editing, and the Current Limits of Next Generation Sequencing. Genes 2023, 14, 1386. https://doi.org/10.3390/genes14071386
Piazzi M, Bavelloni A, Salucci S, Faenza I, Blalock WL. Alternative Splicing, RNA Editing, and the Current Limits of Next Generation Sequencing. Genes. 2023; 14(7):1386. https://doi.org/10.3390/genes14071386
Chicago/Turabian StylePiazzi, Manuela, Alberto Bavelloni, Sara Salucci, Irene Faenza, and William L. Blalock. 2023. "Alternative Splicing, RNA Editing, and the Current Limits of Next Generation Sequencing" Genes 14, no. 7: 1386. https://doi.org/10.3390/genes14071386