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Molecular Mechanisms of mRNA Transcriptional Regulation 2.0
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Special Issue "Molecular Mechanisms of mRNA Transcriptional Regulation 2.0"

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: 30 November 2023 | Viewed by 561

Special Issue Editor

Dr. Andrey Turchinovich

E-Mail Website1 Website2
Guest Editor
1. Cancer Genome Research (B063), German Cancer Research Center, 69120 Heidelberg, Germany
2. Heidelberg Biolabs GmbH, 69120 Heidelberg, Germany
Interests: regulation of gene expression; non-coding RNA; cell-free RNA; cancer biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues, 

Regulation of mRNA transcription is a highly dynamic process mediated by various molecular events which include specific DNA–protein, RNA–protein, RNA-RNA as well as DNA–RNA interactions. This complex process can be controlled at several steps, including the initial recruitment and assembly of the transcriptional machinery, transcription initiation, transcription pausing, transcription elongation, as well as termination phases. In addition, regulation of mRNA biogenesis and degradation involves the participation of various non-coding RNAs (ncRNAs), such as microRNAs, endogenous siRNAs, small nuclear RNAs, long ncRNAs, circular RNAs, and enhancer RNAs. This Special Issue focuses on the roles of different classes of RNAs and proteins regulating mRNA expression in various cell types. In particular, studies involving advanced deep sequencing, proteomics, and novel bioinformatics algorithms for RNA research are highly welcomed. The formats for submission include original research reports, reviews, and communications.

Dr. Andrey Turchinovich
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • transcriptoion factors (TFs)
  • cis-regulatory elements (CREs)
  • long non-coding RNAs (lncRNAs)
  • short non-coding RNAs (sncRNAs)
  • small nuclear RNAs (snRNAs)
  • microRNA (miRNA)
  • circular RNA (circRNA)
  • DNA methylation
  • chromatin regulators

Published Papers (1 paper)

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Article
Transcriptomic Analysis of Metarhizium anisopliae-Induced Immune-Related Long Non-Coding RNAs in Polymorphic Worker Castes of Solenopsis invicta
by
Junaid Zafar
,
Hongxin Wu
,
Yating Xu
,
Liangjie Lin
,
Zehong Kang
,
Jie Zhang
,
Ruonan Zhang
,
Yongyue Lu
,
Fengliang Jin
and
Xiaoxia Xu
Int. J. Mol. Sci. 2023, 24(18), 13983; https://doi.org/10.3390/ijms241813983 - 12 Sep 2023
Viewed by 263
Abstract
Long non-coding RNAs (lncRNAs) represent a class of RNA molecules that do not encode proteins. Generally studied for their regulatory potential in model insects, relatively little is known about their immunoregulatory functions in different castes of eusocial insects, including Solenopsis invicta, a [...] Read more.
Long non-coding RNAs (lncRNAs) represent a class of RNA molecules that do not encode proteins. Generally studied for their regulatory potential in model insects, relatively little is known about their immunoregulatory functions in different castes of eusocial insects, including Solenopsis invicta, a notoriously invasive insect pest. In the current study, we used Metarhizium anisopliae, an entomopathogenic fungus, to infect the polymorphic worker castes (Major and Minor Workers) and subjected them to RNA sequencing at different intervals (6, 24, and 48 h post-infection (hpi)). Comprehensive bioinformatic analysis identified 5719 (1869 known and 3850 novel) lncRNAs in all libraries. Genomic characteristics analysis showed that S. invicta lncRNAs exhibited structural similarities with lncRNAs from other eusocial insects, including lower exon numbers, shorter intron and exon lengths, and a lower expression profile. A comparison of lncRNAs in major and minor worker ants revealed that several lncRNAs were exclusively expressed in one worker caste and remained absent in the other. LncRNAs such as MSTRG.12029.1, XR_005575440.1 (6 h), MSTRG.16728.1, XR_005575440.1 (24 h), MSTRG.20263.41, and MSTRG.11994.5 (48 h) were only present in major worker ants, while lncRNAs such as MSTRG.8896.1, XR_005574239.1 (6 h), MSTRG.20289.8, XR_005575051.1 (24 h), MSTRG.20289.8, and MSTRG.6682.1 (48 h) were only detected in minor workers. Additionally, we performed real-time quantitative PCR and experimentally validated these findings. Functional annotation of cis-acting lncRNAs in major worker ants showed that lncRNAs targeted genes such as serine protease, trypsin, melanization protease-1, spaetzle-3, etc. In contrast, apoptosis and autophagy-related genes were identified as targets of lncRNAs in minor ants. Lastly, we identified several lncRNAs as precursors of microRNAs (miRNAs), such as miR-8, miR-14, miR-210, miR-6038, etc., indicating a regulatory relationship between lncRNAs, miRNAs, and mRNAs in antifungal immunity. These findings will serve as a genetic resource for lncRNAs in polymorphic eusocial ants and provide a theoretical basis for exploring the function of lncRNAs from a unique and novel perspective. Full article
(This article belongs to the Special Issue Molecular Mechanisms of mRNA Transcriptional Regulation 2.0)
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