S. L. Devos and T. M. Miller, Antisense oligonucleotides: Treating neurodegeneration at the level of RNA, Neurotherapeutics, vol.10, pp.486-497, 2013.

E. Beaudoing, S. Freier, J. R. Wyatt, J. M. Claverie, and D. Gautheret, Patterns of variant poly(A)denylation signal usage in human genes, Genome Res, vol.10, pp.1001-1010, 2000.

A. J. Gruber, R. Schmidt, A. R. Gruber, G. Martin, S. Ghosh et al., A comprehensive analysis of 3 end sequencing data sets reveals novel poly(A)denylation signals and the repressive role of heterogeneous ribonucleoprotein c on cleavage and poly(A)denylation, Genome Res, vol.26, pp.1145-1159, 2016.

B. Tian, J. Hu, H. Zhang, and C. S. Lutz, A large-scale analysis of mRNA poly(A)denylation of human and mouse genes, Nucleic Acids Res, vol.33, pp.201-212, 2005.

N. J. Proudfoot and G. G. Brownlee, 3 non-coding region sequences in eukaryotic messenger rna, Nature, vol.263, pp.211-214, 1976.

P. G. Ferreira, M. Oti, M. Barann, T. Wieland, S. Ezquina et al., Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing, Sci. Rep, vol.6, 2016.

A. Curinha, S. Oliveira-braz, I. Pereira-castro, A. Cruz, and A. Moreira, Implications of poly(A)denylation in health and disease, Nucleus, vol.5, pp.508-519, 2014.

A. Gil and N. J. Proudfoot, Position-dependent sequence elements downstream of AAUAAA are required for efficient rabbit beta-globin mRNA 3 end formation, Cell, vol.49, pp.399-406, 1987.

J. Hu, C. S. Lutz, J. Wilusz, and B. Tian, Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA poly(A)denylation. RNA, vol.11, pp.1485-1493, 2005.

M. I. Zarudnaya, I. M. Kolomiets, A. L. Potyahaylo, and D. M. Hovorun, Downstream elements of mammalian pre-mRNA poly(A)denylation signals: Primary, secondary and higher-order structures, Nucleic Acids Res, vol.31, pp.1375-1386, 2003.

S. Danckwardt, N. H. Gehring, G. Neu-yilik, P. Hundsdoerfer, M. Pforsich et al., The prothrombin 3 end formation signal reveals a unique architecture that is sensitive to thrombophilic gain-of-function mutations, Blood, vol.104, pp.428-435, 2004.

N. M. Nunes, W. Li, B. Tian, and A. Furger, A functional human poly(a) site requires only a potent dse and an a-rich upstream sequence, EMBO J, vol.29, pp.1523-1536, 2010.

E. Pauws, A. H. Van-kampen, S. A. Van-de-graaf, and J. J. De-vijlder, Ris-Stalpers, C. Heterogeneity in poly(A)denylation cleavage sites in mammalian mRNA sequences: Implications for sage analysis, Nucleic Acids Res, vol.29, pp.1690-1694, 2001.

, Int. J. Mol. Sci, vol.19, p.1347, 2018.

F. Chen, C. C. Macdonald, and J. Wilusz, Cleavage site determinants in the mammalian poly(A)denylation signal, Nucleic Acids Res, vol.23, pp.2614-2620, 1995.

W. Li, R. S. Laishram, and R. A. Anderson, The novel poly(A) polymerase Star-PAP is a signal-regulated switch at the 3 -end of mRNAs, Adv. Biol. Regul, vol.53, pp.64-76, 2013.

M. Dalziel, N. M. Nunes, and A. Furger, Two g-rich regulatory elements located adjacent to and 440 nucleotides downstream of the core poly(a) site of the intronless melanocortin receptor 1 gene are critical for efficient 3 end processing, Mol. Cell. Biol, vol.27, pp.1568-1580, 2007.

D. Oberg, J. Fay, H. Lambkin, and S. Schwartz, A downstream poly(A)denylation element in human papillomavirus type 16 L2 encodes multiple GGG motifs and interacts with hnRNP H, J. Virol, vol.79, pp.9254-9269, 2005.

D. T. Kandala, N. Mohan, and R. S. Laishram, CstF-64 and 3 -UTR cis-element determine Star-PAP specificity for target mRNA selection by excluding PAP?, Nucleic Acids Res, vol.44, pp.811-823, 2016.

R. S. Laishram and . Poly, A) polymerase (PAP) diversity in gene expression-Star-PAP vs canonical PAP, FEBS Lett, vol.588, pp.2185-2197, 2014.

R. S. Laishram and R. A. Anderson, The poly A polymerase Star-PAP controls 3 -end cleavage by promoting CPSF interaction and specificity toward the pre-mRNA, EMBO J, vol.29, pp.4132-4145, 2010.

D. L. Mellman, M. L. Gonzales, C. Song, C. A. Barlow, P. Wang et al., 5P2-regulated nuclear poly(A) polymerase controls expression of select mRNAs, Nature, vol.451, pp.1013-1017, 2008.

N. Peart and E. J. Wagner, A distal auxiliary element facilitates cleavage and poly(A)denylation of Dux4 mRNA in the pathogenic haplotype of FSHD, Hum. Genet, vol.136, pp.1291-1301, 2017.

J. Neve, R. Patel, Z. Wang, A. Louey, and A. M. Furger, Cleavage and poly(A)denylation: Ending the message expands gene regulation, RNA Biol, vol.14, pp.865-890, 2017.

Y. Shi and J. L. Manley, The end of the message: Multiple protein-rna interactions define the mRNA poly(A)denylation site, Genes Dev, vol.29, pp.889-897, 2015.

O. Chambers, J. Milenkovic, A. Praznikar, and J. F. Tasic, Computer-based assessment for facioscapulohumeral dystrophy diagnosis, Comput. Methods Programs Biomed, vol.120, pp.37-48, 2015.

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

Y. Shi, D. C. Di-giammartino, D. Taylor, A. Sarkeshik, W. J. Rice et al., Molecular architecture of the human pre-mRNA 3 processing complex, Mol. Cell, vol.33, pp.365-376, 2009.

Y. Takagaki and J. L. Manley, Complex protein interactions within the human poly(A)denylation machinery identify a novel component, Mol. Cell. Biol, vol.20, pp.1515-1525, 2000.

Z. Dominski, X. Yang, M. Purdy, E. J. Wagner, and W. F. Marzluff, A CPSF-73 homologue is required for cell cycle progression but not cell growth and interacts with a protein having features of CPSF-100, Mol. Cell. Biol, vol.25, pp.1489-1500, 2005.

K. D. Sullivan, M. Steiniger, and W. F. Marzluff, A core complex of CPSF73, CPSF100, and symplekin may form two different cleavage factors for processing of poly(a) and histone mRNAs, Mol. Cell, vol.34, pp.322-332, 2009.

C. R. Mandel, S. Kaneko, H. Zhang, D. Gebauer, V. Vethantham et al., Polyadenylation factor CPSF-73 is the pre-mRNA 3 -end-processing endonuclease, Nature, vol.444, pp.953-956, 2006.

K. Ryan, O. Calvo, and J. L. Manley, Evidence that poly(A)denylation factor CPSF-73 is the mRNA 3 processing endonuclease, RNA, vol.10, pp.565-573, 2004.

S. L. Chan, I. Huppertz, C. Yao, L. Weng, J. J. Moresco et al., CPSF30 and Wdr33 directly bind to AAUAAA in mammalian mRNA 3 processing, Genes Dev, vol.28, pp.2370-2380, 2014.

M. Clerici, M. Faini, R. Aebersold, and M. Jinek, Structural insights into the assembly and poly(A) signal recognition mechanism of the human CPSF complex, vol.6, p.33111, 2017.

B. Dichtl, D. Blank, M. Sadowski, W. Hubner, S. Weiser et al., Yhh1p/Cft1p directly links poly(A) site recognition and RNA polymerase ii transcription termination, EMBO J, vol.21, pp.4125-4135, 2002.

, Int. J. Mol. Sci, vol.19, p.1347, 2018.

L. Schönemann, U. Kuhn, G. Martin, P. Schafer, A. R. Gruber et al., Reconstitution of CPSF active in poly(A)denylation: Recognition of the poly(A)denylation signal by Wdr33, Genes Dev, vol.28, pp.2381-2393, 2014.

K. G. Murthy and J. L. Manley, The 160-kD subunit of human cleavage-poly(A)denylation specificity factor coordinates pre-mRNA 3 -end formation, Genes Dev, vol.9, pp.2672-2683, 1995.

G. M. Gilmartin and J. R. Nevins, An ordered pathway of assembly of components required for poly(A)denylation site recognition and processing, Genes Dev, vol.3, pp.2180-2190, 1989.

Y. Takagaki, L. C. Ryner, and J. L. Manley, Four factors are required for 3 -end cleavage of pre-mRNAs, Genes Dev, vol.3, pp.1711-1724, 1989.

M. Moreno-morcillo, L. Minvielle-sebastia, C. Mackereth, and S. B. Fribourg, Hexameric architecture of CstF supported by CstF-50 homodimerization domain structure, RNA, vol.17, pp.412-418, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02474033

J. M. Perez-canadillas and G. Varani, Recognition of GU-rich poly(A)denylation regulatory elements by human CstF-64 protein, EMBO J, vol.22, pp.2821-2830, 2003.

C. Yao, J. Biesinger, J. Wan, L. Weng, Y. Xing et al., Transcriptome-wide analyses of CstF64-rna interactions in global regulation of mRNA alternative poly(A)denylation, Proc. Natl. Acad. Sci, vol.109, pp.18773-18778, 2012.

F. E. Kleiman and J. L. Manley, The BARD1-CstF-50 interaction links mRNA 3 end formation to DNA damage and tumor suppression, Cell, vol.104, pp.743-753, 2001.

N. Fong and D. L. Bentley, Capping, splicing, and 3 processing are independently stimulated by RNA polymerase II: Different functions for different segments of the CTD, Genes Dev, vol.15, pp.1783-1795, 2001.

M. Ruepp, C. Schweingruber, N. Kleinschmidt, and D. Schümperli, Interactions of CstF-64, CstF-77, and symplekin: Implications on localisation and function, Mol. Biol. Cell, vol.22, pp.91-104, 2011.

A. R. Gruber, G. Martin, W. Keller, and M. Zavolan, Cleavage factor im is a key regulator of 3 UTR length, RNA Biol, vol.9, pp.1405-1412, 2012.

J. Katahira, D. Okuzaki, H. Inoue, Y. Yoneda, K. Maehara et al., Human TREX component Thoc5 affects alternative poly(A)denylation site choice by recruiting mammalian cleavage factor I, Nucleic Acids Res, vol.41, pp.7060-7072, 2013.

C. P. Masamha, Z. Xia, J. Yang, T. R. Albrecht, M. Li et al., CFIm25 links alternative poly(A)denylation to glioblastoma tumor suppression, Nature, vol.510, pp.412-416, 2014.

M. Ruepp, C. Aringhieri, S. Vivarelli, S. Cardinale, S. Paro et al., Mammalian pre-mRNA 3 end processing factor cf I M 68 functions in mRNA export, Mol. Biol. Cell, vol.20, pp.5211-5223, 2009.

Y. Zhu, X. Wang, E. Forouzmand, J. Jeong, F. Qiao et al., Molecular mechanisms for CFIm-mediated regulation of mRNA alternative poly(A)denylation, Mol. Cell, vol.69, pp.62-74, 2018.

M. Coseno, G. Martin, C. Berger, G. Gilmartin, W. Keller et al., Crystal structure of the 25 kDa subunit of human cleavage factor I m, Nucleic Acids Res, vol.36, pp.3474-3483, 2008.

U. Ruegsegger, K. Beyer, and W. Keller, Purification and characterization of human cleavage factor im involved in the 3 end processing of messenger RNA precursors, J. Biol. Chem, vol.271, pp.6107-6113, 1996.

U. Ruegsegger, D. Blank, and W. Keller, Human pre-mRNA cleavage factor I m is related to spliceosomal SR proteins and can be reconstituted in vitro from recombinant subunits, Mol. Cell, vol.1, pp.243-253, 1998.

Q. Yang, M. Coseno, G. M. Gilmartin, and S. Doublie, Crystal structure of a human cleavage factor CFI(m)25/CFI(m)68/RNA complex provides an insight into poly(A) site recognition and RNA looping, Structure, vol.19, pp.368-377, 2011.

K. M. Brown and G. M. Gilmartin, A mechanism for the regulation of pre-mRNA 3 processing by human cleavage factor im, Mol. Cell, vol.12, pp.1467-1476, 2003.

Q. Yang, G. M. Gilmartin, and S. Doublié, Structural basis of ugua recognition by the nudix protein CFI(m)25 and implications for a regulatory role in mRNA 3 processing, Proc. Natal. Acad. Sci, vol.107, pp.10062-10067, 2010.

, Int. J. Mol. Sci, vol.19, p.1347, 2018.

D. F. Colgan and J. L. Manley, Mechanism and regulation of mRNA poly(A)denylation, Genes Dev, vol.11, pp.2755-2766, 1997.

C. R. Mandel, Y. Bai, and L. Tong, Protein factors in pre-mRNA 3 -end processing, Cell. Mol. Life Sci. CMLS, vol.65, pp.1099-1122, 2008.

J. Zhao, L. Hyman, and C. Moore, Formation of mRNA 3 ends in eukaryotes: Mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol, Mol. Biol. Rev. MMBR, vol.63, pp.405-445, 1999.

T. Raabe, F. J. Bollum, and J. L. Manley, Primary structure and expression of bovine poly(A) polymerase, Nature, vol.353, pp.229-234, 1991.

E. Wahle, Purification and characterization of a mammalian poly(A)denylate polymerase involved in the 3 end processing of messenger RNA precursors, J. Biol. Chem, vol.266, pp.3131-3139, 1991.

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

S. Bienroth, W. Keller, and E. Wahle, Assembly of a processive messenger RNA poly(A)denylation complex, EMBO J, vol.12, pp.585-594, 1993.

Y. Kerwitz, U. Kühn, H. Lilie, A. Knoth, T. Scheuermann et al., Stimulation of poly(A) polymerase through a direct interaction with the nuclear poly(A) binding protein allosterically regulated by rna, EMBO J, vol.22, pp.3705-3714, 2003.

U. Kuhn and E. Wahle, Structure and function of poly(A) binding proteins, Biochim. Biophys. Acta, vol.1678, pp.67-84, 2004.

L. H. Apponi, S. W. Leung, K. R. Williams, S. R. Valentini, A. H. Corbett et al., Loss of nuclear poly(A)-binding protein 1 causes defects in myogenesis and mRNA biogenesis, Hum. Mol. Genet, vol.19, pp.1058-1065, 2010.

Z. Chen, Y. Li, and R. M. Krug, Influenza a virus ns1 protein targets poly(A)-binding protein II of the cellular 3 -end processing machinery, EMBO J, vol.18, pp.2273-2283, 1999.

Y. J. Lee and B. A. Glaunsinger, Aberrant herpesvirus-induced poly(A)denylation correlates with cellular messenger RNA destruction, PLoS Biol, 2009.

D. L. Bentley, Rules of engagement: Co-transcriptional recruitment of pre-mRNA processing factors, Curr. Opin. Cell Biol, vol.17, pp.251-256, 2005.

Y. Hirose and J. L. Manley, RNA polymerase II and the integration of nuclear events, Genes Dev, vol.14, pp.1415-1429, 2000.

Y. Hirose and J. L. Manley, Rna polymerase II is an essential mRNA poly(A)denylation factor, Nature, vol.395, pp.93-96, 1998.

S. Mccracken, N. Fong, K. Yankulov, S. Ballantyne, G. Pan et al., The C-terminal domain of RNA polymerase II couples mRNA processing to transcription, Nature, vol.385, pp.357-361, 1997.

M. Sadowski, B. Dichtl, W. Hübner, and W. Keller, Independent functions of yeast Pcf11p in pre-mRNA 3 end processing and in transcription termination, EMBO J, vol.22, pp.2167-2177, 2003.

S. Mccracken, N. Fong, E. Rosonina, K. Yankulov, G. Brothers et al., 5 -capping enzymes are targeted to pre-mRNA by binding to the phosphorylated carboxy-terminal domain of RNA polymerase II, Genes Dev, vol.11, pp.3306-3318, 1997.

S. M. Flaherty, P. Fortes, E. Izaurralde, I. W. Mattaj, and G. M. Gilmartin, Participation of the nuclear cap binding complex in pre-mRNA 3 processing, Proc. Natl. Acad. Sci, vol.94, pp.11893-11898, 1997.

X. Jiao, J. H. Chang, T. Kilic, L. Tong, and M. Kiledjian, A mammalian pre-mRNA 5 end capping quality control mechanism and an unexpected link of capping to pre-mRNA processing, Mol. Cell, vol.50, pp.104-115, 2013.

S. Danckwardt, M. W. Hentze, and A. E. Kulozik, 3 end mRNA processing: Molecular mechanisms and implications for health and disease, EMBO J, vol.27, pp.482-498, 2008.

W. Keller, S. Bienroth, K. M. Lang, and G. Christofori, Cleavage and poly(A)denylation factor cpf specifically interacts with the pre-mRNA 3 processing signal AAUAAA, EMBO J, vol.10, pp.4241-4249, 1991.

J. C. Dantonel, K. G. Murthy, J. L. Manley, and L. Tora, Transcription factor tfiid recruits factor CPSF for formation of 3 end of mRNA, Nature, vol.389, pp.399-402, 1997.

, Int. J. Mol. Sci, vol.19, p.1347, 2018.

Y. Takagaki and J. L. Manley, RNA recognition by the human poly(A)denylation factor CstF, Mol. Cell. Biol, vol.17, pp.3907-3914, 1997.

M. Kim, N. J. Krogan, L. Vasiljeva, O. J. Rando, E. Nedea et al., The yeast rat1 exonuclease promotes transcription termination by RNA polymerase II, Nature, vol.432, pp.517-522, 2004.

S. West, N. Gromak, and N. J. Proudfoot, Human 5 ? 3 exonuclease Xrn2 promotes transcription termination at co-transcriptional cleavage sites, Nature, vol.432, pp.522-525, 2004.

D. A. Mangus, M. C. Evans, and A. Jacobson, Poly(A)-binding proteins: Multifunctional scaffolds for the post-transcriptional control of gene expression, Genome Biol, vol.4, 2003.

S. Millevoi and S. Vagner, Molecular mechanisms of eukaryotic pre-mRNA 3 end processing regulation, Nucleic Acids Res, vol.38, pp.2757-2774, 2010.

A. Derti, P. Garrett-engele, K. D. Macisaac, R. C. Stevens, S. Sriram et al., A quantitative atlas of poly(A)denylation in five mammals, Genome Res, vol.22, pp.1173-1183, 2012.

M. Hoque, Z. Ji, D. Zheng, W. Luo, W. Li et al., Analysis of alternative cleavage and poly(A)denylation by 3 region extraction and deep sequencing, Nat. Methods, vol.10, pp.133-139, 2013.

R. Sandberg, J. R. Neilson, A. Sarma, P. A. Sharp, and C. B. Burge, Proliferating cells express mRNAs with shortened 3 untranslated regions and fewer microrna target sites, Science, vol.320, pp.1643-1647, 2008.

Z. Ji, J. Y. Lee, Z. Pan, B. Jiang, and B. Tian, Progressive lengthening of 3 untranslated regions of mRNAs by alternative poly(A)denylation during mouse embryonic development, Proc. Natl. Acad. Sci, vol.106, pp.7028-7033, 2009.

R. M. Denome and C. N. Cole, Patterns of poly(A)denylation site selection in gene constructs containing multiple poly(A)denylation signals, Mol. Cell. Biol, vol.8, pp.4829-4839, 1988.

P. A. Pinto, T. Henriques, M. O. Freitas, T. Martins, R. G. Domingues et al., Rna polymerase II kinetics in polo poly(A)denylation signal selection, EMBO J, vol.30, pp.2431-2444, 2011.

M. L. Peterson, S. Bertolino, and F. Davis, An RNA polymerase pause site is associated with the immunoglobulin mus poly(A) site, Mol. Cell. Biol, vol.22, pp.5606-5615, 2002.

W. A. Kellner, J. S. Bell, and P. M. Vertino, GC skew defines distinct RNA polymerase pause sites in CpG island promoters, Genome Res, vol.25, pp.1600-1609, 2015.

A. J. Wood, R. Schulz, K. Woodfine, K. Koltowska, C. V. Beechey et al., Regulation of alternative poly(A)denylation by genomic imprinting, Genes Dev, vol.22, pp.1141-1146, 2008.

Y. Takagaki, R. L. Seipelt, M. L. Peterson, and J. L. Manley, The poly(A)denylation factor CstF-64 regulates alternative processing of igm heavy chain pre-mRNA during b cell differentiation, Cell, vol.87, pp.941-952, 1996.

J. G. Hardy and C. J. Norbury, Cleavage factor im (CFIm) as a regulator of alternative poly(A)denylation, Biochem. Soc. Trans, vol.44, pp.1051-1057, 2016.

G. Martin, A. R. Gruber, W. Keller, and M. Zavolan, 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, vol.1, pp.753-763, 2012.

W. Li, B. You, M. Hoque, D. Zheng, W. Luo et al., Systematic profiling of poly(A)+ transcripts modulated by core 3 end processing and splicing factors reveals regulatory rules of alternative cleavage and poly(A)denylation, PLoS Genet, vol.11, 2015.

C. Y. Lee and L. Chen, Alternative poly(A)denylation sites reveal distinct chromatin accessibility and histone modification in human cell lines, Bioinformatics, vol.29, pp.1713-1717, 2013.

H. Huang, J. Chen, H. Liu, and X. Sun, The nucleosome regulates the usage of poly(A)denylation sites in the human genome, BMC Genom, vol.14, 2013.

D. Kaida, M. G. Berg, I. Younis, M. Kasim, L. N. Singh et al., U1 snrnp protects pre-mRNAs from premature cleavage and poly(A)denylation, Nature, vol.468, pp.664-668, 2010.

M. G. Berg, L. N. Singh, I. Younis, Q. Liu, A. M. Pinto et al., U1 snrnp determines mRNA length and regulates isoform expression, Cell, vol.150, pp.53-64, 2012.

A. R. Gruber, G. Martin, P. Muller, A. Schmidt, A. J. Gruber et al., Global 3 UTR shortening has a limited effect on protein abundance in proliferating T cells, Nat. Commun, vol.5, 2014.

N. Spies, C. B. Burge, and D. P. Bartel, UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts, Genome Res, vol.23, pp.2078-2090, 2013.

J. W. Nam, O. S. Rissland, D. Koppstein, C. Abreu-goodger, C. H. Jan et al., Global analyses of the effect of different cellular contexts on microrna targeting, Mol. Cell, vol.53, pp.1031-1043, 2014.

J. Neve, K. Burger, W. Li, M. Hoque, R. Patel et al., Subcellular RNA profiling links splicing and nuclear dicer1 to alternative cleavage and poly(A)denylation, Genome Res, vol.26, pp.24-35, 2016.

C. Mayr, Evolution and biological roles of alternative 3 UTRs, Trends Cell Biol, vol.26, pp.227-237, 2016.

M. Chiabudini, C. Conz, F. Reckmann, and S. Rospert, Ribosome-associated complex and SSB are required for translational repression induced by polylysine segments within nascent chains, Mol. Cell. Biol, vol.32, pp.4769-4779, 2012.

A. A. Klauer and A. Van-hoof, Degradation of mRNAs that lack a stop codon: A decade of nonstop progress, Wiley Interdiscip. Rev, vol.3, pp.649-660, 2012.

Z. Mbita, M. Meyer, A. Skepu, M. Hosie, J. Rees et al., De-regulation of the RBBP6 isoform 3/DWNN in human cancers, Mol. Cell. Biochem, vol.362, pp.249-262, 2012.

D. C. Di-giammartino, W. Li, K. Ogami, J. J. Yashinskie, M. Hoque et al., RBBP6 isoforms regulate the human poly(A)denylation machinery and modulate expression of mRNAs with

. Utrs, Genes Dev, vol.28, pp.2248-2260, 2014.

Z. Ji and B. Tian, Reprogramming of 3 untranslated regions of mRNAs by alternative poly(A)denylation in generation of pluripotent stem cells from different cell types, PLoS ONE, vol.4, p.8419, 2009.

F. W. Alt, A. L. Bothwell, M. Knapp, E. Siden, E. Mather et al., Synthesis of secreted and membrane-bound immunoglobulin mu heavy chains is directed by mRNAs that differ at their 3 ends, Cell, vol.20, pp.293-301, 1980.

M. L. Peterson, Mechanisms controlling production of membrane and secreted immunoglobulin during B cell development, Immunol. Res, vol.37, pp.33-46, 2007.

V. Raz, M. Riaz, Z. Tatum, S. M. Kielbasa, and P. A. Hoen, The distinct transcriptomes of slow and fast adult muscles are delineated by noncoding RNAs, FASEB J, 2018.

S. C. Boutet, T. H. Cheung, N. L. Quach, L. Liu, S. L. Prescott et al., Alternative poly(A)denylation mediates microrna regulation of muscle stem cell function, Cell Stem Cell, vol.10, pp.327-336, 2012.

E. Vorobyov and J. Horst, Expression of two protein isoforms of PAX7 is controlled by competing cleavage-poly(A)denylation and splicing, Gene, vol.342, pp.107-112, 2004.

K. E. Vest, A. L. Paskavitz, J. B. Lee, and T. Padilla-benavides, Dynamic changes in copper homeostasis and post-transcriptional regulation of Atp7a during myogenic differentiation, Metallomics, vol.10, pp.309-322, 2018.

D. J. Kim, B. Oh, and Y. Y. Kim, Splicing factor ASF/SF2 and transcription factor PPAR-gamma cooperate to directly regulate transcription of uncoupling protein-3, Biochem. Biophys. Res. Commun, vol.378, pp.877-882, 2009.

R. Joubert, S. Metayer-coustard, Q. Swennen, V. Sibut, S. Crochet et al., The beta-adrenergic system is involved in the regulation of the expression of avian uncoupling protein in the chicken, Domest. Anim. Endocrinol, vol.38, pp.115-125, 2010.

M. S. Yoon, Mtor as a key regulator in maintaining skeletal muscle mass, Front. Physiol, vol.8, 2017.

, Int. J. Mol. Sci, vol.19, p.1347, 2018.

J. W. Chang, W. Zhang, H. S. Yeh, E. P. Jong, S. Jun et al., mRNA 3 -UTR shortening is a molecular signature of mTORC1 activation, Nat. Commun, vol.6, 2015.

Y. Zhang, O. D. King, F. Rahimov, T. I. Jones, C. W. Ward et al., Human skeletal muscle xenograft as a new preclinical model for muscle disorders, Hum. Mol. Genet, vol.23, pp.3180-3188, 2014.

D. A. Monks and M. M. Holmes, Androgen receptors and muscle: A key mechanism underlying life history trade-offs, J. Comp. Physiol, vol.204, pp.51-60, 2018.

R. Hu, T. A. Dunn, S. Wei, S. Isharwal, R. W. Veltri et al., Ligand-independent androgen receptor variants derived from splicing of cryptic exons signify hormone-refractory prostate cancer, Cancer Res, vol.69, pp.16-22, 2009.

J. P. Tavanez, P. Calado, J. Braga, M. Lafarga, and M. Carmo-fonseca, In vivo aggregation properties of the nuclear poly(A)-binding protein pabpn1, RNA, vol.11, pp.752-762, 2005.

M. Jenal, R. Elkon, F. Loayza-puch, G. Van-haaften, U. Kuhn et al., The poly(A)-binding protein nuclear 1 suppresses alternative cleavage and poly(A)denylation sites, Cell, vol.149, pp.538-553, 2012.

E. De-klerk, A. Venema, S. Y. Anvar, J. J. Goeman, O. Hu et al., A) binding protein nuclear 1 levels affect alternative poly(A)denylation, Nucleic Acids Res, vol.40, pp.9089-9101, 2012.

A. Banerjee, L. H. Apponi, G. K. Pavlath, A. H. Corbett, and . Pabpn1, Molecular function and muscle disease, FEBS J, vol.280, pp.4230-4250, 2013.

R. Batra, K. Charizanis, M. Manchanda, A. Mohan, M. Li et al., Loss of mbnl leads to disruption of developmentally regulated alternative poly(A)denylation in rna-mediated disease, Mol. Cell, vol.56, pp.311-322, 2014.

B. Udd and R. Krahe, The myotonic dystrophies: Molecular, clinical, and therapeutic challenges, Lancet, vol.11, pp.891-905, 2012.

J. D. Brook, M. E. Mccurrach, H. G. Harley, A. J. Buckler, D. Church et al., Molecular basis of myotonic dystrophy: Expansion of a trinucleotide (CTG) repeat at the 3 end of a transcript encoding a protein kinase family member, Cell, vol.68, pp.799-808, 1992.

B. Tian, R. J. White, T. Xia, S. Welle, D. H. Turner et al., Expanded CUG repeat RNAs form hairpins that activate the double-stranded rna-dependent protein kinase PKR, RNA, vol.6, pp.79-87, 2000.

O. J. Pettersson, L. Aagaard, T. G. Jensen, and C. K. Damgaard, Molecular mechanisms in DM1-A focus on foci, Nucleic Acids Res, vol.43, pp.2433-2441, 2015.

M. Ferreboeuf, V. Mariot, D. Furling, G. Butler-browne, V. Mouly et al., Nuclear protein spreading: Implication for pathophysiology of neuromuscular diseases, Hum. Mol. Genet, vol.23, pp.4125-4133, 2014.

Y. Gao, X. Guo, K. Santostefano, Y. Wang, T. Reid et al., Genome therapy of myotonic dystrophy type 1 iPS cells for development of autologous stem cell therapy, Mol. Ther, vol.24, pp.1378-1387, 2016.

J. C. Chen, O. D. King, Y. Zhang, N. P. Clayton, C. Spencer et al., Morpholino-mediated knockdown of DUX4 toward facioscapulohumeral muscular dystrophy therapeutics, Mol. Ther, vol.24, pp.1405-1411, 2016.

A. C. Marsollier, L. Ciszewski, V. Mariot, L. Popplewell, T. Voit et al., Antisense targeting of 3 end elements involved in DUX4 mRNA processing is an efficient therapeutic strategy for facioscapulohumeral dystrophy: A new gene-silencing approach, Hum. Mol. Genet, vol.25, pp.1468-1478, 2016.

R. Tawil, Facioscapulohumeral muscular dystrophy, Neurotherapeutics, vol.5, pp.601-606, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00770764

G. Tasca, M. Monforte, E. Iannaccone, F. Laschena, P. Ottaviani et al., Upper girdle imaging in facioscapulohumeral muscular dystrophy, PLoS ONE, vol.9, 2014.

C. Wijmenga, J. E. Hewitt, L. A. Sandkuijl, L. N. Clark, T. J. Wright et al., Chromosome 4q DNA rearrangements associated with facioscapulohumeral muscular dystrophy, Nat. Genet, vol.2, pp.26-30, 1992.

R. J. Lemmers, . Van-der, P. J. Vliet, R. Klooster, S. Sacconi et al., A unifying genetic model for facioscapulohumeral muscular dystrophy, Science, vol.329, pp.1650-1653, 2010.

M. Dixit, E. N. Ansseau, A. Tassin, S. Winokur, R. Shi et al., DUX4, a candidate gene of facioscapulohumeral muscular dystrophy, encodes a transcriptional activator of PITX1, Proc. Natl. Acad. Sci, vol.104, pp.18157-18162, 2007.

R. J. Lemmers, M. Wohlgemuth, R. R. Frants, G. W. Padberg, E. Morava et al., Contractions of D4Z4 on 4qB subtelomeres do not cause facioscapulohumeral muscular dystrophy, Am. J. Hum. Genet, vol.75, pp.1124-1130, 2004.

R. J. Lemmers, R. Tawil, L. M. Petek, J. Balog, G. J. Block et al., Digenic inheritance of an smchd1 mutation and an FSHD-permissive D4Z4 allele causes facioscapulohumeral muscular dystrophy type 2, Nat. Genet, vol.44, pp.1370-1374, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00770764

M. L. Van-den-boogaard, R. Lemmers, J. Balog, M. Wohlgemuth, M. Auranen et al., Mutations in DNMT3b modify epigenetic repression of the D4Z4 repeat and the penetrance of facioscapulohumeral dystrophy, Am. J. Hum. Genet, vol.98, pp.1020-1029, 2016.

N. Caruso, B. Herberth, M. Bartoli, F. Puppo, J. Dumonceaux et al., Deregulation of the protocadherin gene FAT1 alters muscle shapes: Implications for the pathogenesis of facioscapulohumeral dystrophy, PLoS Genet, vol.9, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00862092

V. Mariot, S. Roche, C. Hourde, D. Portilho, S. Sacconi et al., Correlation between low FAT1 expression and early affected muscle in facioscapulohumeral muscular dystrophy, Ann. Neurol, vol.78, pp.387-400, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01431338

M. Ferreboeuf, V. Mariot, B. Bessieres, A. Vasiljevic, T. Attie-bitach et al., DUX4 and DUX4 downstream target genes are expressed in fetal FSHD muscles, Hum. Mol. Genet, vol.23, pp.171-181, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01907613

N. Broucqsault, J. Morere, M. C. Gaillard, J. Dumonceaux, J. Torrents et al., Dysregulation of 4q35-and muscle-specific genes in fetuses with a short D4Z4 array linked to facio-scapulo-humeral dystrophy, Hum. Mol. Genet, vol.22, pp.4206-4214, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01662672

L. Snider, A. Asawachaicharn, A. E. Tyler, L. N. Geng, L. M. Petek et al., Rna transcripts, miRNA-sized fragments and proteins produced from D4Z4 units: New candidates for the pathophysiology of facioscapulohumeral dystrophy, Hum. Mol. Genet, vol.18, pp.2414-2430, 2009.

M. C. Gaillard, S. Roche, C. Dion, A. Tasmadjian, G. Bouget et al., Differential DNA methylation of the D4Z4 repeat in patients with FSHD and asymptomatic carriers, Neurology, vol.83, pp.733-742, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01610019

Z. Yao, L. Snider, J. Balog, R. J. Lemmers, S. M. Van-der-maarel et al., DUX4-induced gene expression is the major molecular signature in FSHD skeletal muscle, Hum. Mol. Genet, vol.23, pp.5342-5352, 2014.

G. Xia, Y. Gao, S. Jin, S. H. Subramony, N. Terada et al., Genome modification leads to phenotype reversal in human myotonic dystrophy type 1 induced pluripotent stem cell-derived neural stem cells, Stem Cells, vol.33, pp.1829-1838, 2015.