Sources of transcription variation in Plasmodium falciparum
Copyright © 2022. Published by Elsevier Ltd..
Variation in transcript abundance can contribute to both short-term environmental response and long-term evolutionary adaptation. Most studies are designed to assess differences in mean transcription levels and do not consider other potentially important and confounding sources of transcriptional variation. Detailed quantification of variation sources will improve our ability to detect and identify the mechanisms that contribute to genome-wide transcription changes that underpin adaptive responses. To quantify innate levels of expression variation, we measured mRNA levels for more than 5000 genes in the malaria parasite, Plasmodium falciparum, among clones derived from two parasite strains across biologically and experimentally replicated batches. Using a mixed effects model, we partitioned the total variation among four sources-between strain, within strain, environmental batch effects, and stochastic noise. We found 646 genes with significant variation attributable to at least one of these sources. These genes were categorized by their predominant variation source and further examined using gene ontology enrichment analysis to associate function with each source of variation. Genes with environmental batch effect and within strain transcript variation may contribute to phenotypic plasticity, while genes with between strain variation may contribute to adaptive responses and processes that lead to parasite strain-specific survival under varied conditions.
| Medienart: |
E-Artikel |
|---|
| Erscheinungsjahr: |
2022 |
|---|---|
| Erschienen: |
2022 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:49 |
|---|---|
| Enthalten in: |
Journal of genetics and genomics = Yi chuan xue bao - 49(2022), 10 vom: 06. Okt., Seite 965-974 |
| Sprache: |
Englisch |
|---|
| Beteiligte Personen: |
Turnbull, Lindsey B [VerfasserIn] |
|---|
| Links: |
|---|
| Themen: |
Cloning |
|---|
| Anmerkungen: |
Date Completed 24.10.2022 Date Revised 21.12.2022 published: Print-Electronic Citation Status MEDLINE |
|---|
| doi: |
10.1016/j.jgg.2022.03.008 |
|---|
| funding: |
|
|---|---|
| Förderinstitution / Projekttitel: |
|
| PPN (Katalog-ID): |
NLM339250852 |
|---|
| LEADER | 01000naa a22002652 4500 | ||
|---|---|---|---|
| 001 | NLM339250852 | ||
| 003 | DE-627 | ||
| 005 | 20231226002458.0 | ||
| 007 | cr uuu---uuuuu | ||
| 008 | 231226s2022 xx |||||o 00| ||eng c | ||
| 024 | 7 | |a 10.1016/j.jgg.2022.03.008 |2 doi | |
| 028 | 5 | 2 | |a pubmed24n1130.xml |
| 035 | |a (DE-627)NLM339250852 | ||
| 035 | |a (NLM)35395422 | ||
| 035 | |a (PII)S1673-8527(22)00089-3 | ||
| 040 | |a DE-627 |b ger |c DE-627 |e rakwb | ||
| 041 | |a eng | ||
| 100 | 1 | |a Turnbull, Lindsey B |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Sources of transcription variation in Plasmodium falciparum |
| 264 | 1 | |c 2022 | |
| 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 24.10.2022 | ||
| 500 | |a Date Revised 21.12.2022 | ||
| 500 | |a published: Print-Electronic | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a Copyright © 2022. Published by Elsevier Ltd. | ||
| 520 | |a Variation in transcript abundance can contribute to both short-term environmental response and long-term evolutionary adaptation. Most studies are designed to assess differences in mean transcription levels and do not consider other potentially important and confounding sources of transcriptional variation. Detailed quantification of variation sources will improve our ability to detect and identify the mechanisms that contribute to genome-wide transcription changes that underpin adaptive responses. To quantify innate levels of expression variation, we measured mRNA levels for more than 5000 genes in the malaria parasite, Plasmodium falciparum, among clones derived from two parasite strains across biologically and experimentally replicated batches. Using a mixed effects model, we partitioned the total variation among four sources-between strain, within strain, environmental batch effects, and stochastic noise. We found 646 genes with significant variation attributable to at least one of these sources. These genes were categorized by their predominant variation source and further examined using gene ontology enrichment analysis to associate function with each source of variation. Genes with environmental batch effect and within strain transcript variation may contribute to phenotypic plasticity, while genes with between strain variation may contribute to adaptive responses and processes that lead to parasite strain-specific survival under varied conditions | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Research Support, N.I.H., Extramural | |
| 650 | 4 | |a Research Support, Non-U.S. Gov't | |
| 650 | 4 | |a Cloning | |
| 650 | 4 | |a Expression variation | |
| 650 | 4 | |a Malaria | |
| 650 | 4 | |a Microarray | |
| 650 | 4 | |a Transcription | |
| 650 | 7 | |a RNA, Messenger |2 NLM | |
| 700 | 1 | |a Button-Simons, Katrina A |e verfasserin |4 aut | |
| 700 | 1 | |a Agbayani, Nestor |e verfasserin |4 aut | |
| 700 | 1 | |a Ferdig, Michael T |e verfasserin |4 aut | |
| 773 | 0 | 8 | |i Enthalten in |t Journal of genetics and genomics = Yi chuan xue bao |d 2007 |g 49(2022), 10 vom: 06. Okt., Seite 965-974 |w (DE-627)NLM169995097 |x 1673-8527 |7 nnns |
| 773 | 1 | 8 | |g volume:49 |g year:2022 |g number:10 |g day:06 |g month:10 |g pages:965-974 |
| 856 | 4 | 0 | |u http://dx.doi.org/10.1016/j.jgg.2022.03.008 |3 Volltext |
| 912 | |a GBV_USEFLAG_A | ||
| 912 | |a GBV_NLM | ||
| 951 | |a AR | ||
| 952 | |d 49 |j 2022 |e 10 |b 06 |c 10 |h 965-974 | ||