Transcriptomics technologies: Difference between revisions

Revision as of 23:41, 20 May 2022

Revision as of 03:40, 24 May 2022

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Transcriptomic profiling also provides crucial information on mechanisms of [[drug resistance]]. Analysis of over 1000 isolates of ''[[Plasmodium falciparum]]'', a virulent parasite responsible for malaria in humans,<ref name="Rich et al">{{cite journal | vauthors = Rich SM, Leendertz FH, Xu G, LeBreton M, Djoko CF, Aminake MN, Takang EE, Diffo JL, Pike BL, Rosenthal BM, Formenty P, Boesch C, Ayala FJ, Wolfe ND | title = The origin of malignant malaria | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 106 | issue = 35 | pages = 14902–7 | date = September 2009 | pmid = 19666593 | pmc = 2720412 | doi = 10.1073/pnas.0907740106 | bibcode = 2009PNAS..10614902R | doi-access = free }}</ref> identified that upregulation of the [[unfolded protein response]] and slower progression through the early stages of the asexual intraerythrocytic [[Plasmodium falciparum#Lifecycle|developmental cycle]] were associated with [[Artemisinin#Resistance|artemisinin resistance]] in isolates from [[Southeast Asia]].<ref name="#25502316">{{cite journal | vauthors = Mok S, Ashley EA, Ferreira PE, Zhu L, Lin Z, Yeo T, Chotivanich K, Imwong M, Pukrittayakamee S, Dhorda M, Nguon C, Lim P, Amaratunga C, Suon S, Hien TT, Htut Y, Faiz MA, Onyamboko MA, Mayxay M, Newton PN, Tripura R, Woodrow CJ, Miotto O, Kwiatkowski DP, Nosten F, Day NP, Preiser PR, White NJ, Dondorp AM, Fairhurst RM, Bozdech Z | display-authors = 6 | title = Drug resistance. Population transcriptomics of human malaria parasites reveals the mechanism of artemisinin resistance | journal = Science | volume = 347 | issue = 6220 | pages = 431–5 | date = January 2015 | pmid = 25502316 | pmc = 5642863 | doi = 10.1126/science.1260403 | bibcode = 2015Sci...347..431M }}</ref>

The use of transcriptomics is also important to investigate responses in the marine environment.<ref name=":0"> {{Cite journal |last1=Page |first1=Tessa M. |last2=Lawley |first2=Jonathan W. |date=2022 |title=The Next Generation Is Here: A Review of Transcriptomic Approaches in Marine Ecology |journal=Frontiers in Marine Science |volume=9 |doi=10.3389/fmars.2022.757921 |issn=2296-7745|doi-access=free }}</ref>. In marine ecology, "[[Stress (biology)|stress]]" and "[[adaptation]]" have been among the most common research topics, especially related to anthropogenic stress, such as [[global change]] and [[pollution]].<ref name=":0" />. Most of the studies in this area have been done in [[Animal|animals]], although [[Invertebrate|invertebrates]] have been underrepresented.<ref name=":0" />. One issue still is a deficiency in functional genetic studies, which hamper [[Gene annotation|gene annotations]], especially for non-model species, and can lead to vague conclusions on the effects of responses studied.<ref name=":0" />.

=== Gene function annotation ===

All transcriptomic techniques have been particularly useful in [[Gene annotation|identifying the functions of genes]] and identifying those responsible for particular phenotypes. Transcriptomics of ''Arabidopsis'' [[ecotype]]s that [[Hyperaccumulator|hyperaccumulate metals]] correlated genes involved in [[Bioinorganic chemistry#Metal ion transport and storage|metal uptake]], tolerance, and [[homeostasis]] with the phenotype.<ref name="#19192189">{{cite journal | vauthors = Verbruggen N, Hermans C, Schat H | title = Molecular mechanisms of metal hyperaccumulation in plants | journal = The New Phytologist | volume = 181 | issue = 4 | pages = 759–76 | date = March 2009 | pmid = 19192189 | doi = 10.1111/j.1469-8137.2008.02748.x | url = https://dipot.ulb.ac.be/dspace/bitstream/2013/58126/3/58126.pdf }}</ref> Integration of RNA-Seq datasets across different tissues has been used to improve annotation of gene functions in commercially important organisms (e.g. [[Cucumis sativus|cucumber]])<ref name="#22047402">{{cite journal | vauthors = Li Z, Zhang Z, Yan P, Huang S, Fei Z, Lin K | title = RNA-Seq improves annotation of protein-coding genes in the cucumber genome | journal = BMC Genomics | volume = 12 | pages = 540 | date = November 2011 | pmid = 22047402 | pmc = 3219749 | doi = 10.1186/1471-2164-12-540 }}</ref> or threatened species (e.g. [[koala]]).<ref name="#25214207">{{cite journal | vauthors = Hobbs M, Pavasovic A, King AG, Prentis PJ, Eldridge MD, Chen Z, Colgan DJ, Polkinghorne A, Wilkins MR, Flanagan C, Gillett A, Hanger J, Johnson RN, Timms P | title = A transcriptome resource for the koala (Phascolarctos cinereus): insights into koala retrovirus transcription and sequence diversity | journal = BMC Genomics | volume = 15 | pages = 786 | date = September 2014 | pmid = 25214207 | pmc = 4247155 | doi = 10.1186/1471-2164-15-786 }}</ref>