Evidence for transcriptome-wide RNA editing among Sus scrofa PRE-1 SINE elements
BACKGROUND: RNA editing by ADAR (adenosine deaminase acting on RNA) proteins is a form of transcriptional regulation that is widespread among humans and other primates. Based on high-throughput scans used to identify putative RNA editing sites, ADAR appears to catalyze a substantial number of adenosine to inosine transitions within repetitive regions of the primate transcriptome, thereby dramatically enhancing genetic variation beyond what is encoded in the genome.
RESULTS: Here, we demonstrate the editing potential of the pig transcriptome by utilizing DNA and RNA sequence data from the same pig. We identified a total of 8550 mismatches between DNA and RNA sequences across three tissues, with 75% of these exhibiting an A-to-G (DNA to RNA) discrepancy, indicative of a canonical ADAR-catalyzed RNA editing event. When we consider only mismatches within repetitive regions of the genome, the A-to-G percentage increases to 94%, with the majority of these located within the swine specific SINE retrotransposon PRE-1. We also observe evidence of A-to-G editing within coding regions that were previously verified in primates.
CONCLUSIONS: Thus, our high-throughput evidence suggests that pervasive RNA editing by ADAR can exist outside of the primate lineage to dramatically enhance genetic variation in pigs.
| Medienart: |
E-Artikel |
|---|
| Erscheinungsjahr: |
2017 |
|---|---|
| Erschienen: |
2017 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:18 |
|---|---|
| Enthalten in: |
BMC genomics - 18(2017), 1 vom: 09. Mai, Seite 360 |
| Sprache: |
Englisch |
|---|
| Beteiligte Personen: |
Funkhouser, Scott A [VerfasserIn] |
|---|
| Links: |
|---|
| Themen: |
Bioinformatics |
|---|
| Anmerkungen: |
Date Completed 25.12.2017 Date Revised 08.04.2022 published: Electronic Citation Status MEDLINE |
|---|
| doi: |
10.1186/s12864-017-3766-7 |
|---|
| funding: |
|
|---|---|
| Förderinstitution / Projekttitel: |
|
| PPN (Katalog-ID): |
NLM271721987 |
|---|
| LEADER | 01000naa a22002652 4500 | ||
|---|---|---|---|
| 001 | NLM271721987 | ||
| 003 | DE-627 | ||
| 005 | 20231224233328.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 231224s2017 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1186/s12864-017-3766-7 |2 doi | |
| 028 | 5 | 2 | |a pubmed24n0905.xml |
| 035 | |a (DE-627)NLM271721987 | ||
| 035 | |a (NLM)28486975 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 100 | 1 | |a Funkhouser, Scott A |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Evidence for transcriptome-wide RNA editing among Sus scrofa PRE-1 SINE elements |
| 264 | 1 | |c 2017 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a ƒaComputermedien |b c |2 rdamedia | ||
| 338 | |a ƒa Online-Ressource |b cr |2 rdacarrier | ||
| 500 | |a Date Completed 25.12.2017 | ||
| 500 | |a Date Revised 08.04.2022 | ||
| 500 | |a published: Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a BACKGROUND: RNA editing by ADAR (adenosine deaminase acting on RNA) proteins is a form of transcriptional regulation that is widespread among humans and other primates. Based on high-throughput scans used to identify putative RNA editing sites, ADAR appears to catalyze a substantial number of adenosine to inosine transitions within repetitive regions of the primate transcriptome, thereby dramatically enhancing genetic variation beyond what is encoded in the genome | ||
| 520 | |a RESULTS: Here, we demonstrate the editing potential of the pig transcriptome by utilizing DNA and RNA sequence data from the same pig. We identified a total of 8550 mismatches between DNA and RNA sequences across three tissues, with 75% of these exhibiting an A-to-G (DNA to RNA) discrepancy, indicative of a canonical ADAR-catalyzed RNA editing event. When we consider only mismatches within repetitive regions of the genome, the A-to-G percentage increases to 94%, with the majority of these located within the swine specific SINE retrotransposon PRE-1. We also observe evidence of A-to-G editing within coding regions that were previously verified in primates | ||
| 520 | |a CONCLUSIONS: Thus, our high-throughput evidence suggests that pervasive RNA editing by ADAR can exist outside of the primate lineage to dramatically enhance genetic variation in pigs | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Research Support, U.S. Gov't, Non-P.H.S. | |
| 650 | 4 | |a Bioinformatics | |
| 650 | 4 | |a PRE-1 | |
| 650 | 4 | |a RNA editing | |
| 650 | 4 | |a Swine | |
| 650 | 7 | |a Retroelements |2 NLM | |
| 700 | 1 | |a Steibel, Juan P |e verfasserin |4 aut | |
| 700 | 1 | |a Bates, Ronald O |e verfasserin |4 aut | |
| 700 | 1 | |a Raney, Nancy E |e verfasserin |4 aut | |
| 700 | 1 | |a Schenk, Darius |e verfasserin |4 aut | |
| 700 | 1 | |a Ernst, Catherine W |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t BMC genomics |d 2000 |g 18(2017), 1 vom: 09. Mai, Seite 360 |w (DE-627)NLM10921594X |x 1471-2164 |7 nnns |
| 773 | 1 | 8 | |g volume:18 |g year:2017 |g number:1 |g day:09 |g month:05 |g pages:360 |
| 856 | 4 | 0 | |u http://dx.doi.org/10.1186/s12864-017-3766-7 |3 Volltext |
| 912 | |a GBV_USEFLAG_A | ||
| 912 | |a GBV_NLM | ||
| 951 | |a AR | ||
| 952 | |d 18 |j 2017 |e 1 |b 09 |c 05 |h 360 | ||