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| Status |
Public on May 14, 2024 |
| Title |
Differential junction usage in paired RNA-seq of white and beige differentiated adipocytes from six human subjects |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Background: The beneficial effect of thermogenic adipocytes in maintaining body weight and protecting against metabolic disorders has raised interest in understanding the regulatory mechanisms defining white and beige adipocyte identity. Although alternative splicing has been shown to propagate adipose browning signals in mice, this has yet to be thoroughly investigated in human adipocytes. Methods: We performed parallel white and beige adipogenic differentiation using primary adipose stem cells from 6 unrelated healthy subjects, and assessed differential gene and isoform expression in mature adipocytes by RNA sequencing. Results: We find 693 exon junctions with robust differential usage between white and beige adipocytes in all 6 subjects, mapping to 507 genes. Importantly, only 8% of these differentially spliced genes are also differentially expressed, indicating that alternative splicing constitutes an additional layer of gene expression regulation during beige adipocyte adipogenic differentiation. Functional classification of alternative isoforms point to a gain of function for key thermogenic regulators such as PPARG, CITED1 and PEMT. We find that a large majority of the splice variants arise from differential usage of transcription start sites (TSSs), with beige-specific TSSs being enriched for PPARĪ³ and MED1 binding compared to white-specific TSSs. Finally, we validate beige specific isoform expression at the protein level for two thermogenic regulators, PPARĪ³ and PEMT. Discussion: These results indicate that differential isoform expression through alternative TSS usage is an important regulatory mechanism for human adipocyte thermogenic specification. Code for data processing and analysis are available at https://github.com/sarahhp/splicing_thermogenesis.
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| Overall design |
To study the differentiation of beige adipocytes in vitro, six human primary adipose stem cell (hASC) lines from female subjects were selected for similar white adipose differentiation capacity based on marker genes and proteins.
hASC cell lines from six subjects were differentiated in triplicate into both beige and white adipocytes in the presence or absence of rosiglitazone, respectively, and harvested for RNA-seq.
We investigated the difference between the white and beige adipocytes using differential gene and exon junction expression. Further, differential exon junctions were annotated with functionality scores from TRIFID.
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| |
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| Contributor(s) |
Hazell Pickering S, Abdelhalim M, Collas P, Briand N |
| Citation(s) |
38859907 |
|
Sarah Hazell Pickering, Mohamed Abdelhalim, Philippe Collas, and Nolwenn Briand. Alternative isoform expression of key thermogenic genes in human beige adipocytes. Front Endocrinol, Vol 15, 2024. doi:10.3389/fendo.2024.1395750
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| |
| Submission date |
Feb 21, 2024 |
| Last update date |
Jun 28, 2024 |
| Contact name |
Philippe Collas |
| Organization name |
University of Oslo
|
| Department |
Institute of Basic Medical Sciences
|
| Street address |
PO Box 1112 Blindern
|
| City |
Oslo |
| ZIP/Postal code |
0317 |
| Country |
Norway |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (36)
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| This SubSeries is part of SuperSeries: |
| GSE256262 |
Alternative isoform expression of key thermogenic genes in human beige adipocytes |
|
| Relations |
| BioProject |
PRJNA1078805 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE256259_beige_day15_rpkm_tmm.tsv.gz |
5.8 Mb |
(ftp)(http) |
TSV |
| GSE256259_leafcutter_three_database_info_all_junctions.tsv.gz |
5.5 Mb |
(ftp)(http) |
TSV |
| GSE256259_perind_numers.junction.counts.gz |
7.3 Mb |
(ftp)(http) |
COUNTS |
| GSE256259_six_donors.merged.nomm.feature.counts.txt.gz |
6.6 Mb |
(ftp)(http) |
TXT |
| GSE256259_subject1_beige.fwd.bw |
263.6 Mb |
(ftp)(http) |
BW |
| GSE256259_subject1_beige.rev.bw |
238.5 Mb |
(ftp)(http) |
BW |
| GSE256259_subject1_white.fwd.bw |
265.0 Mb |
(ftp)(http) |
BW |
| GSE256259_subject1_white.rev.bw |
242.6 Mb |
(ftp)(http) |
BW |
| GSE256259_subject2_beige.fwd.bw |
201.8 Mb |
(ftp)(http) |
BW |
| GSE256259_subject2_beige.rev.bw |
183.1 Mb |
(ftp)(http) |
BW |
| GSE256259_subject2_white.fwd.bw |
219.1 Mb |
(ftp)(http) |
BW |
| GSE256259_subject2_white.rev.bw |
199.8 Mb |
(ftp)(http) |
BW |
| GSE256259_subject3_beige.fwd.bw |
211.4 Mb |
(ftp)(http) |
BW |
| GSE256259_subject3_beige.rev.bw |
190.9 Mb |
(ftp)(http) |
BW |
| GSE256259_subject3_white.fwd.bw |
227.7 Mb |
(ftp)(http) |
BW |
| GSE256259_subject3_white.rev.bw |
206.7 Mb |
(ftp)(http) |
BW |
| GSE256259_subject4_beige.fwd.bw |
223.5 Mb |
(ftp)(http) |
BW |
| GSE256259_subject4_beige.rev.bw |
199.9 Mb |
(ftp)(http) |
BW |
| GSE256259_subject4_white.fwd.bw |
215.7 Mb |
(ftp)(http) |
BW |
| GSE256259_subject4_white.rev.bw |
196.7 Mb |
(ftp)(http) |
BW |
| GSE256259_subject5_beige.fwd.bw |
229.8 Mb |
(ftp)(http) |
BW |
| GSE256259_subject5_beige.rev.bw |
207.2 Mb |
(ftp)(http) |
BW |
| GSE256259_subject5_white.fwd.bw |
210.5 Mb |
(ftp)(http) |
BW |
| GSE256259_subject5_white.rev.bw |
191.5 Mb |
(ftp)(http) |
BW |
| GSE256259_subject6_beige.fwd.bw |
194.0 Mb |
(ftp)(http) |
BW |
| GSE256259_subject6_beige.rev.bw |
176.2 Mb |
(ftp)(http) |
BW |
| GSE256259_subject6_white.fwd.bw |
178.8 Mb |
(ftp)(http) |
BW |
| GSE256259_subject6_white.rev.bw |
162.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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