| Literature DB >> 34616359 |
Rong-Hua Song1, Peng Du1, Chao-Qun Gao1, Xue-Rong Liu1, Jin-An Zhang1.
Abstract
Objective: Epigenetic modifications in RNA are known to play critical roles in cell differentiation through regulating expressions of some key genes including members of the suppressor of cytokine signaling (SOCS) family. The present study aimed to unveil the relationship of SOCS mRNA methylation induced by methyltransferase like 3 (METTL3) with Graves' disease (GD).Entities:
Keywords: Graves’ disease (GD); RNA methyltransferase; RNA modification; methyltransferase like 3 (METTL3); suppressor of cytokine signaling (SOCS)
Mesh:
Substances:
Year: 2021 PMID: 34616359 PMCID: PMC8488398 DOI: 10.3389/fendo.2021.666393
Source DB: PubMed Journal: Front Endocrinol (Lausanne) ISSN: 1664-2392 Impact factor: 5.555
Figure 1METTL3 mRNA expressions in thyroid from GD and controls.
Figure 2The mRNA expression of SOCS family main members in in thyroid from GD and controls.
Figure 3WGCNA found several GD related key gene expression modules (The most significant is the black module).
GD related key gene co-expression modules---blue module gene function riched GO pathway.
| Pathway ID | Number of gene | Name of pathways | Bonferoni P-value |
|---|---|---|---|
| GO:0006955 | 165 | Immune response | 1.14E-49 |
| GO:0002376 | 195 | Immune system process | 2.36E-44 |
| GO:0002682 | 129 | Regulation of immune system process | 4.65E-34 |
| GO:0006952 | 140 | Defense response | 4.68E-34 |
| GO:0050776 | 98 | Regulation of immune response | 1.51E-29 |
| GO:0002684 | 99 | Positive regulation of immune system process | 9.93E-27 |
| GO:0045321 | 95 | Leukocyte activation | 2.88E-26 |
| GO:0045087 | 90 | Innate immune response | 3.18E-23 |
| GO:0050778 | 76 | Positive regulation of immune response | 3.40E-23 |
| GO:0001775 | 101 | Cell activation | 1.33E-21 |
| GO:0002250 | 58 | Adaptive immune response | 2.92E-20 |
| GO:0007159 | 68 | Leukocyte cell-cell adhesion | 2.28E-18 |
| GO:0070486 | 65 | Leukocyte aggregation | 1.14E-17 |
| GO:0071593 | 64 | Lymphocyte aggregation | 1.93E-17 |
| GO:0042110 | 63 | T cell activation | 6.80E-17 |
GD related key gene co-expression modules---green module gene function riched GO pathway.
| Pathway ID | Number of gene | Name of pathways | Bonferoni P-value |
|---|---|---|---|
| GO:0006396 | 85 | RNA processing | 4.02E-11 |
| GO:0006613 | 33 | Cotranslational protein targeting to membrane | 2.48E-10 |
| GO:0006614 | 31 | SRP-dependent cotranslational protein targeting to membrane | 2.36E-09 |
| GO:0045047 | 31 | Protein targeting to ER | 2.36E-09 |
| GO:0006612 | 37 | Protein targeting to membrane | 1.05E-08 |
| GO:0072599 | 31 | Establishment of protein localization to endoplasmic reticulum | 1.47E-08 |
| GO:0016071 | 64 | mRNA metabolic process | 1.52E-08 |
| GO:0000184 | 32 | Nuclear-transcribed mRNA catabolic process, nonsense-mediated decay | 2.59E-08 |
| GO:0003723 | 129 | RNA binding | 4.78E-08 |
| GO:0005840 | 36 | Ribosome | 1.04E-07 |
| GO:0022626 | 30 | Cytosolic ribosome | 2.19E-07 |
| GO:0000956 | 37 | Nuclear-transcribed mRNA catabolic process | 3.99E-07 |
| GO:0070972 | 32 | Protein localization to endoplasmic reticulum | 4.64E-07 |
| GO:0006364 | 40 | rRNA processing | 5.33E-07 |
| GO:0016072 | 40 | rRNA metabolic process | 5.33E-07 |
| GO:0006402 | 37 | mRNA catabolic process | 1.16E-06 |
| GO:0006413 | 39 | Translational initiation | 1.34E-06 |
| GO:0003735 | 34 | Structural constituent of ribosome | 2.38E-06 |
| GO:0015934 | 21 | Large ribosomal subunit | 3.10E-06 |
| GO:0006396 | 85 | RNA processing | 4.02E-11 |
| GO:0006613 | 33 | Cotranslational protein targeting to membrane | 2.48E-10 |
| GO:0006614 | 31 | SRP-dependent cotranslational protein targeting to membrane | 2.36E-09 |
Figure 4mRNA modification key enzymes’ expressions in CD4+T cells of GD.
m6A modification loci in the mRNA of SOCS family members (main part).
| SOCS members | Chromosome | ModID | Motif score | region |
|---|---|---|---|---|
| SOCS1 | Chr16(11348442-11348443) | m6A_site_162250 | 369.74 | 3'UTR |
| SOCS1 | Chr16(11348969-11348970) | m6A_site_162254 | 369.74 | CDS |
| SOCS2 | Chr12(93966490-93966491) | m6A_site_105936 | 419.59 | 5'UTR |
| SOCS2 | Chr12(93966573-93966574) | m6A_site_105938 | 419.59 | 5'UTR |
| SOCS2 | Chr12(93968677-93968678) | m6A_site_105949 | 419.59 | CDS/3'UTR |
| SOCS2 | Chr12(93968897-93968898) | m6A_site_105953 | 419.59 | CDS/3'UTR |
| SOCS2 | Chr12(93966560-93966561) | m6A_site_105937 | 371.87 | 5'UTR |
| SOCS2 | Chr12(93968769-93968770) | m6A_site_105951 | 371.87 | CDS/3'UTR |
| SOCS2 | Chr12(93966736-93966737) | m6A_site_105940 | 369.74 | CDS |
| SOCS3 | Chr17(76353316-763533167) | m6A_site_206141 | 419.59 | 3'UTR |
| SOCS3 | Chr17(76353537-76353538) | m6A_site_206143 | 419.59 | 3'UTR |
| SOCS3 | Chr17(76354571-76354572) | m6A_site_206160 | 419.59 | CDS |
| SOCS3 | Chr17(76356144-76356145) | m6A_site_206173 | 419.59 | 5'UTR |
| SOCS3 | Chr17(76353702-76353703) | m6A_site_206146 | 371.87 | 3'UTR |
| SOCS3 | Chr17(76353887-76353888) | m6A_site_206148 | 371.87 | 3'UTR |
| SOCS3 | Chr17(76354182-76354183) | m6A_site_206155 | 371.87 | 3'UTR |
| SOCS3 | Chr17(76354370-76354371) | m6A_site_206158 | 371.87 | 3'UTR |
| SOCS3 | Chr17(76355126-76355127) | m6A_site_206169 | 371.87 | CDS |
| SOCS4 | Chr14(55498662-55498663) | m6A_site_129198 | 419.59 | 5'UTR/Exon |
| SOCS4 | Chr14(55509988-55509989) | m6A_site_129204 | 419.59 | CDS |
| SOCS4 | Chr14(55510908-55510909) | m6A_site_129222 | 419.59 | CDS |
| SOCS4 | Chr14(55494015-55494016) | m6A_site_129195 | 369.74 | 5'UTR/Exon |
| SOCS4 | Chr14(55510855-55510856) | m6A_site_129220 | 369.74 | CDS |
| SOCS5 | Chr2(46926501-46926502) | m6A_site_259666 | 419.59 | 5'UTR |
| SOCS5 | Chr2(46986112-46986113) | m6A_site_259676 | 419.59 | CDS |
| SOCS5 | Chr2(46986888-46986889) | m6A_site_259689 | 419.59 | CDS |
| SOCS5 | Chr2(46986903-46986904) | m6A_site_259690 | 419.59 | CDS |
| SOCS6 | Chr18(67992545-67992546) | m6A_site_216257 | 419.59 | CDS |
| SOCS6 | Chr18(67992559-67992560) | m6A_site_216258 | 419.59 | CDS |
| SOCS6 | Chr18(67992887-67992888) | m6A_site_216263 | 419.59 | CDS |
| SOCS6 | Chr18(67993294-67992546) | m6A_site_216271 | 419.59 | CDS |
| SOCS7 | Chr17(36508291-36508292) | m6A_site_192042 | 419.59 | CDS |
| SOCS7 | Chr17(36508629-36508630) | m6A_site_192046 | 419.59 | CDS/Exon |
| SOCS7 | Chr17(36555962-36555963) | m6A_site_192056 | 419.59 | 3'UTR |
| SOCS7 | Chr17(36556240-36556241) | m6A_site_192060 | 419.59 | 3'UTR |
| CISH | Chr3(50644562-50644563) | m6A_site_325389 | 419.59 | 3'UTR/Exon |
| CISH | Chr3(50644971-50644972) | m6A_site_325396 | 419.59 | 3'UTR/Exon |
| CISH | Chr3(50645098-50645099) | m6A_site_325398 | 419.59 | CDS/Exon |
| CISH | Chr3(50645392- 50645393) | m6A_site_325400 | 419.59 | CDS/Exon |
Figure 5mRNA modification key enzymes’ expressions in PBMCs of GD.
Figure 6mRNA expressions of SOCS family members in METTL3 knock-down RAW 264.7 cells. (A) It showed the significant lower expression of METTL3 after METTL3 knock-down; (B) SOCS1 mRNA expression after METTL3 knock-down; (C) SOCS2 mRNA expression after METTL3 knock-down; (D) SOCS3 mRNA expression after METTL3 knock-down; (E) SOCS4 mRNA expression after METTL3 knock-down; (F) SOCS5 mRNA expression after METTL3 knock-down; (G) SOCS6 mRNA expression after METTL3 knock-down; (H) SOCS7 mRNA expression after METTL3 knock-down.