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Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells

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HITS-CLIP yields genome-wide insights into brain alternative RNA processing

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Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites

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IFITM Proteins Mediate the Innate Immune Response to Influenza A H1N1 Virus, West Nile Virus and Dengue Virus

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Integrating mRNA Processing with Transcription

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Context-dependent control of alternative splicing by RNA-binding proteins

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The General Transcription Machinery and General Cofactors

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Large-Scale Proteomic Analysis of the Human SpliceosomePreprint

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Crosstalk of promoter and terminator during RNA polymerase II transcription cycle

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Splicing regulation and dysregulation of cholinergic genes expressed at the neuromuscular junction

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Therapeutic targeting of CPSF3-dependent transcriptional termination in ovarian cancer

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The Length of the Expressed 3′ UTR Is an Intermediate Molecular Phenotype Linking Genetic Variants to Complex Diseases

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Epidermal progenitors suppress GRHL3-mediated differentiation through intronic polyadenylation promoted by CPSF-HNRNPA3 collaboration

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Structural basis of mRNA maturation: Time to put it together

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CYCLIN K down-regulation induces androgen receptor gene intronic polyadenylation, variant expression and PARP inhibitor vulnerability in castration-resistant prostate cancer

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Poly(A) code analyses reveal key determinants for tissue-specific mRNA alternative polyadenylation

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Targeting the Polyadenylation Signal of Pre-mRNA: A New Gene Silencing Approach for Facioscapulohumeral Dystrophy

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Structural transitions in poly(A), poly(C), poly(U), and poly(G) and their possible biological roles

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Dynamic mRNP Remodeling in Response to Internal and External Stimuli

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Regulation of neuronal RNA signatures by ELAV /Hu proteins

Hilgers, V. (2022) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1733 · Cited by 26

IntS6 and the Integrator phosphatase module tune the efficiency of select premature transcription termination events

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A transcriptome-wide antitermination mechanism sustaining identity of embryonic stem cells

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Glucose stress causes mRNA retention in nuclear Nab2 condensates

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Dissociation of Rpb4 from RNA polymerase II is important for yeast functionality

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Biophysical characterizations of the recognition of the AAUAAA polyadenylation signal

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CRISPR-iPAS: a novel dCAS13-based method for alternative polyadenylation interference

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Macrophage differentiation is marked by increased abundance of the mRNA 3’ end processing machinery, altered poly(A) site usage, and sensitivity to the level of CstF64

Mukherjee, S., Graber, J. H., & Moore, C. L. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1091403 · Cited by 21

The emerging theme of 3′UTR mRNA isoform regulation in reprogramming of cell metabolism

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RNA recognition by Roquin in posttranscriptional gene regulation

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snoRNAs associate with mRNA 3′ processing complex: New wine in old bottles

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A Detailed Analysis of the BR1 Locus Suggests a New Mechanism for Bolting after Winter in Sugar Beet (Beta vulgaris L.)

Tränkner, C., Lemnian, I., Emrani, N., Pfeiffer, N., Tiwari, S. P., Kopisch-Obuch, F., Vogt, S. H., MÜLLER, A. E., Schilhabel, M. B., Jung, C., et al. (2016) · Frontiers in Plant Science · doi:10.3389/fpls.2016.01662 · Cited by 21

Connections between 3′ end processing and DNA damage response: Ten years later

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Small Nucleolar RNAs: Biological Functions and Diseases

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CPSF3 inhibition blocks pancreatic cancer cell proliferation through disruption of core histone mRNA processing

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The DEAD-box RNA helicase SHI2 functions in repression of salt-inducible genes and regulation of cold-inducible gene splicing

Wang, B., Chai, H., Zhong, Y., Shen, Y., Yang, W., Chen, J., Xin, Z., & Shi, H. (2019) · Journal of Experimental Botany · doi:10.1093/jxb/erz523 · Cited by 20

Requirement for cleavage factor II m in the control of alternative polyadenylation in breast cancer cells

Turner, R. E., Henneken, L. M., Liem-Weits, M., Harrison, P. F., Swaminathan, A., Vary, R., Nikolić, I., Simpson, K. J., Powell, D., Beilharz, T. H., et al. (2020) · RNA · doi:10.1261/rna.075226.120 · Cited by 20

A missense mutation in the CSTF2 gene that impairs the function of the RNA recognition motif and causes defects in 3′ end processing is associated with intellectual disability in humans

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Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens using a dual fluorescence readthrough reporter

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The anticancer compound JTE-607 reveals hidden sequence specificity of the mRNA 3′ processing machinery

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At the Interface of Three Nucleic Acids: The Role of RNA-Binding Proteins and Poly(ADP-ribose) in DNA Repair

Alemasova, E. E., & Lavrik, O. I. (2017) · Acta Naturae · doi:10.32607/20758251-2017-9-2-4-16 · Cited by 20

Impaired stem cell differentiation and somatic cell reprogramming in DIDO3 mutants with altered RNA processing and increased R-loop levels

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Generation of Drosophila sisRNAs by Independent Transcription from Cognate Introns

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SIZ1-mediated SUMOylation of CPSF100 promotes plant thermomorphogenesis by controlling alternative polyadenylation

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U7 deciphered: the mechanism that forms the unusual 3′ end of metazoan replication-dependent histone mRNAs

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Analysis of mRNA-derived siRNAs in mutants of mRNA maturation and surveillance pathways in Arabidopsis thaliana

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Alternative Polyadenylation Is a Novel Strategy for the Regulation of Gene Expression in Response to Stresses in Plants

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Post-transcriptional control of haemostatic genes: mechanisms and emerging therapeutic concepts in thrombo-inflammatory disorders

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Useful Bicistronic Reporter System for Studying Poly(A) Site-Defining cis Elements and Regulation of Alternative Polyadenylation

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CRISPRpas: programmable regulation of alternative polyadenylation by dCas9

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PQBP1: The Key to Intellectual Disability, Neurodegenerative Diseases, and Innate Immunity

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Molecular mechanism for the interaction between human CPSF30 and hFip1Preprint

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Polyploid giant cancer cells: Underlying Mechanisms, Signaling Pathways, and Therapeutic Strategies.

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Nudt21-mediated alternative polyadenylation of MZT1 3′UTR contributes to pancreatic cancer progression

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Transcript shortening via alternative polyadenylation promotes gene expression during fracture healing

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Distinct roles of Pcf11 zinc-binding domains in pre-mRNA 3′-end processing

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Pcf11/Spt5 condensates stall RNA polymerase II to facilitate termination and piRNA-guided heterochromatin formation

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Canonical and noncanonical RNA polyadenylation

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A distal auxiliary element facilitates cleavage and polyadenylation of Dux4 mRNA in the pathogenic haplotype of FSHD

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Virulence‐ and signaling‐associated genes display a preference for long 3′ UTR s during rice infection and metabolic stress in the rice blast fungus

Rodríguez‐Romero, J., Marconi, M., Ortega‐Campayo, V., Demuez, M., Wilkinson, M. D., & Sesma, A. (2018) · New Phytologist · doi:10.1111/nph.15405 · Cited by 16

Intronic Polyadenylation in Acquired Cancer Drug Resistance Circumvented by Utilizing CRISPR/Cas9 with Homology-Directed Repair: The Tale of Human DNA Topoisomerase IIα

Elton, T. S., Hernandez, V. A., Carvajal‐Moreno, J., Wang, X., Ipinmoroti, D., & Yalowich, J. C. (2022) · Cancers · doi:10.3390/cancers14133148 · Cited by 15

Suboptimal RNA–RNA interaction limits U1 snRNP inhibition of canonical mRNA 3’ processing

Shi, J., Deng, Y., Huang, S., Huang, C., Wang, J., Xiang, A. P., & Yao, C. (2019) · RNA Biology · doi:10.1080/15476286.2019.1636596 · Cited by 14

Alternative mRNA polyadenylation regulates macrophage hyperactivation via the autophagy pathway

Chen, Y., Chen, B., Li, J., Li, H., Wang, G., Cai, X., Zhang, Q., Liu, X., Chen, K., Wang, Z., et al. (2024) · Cellular and Molecular Immunology · doi:10.1038/s41423-024-01237-8 · Cited by 13

Differential alternative polyadenylation of homoeologous genes of allohexaploid wheat ABD subgenomes during drought stress response

Ma, H., Lin, J., Mei, F., Mao, H., & Li, Q. Q. (2023) · The Plant Journal · doi:10.1111/tpj.16150 · Cited by 13

Alu exaptation enriches the human transcriptome by introducing new gene ends

Lavi, E., & Carmel, L. (2018) · RNA Biology · doi:10.1080/15476286.2018.1429880 · Cited by 13

PABPN1, a Target of p63, Modulates Keratinocyte Differentiation through Regulation of p63α mRNA Translation

Mohibi, S., Zhang, J., & Chen, X. (2020) · Journal of Investigative Dermatology · doi:10.1016/j.jid.2020.03.942 · Cited by 13

Sequential Polyadenylation to Enable Alternative mRNA 3’ End Formation

Hao, Y., Cai, T., Liu, C., Zhang, X., & Fu, X. (2023) · Molecules and Cells · doi:10.14348/molcells.2023.2176 · Cited by 12

Effect of CFIm25 knockout on RNA polymerase II transcription

Tellier, M., Hardy, J. G., Norbury, C. J., & Murphy, S. (2018) · BMC Research Notes · doi:10.1186/s13104-018-4006-1 · Cited by 12

Genome-wide Identification and Expression Analysis of the YTH Domain-containing RNA-binding Protein Family in Citrus Sinensis

Ouyang, Z., Duan, H., Mi, L., Hu, W., Chen, J., Li, X., & Zhong, B. (2019) · Journal of the American Society for Horticultural Science · doi:10.21273/jashs04567-18 · Cited by 12

Thr 4 phosphorylation on RNA Pol II occurs at early transcription regulating 3′-end processing

Moreno, R. Y., Panina, S., Irani, S., Hardtke, H. A., Stephenson, R., Floyd, B. M., Marcotte, E. M., Zhang, Q., & Zhang, Y. (2024) · Science Advances · doi:10.1126/sciadv.adq0350 · Cited by 11

RNA interference and turnover in plants -a complex partnership

Krzysztoń, M., Kufel, J., & Zakrzewska‐Placzek, M. (2025) · Frontiers in Plant Science · doi:10.3389/fpls.2025.1608888 · Cited by 11

Identification of nucleotide sequences and some proteins involved in polyadenylation of RNA transcribed by Pol III from SINEs

Ustyantsev, I. G., Borodulina, O. R., & Kramerov, D. A. (2020) · RNA Biology · doi:10.1080/15476286.2020.1857942 · Cited by 11

Premature transcription termination complex proteins PCF11 and WDR82 silence HIV-1 expression in latently infected cells

Said, M. A., Bejjani, F., Abdouni, A., Ségéral, E., & Emiliani, S. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2313356120 · Cited by 10

Regulation of the Ysh1 endonuclease of the mRNA cleavage/polyadenylation complex by ubiquitin-mediated degradation

Lee, S. D., Liu, H., Graber, J. H., Heller-Trulli, D., Michaels, K. K., Cerezo, J. F., & Moore, C. L. (2020) · RNA Biology · doi:10.1080/15476286.2020.1724717 · Cited by 10

Alternative polyadenylated mRNAs behave as asynchronous rhythmic transcription in Arabidopsis

Lin, J., Yu, Z., Ye, C., Hong, L., Chu, Y., Shen, Y., & Li, Q. Q. (2021) · RNA Biology · doi:10.1080/15476286.2021.1933732 · Cited by 12

A real-time fluorescence assay for CPSF73, the nuclease for pre-mRNA 3′-end processing

Gutierrez, P. A., Baughman, K. M., Sun, Y., & Tong, L. (2021) · RNA · doi:10.1261/rna.078764.121 · Cited by 11

Reduced function of the RNA-binding protein FPA rescues a T-DNA insertion mutant in the Arabidopsis ZHOUPI gene by promoting transcriptional read-through

Zhang, Y., Li, X., Goodrich, J., Wu, C., Wei, H., Yang, S., & Feng, X. (2016) · Plant Molecular Biology · doi:10.1007/s11103-016-0487-2 · Cited by 10

Identification of Myoferlin, a Potential Serodiagnostic Antigen of Clonorchiasis, via Immunoproteomic Analysis of Sera From Different Infection Periods and Excretory-Secretory Products of Clonorchis sinensis

Ma, X.-X., Qiu, Y., Chang, Z., Gao, J., Jiang, R.-R., Li, C.-L., Wang, C., & Chang, Q. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.779259 · Cited by 10

MPP6 stimulates both RRP6 and DIS3 to degrade a specified subset of MTR4-sensitive substrates in the human nucleus

Fujiwara, N., Shigemoto, M., Hirayama, M., Fujita, K., Seno, S., Matsuda, H., Nagahama, M., & Masuda, S. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac559 · Cited by 10

An examination of the metal ion content in the active sites of human endonucleases CPSF73 and INTS11

Huang, J. W., Liu, X., Sun, Y., Li, Z., Lin, M.-H., Hamilton, K., Mandel, C. R., Sandmeir, F., Conti, E., Oyala, P. H., et al. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2023.103047 · Cited by 10

Reconstitution and biochemical assays of an active human histone pre-mRNA 3′-end processing machinery

Sun, Y., Aik, W. S., Yang, X.-C., Marzluff, W. F., Domiński, Z., & Tong, L. (2021) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2021.03.021 · Cited by 10

Emerging value of the viroid model in molecular biology and beyond

Ma, J., Mudiyanselage, S. D. D., & Wang, Y. (2022) · Virus Research · doi:10.1016/j.virusres.2022.198730 · Cited by 10

Cleavage stimulation factor 2 promotes malignant progression of liver hepatocellular carcinoma by activating phosphatidylinositol 3′-kinase/protein kinase B/mammalian target of rapamycin pathway

Zhang, M., & Liu, J. (2022) · Bioengineered · doi:10.1080/21655979.2022.2063100 · Cited by 9

Molecular basis for the recognition of the AUUAAA polyadenylation signal by mPSF

Gutierrez, P. A., Jia, W., Sun, Y., & Tong, L. (2022) · RNA · doi:10.1261/rna.079322.122 · Cited by 9

Restrictor slows RNAPII elongation to promote termination at noncoding RNA lociPreprint

Mimoso, C. A., Vlaming, H., Wagenaar, N. P. V.-D., Siegenfeld, A. P., & Adelman, K. (2025) · Genes & Development · doi:10.1101/gad.352654.125 · Cited by 9

Evidence that a threshold of serine/arginine-rich (SR) proteins recruits CFIm to promote rous sarcoma virus mRNA 3′ end formation

Hudson, S. W., McNally, L. M., & McNally, M. T. (2016) · Virology · doi:10.1016/j.virol.2016.08.021 · Cited by 8

Functional inhibition of core spliceosomal machinery activates intronic premature cleavage and polyadenylation of pre-mRNAs

Feng, Q., Lin, Z., Zhao, D., Li, M., Yang, S., Xiang, A. P., Ye, C., & Yao, C. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115376 · Cited by 8

The Nrd1–Nab3–Sen1 transcription termination complex from a structural perspective

Chaves‐Arquero, B., & Pérez‐Cañadillas, J. M. (2023) · Biochemical Society Transactions · doi:10.1042/bst20221418 · Cited by 7

TRENDseq—A highly multiplexed high throughput RNA 3′ end sequencing for mapping alternative polyadenylation

Ogorodnikov, A., & Danckwardt, S. (2021) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2021.03.022 · Cited by 7

In vivo discovery of RNA proximal proteins in human cells via proximity-dependent biotinylationPreprint

Lin, X., Fonseca, M. A., Corona, R. I., & Lawrenson, K. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.02.28.970442 · Cited by 7

Isoform-specific regulation of rhythmic gene expression by alternative polyadenylationPreprint

Greenwell, B. J., Beytebiere, J. R., Lamb, T. M., Bell‐Pedersen, D., Merlin, C., & Menet, J. S. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.12.12.422514 · Cited by 5

Exploring the Impact of Cleavage and Polyadenylation Factors on Pre-mRNA Splicing Across Eukaryotes

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DEAD-box ATPase Dbp2 is the key enzyme in an mRNP assembly checkpoint at the 3’-end of genes and involved in the recycling of cleavage factors

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