TY - JOUR
T1 - New insights into minor splicing-a transcriptomic analysis of cells derived from TALS patients
AU - Cologne, Audric
AU - Benoit-Pilven, Clara
AU - Besson, Alicia
AU - Putoux, Audrey
AU - Campan-Fournier, Amandine
AU - Bober, Michael B.
AU - De Die-Smulders, Christine E. M.
AU - PAULUSSEN, Aimee D. C.
AU - Pinson, Lucile
AU - Toutain, Annick
AU - Roifman, Chaim M.
AU - Leutenegger, Anne-Louise
AU - Mazoyer, Sylvie
AU - Edery, Patrick
AU - Lacroix, Vincent
N1 - Funding Information:
This work was supported by CNRS, Inserm, Université Paris 7 and Université Lyon 1 through recurrent funding, the ANR Aster (no. ANR-16-CE23-0001) and U4ATAC-BRAIN (no. ANR-18-CE12-0007-01) grants and an Inserm/Hospices Civils de Lyon grant to P.E. (Contrat d'Interface pour Hospitaliers). A.C. was supported by a grant from Inria (Thése Inria-Inserm “Médecine Numérique” - 2016) and C.B.P. by a grant from the Fondation pour la Recherche Médicale to P.E. (Financement d‘un ingénieur -ING20160435660). We thank the families for their participation in this study, the CBC Biotec biobank for sample management (Emilie Chopin, Isabelle Rouvet), the students for their contribution (Clément Saccaro, Gabriel Sala, Nabil Sersoub), Integragen SA for performing the RNA-seq experiments, Daniele Merico for critical reading of the manuscript and helpful suggestions, Tyler Alioto for providing us with the scripts for predicting U12 introns and Cyril Bourgeois, Vincent Navratil and Marion Delous for stimulating discussions.
Funding Information:
This work was supported by CNRS, Inserm, Universit? Paris 7 and Universit? Lyon 1 through recurrent funding, the ANR Aster (no. ANR-16-CE23-0001) and U4ATAC-BRAIN (no. ANR-18-CE12-0007-01) grants and an Inserm/Hospices Civils de Lyon grant to P.E. (Contrat d'Interface pour Hospitaliers). A.C. was supported by a grant from Inria (Th?se Inria-Inserm ?M?decine Num?rique? - 2016) and C.B.P. by a grant from the Fondation pour la Recherche M?dicale to P.E. (Financement d?un ing?nieur - ING20160435660). We thank the families for their participation in this study, the CBC Biotec biobank for sample management (Emilie Chopin, Isabelle Rouvet), the students for their contribution (Cl?ment Saccaro, Gabriel Sala, Nabil Sersoub), Integragen SA for performing the RNA-seq experiments, Daniele Merico for critical reading of the manuscript and helpful suggestions, Tyler Alioto for providing us with the scripts for predicting U12 introns and Cyril Bourgeois, Vincent Navratil and Marion Delous for stimulating discussions.
Publisher Copyright:
© 2019 Cologne et al.
PY - 2019/9
Y1 - 2019/9
N2 - Minor intron splicing plays a central role in human embryonic development and survival. Indeed, biallelic mutations in RNU4ATAC, transcribed into the minor spliceosomal U4atac snRNA, are responsible for three rare autosomal recessive multimalformation disorders named Taybi-Linder (TALS/MOPD1), Roifman (RFMN), and Lowry-Wood (LWS) syndromes, which associate numerous overlapping signs of varying severity. Although RNA-seq experiments have been conducted on a few RFMN patient cells, none have been performed in TALS, and more generally no in-depth transcriptomic analysis of the similar to 700 human genes containing a minor (U12-type) intron had been published as yet. We thus sequenced RNA from cells derived from five skin, three amniotic fluid, and one blood biosamples obtained from seven unrelated TALS cases and from age- and sex-matched controls. This allowed us to describe for the first time the mRNA expression and splicing profile of genes containing U12-type introns, in the context of a functional minor spliceosome. Concerning RNU4ATAC-mutated patients, we show that as expected, they display distinct U12-type intron splicing profiles compared to controls, but that rather unexpectedly mRNA expression levels are mostly unchanged. Furthermore, although U12-type intron missplicing concerns most of the expressed U12 genes, the level of U12-type intron retention is surprisingly low in fibroblasts and amniocytes, and much more pronounced in blood cells. Interestingly, we found several occurrences of introns that can be spliced using either U2, U12, or a combination of both types of splice site consensus sequences, with a shift towards splicing using preferentially U2 sites in TALS patients' cells compared to controls.
AB - Minor intron splicing plays a central role in human embryonic development and survival. Indeed, biallelic mutations in RNU4ATAC, transcribed into the minor spliceosomal U4atac snRNA, are responsible for three rare autosomal recessive multimalformation disorders named Taybi-Linder (TALS/MOPD1), Roifman (RFMN), and Lowry-Wood (LWS) syndromes, which associate numerous overlapping signs of varying severity. Although RNA-seq experiments have been conducted on a few RFMN patient cells, none have been performed in TALS, and more generally no in-depth transcriptomic analysis of the similar to 700 human genes containing a minor (U12-type) intron had been published as yet. We thus sequenced RNA from cells derived from five skin, three amniotic fluid, and one blood biosamples obtained from seven unrelated TALS cases and from age- and sex-matched controls. This allowed us to describe for the first time the mRNA expression and splicing profile of genes containing U12-type introns, in the context of a functional minor spliceosome. Concerning RNU4ATAC-mutated patients, we show that as expected, they display distinct U12-type intron splicing profiles compared to controls, but that rather unexpectedly mRNA expression levels are mostly unchanged. Furthermore, although U12-type intron missplicing concerns most of the expressed U12 genes, the level of U12-type intron retention is surprisingly low in fibroblasts and amniocytes, and much more pronounced in blood cells. Interestingly, we found several occurrences of introns that can be spliced using either U2, U12, or a combination of both types of splice site consensus sequences, with a shift towards splicing using preferentially U2 sites in TALS patients' cells compared to controls.
KW - MOPD1
KW - RNU4ATAC
KW - minor splicing
KW - U12-type introns
KW - RNA sequencing
KW - intron retention
KW - MESSENGER-RNA
KW - INTRON RETENTION
KW - DEVELOPMENTAL DISORDER
KW - U12-DEPENDENT INTRONS
KW - U12-TYPE INTRONS
KW - MUTATIONS
KW - SPLICEOSOME
KW - COMPONENT
KW - TWINTRON
U2 - 10.1261/rna.071423.119
DO - 10.1261/rna.071423.119
M3 - Article
C2 - 31175170
SN - 1355-8382
VL - 25
SP - 1130
EP - 1149
JO - Rna-A Publication of the Rna Society
JF - Rna-A Publication of the Rna Society
IS - 9
ER -