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Series GSE199930 Query DataSets for GSE199930
Status Public on Aug 01, 2022
Title Alternative splicing of a transposable element into the human long noncoding RNA CARMEN is a switch for cardiac precursor cell specification
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Other
Summary The major cardiac cell types composing the adult heart arise from common multipotent precursor cells. Cardiac lineage decisions are guided by extrinsic and cell-autonomous factors, including recently discovered long noncoding RNAs (lncRNAs). The CARMEN locus, which is known to dictate specification towards the cardiomyocyte (CM) and the smooth muscle cell (SMC) fates, generates a diversity of alternatively spliced lncRNAs. Here, we identify one of these isoforms, CARMEN-201, to be crucial for SMC commitment. CARMEN-201 activity is encoded within an alternatively-spliced exon containing a MIRc short interspersed nuclear element. This element binds the transcriptional repressor REST (RE1 Silencing Transcription Factor), targets it to cardiogenic loci, including ISL1, IRX1, IRX5, and SFRP1, and thereby blocks the CM gene program. In turn, genes regulating SMC differentiation are induced. These data show how a critical physiological switch is wired by alternative splicing and functional transposable elements in a long noncoding RNA.
 
Overall design Human fetal cardiac precursor cells (CPCs) were infected with lentivirus expressing CARMEN7 Exon2 bearing either a native WT MIRc (D1FCPCLV and D7PFCPCLV) or a scrambled (D1FCPCMV and D7FCPCMV) MIRc, with conservation of base composition. The cells were cultured in differentiation consitions and total cellular RNA was extracted 1 day (D1) or 7 days (D7) after initiation of differentaition. Uninfected fetal human CPCs maintained under proliferation conditions (PFCPC) were included as controls. Additionally, uninfected cells were also also subjected to differentiation and harvested 1 day (D1FCPC) or 7 days (D7FCPC) post initiation of differentiation. Triplicate samples were used for each biological condition. RNA samples were subjected to RNASeq analysis. For RNA immunoprescipitation, adult control CPCs (DIFFCTRL and PROCTRL) and CPCs lacking CARMEN C201 (DKOC201 and PKOC201) were grown under differentiation (DIFFCTRL and DKOC201) or proliferation (PROCTRL and PKOC201) conditions, then RIP was performed using anti-REST IgG. REST-associated transcripts were purified from differentiated adult CPCs using the RNeasy isolation kit (Qiagen). Sequencing libraries were prepared from 3 samples for each condition according to Illumina RNA Seq library kit instructions with Poly(A) selection. Libraries were sequenced with the Illumina HiSeq4000.
 
Contributor(s) Plaisance I, Chouvardas P, Sun Y, Nemir M, Aghagolzadeh P, Aminfar F, Shen S, Rochais F, Johnson R, Palpant N, Pedrazzini T
Citation(s) 36537036
Submission date Apr 01, 2022
Last update date Sep 08, 2023
Contact name Mohamed Nemir
E-mail(s) Mohamed.Nemir@chuv.ch
Organization name Lausanne University Hospital
Department Cœur et Vaisseau
Lab Experimental Cardiology Unit
Street address Bugnon 27
City Lausanne
State/province Vaud
ZIP/Postal code 1011
Country Switzerland
 
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (33)
GSM5993875 Diff (day1)_FetalCPC_Lentivirus(exon2CARMN7)_Sample1
GSM5993876 Diff (day1)_FetalCPC_Lentivirus(exon2CARMN7)_Sample3
GSM5993877 Diff (day1)_FetalCPC_Lentivirus(exon2CARMN7)_Sample4
Relations
BioProject PRJNA822122

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE199930_C201Ex2OE_DEGs.xlsx 2.2 Mb (ftp)(http) XLSX
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