TET dioxygenases localize at splicing speckles and promote RNA splicing
Open accessPublished version of a preprint
Abstract
The dynamic regulation of RNA metabolism plays a crucial part in cellular function, with emerging evidence suggesting an important role for RNA modifications in this process. This study explores the relationship between RNA splicing and the TET dioxygenase activity, shedding light on the role of hm5C (RNA 5-hydroxymethylcytosine), and TET proteins in RNA metabolism. Integrating data from mass spectrometry, AlphaFold structural modeling, microscopic analysis, and different functional assays, including in vitro splicing, TET proteins were found to regulate splicing. We show that TET1, TET2, and TET3 interact with the splicing factors U2AF1 and U2AF2. Interestingly, TET dioxygenases localize in splicing speckles in mammalian and Drosophila cells. TET speckles association was found to be RNA-dependent, but also rely on its interaction with splicing factors. Furthermore, cellular splicing assays revealed that all three TET proteins promote splicing efficiency independent of their catalytic activity. Interestingly, though, the oxidation of m5C to hm5C restores splicing efficiency in vitro. The latter highlights the regulatory role of cytosine modifications in RNA metabolism. These findings provide insights into the complex interplay between RNA modifications and splicing, suggesting a multifaceted role for TET proteins in RNA metabolism beyond their canonical function in the oxidation of 5mC in DNA.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Accurate structure prediction of biomolecular interactions with AlphaFold 3
Abramson, J., Adler, J., Dunger, J., Evans, R., Green, T., Pritzel, A., Ronneberger, O., Willmore, L., Ballard, A. J., Bambrick, J., et al. (2024) · Nature · doi:10.1038/s41586-024-07487-w · Cited by 15,861 · cited 1× · see citing works
“For transfection of mouse embryonic stem cells (mESC), the Neon electroporation system was used (ThermoFisher Scientific) following the manufacturer’s instructions.”
Cox, J., & Mann, M. (2008) · Nature Biotechnology · doi:10.1038/nbt.1511 · Cited by 14,855 · cited 2× · see citing works
“For data analysis, all raw files were analyzed using the MaxQuant computational proteomics platform (version 1.4.1.6) [52] as described in [51].”
InfluentialUCSF ChimeraX : Structure visualization for researchers, educators, and developers
Pettersen, E. F., Goddard, T. D., Huang, C. C., Meng, E. C., Couch, G. S., Croll, T. I., Morris, J. H., & Ferrin, T. E. (2020) · Protein Science · doi:10.1002/pro.3943 · Cited by 9,327 · cited 1× · see citing works
“Protein structure images were generated with ChimeraX [60,61].”
UniProt: the Universal Protein Knowledgebase in 2023
The UniProt Consortium, Bateman, A., Martin, M.-J., Orchard, S., Magrane, M., Ahmad, S., Alpi, E., Bowler-Barnett, E. H., Britto, R., Bye-A-Jee, H., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac1052 · Cited by 7,210 · cited 1× · see citing works
“GO analysis was done with STRING using the rank list enrichment analysis.”
DNA methylation patterns and epigenetic memory
Bird, A. (2002) · Genes & Development · doi:10.1101/gad.947102 · Cited by 7,124 · cited 1× · see citing works
“5mC is generated and maintained by DNA methyltrans-ferases (MTases) called Dnmts [21] and is mainly found in CpG dinucleotide-rich sites, resulting in dense packing of chromatin [22].”
Okano, M., Bell, D. W., Haber, D. A., & Li, E. (1999) · Cell · doi:10.1016/s0092-8674(00)81656-6 · Cited by 6,143 · see citing works
N6-Methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO
Jia, G., Fu, Y., Zhao, X., Dai, Q., Zheng, G., Yang, Y., Yi, C., Lindahl, T., Pan, T., Yang, Y.-G., et al. (2011) · Nature Chemical Biology · doi:10.1038/nchembio.687 · Cited by 4,106 · see citing works
Protein complex prediction with AlphaFold-Multimer
Evans, R., O’Neill, M., Pritzel, A., Antropova, N., Senior, A., Green, T., Žídek, A., Bates, R., Blackwell, S., Yim, J., et al. (2021) · doi:10.1101/2021.10.04.463034 · Cited by 3,808 · see citing works
Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine
Ito, S., Shen, L., Dai, Q., Wu, S. C., Collins, L. B., Swenberg, J. A., He, C., & Zhang, Y. (2011) · Science · doi:10.1126/science.1210597 · Cited by 3,451 · cited 2× · see citing works
“NMD affects mRNAs containing premature translation termination codons (PTCs), which recruit the ATP-dependent RNA helicases Upf1–34.”
Scoring function for automated assessment of protein structure template quality
Zhang, Y., & Skolnick, J. (2004) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.20264 · Cited by 2,392 · cited 1× · see citing works
“The predicted template modeling score (pTM) and the interface-predicted template modeling (ipTM) are measures of the accuracy of the entire structure [54,55].”
Varadi, M., Bertoni, D., Magana, P., Paramval, U., Pidruchna, I., Radhakrishnan, M., Tsenkov, M., Nair, S., Mirdita, M., Yeo, J., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkad1011 · Cited by 2,052 · cited 1× · see citing works
“GO analysis was done with STRING using the rank list enrichment analysis.”
The DNA methyltransferases of mammals
Bestor, T. H. (2000) · Human Molecular Genetics · doi:10.1093/hmg/9.16.2395 · Cited by 2,045 · cited 1× · see citing works
“5mC is generated and maintained by DNA methyltrans-ferases (MTases) called Dnmts [21] and is mainly found in CpG dinucleotide-rich sites, resulting in dense packing of chromatin [22].”
Karikó, K., Muramatsu, H., Welsh, F. A., Ludwig, J., Kato, H., Akira, S., & Weissman, D. (2008) · Molecular Therapy · doi:10.1038/mt.2008.200 · Cited by 1,930 · cited 1× · see citing works
“Translational capacity is also dependent on RNA modifications like the incorporation of pseudouridine [17] or N6-methyladenosine (m6A) [18].”
Spliceosome Structure and Function
Will, C. L., & Luhrmann, R. (2011) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a003707 · Cited by 1,829 · cited 1× · see citing works
“Splicing enhancer sequences within the exon (ESEs) recruit proteins of the SR protein family (among them SC35), which establish a network of protein–protein interactions between the different components of the spliceosome (Figure 2A) [77].”
Loss of the Suv39h Histone Methyltransferases Impairs Mammalian Heterochromatin and Genome Stability
Peters, A. H. F. M., O'Carroll, D., Scherthan, H., Mechtler, K., Sauer, S., Schöfer, C., Weipoltshammer, K., Pagani, M., Lachner, M., Kohlmaier, A., et al. (2001) · Cell · doi:10.1016/s0092-8674(01)00542-6 · Cited by 1,766 · see citing works
Methylation of tRNA Asp by the DNA Methyltransferase Homolog Dnmt2
Goll, M. G., Kirpekar, F., Maggert, K. A., Yoder, J. A., Hsieh, C., Zhang, X., Golic, K. G., Jacobsen, S. E., & Bestor, T. H. (2006) · Science · doi:10.1126/science.1120976 · Cited by 1,192 · cited 1× · see citing works
“Similar to DNA, methylation of cytosines in RNA is catalyzed by specific RNA MTases (RMTases) like TRDMT1 and the nucleolar protein 1 (NOL1)/NSUN protein family [27,28].”
An extensive network of coupling among gene expression machines
Maniatis, T., & Reed, R. (2002) · Nature · doi:10.1038/416499a · Cited by 1,148 · cited 2× · see citing works
“Splicing speckles localize in the proximity of transcription sites and form subcellular domains called gene expression factories [88].”
How significant is a protein structure similarity with TM-score = 0.5?
Xu, J., & Zhang, Y. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq066 · Cited by 1,142 · cited 1× · see citing works
“The predicted template modeling score (pTM) and the interface-predicted template modeling (ipTM) are measures of the accuracy of the entire structure [54,55].”
mRNA localization: Gene expression in the spatial dimension
Martin, K. C., & Ephrussi, A. (2009) · Cell · doi:10.1016/j.cell.2009.01.044 · Cited by 1,048 · cited 1× · see citing works
“Internal base editing and splicing guarantee the exclusive continu-ance of coding sections, while distinct modifications at the 5´ and 3´ untranslated regions (UTR) ensure mRNA stability and correct subcellular localization [16].”
Wu, J. Y., & Maniatis, T. (1993) · Cell · doi:10.1016/0092-8674(93)90316-i · Cited by 755 · cited 2× · see citing works
“This again confirmed our AlphaFold protein–protein interaction predictions, showing that U2AF1 and U2AF2 proteins form a multimer complex [10] that interacts directly with the catalytic domain of TET proteins.”
A Versatile Nanotrap for Biochemical and Functional Studies with Fluorescent Fusion Proteins
Rothbauer, U., Zolghadr, K., Muyldermans, S., Schepers, A., Cardoso, M. C., & Leonhardt, H. (2007) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700342-mcp200 · Cited by 678 · cited 2× · see citing works
“For the binding fractions, the rest of the lysate was incubated with GFP-binder beads [75].”
Self-citationThe superfamily of arginine/serine-rich splicing factors.
Fu, X. (1995) · PubMed · Cited by 674 · see citing works
General Translational Repression by Activators of mRNA Decapping
Coller, J. M., & Parker, R. (2005) · Cell · doi:10.1016/j.cell.2005.07.012 · Cited by 629 · cited 1× · see citing works
“The latter was shown to be coupled with translational repression [98].”
Facultative Heterochromatin: Is There a Distinctive Molecular Signature?
Trojer, P., & Reinberg, D. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.09.011 · Cited by 609 · cited 1× · see citing works
“In mammals, it is well established that DNA cytosine base modifications, especially 5mC, are important epigenetic marks and fulfill crucial functions in cellular processes [20].”
RNA splicing dysregulation and the hallmarks of cancer
Bradley, R. K., & Anczuków, O. (2023) · Nature Reviews Cancer · doi:10.1038/s41568-022-00541-7 · Cited by 579 · cited 1× · see citing works
“Furthermore, alternative splicing events increase transcript diversity in different cell types and under variant conditions [15].”
Cloning and domain structure of the mammalian splicing factor U2AF
Zamore, P. D., Patton, J. G., & Green, M. R. (1992) · Nature · doi:10.1038/355609a0 · Cited by 568 · cited 1× · see citing works
“One of them is the U2 small ribonucleoprotein particle (snRNP) auxiliary factor 2 (U2AF2), with an N-terminal SR domain and three C-terminal RNA-binding domains [7,8].”
Wansink, D. G., Schul, W., van der Kraan, I., van Steensel, B., DRIEL, R. V., & de Jong, L. (1993) · The Journal of Cell Biology · doi:10.1083/jcb.122.2.283 · Cited by 547 · cited 1× · see citing works
“Its localization is mainly restricted to so-called nuclear speckles, also referred to as ‘SC35 domains’ [2], RNA – protein interchromatin granules found in the nucleoplasm of eukaryotic cells.”
Tsumura, A., Hayakawa, T., Kumaki, Y., Takebayashi, S., Sakaue, M., Matsuoka, C., Shimotohno, K., Ishikawa, F., Li, E., Ueda, H. R., et al. (2006) · Genes to Cells · doi:10.1111/j.1365-2443.2006.00984.x · Cited by 544 · cited 1× · see citing works
“Therefore, we used mESCs triple knockouts of DNMT proteins, with residual levels of 5-methylcy-tosine [100,101].”
Associations between distinct pre‐mRNA splicing components and the cell nucleus.
Spector, D. L., Fu, X., & Maniatis, T. (1991) · The EMBO Journal · doi:10.1002/j.1460-2075.1991.tb04911.x · Cited by 522 · cited 2× · see citing works
“Interestingly, SC35 distribution is unaffected by RNase A digestion, indicating that the association with speckles is based on protein– protein interactions rather than protein–RNA interactions [4].”
Distinct 5-methylcytosine profiles in poly(A) RNA from mouse embryonic stem cells and brain
Amort, T., Rieder, D., Wille, A., Khokhlova-Cubberley, D., Riml, C., Trixl, L., Jia, X.-Y., Micura, R., & Lusser, A. (2017) · Genome biology · doi:10.1186/s13059-016-1139-1 · Cited by 496 · cited 1× · see citing works
“The distribution of m5C varies among cell types [106], and modifications at specific positions on mRNA can have different regulatory roles promoting or inhibiting translation [107,108].”
Nuclear speckles: molecular organization, biological function and role in disease
Gałgański, Ł., Urbanek-Trzeciak, M. O., & Krzyżosiak, W. J. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx759 · Cited by 489 · cited 1× · see citing works
“The term ‘speck-les’ was first used in 1961, and 2 years later, these speckles were identified as RNA-containing inter-chromatin particles [3].”
FTO-mediated formation of N6-hydroxymethyladenosine and N6-formyladenosine in mammalian RNA
Fu, Y., Jia, G., Pang, X., Wang, R. N., Wang, X., Li, C. J., Smemo, S., Dai, Q., Bailey, K. A., Nóbrega, M. A., et al. (2013) · Nature Communications · doi:10.1038/ncomms2822 · Cited by 478 · cited 1× · see citing works
“This modification was shown to be the substrate for iterative oxidation to N6–hydroxymethyl adenosine and further to N6-formyladenosine, in a reaction catalyzed by the AlkB protein family of dioxygenases [31,32].”
Crystal Structure of TET2-DNA Complex: Insight into TET-Mediated 5mC Oxidation
Hu, L., Li, Z., Cheng, J., Rao, Q., Gong, W., Liu, M., Shi, Y. G., Zhu, J., Wang, P., & Xu, Y. (2013) · Cell · doi:10.1016/j.cell.2013.11.020 · Cited by 448 · cited 2× · see citing works
“The mammalian TET family consists of three members, TET1, TET2, and TET3, sharing a conserved catalytic domain at the C-terminus [33].”
Yıldırım, Ö., Li, R., Hung, J., Chen, P. B., Dong, X., Ee, L.-S., Weng, Z., Rando, O. J., & Fazzio, T. G. (2011) · Cell · doi:10.1016/j.cell.2011.11.054 · Cited by 446 · cited 1× · see citing works
“In the past, the link between TET1 and the NuRD chromatin remodeling complex was reported [110], which mediates gene repression to maintain the pluripotent state of ESCs.”
Transcriptome-wide distribution and function of RNA hydroxymethylcytosine
Delatte, B., Wang, F., Ngoc, L. V., Collignon, É., Bonvin, E., Deplus, R., Calonne, E., Hassabi, B., Putmans, P., Awe, S., et al. (2016) · Science · doi:10.1126/science.aac5253 · Cited by 441 · cited 3× · see citing works
“Interestingly, TET has been shown to interact with microRNAs regulating hm5C in the adult brain [40], and hm5C was found in the RNA of Drosophila S2 cells [41].”
InfluentialFedeles, B. I., Singh, V., Delaney, J. C., Li, D., & Essigmann, J. M. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.r115.656462 · Cited by 416 · cited 1× · see citing works
“The AlkB family of dioxy-genases can use DNA and RNA as substrates [35,36]; however, whether the related TET proteins do the same was unclear.”
MODOMICS: a database of RNA modifications and related information. 2023 update
Cappannini, A., Ray, A., Purta, E., Mukherjee, S., Boccaletto, P., Moafinejad, S. N., Lechner, A., Barchet, C., Klaholz, B. P., Stefaniak, F., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad1083 · Cited by 412 · see citing works
Tet-Mediated Formation of 5-Hydroxymethylcytosine in RNA
Fu, L., Guerrero, C. R., Zhong, N., Amato, N. J., Liu, Y., Liu, S., Cai, Q., Ji, D., Jin, S., Niedernhofer, L. J., et al. (2014) · Journal of the American Chemical Society · doi:10.1021/ja505305z · Cited by 405 · cited 5× · see citing works
“Accordingly, previous studies detected hm5C in RNA of different tissues, like the heart and spleen [37].”
InfluentialTranscription-dependent colocalization of the U1, U2, U4/U6, and U5 snRNPs in coiled bodies
Carmo‐Fonseca, M., Pepperkok, R., Carvalho, M., & Lamond, A. I. (1992) · The Journal of Cell Biology · doi:10.1083/jcb.117.1.1 · Cited by 403 · cited 1× · see citing works
“One of them is the U2 small ribonucleoprotein particle (snRNP) auxiliary factor 2 (U2AF2), with an N-terminal SR domain and three C-terminal RNA-binding domains [7,8].”
5-methylcytosine in RNA: detection, enzymatic formation and biological functions
Motorin, Y., Lyko, F., & Helm, M. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp1117 · Cited by 386 · cited 2× · see citing works
“These proteins use S-adenosylmethionine (SAM) as a methyl group donor [24].”
Loss of Tet Enzymes Compromises Proper Differentiation of Embryonic Stem Cells
Dawlaty, M. M., Breiling, A., Le, T., Barrasa, M. I., Raddatz, G., Gao, Q., Powell, B. E., Cheng, A. W., Faull, K. F., Lyko, F., et al. (2014) · Developmental Cell · doi:10.1016/j.devcel.2014.03.003 · Cited by 338 · see citing works
Visualization of gene activity in living cells
Tsukamoto, T., Hashiguchi, N., Janicki, S. M., Tumbar, T., Belmont, A. S., & Spector, D. L. (2000) · Nature Cell Biology · doi:10.1038/35046510 · Cited by 305 · cited 1× · see citing works
“In this essay, the mRNA mimic (pms2-PABPC1-mCherry) is cotransfected in BHK cells [95] together with an RNA trap (MCP-EGFP-LacI), and the protein of interest, in this case PABPC1-mCherry (known to interact with the mRNA mimic) [70] or mCherry-TET1-CD.”
Deckert, J., Hartmuth, K., Boehringer, D., Behzadnia, N., Will, C. L., Kastner, B., Stark, H., Urlaub, H., & Lührmann, R. (2006) · Molecular and Cellular Biology · doi:10.1128/mcb.00582-06 · Cited by 301 · cited 2× · see citing works
“For this purpose, we performed an in vitro splicing assay using MINX-M3 pre-mRNA reporter construct [73].”
Qiu, L., Li, X., Tang, H., Jiang, B., Dou, Y., Gorospe, M., & Wang, W. (2017) · Journal of Cellular Biochemistry · doi:10.1002/jcb.25957 · Cited by 284 · cited 1× · see citing works
“Perseus software (version 1.5.0.15) [52]”
InfluentialPrecise temporal regulation of alternative splicing during neural development
Weyn‐Vanhentenryck, S. M., Feng, H., Ustianenko, D., Duffié, R., Yan, Q., Jacko, M., Martinez, J. C., Goodwin, M., Zhang, X., Hengst, U., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-04559-0 · Cited by 271 · cited 1× · see citing works
“In this process, the precise regulation of alternative splicing is crucial [105].”
Dnmt2-dependent methylomes lack defined DNA methylation patterns
Raddatz, G., Guzzardo, P. M., Olova, N. N., Fantappíé, M. R., Rampp, M., Schaefer, M., Reik, W., Hannon, G. J., & Lyko, F. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1306723110 · Cited by 258 · cited 1× · see citing works
“Since Drosophila lacks 5mC in DNA [93] but still has a TET gene highly homologous to the vertebrate TET proteins, we hypothesized a DNA methyla-tion-independent function of TET proteins in chromatin-associated regulation of transcription.”
Capuano, F., Mülleder, M., Kok, R., Blom, H. J., & Ralser, M. (2014) · Analytical Chemistry · doi:10.1021/ac500447w · Cited by 250 · cited 1× · see citing works
“For transfection of mouse embryonic stem cells (mESC), the Neon electroporation system was used (ThermoFisher Scientific) following the manufacturer’s instructions.”
Wang, E., & Aifantis, I. (2020) · Trends in cancer · doi:10.1016/j.trecan.2020.04.011 · Cited by 242 · cited 1× · see citing works
“Furthermore, alternative splicing events increase transcript diversity in different cell types and under variant conditions [15].”
mRNA quality control: An ancient machinery recognizes and degrades mRNAs with nonsense codons
Behm‐Ansmant, I., Kashima, I., Rehwinkel, J., Saulière, J., Wittkopp, N., & Izaurralde, E. (2007) · FEBS Letters · doi:10.1016/j.febslet.2007.05.027 · Cited by 213 · cited 1× · see citing works
“Nonsense-mediated mRNA decay (NMD) is a conserved mRNA surveillance mechanism to mitigate deleterious effects caused by gene mutations or transcriptional errors (reviewed in [97].”
Immunoelectron microscopic localization of snRNPs
Spector, D. L., Schrier, W. H., & Busch, H. (1984) · Biology of the Cell · doi:10.1111/j.1768-322x.1984.tb00215.x · Cited by 208 · see citing works
Stevens, L. C. (1973) · JNCI Journal of the National Cancer Institute · doi:10.1093/jnci/50.1.235 · Cited by 206 · see citing works
Distribution of 5-methylcytosine in chromatin.
Razin, A., & Cedar, H. (1977) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.74.7.2725 · Cited by 205 · cited 1× · see citing works
“On the one hand, TET1 could play a role in chromatin reorganization and decondensation by erasing 5mC, which keeps chromatin in a densely packed state [80].”
Splice site m6A methylation prevents binding of U2AF35 to inhibit RNA splicing
Mendel, M., Delaney, K., Pandey, R. R., Chen, K., Wenda, J. M., Vågbø, C. B., Steiner, F. A., Homolka, D., & Pillai, R. S. (2021) · Cell · doi:10.1016/j.cell.2021.03.062 · Cited by 200 · cited 1× · see citing works
“Translational capacity is also dependent on RNA modifications like the incorporation of pseudouridine [17] or N6-methyladenosine (m6A) [18].”
Zillmann, M., Zapp, M. L., & Berget, S. M. (1988) · Molecular and Cellular Biology · doi:10.1128/mcb.8.2.814 · Cited by 191 · see citing works
Formation and Abundance of 5‐Hydroxymethylcytosine in RNA
Huber, S. M., van Delft, P., Mendil, L., Bachman, M., Smollett, K. L., Werner, F., Miska, E. A., & Balasubramanian, S. (2015) · ChemBioChem · doi:10.1002/cbic.201500013 · Cited by 187 · cited 1× · see citing works
“The iterative oxidation of m5C to hm5C in total RNA was demonstrated in a mouse model, suggesting a conserved process that could have critical regulatory functions inside cells [38].”
Exposition of a family of RNA m5C methyltransferases from searching genomic and proteomic sequences
Reid, R. C., Greene, P. J., & Santi, D. V. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.15.3138 · Cited by 168 · cited 1× · see citing works
“Similar to DNA, methylation of cytosines in RNA is catalyzed by specific RNA MTases (RMTases) like TRDMT1 and the nucleolar protein 1 (NOL1)/NSUN protein family [27,28].”
Hoernes, T. P., Clementi, N., Faserl, K., Glasner, H., Breuker, K., Lindner, H. H., Hüttenhofer, A., & Erlacher, M. D. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1182 · Cited by 166 · cited 1× · see citing works
“The distribution of m5C varies among cell types [106], and modifications at specific positions on mRNA can have different regulatory roles promoting or inhibiting translation [107,108].”
Prasanth, K. V., Rajendra, T. K., Lal, A. K., & Lakhotia, S. C. (2000) · Journal of Cell Science · doi:10.1242/jcs.113.19.3485 · Cited by 151 · see citing works
Bauer, C., Göbel, K., Nagaraj, N., Colantuoni, C., Wang, M., Müller, U., Kremmer, E., Rottach, A., & Leonhardt, H. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.605881 · Cited by 138 · cited 3× · see citing works
“For data analysis, all raw files were analyzed using the MaxQuant computational proteomics platform (version 1.4.1.6) [52] as described in [51].”
InfluentialSelf-citationSubstrate specificities of bacterial and human AlkB proteins
Falnes, P. Ø. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh655 · Cited by 132 · cited 1× · see citing works
“The AlkB family of dioxy-genases can use DNA and RNA as substrates [35,36]; however, whether the related TET proteins do the same was unclear.”
The existence of 5-hydroxymethylcytosine and 5-formylcytosine in both DNA and RNA in mammals
Zhang, H.-Y., Xiong, J., Qi, B.-L., Feng, Y., & Yuan, B. (2015) · Chemical Communications · doi:10.1039/c5cc07354e · Cited by 124 · cited 1× · see citing works
“In addition, 5-formylcytidine (f5C) was detected in mammalian RNA, where its formation is currently assumed to be catalyzed by TET proteins [39].”
Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation
Lee, C. Y., Hubrich, D., Varga, J. K., Schäfer, C., Welzel, M., Schumbera, E., Djokic, M., Strom, J. M., Schönfeld, J., Geist, J. L., et al. (2024) · Molecular Systems Biology · doi:10.1038/s44320-023-00005-6 · Cited by 105 · cited 1× · see citing works
“Previous studies reported significant decreases in the sensitivity of AlphaFold for complex structure predictions when using full-length sequences [78].”
Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation
Lee, C. Y., Hubrich, D., Varga, J. K., Schäfer, C., Welzel, M., Schumbera, E., Đokić, M., Strom, J. M., Schönfeld, J., Geist, J. L., et al. (2023) · doi:10.1101/2023.08.07.552219 · Cited by 105 · see citing works
Differential recruitment of DNA Ligase I and III to DNA repair sites
Mortusewicz, O. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl492 · Cited by 102 · cited 1× · see citing works
“The SDS-PAGE and Western blotting experiments were performed as in [76].”
Mapping and Use of a Sequence that Targets DNA Ligase I to Sites of DNA Replication In Vivo
Cardoso, M. C., Joseph, C., Rahn, H.-P., Reusch, R., Nadal‐Ginard, B., & Leonhardt, H. (1997) · The Journal of Cell Biology · doi:10.1083/jcb.139.3.579 · Cited by 101 · cited 1× · see citing works
“Protein structure images were generated with ChimeraX [60,61].”
Self-citationTET enzymes and DNA hydroxymethylation in neural development and function — How critical are they?
Santiago, M., Antunes, C., Guedes, M., Sousa, N., & Marques, C. J. (2014) · Genomics · doi:10.1016/j.ygeno.2014.08.018 · Cited by 98 · cited 1× · see citing works
“For these experiments, we focused mostly on TET1 since it showed the highest interaction score with U2AF2, and it is abundantly distributed in a higher number of cell lines and tissues [79].”
TET-mediated oxidation of methylcytosine causes TDG or NEIL glycosylase dependent gene reactivation
Müller, U., Bauer, C., Siegl, M., Rottach, A., & Leonhardt, H. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku552 · Cited by 97 · cited 1× · see citing works
“Cell lysis and immunoprecipitation with the GFP-Trap (ChromoTek GmbH, Martinsried, Germany) were performed as described previously [50].”
Self-citationEpitranscriptome: Review of Top 25 Most-Studied RNA Modifications
Arzumanian, V. A., Dolgalev, G. V., Kurbatov, I. Y., Kiseleva, O. I., & Poverennaya, E. V. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms232213851 · Cited by 94 · see citing works
Guo, G., Pan, K., Su, F., Ye, L., Tong, X., Wang, Z., Xue, X., & Zhang, H. (2021) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2021.08.020 · Cited by 92 · cited 1× · see citing works
“In tRNA and rRNA, m5C has been extensively studied, but little is known about its role in mRNA, in part, due to the lack of effective separation and purification technologies [26].”
MeCP2 Rett mutations affect large scale chromatin organization
Agarwal, N., Becker, A., Jost, K. L., Haase, S., Thakur, B. K., Brero, A., Hardt, T., Kudo, S., Leonhardt, H., & Cardoso, M. C. (2011) · Human Molecular Genetics · doi:10.1093/hmg/ddr346 · Cited by 86 · cited 1× · see citing works
“: 40827–7, Sigma-Aldrich Chemie GmbH, Steinheim, Germany) as previously described [48].”
Self-citationPre-mRNA splicing and its cotranscriptional connections
Shenasa, H., & Bentley, D. L. (2023) · Trends in Genetics · doi:10.1016/j.tig.2023.04.008 · Cited by 84 · cited 1× · see citing works
“5mC is generated and maintained by DNA methyltrans-ferases (MTases) called Dnmts [21] and is mainly found in CpG dinucleotide-rich sites, resulting in dense packing of chromatin [22].”
SRSF2 plays an unexpected role as reader of m5C on mRNA, linking epitranscriptomics to cancer
Ma, H., Bizet, M., Costa, C. S. D., Murisier, F., de Bony, E. J., Wang, M., Yoshimi, A., Lin, K., Riching, K. M., Wang, X., et al. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.11.003 · Cited by 83 · cited 1× · see citing works
“Perseus software (version 1.5.0.15) [52]”
InfluentialThomas, J. A., Palusa, S. G., Prasad, K. V. S. K., Ali, G. S., Surabhi, G., Ben‐Hur, A., Abdel‐Ghany, S. E., & Reddy, A. S. N. (2012) · The Plant Journal · doi:10.1111/tpj.12004 · Cited by 72 · cited 1× · see citing works
“One of its components is SC35, belonging to the family of serine-arginine-rich proteins (SR proteins), which is involved in intron recognition and spliceosome assembly [1].”
A novel isoform of TET1 that lacks a CXXC domain is overexpressed in cancer
Good, C. R., Madžo, J., Patel, B. G., Maegawa, S., Engel, N., Jelı́nek, J., & Issa, J. J. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx435 · Cited by 70 · cited 1× · see citing works
“32P-labeled transcripts were subjected to in vitro splicing using HeLa nuclear extracts, a tumor-derived cell line with high levels of TET1 protein [102].”
A small, portable RNA device for the control of exon skipping in mammalian cells
Vogel, M. O., Weigand, J. E., Kluge, B., Grez, M., & Suess, B. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky062 · Cited by 68 · cited 1× · see citing works
“The vectors pWHE237 (pc3336) and pWHE237mod-WT (pc3337) were used for luciferase reporter gene assays (generated by C. Berens´s laboratory) and published in [43].”
DNA Methylation in Drosophila—A Critical Evaluation
Krauß, V., & Reuter, G. (2011) · Progress in molecular biology and translational science · doi:10.1016/b978-0-12-387685-0.00003-2 · Cited by 66 · cited 1× · see citing works
“For transfection of mouse embryonic stem cells (mESC), the Neon electroporation system was used (ThermoFisher Scientific) following the manufacturer’s instructions.”
Chrysanthou, S., Tang, Q., Lee, J., Taylor, S. J., Zhao, Y., Steidl, U. G., Zheng, D., & Dawlaty, M. M. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac089 · Cited by 64 · see citing works
Erect wing regulates synaptic growth in Drosophilaby integration of multiple signaling pathways
Haussmann, I. U., White, K., & Soller, M. (2008) · Genome biology · doi:10.1186/gb-2008-9-4-r73 · Cited by 63 · cited 1× · see citing works
“Antibody in-situ stainings were done as described previously [64] using rabbit anti-HA (1:1000; Sigma), mouse anti-SC35 (Sigma-Aldrich S4045 ascites, 1:1000), rat anti-RNA Pol II (anti-Ser 2, clone 3E10, 04–1571 Merck-Millipore, 1:1000) and visualized with Alexa Fluor 488 (1:250; Molecular Probes),…”
Self-citationThe CTD role in cotranscriptional RNA processing and surveillance
de Almeida, S. F., & Carmo‐Fonseca, M. (2008) · FEBS Letters · doi:10.1016/j.febslet.2008.04.019 · Cited by 60 · see citing works
Cytosine base modifications regulate DNA duplex stability and metabolism
Rausch, C., Zhang, P., Casas-Delucchi, C. S., Daiß, J. L., Engel, C., Coster, G., Hastert, F. D., Weber, P., & Cardoso, M. C. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab509 · Cited by 51 · cited 1× · see citing works
“In this scenario, the oxidation of methylated cytosines reverses the duplex stability and genome metabolic effects of the unmodified cytosine [103].”
Self-citationSpliceosome Malfunction Causes Neurodevelopmental Disorders with Overlapping Features
Li, D., Wang, Q., Bayat, A., Battig, M. R., Zhou, Y., Bosch, D. G. M., van Haaften, G., Granger, L., Petersen, A. K., Pérez-Jurado, L. A., et al. (2024) · Journal of Clinical Investigation · doi:10.1172/jci171235 · Cited by 46 · cited 1× · see citing works
“Overall, our results provide novel insights into how RNA splicing is regulated, with TET proteins and their oxidation product hm5C having an impact on it.”
RNA splicing regulators play critical roles in neurogenesis
Fisher, E., & Feng, J. (2022) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1728 · Cited by 45 · cited 3× · see citing works
“Internal base editing and splicing guarantee the exclusive continu-ance of coding sections, while distinct modifications at the 5´ and 3´ untranslated regions (UTR) ensure mRNA stability and correct subcellular localization [16].”
InfluentialBinding of MBD proteins to DNA blocks Tet1 function thereby modulating transcriptional noise
Ludwig, A. K., Zhang, P., Hastert, F. D., Meyer, S., Rausch, C., Herce, H. D., Müller, U., Lehmkuhl, A., Hellmann, I., Trummer, C., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1197 · Cited by 44 · cited 1× · see citing works
“…stainings were done as described previously [64] using rabbit anti-HA (1:1000; Sigma), mouse anti-SC35 (Sigma-Aldrich S4045 ascites, 1:1000), rat anti-RNA Pol II (anti-Ser 2, clone 3E10, 04–1571 Merck-Millipore, 1:1000) and visualized with Alexa Fluor 488 (1:250; Molecular Probes), Alexa…”
Self-citationStolz, P., Mantero, A. S., Tvardovskiy, A., Ugur, E., Wange, L. E., Mulholland, C. B., Cheng, Y., Wierer, M., Enard, W., Schneider, R., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac642 · Cited by 44 · cited 1× · see citing works
“Peak lists were searched against the UniProt database (https://www.uni prot.org/) with an initial mass deviation of 7 ppm and fragment ion deviation of 0.5 Thomson using carbamidomethylation as a fixed modification.”
InfluentialSelf-citationDrosophila Genomic Methylation: new Evidence and new Questions
Dunwell, T. L., & Pfeifer, G. P. (2014) · Epigenomics · doi:10.2217/epi.14.46 · Cited by 42 · cited 1× · see citing works
“However, previous studies have shown that DNA methylation in Drosophila is nearly undetectable [84–86], while RNA methylation-associated processes are present and functionally important.”
Huber, L., Ulrich, S., Leuenberger, C., Gassmann, M., Vogel, J., von Blotzheim, L. G., Speich, R., Kohler, M., & Brock, M. (2015) · Experimental Biology and Medicine · doi:10.1177/1535370215579018 · Cited by 42 · cited 1× · see citing works
“Furthermore, it can take part in the generation of individual sets of mRNAs by affecting the metabolism of microRNAs [25].”
Allemand, E., Gattoni, R. C., Bourbon, H.-M. G., Stévenin, J., Cáceres, J. F., Soret, J., & Tazi, J. (2001) · Molecular and Cellular Biology · doi:10.1128/mcb.21.4.1345-1359.2001 · Cited by 41 · cited 1× · see citing works
“For transfection of mouse embryonic stem cells (mESC), the Neon electroporation system was used (ThermoFisher Scientific) following the manufacturer’s instructions.”
Poly(ADP-ribosyl)ation of Methyl CpG Binding Domain Protein 2 Regulates Chromatin Structure
Becker, A., Zhang, P., Allmann, L., Meilinger, D., Bertulat, B., Eck, D., Hofstaetter, M., Bartolomei, G., Hottiger, M. O., Schreiber, V., et al. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.698357 · Cited by 37 · see citing works
Self-citationInterplay between TETs and microRNAs in the adult brain for memory formation
Kremer, E. A., Gaur, N., Lee, M. A., Engmann, O., Bohacek, J., & Mansuy, I. M. (2018) · Scientific Reports · doi:10.1038/s41598-018-19806-z · Cited by 35 · cited 1× · see citing works
“Interestingly, TET has been shown to interact with microRNAs regulating hm5C in the adult brain [40], and hm5C was found in the RNA of Drosophila S2 cells [41].”
Haussmann, I. U., Wu, Y., Nallasivan, M. P., Archer, N., Bódi, Z., Hebenstreit, D., Waddell, S., Fray, R. G., & Soller, M. (2022) · Nature Communications · doi:10.1038/s41467-022-28549-5 · Cited by 33 · cited 1× · see citing works
“For luciferase splicing reporter assay, HEK cells were transfected with PEI using 2 µg of mCherry-tagged TET1 constructs (TET1-CD/TET1-CDmut) or mCherry alone, in combination with 2 µg of plasmid DNA encoding firefly luciferase constructs with either one (pc3336) or two introns (pc3337).”
Self-citationDrosophila Tet Is Expressed in Midline Glia and Is Required for Proper Axonal Development
Ismail, J. N., Badini, S., Frey, F., Abou-Kheir, W. G., & Shirinian, M. (2019) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2019.00252 · Cited by 32 · cited 1× · see citing works
“GO analysis for changes focused on alternative 5’ splice sites revealed a significant enrichment ( p 0.05) in neuro-developmental genes, which is consistent with the defects in TETnull mutants [41,92].”
InfluentialTet protein function during Drosophila development
Wang, F., Minakhina, S., Tran, H., Changela, N., Kramer, J. J., & Steward, R. (2018) · PLoS ONE · doi:10.1371/journal.pone.0190367 · Cited by 31 · cited 1× · see citing works
“Error bars represent the standard deviation. isoform without this motif resembles vertebrate TET2 [87].”
Epigenetic reprogramming by TET enzymes impacts co-transcriptional R-loops
Sabino, J. C., de Almeida, M. R., Abreu, P. L., Ferreira, A. M., Caldas, P., Domingues, M. M., Santos, N. C., Azzalin, C. M., Grosso, A. R., & de Almeida, S. F. (2022) · eLife · doi:10.7554/elife.69476 · Cited by 30 · see citing works
Haussmann, I. U., Ustaoğlu, P., Bräuer, U., Hemani, Y., Dix, T. C., & Soller, M. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1254 · Cited by 29 · cited 1× · see citing works
“Recombineering was used to clone the genomic part of the core TET gene into pUC 3GLA UAS from a genomic BAC clone as described [65,66] by adding a HA Tev FLAG C-terminal tag.”
Self-citationBase pairing and structural insights into the 5-formylcytosine in RNA duplex
Wang, R., Luo, Z., He, K., Delaney, M. O., Chen, D., & Sheng, J. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw235 · Cited by 28 · cited 1× · see citing works
“Similar results were published for f5C [96], which was shown to favor RNA duplex structures.”
Effect of light on the nucleotide composition of rRNA of wheat seedlings
R�cz, I., Kir�ly, I., & L�sztily, D. (1978) · Planta · doi:10.1007/bf00385075 · Cited by 26 · cited 1× · see citing works
“In 1978, m5C was also detected in the rRNA of wheat seedlings [23], raising the question of whether it can fulfill regulatory functions in RNA.”
Biological function molecular pathways and druggability of DNMT2/TRDMT1.
Li, H., Liu, H.-R., Zhu, D., Dou, C., Gang, B., Zhang, M., & Wan, Z. (2024) · Pharmacological Research · doi:10.1016/j.phrs.2024.107222 · Cited by 24 · cited 1× · see citing works
“All cell lines’ characteristics, sources, and references are listed in Supplementary Table S2.”
Mechanisms of Drosophila Dscam mutually exclusive splicing regulation
Hemani, Y., & Soller, M. (2012) · Biochemical Society Transactions · doi:10.1042/bst20120060 · Cited by 24 · cited 1× · see citing works
“In Drosophila, this is one of the most complex alternatively spliced genes harboring three variable clusters, exon 4, exon 6, and exon 9, with 12, 48, and 33 variables, respectively [91].”
Self-citationKetchum, H. C., Suzuki, M., & Dawlaty, M. M. (2024) · Communications Biology · doi:10.1038/s42003-024-06120-w · Cited by 23 · cited 1× · see citing works
“For transfection of mouse embryonic stem cells (mESC), the Neon electroporation system was used (ThermoFisher Scientific) following the manufacturer’s instructions.”
Herce, H. D., Casas-Delucchi, C. S., & Cardoso, M. C. (2013) · Journal of Microscopy · doi:10.1111/jmi.12008 · Cited by 22 · cited 1× · see citing works
“Detailed colocalization analysis was performed by implementing the Python-based image analysis platform Priithon (http://code.google.com/p/priithon/), which was used to calculate the H-coefficient for the different conditions as in [69].”
Self-citationRNA splicing during terminal erythropoiesis
Conboy, J. G. (2017) · Current Opinion in Hematology · doi:10.1097/moh.0000000000000329 · Cited by 21 · cited 1× · see citing works
“Important roles for splicing are also related to biological processes like terminal ery-thropoiesis [14] or neurogenesis [15].”
Arroyo, M. D. C. G., Hastert, F. D., Zhadan, A., Schelter, F., Zimbelmann, S., Rausch, C., Ludwig, A. K., Carell, T., & Cardoso, M. C. (2022) · Nature Communications · doi:10.1038/s41467-022-32799-8 · Cited by 20 · cited 4× · see citing works
“Isolated RNA was then analyzed on 14% denaturing PAGE and visualized with autoradiography.”
InfluentialSelf-citationPerraud, M., Gioud, M., & Monier, J. C. (1979) · PubMed · Cited by 16 · see citing works
RNA splicing: a dual-edged sword for hepatocellular carcinoma
Kashyap, A., Tripathi, G., Tripathi, A., Rao, R., Kashyap, M., Bhat, A., Kumar, D., Rajhans, A., Kumar, P., Chandrashekar, D. S., et al. (2022) · Medical Oncology · doi:10.1007/s12032-022-01726-8 · Cited by 14 · cited 1× · see citing works
“Furthermore, alternative splicing events increase transcript diversity in different cell types and under variant conditions [15].”
Visualization and characterization of RNA–protein interactions in living cells
Duan, N., Arroyo, M. D. C. G., Deng, W., Cardoso, M. C., & Leonhardt, H. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab614 · Cited by 13 · cited 4× · see citing works
“To verify this observation, we performed a fluorescent three-hybrid assay [70] in live cells to test the direct interaction of TET1-CD with an mRNA mimic.”
InfluentialSelf-citationKanto, S., Grynberg, M., Kaneko, Y., Fujita, J., & Satake, M. (2016) · PeerJ · doi:10.7717/peerj.1862 · Cited by 12 · see citing works
Boulet, M., Gilbert, G., Renaud, Y., Schmidt, M., Auxerre-Plantié, E., Bertrand, R., Nan, X., Jurkowski, T. P., Helm, M., Vandel, L., et al. (2023) · eLife · doi:10.7554/elife.91655 · Cited by 12 · cited 2× · see citing works
“For transfection of mouse embryonic stem cells (mESC), the Neon electroporation system was used (ThermoFisher Scientific) following the manufacturer’s instructions.”
Poly(ADP-ribosyl)ation of methyl CpG binding protein 2 regulates chromatin structure.
Becker, A., Zhang, P., Allmann, L., Meilinger, D., Bertulat, B., Eck, D., Hofstaetter, M., Bartolomei, G., Hottiger, M. O., Schreiber, V., et al. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.a115.698357 · Cited by 7 · cited 1× · see citing works
“To analyze the protein–protein interaction between TET and splicing factors, we performed co-immunoprecipitation experiments as described in [62,74].”
Self-citationDNA base flipping analytical pipeline
Zhang, P., Hastert, F. D., Ludwig, A. K., Breitwieser, K., Hofstätter, M., & Cardoso, M. C. (2017) · Biology Methods and Protocols · doi:10.1093/biomethods/bpx010 · Cited by 5 · cited 1× · see citing works
“03.1–446, https://rstudio.com/) and Microsoft® Excel® for Mac 2011 (Version 14.7.7) were used for data visualization, analysis, statistics, and plotting (unless stated otherwise).”
InfluentialSelf-citationDix, T. C., Lassota, A., Bräuer, U., Haussmann, I. U., & Soller, M. (2024) · BMC Methods · doi:10.1186/s44330-024-00011-6 · Cited by 5 · cited 1× · see citing works
“The LacO was segmented in each nucleus for image analysis using the GFP signal and generating an ROI (region of interest).”
Self-citationArroyo, M. D. C. G., Cardoso, M. C., & Hastert, F. D. (2023) · BIO-PROTOCOL · doi:10.21769/bioprotoc.4716 · Cited by 3 · cited 1× · see citing works
“Incubations were performed in humid dark chambers overnight [63].”
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
MeCP2-driven chromatin organization controls nuclear stiffness
Romero, H., Amiri, A., Pabba, M. K., Zhang, H., Berg, V., Arroyo, M. D. C. G., Prorok, P., Zhadan, A., Mahmoud, M., Trautwein, N., et al. (2025) · Communications Biology · doi:10.1038/s42003-025-09328-6 · Cited by 4 · see citing works
Self-citationThe m5C demethylase TET1 is identified as a key regulator of scleral remodeling in myopia
Jia, S., Yang, L., Wei, P., Yu, J., Han, G., & Wang, Y. (2026) · Clinical Epigenetics · doi:10.1186/s13148-026-02099-9 · Cited by 1 · see citing works
“Concurrently, their catalytic activity (oxidizing RNA-m 5 C) can also restore splicing efficiency in vitro, highlighting the potential for direct chemical modifica-tion-mediated regulation of RNA processing [31].”
Genes and physiological strategies in bacterial antibiotic resistance
Nadeem, M. S., Rasool, R., Afzal, M., Ullah, I., Murtaza, B. N., Daoub, R. M. A., Chaieb, K., Alzarea, S. I., Kazmi, I. A., & Ashraf, G. M. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1811959 · Cited by 1 · see citing works
“Overexpression of efflux pumps is a common cause of antimicrobial treatment failure (Ebbensgaard et al., 2020; Hastert et al., 2025).”
Zhang, H., Ugur, E., Hake, C., Romero, H., Arroyo, M., Mahmoud, M., Lermyte, F., Leonhardt, H., & Cardoso, M. C. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf1380
“We performed co-immunoprecipitation experiments as described in [ 32 –34 ] to analyze protein-protein interactions be-tween MBD2 isoforms and Hdac11 and Kat7.”
Self-citationDynamic anatomy of the replisome under stressPreprint
Schulte, L., Pabba, M. K., Kamkaew, M., Prorok, P., Arroyo, M., & Cardoso, M. C. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.01.729259 · Cited by 1 · see citing works
Self-citation
- Authors
- Hastert, F. D., Weber, J., Bauer, C., Zhadan, A., Singh, D. N. D., Dix, T. C., Arnold, R., Bessonov, S., Soller, M., Leonhardt, H., Cardoso, M. C., & Arroyo, M.
- Affiliations
- Technische Universität Darmstadt (DE)
- Ludwig-Maximilians-Universität München (DE)
- University of Birmingham (GB)
- Max Planck Society (DE)
- University of Manchester (GB)
- Corresponding author
- Cardoso, M. Cristina
- Arroyo, Maria
- ORCID
- Venue
- Nucleus
- Publisher
- Informa UK Limited
- Published
- 2025-07-27
- Volume
- 16
- Issue
- 1
- Pages
- 2536902-2536902
- ISSN
- 1949-1034 (ISSN-L)
- 1949-1042
- PMC
- PMC12309557
- OpenAlex
- W4412725949
- Cited by
- 5
- References
- 110
- Citations by year
- 2026: 3 · 2025: 2
- FWCI
- 1.50
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleus (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Research Explorer (The University of Manchester) (publishedVersion)
- TUbilio (Technical University of Darmstadt) (acceptedVersion)
- University of Birmingham Research Portal (University of Birmingham) (submittedVersion, cc-by-nc)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- GoeScholar The Publication Server of the Georg-August-Universität Göttingen (Georg-August-Universität Göttingen) (submittedVersion, cc-by-nc)
- Funders
- Deutsche Forschungsgemeinschaft (CA 198/16–1 project number 425470807)
- Biotechnology and Biological Science Research Council
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Keywords
- TET enzymes, RNA splicing, nuclear speckles, 5-hydroxymethylcytosine, U2AF1, U2AF2, RNA modification, RNA metabolism, TET1, TET2, TET3, Drosophila cells
- MeSH terms
- Splicing Factor U2AF, Animals, DNA-Binding Proteins, HeLa Cells, Humans, Mixed Function Oxygenases, Proto-Oncogene Proteins, RNA Splicing, Dioxygenases
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
