Beyond the transcript: Chromatin implications in trans-splicing in Trypanosomatids

Romina Trinidad Zambrano Siri; Paula Beati; Lucas Inchausti; Pablo Smircich; Guillermo Daniel Alonso; Josefina Ocampo

doi:10.1371/journal.pone.0343367

Peer Review History

Original SubmissionDecember 4, 2025
4 Dec 2025 Author Response Attachments Attachment Submitted filename: 159949_1_rebuttal_3547474_t6ljwx.docx https://doi.org/10.1371/journal.pone.0343367.r001
10 Dec 2025 Decision Letter - Alexander Palazzo, Editor Dear Dr. Ocampo, Going over the documents, we see that the plan you submitted as part of the Review Commons process includes an update of the code deposited at Github (https://github.com/paulati/nucleosome); however, as far as we can tell this has not been done - please provide this information (updated code/pipeline with a link to the repository) so that we can make a decision. plosone@plos.org . When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols . Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols . We look forward to receiving your revised manuscript. Kind regards, Alexander F. Palazzo, Ph.D. Academic Editor PLOS One Journal Requirements: 1. When submitting your revision, we need you to address these additional requirements.-->--> -->-->Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at -->-->https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and -->-->https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf-->--> -->-->2. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match. -->--> -->-->When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section.-->--> -->-->3. Thank you for stating the following financial disclosure: -->-->International Development Research Centre (IDRC):Guillermo Alonso 109929; Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación (agenciaidiar):Josefina Ocampo PICT-2020-00473; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET):Josefina Ocampo PIBBA 2020-28720210100100CO; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET):Guillermo Alonso PIP 2021-2023-03073  -->--> -->-->Please state what role the funders took in the study.  If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." -->-->If this statement is not correct you must amend it as needed. -->-->Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf.-->--> -->-->4. Thank you for stating the following in the Acknowledgments Section of your manuscript: -->-->We are grateful to Dr. David Clark for valuable discussions and to Santiago Carena for reading our manuscript. J.O. and G.D.A are members of the Research Career of CONICET. R.T.Z.S. is Ph.D. fellow supported by ANPCYT and her PhD thesis is carried out at Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires.-->--> -->-->We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. -->-->Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: -->-->International Development Research Centre (IDRC):Guillermo Alonso 109929; Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación (agenciaidiar):Josefina Ocampo PICT-2020-00473; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET):Josefina Ocampo PIBBA 2020-28720210100100CO; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET):Guillermo Alonso PIP 2021-2023-03073 -->--> -->-->Please include your amended statements within your cover letter; we will change the online submission form on your behalf.-->--> -->-->5. When completing the data availability statement of the submission form, you indicated that you will make your data available on acceptance. We strongly recommend all authors decide on a data sharing plan before acceptance, as the process can be lengthy and hold up publication timelines. Please note that, though access restrictions are acceptable now, your entire data will need to be made freely accessible if your manuscript is accepted for publication. This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If you are unable to adhere to our open data policy, please kindly revise your statement to explain your reasoning and we will seek the editor's input on an exemption. Please be assured that, once you have provided your new statement, the assessment of your exemption will not hold up the peer review process.-->--> -->-->6. Please upload a new copy of Figure 3 as the detail is not clear. Please follow the link for more information:  https://journals.plos.org/plosone/s/figures-->--> -->-->7. Please remove your figures from within your manuscript file, leaving only the individual TIFF/EPS image files, uploaded separately. These will be automatically included in the reviewers’ PDF.-->--> -->-->8. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information.-->--> -->-->9. If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise. ?> 10. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. [Note: HTML markup is below. Please do not edit.] To ensure your figures meet our technical requirements, please review our figure guidelines: https://journals.plos.org/plosone/s/figures You may also use PLOS’s free figure tool, NAAS, to help you prepare publication quality figures: https://journals.plos.org/plosone/s/figures#loc-tools-for-figure-preparation. NAAS will assess whether your figures meet our technical requirements by comparing each figure against our figure specifications. https://doi.org/10.1371/journal.pone.0343367.r002
Revision 1
4 Feb 2026 Author Response 1. When submitting your revision, we need you to address these additional requirements. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf We have checked thoroughly the format requirements and we are uploading a revised version of the manuscript with track changes (Revised Manuscript with Track Changes) and a plain version (Manuscript). 2. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match. When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section. We corroborated that the correct grant numbers for the awards we used for this study are correctly state in the ‘Funding Information’ section. 3. Thank you for stating the following financial disclosure: International Development Research Centre (IDRC):Guillermo Alonso 109929; Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación (agenciaidiar):Josefina Ocampo PICT-2020-00473; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET):Josefina Ocampo PIBBA 2020-28720210100100CO; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET):Guillermo Alonso PIP 2021-2023-03073 Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. The funders of our study had no involvement during the execution. Therefore, we state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." 4. Thank you for stating the following in the Acknowledgments Section of your manuscript: We are grateful to Dr. David Clark for valuable discussions and to Santiago Carena for reading our manuscript. J.O. and G.D.A are members of the Research Career of CONICET. R.T.Z.S. is Ph.D. fellow supported by ANPCYT and her PhD thesis is carried out at Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: International Development Research Centre (IDRC):Guillermo Alonso 109929; Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación (agenciaidiar):Josefina Ocampo PICT-2020-00473; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET):Josefina Ocampo PIBBA 2020-28720210100100CO; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET):Guillermo Alonso PIP 2021-2023-03073 Please include your amended statements within your cover letter; we will change the online submission form on your behalf. We have removed the funding-related text from the manuscript. You need to fix a small detail in the current statement bolded below: International Development Research Centre (IDRC):Guillermo Alonso 109929; Agencia Nacional de Promoción de la Investigación, el Desarrollo Tecnológico y la Innovación (agenciaidiar):Josefina Ocampo PICT-2020-00473; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET):Josefina Ocampo PIBBA 2020-28720210100100CO; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET):Guillermo Alonso PIP 2021-2023-03073; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). We are also including the amended statement in the cover letter. 5. When completing the data availability statement of the submission form, you indicated that you will make your data available on acceptance. We strongly recommend all authors decide on a data sharing plan before acceptance, as the process can be lengthy and hold up publication timelines. Please note that, though access restrictions are acceptable now, your entire data will need to be made freely accessible if your manuscript is accepted for publication. This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If you are unable to adhere to our open data policy, please kindly revise your statement to explain your reasoning and we will seek the editor's input on an exemption. Please be assured that, once you have provided your new statement, the assessment of your exemption will not hold up the peer review process. All data used in this manuscript is fully available we have now included a source code for the analytical procedures at https://github.com/romizambrano/TAS. We have modifyied our statement to make it clearer as follows: “All relevant data are within this manuscript and its Supporting Information files or extracted from previous published articles. Additionally, a source code for the analytical proceedures here described is available at https://github.com/romizambrano/TAS”. 6. Please upload a new copy of Figure 3 as the detail is not clear. Please follow the link for more information: https://journals.plos.org/plosone/s/figures We are uploading a new copy of Fig 3 with improved quality. 7. Please remove your figures from within your manuscript file, leaving only the individual TIFF/EPS image files, uploaded separately. These will be automatically included in the reviewers’ PDF. We have removed the figures from the updated version of the manuscript. 8. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. We have included captions for our supporting Information files at the end of the manuscript. 9. If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise. We only updated the reference style according to the Journal style. 10. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. No further changes in the reference list have been made. Attachments Attachment Submitted filename: Response_to_reviewers.pdf https://doi.org/10.1371/journal.pone.0343367.r003
6 Feb 2026 Decision Letter - Alexander Palazzo, Editor Beyond the transcript: chromatin implications in trans-splicing in Trypanosomatids PONE-D-25-64632R1 Dear Dr. Ocampo, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact billing support . If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Alexander F. Palazzo, Ph.D. Academic Editor PLOS One Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0343367.r004
Formally Accepted
Acceptance Letter - Alexander Palazzo, Editor PONE-D-25-64632R1 PLOS One Dear Dr. Ocampo, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS One. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. You will receive an invoice from PLOS for your publication fee after your manuscript has reached the completed accept phase. If you receive an email requesting payment before acceptance or for any other service, this may be a phishing scheme. Learn how to identify phishing emails and protect your accounts at https://explore.plos.org/phishing. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Alexander F. Palazzo Academic Editor PLOS One https://doi.org/10.1371/journal.pone.0343367.r005

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