Islam, RA

Rallis, C

Epigenomes

English

Queen Mary Research Online

Citation: Islam, R.A.; Rallis, C.Correction: Islam, R.A.; Rallis, C.Ribosomal Biogenesis andHeterogeneity in Development,Disease, and Aging. Epigenomes 2023,7, 17. Epigenomes 2023, 7, 26. https://doi.org/10.3390/epigenomes7040026Received: 6 September 2023Accepted: 4 October 2023Published: 26 October 2023Copyright: © 2023 by the authors.Licensee MDPI, Basel, Switzerland.This article is an open access articledistributed under the terms andconditions of the Creative CommonsAttribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).epigenomesCorrectionCorrection: Islam, R.A.; Rallis, C. Ribosomal Biogenesis andHeterogeneity in Development, Disease, and Aging.Epigenomes 2023, 7, 17Rowshan Ara Islam 1,2 and Charalampos Rallis 1,2,*1 School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK; ri22394@essex.ac.uk2 School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road,London E1 4NS, UK* Correspondence: c.rallis@qmul.ac.ukCitation Correction23. Akirtava, C.; May, G.E.; McManus, C.J. False-Positive IRESes from Hoxa9 andOther Genes Resulting from Errors in Mam-malian 5’ UTR Annotations. Proc. Natl. Acad.Sci. USA 2022, 119, e2122170119. https://doi.org/10.1073/pnas.2122170119.Should be revised to:23. Leppek, K.; Fujii, K.; Quade, N.; Susanto, T.T.; Boehringer, D.; Lenarčič, T.;Xue, S.; Genuth, N.R.; Ban, N.; Barna, M. Gene- and Species-Specific Hox MRNATranslation by Ribosome Expansion Segments. Mol. Cell 2020, 80, 980–995.e13.https://doi.org/10.1016/j.molcel.2020.10.023.In the original publication [1], the study by Akirtava et al was incorrectly cited insteadof Leppek et al. Leppek et al and Ivanov et al were not cited in the original article. Thecorrection reports the study by Leppek et al and Akirtava et al correctly and includes thereference from Ivanov et al to provide a different point of view about IRES reported byLeppek et al. The citation order of the references in the corrected manuscript have beenadjusted accordingly following the numerical order after the change.Text CorrectionAs there are studies challenging the idea of an “Internal Ribosome Entry Site (IRES)”described in the original publication, it is ideal and fair to include the contradictory findingsas well. Therefore, we added further text and relevant citations to Section 2.2. Evolution of the Idea of Ribosome Heterogeneity and Its Key FactorsParagraph Number 3. Additional text has been added and the paragraph should read:In 2002, Mauro and Edelman found that before translation starts, the small sub-unit scrutinises and decides which mRNAs to translate and to what extent. Thisfiltering preference may change with different heterogeneous ribosomes [22].Generally, the 7-methylguanosine cap on the 5′ end of mRNAs interacts withthe initiation factors to load onto the ribosome to start the translation process.However, recent studies showed that in special situations, such as stress whenthe initiation factors are repressed, the expansion segments (ES) of ribosomesmay recognise mRNAs with 5′ internal ribosome entry sites (IRESs), shown incase of Hoxa9 mRNA by Maria Barna’s lab as a part of their detailed work onspecialised ribosome [23]. First identified in viruses, IRES elements help translateviral mRNAs by recruiting the host’s cellular machinery in a cap-independentmanner [24]. IRES-mediated translation was observed for selected cellular mR-NAs when cap-dependent translation was downregulated (c-myc, XIAP, Apaf-1,p53 mRNAs) during stress [25], or sometimes this is a chosen means for somemRNAs (i.e., Hox mRNA with a translation inhibitor element (TIE) at 5′ UTR,Epigenomes 2023, 7, 26. https://doi.org/10.3390/epigenomes7040026 https://www.mdpi.com/journal/epigenomesEpigenomes 2023, 7, 26 2 of 3which inhibits its cap-dependent translation in physiological condition) [25]. Inthe case of IRES-dependent translation of viral mRNAs, studies found RPS25and RACK1 (ribosomal protein receptor for activated C kinase 1, an SSU pro-tein) to be important in ribosomal composition [26,27]. But in the case of HoxmRNAs (transcribed from Hox genes responsible for embryonic body plan), ribo-somes require RPL38, an otherwise dispensable ribosomal protein [25]. However,it is worth mentioning that a few recent studies contradicted with the idea ofIRES-mediated cellular translation. One such study by McManus lab showedthat most of the hyperconserved transcript leaders (hTLs), where the putativeIRESes are, overlap transcriptional promoters, enhancers, and 3’splice sites, workas transcription factor binding site (E-box) for numerous transcription factorsincluding USF1 and USF2, and the putative IRES sequences are rarely includedin the transcript leader which argued the reported interaction of Hoxa9 IRESwith ES (ES9S specifically) [28]. Their research attributed the putative IRES-likeelements to mis-annotation and false positive result caused by monocistronictranscripts from internal promoters or cryptic splicing in the IRES test sequencein the bicistronic reporter assays [28]. As the McManus lab refuted the conceptof IRES, the explanation of the observed IRES-like activity in this context canbe found in a study done by Ivanov et al. [29]. Their study of ‘cap analysis ofgene expression sequencing (CAGE-seq)’ of published data and mouse somitesreported much shorter transcript leaders with conserved uORFs and absence ofthe putative IRESes in the Hox mRNAs. Translation may start at the start codon(AUG) or its near-cognate codon (CUG or UUG) at upstream ORF (uORF) ormain ORF (mORF). Stringency of start codon selection depends on the flankingcontext nucleotides and the relative level of translation initiation factors eIF1and eIF5. During high stringency (high level of eIF1 relative to eIF5, as seenduring meiosis), Hox genes with ‘conserved poor mORF start codon context’ areinhibited, while mRNAs (Hoxa1, Hoxa9, Hoxa11) with ‘conserved inhibitoryuORF with poor start codon context’ are induced. eIF1/eIF5 ratio is also increasedduring perturbation in global translation due to inhibition of ribosomal proteins(RPL11 in this study) which Ivanov et al. attributed as the reason of putative IREScontaining Hox mRNAs’ connection with RPL38 reported by Barna group [29].To adjust with the new insertion in Section 2. Evolution of the Idea of RibosomeHeterogeneity and Its Key Factors, Paragraph Number 3, we will move the last sentenceof Paragraph 3 of original publication to the beginning of Paragraph 4 of the originalpublication, and should read:While heterogeneity of ribosomes is a natural means of translation regulationand may depend on cell type, growth, differentiation states, or cellular responseto infections or other external stimuli [3,30,31], the association of certain RPs tospecial cellular conditions or specific mRNAs, such as the examples mentionedabove, suggests the specialised roles of ribosomes. The concept of variable rolesof individual RPs arises from the observation of different phenotypes causedby change in different proteins [5]. Comparative studies of phenotypes causedby loss-of-function mutations of RPs in eukaryotic organisms, namely, buddingyeast, worm, drosophila, zebrafish, and mouse, showed a broad spectrum ofphenotypes, including lethality, reduced organ/organism size, and delayed de-velopment. Haploinsufficiency due to the loss of one allele caused by mutation ordeletion is more evident in tissues where the alleles of interest are more highly ex-pressed [32]. RPs expressed selectively in certain cellular conditions and of variedstoichiometry are usually found on the surface of the ribosomes, near the mRNAentry/exit tunnel or L1 stalk, where they are in contact with the mRNAs [33].The authors state that the scientific conclusions are unaffected. This correction wasapproved by the Academic Editor. The original publication has also been updated.Epigenomes 2023, 7, 26 3 of 3Reference1. Islam, R.A.; Rallis, C. Ribosomal Biogenesis and Heterogeneity in Development, Disease, and Aging. Epigenomes 2023, 7, 17.[CrossRef] [PubMed]Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individualauthor(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury topeople or property resulting from any ideas, methods, instructions or products referred to in the content.

Correction: Islam, R.A.; Rallis, C. Ribosomal Biogenesis and Heterogeneity in Development, Disease, and Aging. Epigenomes 2023, 7, 17

https://qmro.qmul.ac.uk/xmlui/bitstream/123456789/92540/2/Rallis%20Correction%3a%20Islam%2c%20R.A.%3b%20Rallis%2c%20C.%20Ribosomal%20Biogenesis%20and%20Heterogeneity%20in%20Development%2c%20Disease%2c%20and%20Aging.%20Epigenomes%202023%2c%207%2c%2017%202023%20Published.pdf

Correction: Islam, R.A.; Rallis, C. Ribosomal Biogenesis and Heterogeneity in Development, Disease, and Aging. Epigenomes 2023, 7, 17

Abstract

Similar works

Full text

Available Versions

Queen Mary Research Online