Preprint / Version 1

LENG8 granule regulates alternative polyadenylation in mammals

This article is a preprint and has not been certified by peer review.

Authors

    Zhi-Cheng Wu,  
    Zhi-Cheng Wu
    Chen Du,  
    Chen Du
    Xue-Ying Huang,  
    Xue-Ying Huang
    You-Wan Qin,  
    You-Wan Qin
    Ai Zhong,  
    Ai Zhong
    Ming Rao,  
    Ming Rao
    Feng-Ming Liu,  
    Feng-Ming Liu
    • National Center for Protein Science Shanghai
    Hong-Wen Zhu,  
    Hong-Wen Zhu
    Yu Zhou,  
    Yu Zhou
    Peng Dai
    Peng Dai
    • Shanghai Key Laboratory of Maternal and Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
Categories
Molecular Biology
Keywords
LENG8 granule; Alternative polyadenylation; liquid-liquid phase separation; nuclear speckle; YTHDC1-m6A

Abstract

Membraneless organelles participate in multiple cellular processes and layers of gene regulation. Alternative polyadenylation (APA) is emerging as a widespread mechanism for controlling gene expression by generating distinct 3′ untranslated regions (UTRs) in transcripts. However, whether specific membraneless organelles exist in mammals to regulate APA remains largely unknown. Here, we unveil a previously unidentified nuclear body, termed LENG8 granule, which functions as an active hub for APA regulation. LENG8 deletion leads to extensive 3′UTR lengthening in both cultured cells and male germ cells. LENG8 granules recruit cleavage and polyadenylation (CPA) factors and promote their local assembly, thereby favoring the utilization of proximal poly(A) sites (pPASs). Additionally, LENG8 granules function both independently and cooperatively with nuclear speckles to regulate mRNA 3' end processing. We also elucidate the pivotal roles of YTHDC1-m6A landscapes in LENG8 granule formation/maintenance and target selection. The 3′UTR length of targets correlates with the formation and properties of LENG8 granules in a cell type-specific and developmental stage-dependent manner. Our findings highlight LENG8 as a key factor in 3′ end processing and uncover a hitherto unrecognized nuclear body involved in mammalian APA regulation, which broadens our understanding of membraneless organelles and their role in poly(A) site selection.

References

1. Tian, B., and Manley, J. L. Alternative polyadenylation of mRNA precursors. Nature reviews. Nat. Rev. Mol. Cell Biol. 18, 18–30 (2017).

2. Mayr C. Regulation by 3'-Untranslated Regions. Annu. Rev. Genet. 51, 171–194 (2017).

3. Mayr C. What Are 3' UTRs Doing? Cold Spring Harb. Perspect. Biol. 11, a034728 (2019).

4. Chen, X., and Mayr, C. A working model for condensate RNA-binding proteins as matchmakers for protein complex assembly. RNA 28, 76–87 (2022).

5. Gallicchio, L., Olivares, G. H., Berry, C. W., and Fuller, M. T. Regulation and function of alternative polyadenylation in development and differentiation. RNA Biol. 20, 908–925 (2023).

6. Derti, A., Garrett-Engele, P., Macisaac, K. D., Stevens, R. C., Sriram, S., Chen, R., Rohl, C. A., Johnson, J. M., and Babak, T. A quantitative atlas of polyadenylation in five mammals. Genome Res. 22, 1173–1183 (2012).

7. Shi Y. Alternative polyadenylation: new insights from global analyses. RNA 18, 2105–2117 (2012).

8. Lianoglou, S., Garg, V., Yang, J. L., Leslie, C. S., and Mayr, C. Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression. Genes Dev. 27, 2380–2396 (2013).

9. Gruber, A. J., and Zavolan, M. Alternative cleavage and polyadenylation in health and disease. Nat. Rev. Genet. 20, 599–614 (2019).

10. MacDonald C. C. Tissue-specific mechanisms of alternative polyadenylation: Testis, brain, and beyond (2018 update). Wiley Interdiscip. Rev. RNA 10, e1526 (2019).

11. Fansler, M. M., Zhen, G. and Mayr, C. Quantification of alternative 3′UTR isoforms from single cell RNA-seq data with scUTRquant. Preprint at bioRxiv, 10.1101/2021.11.22.469635 (2021).

12. Shi, Y., Di Giammartino, D. C., Taylor, D., Sarkeshik, A., Rice, W. J., Yates, J. R., 3rd, Frank, J., and Manley, J. L. Molecular architecture of the human pre-mRNA 3' processing complex. Mol. Cell 33, 365–376 (2009).

13. Schönemann, L., Kühn, U., Martin, G., Schäfer, P., Gruber, A. R., Keller, W., Zavolan, M., and Wahle, E. Reconstitution of CPSF active in polyadenylation: recognition of the polyadenylation signal by WDR33. Genes Dev. 28, 2381–2393 (2014).

14. Chan, S. L., Huppertz, I., Yao, C., Weng, L., Moresco, J. J., Yates, J. R., 3rd, Ule, J., Manley, J. L., and Shi, Y. CPSF30 and Wdr33 directly bind to AAUAAA in mammalian mRNA 3' processing. Genes Dev. 28, 2370-2380 (2014).

15. Bogard, N., Linder, J., Rosenberg, A. B., and Seelig, G. A Deep Neural Network for Predicting and Engineering Alternative Polyadenylation. Cell 178, 91–106 (2019).

16. Liu, H., and Moore, C. L. On the Cutting Edge: Regulation and Therapeutic Potential of the mRNA 3' End Nuclease. Trends Biochem. Sci. 46, 772–784 (2021).

17. Mitra, M., Johnson, E. L., Swamy, V. S., Nersesian, L. E., Corney, D. C., Robinson, D. G., Taylor, D. G., Ambrus, A. M., Jelinek, D., Wang, W., Batista, S. L., and Coller, H. A. Alternative polyadenylation factors link cell cycle to migration. Genome Biol. 19, 176 (2018).

18. Tan, S., Zhang, M., Shi, X., Ding, K., Zhao, Q., Guo, Q., Wang, H., Wu, Z., Kang, Y., Zhu, T., Sun, J., and Zhao, X. CPSF6 links alternative polyadenylation to metabolism adaption in hepatocellular carcinoma progression. J. Exp. Clin. Cancer Res. 40, 85 (2021).

19. Liu, S., Wu, R., Chen, L., Deng, K., Ou, X., Lu, X., Li, M., Liu, C., Chen, S., Fu, Y., and Xu, A. CPSF6 regulates alternative polyadenylation and proliferation of cancer cells through phase separation. Cell Rep. 42, 113197 (2023).

20. Dai, X. X., Pi, S. B., Zhao, L. W., Wu, Y. W., Shen, J. L., Zhang, S. Y., Sha, Q. Q., and Fan, H. Y. PABPN1 functions as a hub in the assembly of nuclear poly(A) domains that are essential for mouse oocyte development. Sci Adv. 8, eabn9016 (2022).

21. Hu, Z., Li, M., Huo, Z., Chen, L., Liu, S., Deng, K., Lu, X., Chen, S., Fu, Y., and Xu, A. U1 snRNP proteins promote proximal alternative polyadenylation sites by directly interacting with 3' end processing core factors. J. Mol. Cell Biol. 14, mjac054 (2022).

22. Fang, X., Wang, L., Ishikawa, R., Li, Y., Fiedler, M., Liu, F., Calder, G., Rowan, B., Weigel, D., Li, P., and Dean, C. Arabidopsis FLL2 promotes liquid-liquid phase separation of polyadenylation complexes. Nature 569, 265–269 (2019).

23. Wende, H., Volz, A., and Ziegler, A. Extensive gene duplications and a large inversion characterize the human leukocyte receptor cluster. Immunogenetics, 51, 703–713 (2000).

24. Baillat, D., Hakimi, M. A., Näär, A. M., Shilatifard, A., Cooch, N., and Shiekhattar, R. Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II. Cell 123, 265–276 (2005).

25. Gaur, U., Xiong, Y. Y., Luo, Q. P., Yuan, F. Y., Wu, H. Y., Qiao, M., Wimmers, K., Li, K., Mei, S. Q., and Liu, G. S. Breed-specific transcriptome response of spleen from six-to eight-week-old piglet after infection with Streptococcus suis type 2. Mol. Biol. Rep. 41, 7865–7873 (2014).

26. Ye, X., Zhang, Y., He, B., Meng, Y., Li, Y., and Gao, Y. Quantitative proteomic analysis identifies new effectors of FOXM1 involved in breast cancer cell migration. Int. J. Clin. Exp. Pathol. 8, 15836–15844 (2015).

27. Farias, T., Augusto, D. G., de Almeida, R. C., Malheiros, D., and Petzl-Erler, M. L. Screening the full leucocyte receptor complex genomic region revealed associations with pemphigus that might be explained by gene regulation. Immunology, 156, 86–93 (2019).

28. Song, J., Liu, Y. D., Su, J., Yuan, D., Sun, F., and Zhu, J. Systematic analysis of alternative splicing signature unveils prognostic predictor for kidney renal clear cell carcinoma. J. Cell Physiol. 234, 22753–22764 (2019).

29. Zhao, Y.X., Wang, X.T., Liu, Y.N., Li, N.N., Wang, S.M., Sun, Z.G., Gao, Z.F., Zhang, X.X., Mao, L.F., Tang, R., Xue, W.Y., Li, C.Y., Guan, J., Yi, H.L., Zhang, N., Ding, Q.R., Liu, F. LENG8 regulation of mRNA processing, is responsible for the control of mitochondrial activity. Preprint at bioRxiv, 10.1101/2021.07.17.452750 (2021).

30. Gomes, E., and Shorter, J. The molecular language of membraneless organelles. J. Biol. Chem. 294, 7115–7127 (2019).

31. Dodson, A. E., and Kennedy, S. Phase Separation in Germ Cells and Development. Dev. Cell 55, 4–17 (2020).

32. Ripin, N., and Parker, R. Formation, function, and pathology of RNP granules. Cell 186, 4737–4756 (2023).

33. Hirose, T., Ninomiya, K., Nakagawa, S., and Yamazaki, T. A guide to membraneless organelles and their various roles in gene regulation. Nat. Rev. Mol. Cell Biol. 24, 288–304 (2023).

34. Griswold M. D. Spermatogenesis: The Commitment to Meiosis. Physiological reviews, 96, 1–17 (2016).

35. Lehtiniemi, T., & Kotaja, N. Germ granule-mediated RNA regulation in male germ cells. Reproduction 155, R77–R91 (2018).

36. Kato, M., Han, T. W., Xie, S., Shi, K., Du, X., Wu, L. C., Mirzaei, H., Goldsmith, E. J., Longgood, J., Pei, J., Grishin, N. V., Frantz, D. E., Schneider, J. W., Chen, S., Li, L., Sawaya, M. R., Eisenberg, D., Tycko, R., and McKnight, S. L. Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels. Cell 149, 753–767 (2012).

37. Zambrano, R., Conchillo-Sole, O., Iglesias, V., Illa, R., Rousseau, F., Schymkowitz, J., Sabate, R., Daura, X., and Ventura, S. PrionW: a server to identify proteins containing glutamine/asparagine rich prion-like domains and their amyloid cores. Nucleic Acids Res. 43, W331–W337 (2015).

38. Sabate, R., Rousseau, F., Schymkowitz, J., and Ventura, S. What makes a protein sequence a prion?. PLoS Comput. Biol. 11, e1004013 (2015).

39. Mittag, T., and Parker, R. Multiple Modes of Protein-Protein Interactions Promote RNP Granule Assembly. J. Mol. Biol. 430, 4636–4649 (2018).

40. Ribbeck, K., and Görlich, D. The permeability barrier of nuclear pore complexes appears to operate via hydrophobic exclusion. EMBO J. 21, 2664–2671(2002).

41. Patel, S. S., Belmont, B. J., Sante, J. M., and Rexach, M. F. Natively unfolded nucleoporins gate protein diffusion across the nuclear pore complex. Cell 129, 83–96 (2007).

42. Kroschwald, S., Maharana, S., Mateju, D., Malinovska, L., Nüske, E., Poser, I., Richter, D., and Alberti, S. Promiscuous interactions and protein disaggregases determine the material state of stress-inducible RNP granules. eLife, 4, e06807 (2015).

43. Molliex, A., Temirov, J., Lee, J., Coughlin, M., Kanagaraj, A. P., Kim, H. J., Mittag, T., and Taylor, J. P. Phase separation by low complexity domains promotes stress granule assembly and drives pathological fibrillization. Cell 163, 123–133 (2015).

44. Wheeler, J. R., Matheny, T., Jain, S., Abrisch, R., and Parker, R. Distinct stages in stress granule assembly and disassembly. eLife 5, e18413 (2016).

45. Muzzopappa, F., Hummert, J., Anfossi, M., Tashev, S. A., Herten, D. P., & Erdel, F. Detecting and quantifying liquid-liquid phase separation in living cells by model-free calibrated half-bleaching. Nature communications 13, 7787 (2022).

46. Lin, Z., Hsu, P. J., Xing, X., Fang, J., Lu, Z., Zou, Q., Zhang, K. J., Zhang, X., Zhou, Y., Zhang, T., Zhang, Y., Song, W., Jia, G., Yang, X., He, C., and Tong, M. H. Mettl3-/Mettl14-mediated mRNA N6-methyladenosine modulates murine spermatogenesis. Cell Res. 27, 1216–1230 (2017).

47. Mitschka, S., and Mayr, C. Context-specific regulation and function of mRNA alternative polyadenylation. Nat. Rev. Mol. Cell Biol. 23, 779–796 (2022).

48. Roden, C., & Gladfelter, A. S. RNA contributions to the form and function of biomolecular condensates. Nat. Rev. Mol. Cell Biol. 22, 183–195 (2021).

49. Shimberg, G. D., Michalek, J. L., Oluyadi, A. A., Rodrigues, A. V., Zucconi, B. E., Neu, H. M., Ghosh, S., Sureschandra, K., Wilson, G. M., Stemmler, T. L., and Michel, S. L. Cleavage and polyadenylation specificity factor 30: An RNA-binding zinc-finger protein with an unexpected 2Fe-2S cluster. Proc. Natl. Acad. Sci. USA 113, 4700–4705 (2016).

50. Clerici, M., Faini, M., Muckenfuss, L. M., Aebersold, R., and Jinek, M. Structural basis of AAUAAA polyadenylation signal recognition by the human CPSF complex. Nat. Struct. Mol. Biol. 25, 135–138 (2018).

51. Sun, Y., Zhang, Y., Hamilton, K., Manley, J. L., Shi, Y., Walz, T., and Tong, L. Molecular basis for the recognition of the human AAUAAA polyadenylation signal. Proc. Natl. Acad. Sci. USA 115, E1419–E1428 (2018).

52. Kaufmann, I., Martin, G., Friedlein, A., Langen, H., and Keller, W. Human Fip1 is a subunit of CPSF that binds to U-rich RNA elements and stimulates poly(A) polymerase. EMBO J. 23, 616–626 (2004).

53. Martin, G., Gruber, A. R., Keller, W., and Zavolan, M. Genome-wide analysis of pre-mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR length. Cell Rep. 1, 753–763 (2012).

54. Lackford, B., Yao, C., Charles, G. M., Weng, L., Zheng, X., Choi, E. A., Xie, X., Wan, J., Xing, Y., Freudenberg, J. M., Yang, P., Jothi, R., Hu, G., and Shi, Y. Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal. EMBO J. 33, 878–889 (2014).

55. Li, W., You, B., Hoque, M., Zheng, D., Luo, W., Ji, Z., Park, J. Y., Gunderson, S. I., Kalsotra, A., Manley, J. L., and Tian, B. Systematic profiling of poly(A)+ transcripts modulated by core 3' end processing and splicing factors reveals regulatory rules of alternative cleavage and polyadenylation. PLoS Genet. 11, e1005166 (2015).

56. Davis, A. G., Johnson, D. T., Zheng, D., Wang, R., Jayne, N. D., Liu, M., Shin, J., Wang, L., Stoner, S. A., Zhou, J. H., Ball, E. D., Tian, B., and Zhang, D. E. Alternative polyadenylation dysregulation contributes to the differentiation block of acute myeloid leukemia. Blood 139, 424–438 (2022).

57. Wahle E. A novel poly(A)-binding protein acts as a specificity factor in the second phase of messenger RNA polyadenylation. Cell 66, 759–768 (1991).

58. Kerwitz, Y., Kühn, U., Lilie, H., Knoth, A., Scheuermann, T., Friedrich, H., Schwarz, E., and Wahle, E. Stimulation of poly(A) polymerase through a direct interaction with the nuclear poly(A) binding protein allosterically regulated by RNA. EMBO J. 22, 3705–3714 (2003).

59. Kühn, U., Gündel, M., Knoth, A., Kerwitz, Y., Rüdel, S., and Wahle, E. Poly(A) tail length is controlled by the nuclear poly(A)-binding protein regulating the interaction between poly(A) polymerase and the cleavage and polyadenylation specificity factor. The Journal of biological chemistry, 284, 22803–22814 (2009).

60. Shi, M., Zhang, H., Wu, X., He, Z., Wang, L., Yin, S., Tian, B., Li, G., and Cheng, H. ALYREF mainly binds to the 5' and the 3' regions of the mRNA in vivo. Nucleic Acids Res. 45, 9640–9653 (2017).

61. Mohibi, S., Zhang, J., and Chen, X. PABPN1, a Target of p63, Modulates Keratinocyte Differentiation through Regulation of p63α mRNA Translation. The Journal of investigative dermatology, 140, 2166–2177.e6 (2020).

62. Zhao, L. W., Zhu, Y. Z., Wu, Y. W., Pi, S. B., Shen, L., and Fan, H. Y. Nuclear poly(A) binding protein 1 (PABPN1) mediates zygotic genome activation-dependent maternal mRNA clearance during mouse early embryonic development. Nucleic Acids Res. 50, 458–472 (2022).

63. Huang, L., Li, G., Du, C., Jia, Y., Yang, J., Fan, W., Xu, Y. Z., Cheng, H., and Zhou, Y. The polyA tail facilitates splicing of last introns with weak 3' splice sites via PABPN1. EMBO Rep. 24, e57128 (2023).

64. Jenal, M., Elkon, R., Loayza-Puch, F., van Haaften, G., Kühn, U., Menzies, F. M., Oude Vrielink, J. A., Bos, A. J., Drost, J., Rooijers, K., Rubinsztein, D. C., and Agami, R. The poly(A)-binding protein nuclear 1 suppresses alternative cleavage and polyadenylation sites. Cell 149, 538–553 (2012).

65. Chen, L., Dong, W., Zhou, M., Yang, C., Xiong, M., Kazobinka, G., Chen, Z., Xing, Y., and Hou, T. PABPN1 regulates mRNA alternative polyadenylation to inhibit bladder cancer progression. Cell Biosci. 13, 45 (2023).

66. Molinie, B., Wang, J., Lim, K. S., Hillebrand, R., Lu, Z. X., Van Wittenberghe, N., Howard, B. D., Daneshvar, K., Mullen, A. C., Dedon, P., Xing, Y., and Giallourakis, C. C. m(6)A-LAIC-seq reveals the census and complexity of the m(6)A epitranscriptome. Nat. Methods 13, 692–698 (2016).

67. Xiao, W., Adhikari, S., Dahal, U., Chen, Y. S., Hao, Y. J., Sun, B. F., Sun, H. Y., Li, A., Ping, X. L., Lai, W. Y., Wang, X., Ma, H. L., Huang, C. M., Yang, Y., Huang, N., Jiang, G. B., et al. Nuclear m(6)A Reader YTHDC1 Regulates mRNA Splicing. Mol Cell 61, 507–519 (2016).

68. Roundtree, I. A., Luo, G. Z., Zhang, Z., Wang, X., Zhou, T., Cui, Y., Sha, J., Huang, X., Guerrero, L., Xie, P., He, E., Shen, B., and He, C. YTHDC1 mediates nuclear export of N6-methyladenosine methylated mRNAs. eLife 6, e31311 (2017).

69. Kasowitz, S. D., Ma, J., Anderson, S. J., Leu, N. A., Xu, Y., Gregory, B. D., Schultz, R. M., and Wang, P. J. Nuclear m6A reader YTHDC1 regulates alternative polyadenylation and splicing during mouse oocyte development. PLoS Genet. 14, e1007412 (2018).

70. Liu, J., Dou, X., Chen, C., Chen, C., Liu, C., Xu, M. M., Zhao, S., Shen, B., Gao, Y., Han, D., and He, C. N6-methyladenosine of chromosome-associated regulatory RNA regulates chromatin state and transcription. Science 367, 580–586 (2020).

71. Chen, C., Liu, W., Guo, J., Liu, Y., Liu, X., Liu, J., Dou, X., Le, R., Huang, Y., Li, C., Yang, L., Kou, X., Zhao, Y., Wu, Y., Chen, J., Wang, H., Shen, B., Gao, Y., and Gao, S. Nuclear m6A reader YTHDC1 regulates the scaffold function of LINE1 RNA in mouse ESCs and early embryos. Protein Cell 12, 455–474 (2021).

72. Cheng, Y., Xie, W., Pickering, B. F., Chu, K. L., Savino, A. M., Yang, X., Luo, H., Nguyen, D. T., Mo, S., Barin, E., Velleca, A., Rohwetter, T. M., Patel, D. J., Jaffrey, S. R., and Kharas, M. G. N6-Methyladenosine on mRNA facilitates a phase-separated nuclear body that suppresses myeloid leukemic differentiation. Cancer cell 39, 958–972.e8 (2021).

73. Liu, J., Gao, M., He, J., Wu, K., Lin, S., Jin, L., Chen, Y., Liu, H., Shi, J., Wang, X., Chang, L., Lin, Y., Zhao, Y. L., Zhang, X., Zhang, M., Luo, G. Z., Wu, G., et al. The RNA m6A reader YTHDC1 silences retrotransposons and guards ES cell identity. Nature 591, 322–326 (2021).

74. Zhu, W., Ding, Y., Meng, J., Gu, L., Liu, W., Li, L., Chen, H., Wang, Y., Li, Z., Li, C., Sun, Y., and Liu, Z. Reading and writing of mRNA m6A modification orchestrate maternal-to-zygotic transition in mice. Genome Biol. 24, 67 (2023).

75. Chen, L., Fu, Y., Hu, Z., Deng, K., Song, Z., Liu, S., Li, M., Ou, X., Wu, R., Liu, M., Li, R., Gao, S., Cheng, L., Chen, S., and Xu, A. Nuclear m6 A reader YTHDC1 suppresses proximal alternative polyadenylation sites by interfering with the 3' processing machinery. EMBO Rep. 23, e54686 (2022).

76. Xu, K., Yang, Y., Feng, G. H., Sun, B. F., Chen, J. Q., Li, Y. F., Chen, Y. S., Zhang, X. X., Wang, C. X., Jiang, L. Y., Liu, C., Zhang, Z. Y., Wang, X. J., Zhou, Q., Yang, Y. G., and Li, W. Mettl3-mediated m6A regulates spermatogonial differentiation and meiosis initiation. Cell Res. 27, 1100–1114 (2017).

77. Tang, C., Klukovich, R., Peng, H., Wang, Z., Yu, T., Zhang, Y., Zheng, H., Klungland, A., and Yan, W. ALKBH5-dependent m6A demethylation controls splicing and stability of long 3'-UTR mRNAs in male germ cells. Proc. Natl. Acad. Sci. USA. 115, E325–E333 (2018).

78. Zhang, H., Lee, J. Y., and Tian, B. Biased alternative polyadenylation in human tissues. Genome Biol. 6, R100 (2005).

79. Wang, E. T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S. F., Schroth, G. P., and Burge, C. B. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470–476 (2008).

80. Ji, Z., Lee, J. Y., Pan, Z., Jiang, B., and Tian, B. Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. Proc. Natl. Acad. Sci. USA. 106, 7028–7033 (2009).

81. Smibert, P., Miura, P., Westholm, J. O., Shenker, S., May, G., Duff, M. O., Zhang, D., Eads, B. D., Carlson, J., Brown, J. B., Eisman, R. C., Andrews, J., Kaufman, T., Cherbas, P., Celniker, S. E., Graveley, B. R., and Lai, E. C. Global patterns of tissue-specific alternative polyadenylation in Drosophila. Cell Rep. 1, 277–289 (2012).

82. Ulitsky, I., Shkumatava, A., Jan, C. H., Subtelny, A. O., Koppstein, D., Bell, G. W., Sive, H., and Bartel, D. P. Extensive alternative polyadenylation during zebrafish development. Genome Biol. 22, 2054–2066 (2012).

83. Miura, P., Shenker, S., Andreu-Agullo, C., Westholm, J. O., and Lai, E. C. Widespread and extensive lengthening of 3' UTRs in the mammalian brain. Genome Res. 23, 812–825 (2013).

84. Sanfilippo, P., Wen, J., and Lai, E. C. Landscape and evolution of tissue-specific alternative polyadenylation across Drosophila species. Genome Biol. 18, 229 (2017).

85. Lee, S., Chen, Y. C., FCA Consortium, Gillen, A. E., Taliaferro, J. M., Deplancke, B., Li, H., and Lai, E. C. Diverse cell-specific patterns of alternative polyadenylation in Drosophila. Nat. Commun. 13, 5372 (2022).

86. Li, W., Park, J. Y., Zheng, D., Hoque, M., Yehia, G., and Tian, B. Alternative cleavage and polyadenylation in spermatogenesis connects chromatin regulation with post-transcriptional control. BMC Biol. 14, 6 (2016).

87. Zhang, Y., Tang, C., Yu, T., Zhang, R., Zheng, H., and Yan, W. MicroRNAs control mRNA fate by compartmentalization based on 3' UTR length in male germ cells. Genome Biol. 18, 105 (2017).

88. Nguyen-Chi, M., Chalmel, F., Agius, E., Vanzo, N., Khabar, K. S., Jégou, B., and Morello, D. Temporally regulated traffic of HuR and its associated ARE-containing mRNAs from the chromatoid body to polysomes during mouse spermatogenesis. PLoS One 4, e4900 (2009).

89. Nguyen-Chi, M., Auriol, J., Jégou, B., Kontoyiannis, D. L., Turner, J. M., de Rooij, D. G., and Morello, D. The RNA-binding protein ELAVL1/HuR is essential for mouse spermatogenesis, acting both at meiotic and postmeiotic stages. Mol. Biol. Cell 22, 2875–2885 (2011).

90. Dai, P., Wang, X., Gou, L. T., Li, Z. T., Wen, Z., Chen, Z. G., Hua, M. M., Zhong, A., Wang, L., Su, H., Wan, H., Qian, K., Liao, L., Li, J., Tian, B., Li, D., Fu, X. D., Shi, H. J., Zhou, Y., and Liu, M. F. A Translation-Activating Function of MIWI/piRNA during Mouse Spermiogenesis. Cell 179, 1566–1581.e16 (2019).

91. Galganski, L., Urbanek, M. O., & Krzyzosiak, W. J. Nuclear speckles: molecular organization, biological function and role in disease. Nucleic Acids Res. 45, 10350–10368 (2017).

92. Bhat, P., Chow, A., Emert, B., Ettlin, O., Quinodoz, S. A., Strehle, M., Takei, Y., Burr, A., Goronzy, I. N., Chen, A. W., Huang, W., Ferrer, J. L. M., Soehalim, E., Goh, S. T., Chari, T., Sullivan, D. K., Blanco, M. R., & Guttman, M. Genome organization around nuclear speckles drives mRNA splicing efficiency. Nature 629, 1165–1173 (2024).

93. Yoon, Y., Bournique, E., Soles, L. V., Yin, H., Chu, H. F., Yin, C., Zhuang, Y., Liu, X., Liu, L., Jeong, J., Yu, C., Valdez, M., Tian, L., Huang, L., Shi, X., Seelig, G., Ding, F., Tong, L., Buisson, R., & Shi, Y. RBBP6 anchors pre-mRNA 3' end processing to nuclear speckles for efficient gene expression. Molecular cell 85, 555–570 (2025).

94. Aravin, A. A., Sachidanandam, R., Bourc'his, D., Schaefer, C., Pezic, D., Toth, K. F., Bestor, T., & Hannon, G. J. A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol. Cell 31, 785–799 (2008).

95. Zeitelhofer, M., Karra, D., Macchi, P., Tolino, M., Thomas, S., Schwarz, M., Kiebler, M., & Dahm, R. Dynamic interaction between P-bodies and transport ribonucleoprotein particles in dendrites of mature hippocampal neurons. J. Neurosci. 28, 7555–7562 (2008).

96. Lachke, S. A., Alkuraya, F. S., Kneeland, S. C., Ohn, T., Aboukhalil, A., Howell, G. R., Saadi, I., Cavallesco, R., Yue, Y., Tsai, A. C., Nair, K. S., Cosma, M. I., Smith, R. S., Hodges, E., Alfadhli, S. M., Al-Hajeri, A., Shamseldin, H. E., Behbehani, A., Hannon, G. J., Bulyk, M. L., … Maas, R. L. Mutations in the RNA granule component TDRD7 cause cataract and glaucoma. Science 331, 1571–1576 (2011).

97. Kedersha, N., Stoecklin, G., Ayodele, M., Yacono, P., Lykke-Andersen, J., Fritzler, M. J., Scheuner, D., Kaufman, R. J., Golan, D. E., & Anderson, P. Stress granules and processing bodies are dynamically linked sites of mRNP remodeling. J. Cell Biol. 169, 871–884 (2005).

98. Bao, J., Vitting-Seerup, K., Waage, J., Tang, C., Ge, Y., Porse, B. T., and Yan, W. UPF2-Dependent Nonsense-Mediated mRNA Decay Pathway Is Essential for Spermatogenesis by Selectively Eliminating Longer 3'UTR Transcripts. PLoS Genet. 12, e1005863 (2016).

99. Ruan, K., Bai, G., Fang, Y., Li, D., Li, T., Liu, X., Lu, B., Lu, Q., Songyang, Z., Sun, S., Wang, Z., Zhang, X., Zhou, W., & Zhang, H. Biomolecular condensates and disease pathogenesis. Sci. China Life Sci. 67, 1792–1832 (2024).

100. Forman-Kay, J. D., Ditlev, J. A., Nosella, M. L., & Lee, H. O. What are the distinguishing features and size requirements of biomolecular condensates and their implications for RNA-containing condensates?. RNA 28, 36–47 (2022).

101. Sahin, C., Leppert, A., & Landreh, M. Advances in mass spectrometry to unravel the structure and function of protein condensates. Nature protocols 18, 3653–3661 (2023).

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https://doi.org/10.65215/LTSpreprints.2026.05.06.000176

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2026-05-06

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Wu, Z.-C., Du, C., Huang, X.-Y., Qin, Y.-W., Zhong, A., Rao, M., Liu, F.-M., Zhu, H.-W., Zhou, Y., & Dai, P. (2026). LENG8 granule regulates alternative polyadenylation in mammals. LangTaoSha Preprint Server. https://doi.org/10.65215/LTSpreprints.2026.05.06.000176

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