Bioinformatic Searching for Optimal RNA Targets of Dimeric Compounds Informs Design of a MicroRNA-27a Inhibitor

: Among the most intensively studied classes of small molecules (molecular weight < 650) in biomedical research are small molecules that non-covalently bind to DNA/RNA, and another intensively studied class is nucleobase derivatives. Both classes have been intensively elaborated in many books and reviews. However, conjugates consisting of DNA/RNA binder covalently linked to nucleobase are much less studied and have not been reviewed in the last two decades. Therefore, this review summarized reports on the design of classical DNA/RNA binder – nucleobase conjugates, as well as data about their interactions with various DNA or RNA targets, and even in some cases protein targets are involved. According to these data, the most important structural aspects of selective or even specific recognition between small molecule and target are proposed, and where possible related biochemical and biomedical aspects were discussed. The general conclusion is that this, rather new class of molecules showed an amazing set of recognition tools for numerous DNA or RNA targets in the last two decades, as well as few intriguing in vitro and in vivo selectivities. Several lead research lines show promising advancements toward either novel, highly selective markers or bioactive, potentially druggable molecules.

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The splicing factor XAB2 interacts with ERCC1-XPF and XPG for R-loop processing

Nature Communications ◽

10.1038/s41467-021-23505-1 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Evi Goulielmaki ◽

Maria Tsekrekou ◽

Nikos Batsiotos ◽

Mariana Ascensão-Ferreira ◽

Eleftheria Ledaki ◽

...

Keyword(s):

Dna Damage ◽

Rna Splicing ◽

Excision Repair ◽

Intron Retention ◽

Dna Lesions ◽

Splicing Factor ◽

Loop Formation ◽

Rna Targets ◽

Underlying Mechanisms

AbstractRNA splicing, transcription and the DNA damage response are intriguingly linked in mammals but the underlying mechanisms remain poorly understood. Using an in vivo biotinylation tagging approach in mice, we show that the splicing factor XAB2 interacts with the core spliceosome and that it binds to spliceosomal U4 and U6 snRNAs and pre-mRNAs in developing livers. XAB2 depletion leads to aberrant intron retention, R-loop formation and DNA damage in cells. Studies in illudin S-treated cells and Csbm/m developing livers reveal that transcription-blocking DNA lesions trigger the release of XAB2 from all RNA targets tested. Immunoprecipitation studies reveal that XAB2 interacts with ERCC1-XPF and XPG endonucleases outside nucleotide excision repair and that the trimeric protein complex binds RNA:DNA hybrids under conditions that favor the formation of R-loops. Thus, XAB2 functionally links the spliceosomal response to DNA damage with R-loop processing with important ramifications for transcription-coupled DNA repair disorders.

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Induction of cryptic pre-mRNA splice-switching by antisense oligonucleotides

Scientific Reports ◽

10.1038/s41598-021-94639-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Kristin A. Ham ◽

Niall P. Keegan ◽

Craig S. McIntosh ◽

May T. Aung-Htut ◽

Khine Zaw ◽

...

Keyword(s):

Rna Splicing ◽

Antisense Oligonucleotides ◽

Live Cells ◽

Splice Sites ◽

Cryptic Splice Site ◽

Exon Definition ◽

Rna Targets ◽

Cryptic Splice Sites ◽

Six Genes ◽

Intended Effect

AbstractAntisense oligomers (AOs) are increasingly being used to modulate RNA splicing in live cells, both for research and for the development of therapeutics. While the most common intended effect of these AOs is to induce skipping of whole exons, rare examples are emerging of AOs that induce skipping of only part of an exon, through activation of an internal cryptic splice site. In this report, we examined seven AO-induced cryptic splice sites in six genes. Five of these cryptic splice sites were discovered through our own experiments, and two originated from other published reports. We modelled the predicted effects of AO binding on the secondary structure of each of the RNA targets, and how these alterations would in turn affect the accessibility of the RNA to splice factors. We observed that a common predicted effect of AO binding was disruption of the exon definition signal within the exon’s excluded segment.

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Development of a Brassica seed cDNA microarray

Genome ◽

10.1139/g07-115 ◽

2008 ◽

Vol 51 (3) ◽

pp. 236-242 ◽

Cited By ~ 18

Author(s):

Daoquan Xiang ◽

Raju Datla ◽

Fengling Li ◽

Adrian Cutler ◽

Meghna R. Malik ◽

...

Keyword(s):

Expression Patterns ◽

Cdna Array ◽

Brassica Species ◽

Crop Species ◽

Rna Targets ◽

Associated Functions ◽

Leaf Tissues ◽

Germinating Seeds ◽

Signal Intensities

Brassica species represent several important crops including canola ( Brassica napus ). Understanding of genetic elements that contribute to seed-associated functions will impact future improvements in the canola crop. Brassica species share a very close taxonomic and molecular relationship with Arabidopsis thaliana. However, there are several subtle but distinct seed-associated agronomic characteristics that differ among the oil seed crop species. To address these, we have generated 67 535 ESTs predominately from Brassica seeds, analyzed these sequences, and identified 10 642 unigenes for the preparation of a targeted seed cDNA array. A set of 10 642 PCR primer pairs was designed and corresponding amplicons were produced for spotting, along with relevant controls. Critical quality control tests produced satisfactory results for use of this microarray in biological experiments. The microarray was also tested with specific RNA targets from embryos, germinating seeds, and leaf tissues. The hybridizations, signal intensities, and overall quality of these slides were consistent and reproducible. Additionally, there are 429 ESTs represented on the array that show no homology with any A. thaliana annotated gene or any gene in the Brassica genome databases or other plant databases; however, all of these probes hybridized to B. napus transcripts, indicating that the array also will be useful in defining expression patterns for genes so far unique to Brassica species.

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Aberrant activation of non-coding RNA targets of transcriptional elongation complexes contributes to TDP-43 toxicity

Nature Communications ◽

10.1038/s41467-018-06543-0 ◽

2018 ◽

Vol 9 (1) ◽

Cited By ~ 21

Author(s):

Chia-Yu Chung ◽

Amit Berson ◽

Jason R. Kennerdell ◽

Ashley Sartoris ◽

Travis Unger ◽

...

Keyword(s):

Transcriptional Elongation ◽

Non Coding Rna ◽

Rna Targets

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Malignant Germ Cell Tumors Display Common MicroRNA Profiles Resulting in Global Changes in Expression of Messenger RNA Targets

Cancer Research ◽

10.1158/0008-5472.can-09-3301 ◽

2010 ◽

Vol 70 (7) ◽

pp. 2911-2923 ◽

Cited By ~ 157

Author(s):

Roger D. Palmer ◽

Matthew J. Murray ◽

Harpreet K. Saini ◽

Stijn van Dongen ◽

Cei Abreu-Goodger ◽

...

Keyword(s):

Germ Cell ◽

Messenger Rna ◽

Germ Cell Tumors ◽

Global Changes ◽

Rna Targets ◽

Malignant Germ Cell Tumors

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The Heptameric SmAP1 and SmAP2 Proteins of the Crenarchaeon Sulfolobus Solfataricus Bind to Common and Distinct RNA Targets

Life ◽

10.3390/life5021264 ◽

2015 ◽

Vol 5 (2) ◽

pp. 1264-1281 ◽

Cited By ~ 4

Author(s):

Birgit Märtens ◽

Gustavo Bezerra ◽

Mathias Kreuter ◽

Irina Grishkovskaya ◽

Andrea Manica ◽

...

Keyword(s):

Sulfolobus Solfataricus ◽

Rna Targets

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Scans of the MYC mRNA reveal multiple stable secondary structures—including a 3′ UTR motif, conserved across vertebrates, that can affect gene expression

10.1101/564864 ◽

2019 ◽

Author(s):

Collin A. O’Leary ◽

Ryan J. Andrews ◽

Van S. Tompkins ◽

Jonathan L. Chen ◽

Jessica L. Childs-Disney ◽

...

Keyword(s):

Internal Ribosomal Entry Site ◽

Folding Energy ◽

Entry Site ◽

Rna Targets ◽

High Propensity ◽

Transcriptional Regulatory ◽

Show Evidence ◽

Analysis Window ◽

Affect Gene Expression ◽

Human Transcription Factor

AbstractThe MYC gene encodes a human transcription factor and proto-oncogene that is dysregulated in over half of all known cancers. To better understand potential post-transcriptional regulatory features affecting MYC expression, we analyzed secondary structure in the MYC mRNA using a program that is optimized for finding small locally-folded motifs with a high propensity for function. This was accomplished by calculating folding metrics across the MYC sequence using a sliding analysis window and generating unique consensus base pairing models weighted by their lower-than-random predicted folding energy. A series of 30 motifs were identified, primarily in the 5’ and 3’ untranslated regions, which show evidence of structural conservation and compensating mutations across vertebrate MYC homologs. This analysis was able to recapitulate known elements found within an internal ribosomal entry site, as well as discover a novel element in the 3’ UTR that is unusually stable and conserved. This novel motif was shown to affect MYC expression: likely via modulation of miRNA target accessibility. In addition to providing basic insights into mechanisms that regulate MYC expression, this study provides numerous, potentially druggable RNA targets for the MYC gene, which is considered “undruggable” at the protein level.

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Degradome comparison between wild and cultivated rice identifies differential targeting by miRNAs

BMC Genomics ◽

10.1186/s12864-021-08288-5 ◽

2022 ◽

Vol 23 (1) ◽

Author(s):

Chenna Swetha ◽

Anushree Narjala ◽

Awadhesh Pandit ◽

Varsha Tirumalai ◽

P. V. Shivaprasad

Keyword(s):

Metabolic Pathways ◽

Wild Rice ◽

Regulation Of Gene Expression ◽

Genome Integrity ◽

Cultivated Rice ◽

Mrna Targets ◽

Ribonucleoprotein Complexes ◽

The Poor ◽

Rna Targets ◽

Secondary Wall Formation

Abstract Background Small non-coding (s)RNAs are involved in the negative regulation of gene expression, playing critical roles in genome integrity, development and metabolic pathways. Targeting of RNAs by ribonucleoprotein complexes of sRNAs bound to Argonaute (AGO) proteins results in cleaved RNAs having precise and predictable 5` ends. While tools to study sliced bits of RNAs to confirm the efficiency of sRNA-mediated regulation are available, they are sub-optimal. In this study, we provide an improvised version of a tool with better efficiency to accurately validate sRNA targets. Results Here, we improvised the CleaveLand tool to identify additional micro (mi)RNA targets that belong to the same family and also other targets within a specified free energy cut-off. These additional targets were otherwise excluded during the default run. We employed these tools to understand the sRNA targeting efficiency in wild and cultivated rice, sequenced degradome from two rice lines, O. nivara and O. sativa indica Pusa Basmati-1 and analyzed variations in sRNA targeting. Our results indicate the existence of multiple miRNA-mediated targeting differences between domesticated and wild species. For example, Os5NG4 was targeted only in wild rice that might be responsible for the poor secondary wall formation when compared to cultivated rice. We also identified differential mRNA targets of secondary sRNAs that were generated after miRNA-mediated cleavage of primary targets. Conclusions We identified many differentially targeted mRNAs between wild and domesticated rice lines. In addition to providing a step-wise guide to generate and analyze degradome datasets, we showed how domestication altered sRNA-mediated cascade silencing during the evolution of indica rice.

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