Cell Type-Selective Expression of Circular RNAs in Human Pancreatic Islets
Abstract
:1. Introduction
2. Results
2.1. Wide-Spread Expression of circRNAs in α- and β-Cells
2.2. Genomic Features of circRNAs in α- and β-Cells
2.3. Alternative Circular Isoforms
2.4. Differentially Expressed circRNAs in β-Cells
2.5. Selectively Expressed circRNAs in α- and β-Cells
2.6. Functional Annotation of α- and β-Cell Selective circRNAs
3. Discussion
4. Materials and Methods
4.1. circRNA Identification and Analysis
4.2. Differential Expression Analysis
4.3. Functional Annotation of circRNAs
4.4. miRNA-circRNA Regulatory Network
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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circRNAs | Genes | |
---|---|---|
α-Cells | 7667 | 3141 |
β-Cells | 8396 | 3291 |
Exocrine-cells | 456 | 388 |
Common circRNAs | 382 | 332 |
Total | 10,830 | 3833 |
circRNA ID | Gene Name | Average Junction Reads (α-Cells) | Average Junction Reads (β-Cells) | circBase ID |
---|---|---|---|---|
1:117402185:117420649 | MAN1A2 | 267 | 354 | hsa_circ_0000118 |
12:97492460:97561047 | RMST | 354 | 220 | - |
11:33286412:33287511 | HIPK3 | 263 | 286 | hsa_circ_0000284 |
4:152411302:152412529 | FBXW7 | 285 | 241 | hsa_circ_0001451 |
5:95755395:95763620 | RHOBTB3 | 137 | 307 | hsa_circ_0007444 |
4:143543508:143543972 | SMARCA5 | 180 | 228 | hsa_circ_0001445 |
7:100023418:100024307 | ZKSCAN1 | 220 | 177 | hsa_circ_0001727 |
10:31908171:31910563 | ARHGAP12 | 174 | 167 | hsa_circ_0000231 |
7:24623665:24668660 | MPP6 | 134 | 144 | hsa_circ_0001686 |
18:9182381:9221999 | ANKRD12 | 101 | 123 | hsa_circ_0000826 |
2:50921868:50925955 | NRXN1 | 106 | 110 | hsa_circ_0001004 |
circRNA | Gene Name | Isoform Name | logFC | p-Value | adj. p-Value |
---|---|---|---|---|---|
Down-Regulated | |||||
2:162183413:162203145 | FAP | ENST00000627638 | −6.34 | 4.40 × 10−8 | 7.23 × 10−5 |
2:190895151:190931637 | GLS | ENST00000320717 | −5.67 | 5.97 × 10−6 | 3.92 × 10−3 |
2:200329430:200419496 | SPATS2L | ENST00000409718 | −5.34 | 4.09 × 10−5 | 1.22 × 10−2 |
11:101062446:101126158 | PGR | ENST00000325455 | −5.22 | 7.83 × 10−5 | 1.98 × 10−2 |
5:95906522:95919545 | ELL2 | ENST00000237853 | −5.07 | 1.77 × 10−4 | 3.53 × 10−2 |
8:61633682:61653660 | ASPH | ENST00000379454 | −5.03 | 2.26 × 10−4 | 4.24 × 10−2 |
9:110972072:110973558 | LPAR1 | ENST00000374431 | −4.07 | 2.45 × 10−9 | 1.61 × 10−5 |
2:190900563:190924593 | GLS | ENST00000320717 | −3.25 | 4.03 × 10−8 | 7.23 × 10−5 |
2:190895151:190910321 | GLS | ENST00000320717 | −3.19 | 1.65 × 10−4 | 3.39 × 10−2 |
10:94030682:94032252 | PLCE1 | ENST00000260766 | −3.11 | 2.67 × 10−5 | 1.03 × 10−2 |
2:190900563:190931637 | GLS | ENST00000320717 | −3.06 | 3.98 × 10−5 | 1.22 × 10−2 |
5:16779544:16783469 | MYO10 | ENST00000274203 | −2.74 | 5.29 × 10−5 | 1.51 × 10−2 |
1:176594523:176595595 | PAPPA2 | ENST00000367661 | −2.74 | 5.93 × 10−5 | 1.56 × 10−2 |
1:95143890:95151419 | TMEM56 | ENST00000370203 | −2.61 | 9.18 × 10−5 | 2.08 × 10−2 |
Up-regulated | |||||
1:91861470:91861644 | TGFBR3 | ENST00000212355 | 6.14 | 3.16 × 10−7 | 3.46 × 10−4 |
7:18666212:18666476 | HDAC9 | ENST00000461159 | 6.07 | 4.91 × 10−7 | 4.24 × 10−4 |
7:14607433:14673027 | DGKB | ENST00000399322 | 5.56 | 1.41 × 10−5 | 7.13 × 10−3 |
16:77816920:77825461 | VAT1L | ENST00000302536 | 5.49 | 2.17 × 10−5 | 8.90 × 10−3 |
4:42485495:42524847 | ATP8A1 | ENST00000381668 | 5.42 | 3.33 × 10−5 | 1.18 × 10−2 |
9:70761600:70784279 | TRPM3 | ENST00000377110 | 5.33 | 5.62 × 10−5 | 1.54 × 10−2 |
9:70681505:70784279 | TRPM3 | ENST00000377110 | 5.25 | 9.04 × 10−5 | 2.08 × 10−2 |
13:69940039:69975802 | KLHL1 | ENST00000377844 | 5.23 | 9.71 × 10−5 | 2.12 × 10−2 |
7:22291174:22318037 | RAPGEF5 | ENST00000344041 | 5.15 | 1.43 × 10−4 | 3.02 × 10−2 |
9:76703336:76713721 | PRUNE2 | ENST00000376718 | 5.11 | 1.85 × 10−4 | 3.58 × 10−2 |
1:65913244:65918835 | PDE4B | ENST00000329654 | 5.09 | 3.28 × 10−8 | 7.23 × 10−5 |
X:154789953:154792285 | MPP1 | ENST00000369534 | 5.05 | 2.37 × 10−4 | 4.33 × 10−2 |
7:75943781:75943916 | SNORA14A | ENST00000364773 | 4.46 | 3.13 × 10−7 | 3.46 × 10−4 |
8:69755423:69761875 | SLCO5A1 | ENST00000260126 | 4.44 | 3.25 × 10−6 | 2.37 × 10−3 |
7:14574211:14673027 | DGKB | ENST00000399322 | 4.27 | 1.62 × 10−5 | 7.60 × 10−3 |
13:26337566:26353880 | CDK8 | ENST00000536792 | 4.10 | 6.81 × 10−6 | 4.06 × 10−3 |
2:144208602:144211579 | GTDC1 | ENST00000392869 | 4.02 | 3.42 × 10−5 | 1.18 × 10−2 |
1:58506059:58539310 | OMA1 | ENST00000371226 | 3.93 | 2.17 × 10−5 | 8.90 × 10−3 |
8:32595827:32616885 | NRG1 | ENST00000523534 | 3.66 | 4.06 × 10−5 | 1.22 × 10−2 |
18:62348167:62349937 | TNFRSF11A | ENST00000269485 | 3.27 | 8.98 × 10−5 | 2.08 × 10−2 |
4:186706562:186709845 | FAT1 | ENST00000441802 | 3.11 | 5.17 × 10−7 | 4.24 × 10−4 |
8:69738039:69761875 | SLCO5A1 | ENST00000260126 | 2.89 | 7.85 × 10−6 | 4.29 × 10−3 |
Selectively Expressed circRNAs | Highly Selective circRNAs | |||
---|---|---|---|---|
circRNAs | Genes | circRNAs | Genes | |
α-Cell | 392 | 343 | 7 | 5 |
β-Cell | 417 | 359 | 1 | 1 |
Exocrine cells | 57 | 52 | - | - |
Gene Name | circ ID | Exon Count | circRNA Length | log2(RC) | Gene Biotype |
---|---|---|---|---|---|
α-cell selective circRNAs | |||||
PLCE1 | 10:94030682:94032252 | 1 | 1570 | 4.43 | protein_coding |
FAP | 2:162183413:162203145 | 9 | 822 | 3.38 | protein_coding |
KANK1 | 9:710803:713464 | 1 | 2661 | 3.27 | protein_coding |
MCU | 10:72715110:72715902 | 2 | 165 | 3.02 | protein_coding |
C1orf168 | 1:56787174:56792803 | 3 | 944 | 2.95 | protein_coding |
FRMPD3 | X:107526581:107533550 | 3 | 304 | 2.93 | protein_coding |
PLCE1 | 10:94245945:94246621 | 1 | 676 | 2.88 | protein_coding |
KIAA1217 | 10:24219625:24219909 | 1 | 284 | 2.70 | protein_coding |
SYTL5 | X:38033533:38034008 | 1 | 475 | 2.70 | protein_coding |
FAM126A | 7:22960255:22991139 | 9 | 1019 | 2.64 | protein_coding |
SPG21 | 15:64974601:64983593 | 4 | 476 | 2.55 | protein_coding |
POU6F2 | 7:39204234:39207620 | 2 | 321 | 2.55 | protein_coding |
PITPNB | 22:27894554:27914347 | 6 | 436 | 2.52 | protein_coding |
PRKCE | 2:46001403:46010517 | 4 | 614 | 2.49 | protein_coding |
SPATS2L | 2:200329430:200419496 | 5 | 517 | 2.49 | protein_coding |
β-cell selective circRNAs | |||||
SNORA14A | 7:75943781:75943916 | 1 | 135 | 4.96 | snoRNA |
PDE4B | 1:65913244:65918835 | 2 | 351 | 4.37 | protein_coding |
TNFRSF11A | 18:62348167:62349937 | 2 | 208 | 4.21 | protein_coding |
NRG1 | 8:32595827:32616885 | 4 | 402 | 3.95 | protein_coding |
SNORD9 | 14:21392149:21392253 | 1 | 104 | 3.63 | snoRNA |
DGKB | 7:14574211:14673027 | 8 | 738 | 3.58 | protein_coding |
GTDC1 | 2:144208602:144211579 | 2 | 267 | 3.48 | protein_coding |
SYNE2 | 14:63998913:64022863 | 12 | 2284 | 3.39 | protein_coding |
HDAC9 | 7:18666212:18666476 | 1 | 264 | 3.36 | protein_coding |
TNRC6B | 22:40117054:40156182 | 3 | 233 | 3.36 | protein_coding |
TGFBR3 | 1:91861470:91861644 | 1 | 174 | 3.29 | protein_coding |
NRD1 | 1:51827795:51834170 | 2 | 228 | 3.29 | protein_coding |
GLCCI1 | 7:8003907:8060248 | 4 | 509 | 3.21 | protein_coding |
ROR1 | 1:64009304:64050716 | 3 | 391 | 3.04 | protein_coding |
TSNAX | 1:231537212:231542611 | 2 | 246 | 2.88 | protein_coding |
Exocrine-cell selective circRNAs | |||||
SNORD26 | 11:62855291:62855366 | 1 | 75 | 5.82 | snoRNA |
PNLIPRP2 | 10:116625945:116627874 | 3 | 373 | 4.78 | polymorphic_pseudogene |
CFTR | 7:117504252:117559655 | 10 | 1531 | 4.29 | protein_coding |
C15orf38-AP3S2 | 15:89903215:89910819 | 4 | 580 | 4.29 | protein_coding |
PNLIPRP2 | 10:116625945:116631357 | 5 | 613 | 4.21 | polymorphic_pseudogene |
RAB3D | 19:11335446:11335783 | 2 | 244 | 4.13 | protein_coding |
SEL1L | 14:81492479:81495137 | 2 | 126 | 3.81 | protein_coding |
TRHDE | 12:72562164:72575542 | 5 | 533 | 3.64 | protein_coding |
TRHDE | 12:72562852:72575542 | 4 | 467 | 3.52 | protein_coding |
SLC7A6 | 16:68266592:68266721 | 1 | 129 | 3.09 | protein_coding |
IKBKB | 8:42325969:42329214 | 2 | 219 | 3.09 | protein_coding |
SLC43A1 | 11:57491223:57491862 | 3 | 322 | 3.09 | protein_coding |
C3orf52 | 3:112109542:112113145 | 2 | 253 | 2.91 | protein_coding |
ARF4 | 3:57583897:57584464 | 2 | 191 | 2.91 | protein_coding |
SNORD58B | 18:49491663:49491729 | 1 | 66 | 2.91 | snoRNA |
α-Cell-Selective circRNAs | ||||
---|---|---|---|---|
Gene Name | CHR | circ ID | circBase or CircNet Id | log2(RC) |
FAP | 2 | 2:162183413:162203145 | hsa-circ-FAP.15 | 3.4 |
SYTL5 | X | X:38033533:38034008 | hsa-circ-SYTL5.3 | 2.7 |
PTPRT | 20 | 20:42448219:42472562 | hsa-circ-PTPRT.2, hsa_circ_0060424 | 1.9 |
PTPRT | 20 | 20:42350627:42352285 | hsa-circ-PTPRT.5 | 1 |
PTPRT | 20 | 20:42756461:42791466 | hsa-circ-PTPRT.15 | 0.2 |
STK32B | 4 | 4:5139904:5168450 | hsa-circ-STK32B.6, hsa_circ_0004536 | 0.5 |
BVES | 6 | 6:105115685:105125578 | hsa-circ-BVES.2, hsa_circ_0077527 | 0.3 |
β-cell-selective circRNAs | ||||
TGFBR3 | 1 | 1:91861470:91861644 | hsa-circ-TGFBR3.25, hsa_circ_0006622 | 3.3 |
© 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
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Kaur, S.; Mirza, A.H.; Pociot, F. Cell Type-Selective Expression of Circular RNAs in Human Pancreatic Islets. Non-Coding RNA 2018, 4, 38. https://doi.org/10.3390/ncrna4040038
Kaur S, Mirza AH, Pociot F. Cell Type-Selective Expression of Circular RNAs in Human Pancreatic Islets. Non-Coding RNA. 2018; 4(4):38. https://doi.org/10.3390/ncrna4040038
Chicago/Turabian StyleKaur, Simranjeet, Aashiq H. Mirza, and Flemming Pociot. 2018. "Cell Type-Selective Expression of Circular RNAs in Human Pancreatic Islets" Non-Coding RNA 4, no. 4: 38. https://doi.org/10.3390/ncrna4040038