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PloS One 2020Poly(A) tails at the 3' end of eukaryotic messenger RNAs control mRNA stability and translation efficiency. Facilitated by various NGS methods, alternative...
Poly(A) tails at the 3' end of eukaryotic messenger RNAs control mRNA stability and translation efficiency. Facilitated by various NGS methods, alternative polyadenylation sites determining the 3'-UTR length of gene transcripts have been extensively studied. However, poly(A) lengths demonstrating dynamic and developmental regulation remain largely unexplored. The recently developed NGS-based methods for genome-wide poly(A) profiling have promoted the study of genom-wide poly(A) dynamics. Here we present a straight forward NGS-method for poly(A) profiling, which applies a direct 3'-end adaptor ligation and the template switching for 5'-end adaptor ligation for cDNA library construction. Poly(A) lengths are directly calculated from base call data using a self-developed pipeline pA-finder. The libraries were directly sequenced from the 3'-UTR regions into the followed poly(A) tails, firstly on NextSeq 500 to produce single-end 300-nt reads, demonstrating the method feasibility and that optimization of the fragmented RNA size for cDNA library construction could detecting longer poly (A) tails. We next applied Poly(A)-seq cDNA libraries containing 40-nt and 120-nt poly(A) tail spike-in RNAs on HiSeq X-ten and NovaSeq 6000 to obtain 150-nt and 250-nt pair-end reads. The sequencing profiles of the spike-in RNAs demonstrated both high accuracy and high quality score in reading poly(A) tails. The poly(A) signal bleeding into the 3' adaptor sequence and a sharp decreased quality score at the junction were observed, allowing the modification of pA-finder to remove homopolymeric signal bleeding. We hope that wide applications of Poly(A)-seq help facilitate the study of the development- and disease-related poly(A) dynamics and regulation, and of the recent emerging mixed tailing regulation.
Topics: 3' Untranslated Regions; Gene Library; Genome; Humans; Poly A; Polyadenylation; Sequence Analysis, RNA; Transcriptome
PubMed: 32544193
DOI: 10.1371/journal.pone.0234696 -
Biomacromolecules Sep 2023While biomaterials have become indispensable for a wide range of tissue repair strategies, second removal procedures oftentimes needed in the case of non-bio-based and...
While biomaterials have become indispensable for a wide range of tissue repair strategies, second removal procedures oftentimes needed in the case of non-bio-based and non-bioresorbable scaffolds are associated with significant drawbacks not only for the patient, including the risk of infection, impaired healing, or tissue damage, but also for the healthcare system in terms of cost and resources. New biopolymers are increasingly being investigated in the field of tissue regeneration, but their widespread use is still hampered by limitations regarding mechanical, biological, and functional performance when compared to traditional materials. Therefore, a common strategy to tune and broaden the final properties of biopolymers is through the effect of different reinforcing agents. This research work focused on the fabrication and characterization of a bio-based and bioresorbable composite material obtained by compounding a poly(3-hydroxybutyrate--3-hydroxyhexanoate) (PHBH) matrix with acetylated cellulose nanocrystals (CNCs). The developed biocomposite was further processed to obtain three-dimensional scaffolds by additive manufacturing (AM). The 3D printability of the PHBH-CNC biocomposites was demonstrated by realizing different scaffold geometries, and the results of in vitro cell viability studies provided a clear indication of the cytocompatibility of the biocomposites. Moreover, the CNC content proved to be an important parameter in tuning the different functional properties of the scaffolds. It was demonstrated that the water affinity, surface roughness, and in vitro degradability rate of biocomposites increase with increasing CNC content. Therefore, this tailoring effect of CNC can expand the potential field of use of the PHBH biopolymer, making it an attractive candidate for a variety of tissue engineering applications.
Topics: Humans; Cellulose; Poly A; Hydroxybutyrates; Printing, Three-Dimensional
PubMed: 37589321
DOI: 10.1021/acs.biomac.3c00263 -
Development (Cambridge, England) Jun 2022As one of the post-transcriptional regulatory mechanisms, uncoupling of transcription and translation plays an essential role in development and adulthood physiology....
As one of the post-transcriptional regulatory mechanisms, uncoupling of transcription and translation plays an essential role in development and adulthood physiology. However, it remains elusive how thousands of mRNAs get translationally silenced while stability is maintained for hours or even days before translation. In addition to oocytes and neurons, developing spermatids display significant uncoupling of transcription and translation for delayed translation. Therefore, spermiogenesis represents an excellent in vivo model for investigating the mechanism underlying uncoupled transcription and translation. Through full-length poly(A) deep sequencing, we discovered dynamic changes in poly(A) length through deadenylation and re-polyadenylation. Deadenylation appeared to be mediated by microRNAs (miRNAs), and transcripts with shorter poly(A) tails tend to be sequestered into ribonucleoprotein (RNP) granules for translational repression and stabilization. In contrast, re-polyadenylation might allow for translocation of the translationally repressed transcripts from RNP granules to polysomes. Overall, our data suggest that miRNA-dependent poly(A) length control represents a previously unreported mechanism underlying uncoupled translation and transcription in haploid male mouse germ cells.
Topics: Animals; Haploidy; Male; Mice; MicroRNAs; Poly A; Protein Biosynthesis; RNA, Messenger; Spermatids
PubMed: 35588208
DOI: 10.1242/dev.199573 -
Chemistry (Weinheim An Der Bergstrasse,... Jul 2022Poly(A)-binding protein (PABP) is an essential element of cellular translational machinery. Recent studies have revealed that poly(A) tail modifications can modulate...
Poly(A)-binding protein (PABP) is an essential element of cellular translational machinery. Recent studies have revealed that poly(A) tail modifications can modulate mRNA stability and translational potential, and that oligoadenylate-derived PABP ligands can act as effective translational inhibitors with potential applications in pain management. Although extensive research has focused on protein-RNA and protein-protein interactions involving PABPs, further studies are required to examine the ligand specificity of PABP. In this study, we developed a microscale thermophoresis-based assay to probe the interactions between PABP and oligoadenylate analogs containing different chemical modifications. Using this method, we evaluated oligoadenylate analogs modified with nucleobase, ribose, and phosphate moieties to identify modification hotspots. In addition, we determined the susceptibility of the modified oligos to CNOT7 to identify those with the potential for increased cellular stability. Consequently, we selected two enzymatically stable oligoadenylate analogs that inhibit translation in rabbit reticulocyte lysates with a higher potency than a previously reported PABP ligand. We believe that the results presented in this study and the implemented methodology can be capitalized upon in the future development of RNA-based biological tools.
Topics: Animals; Ligands; Poly A; Poly(A)-Binding Proteins; Protein Binding; Protein Biosynthesis; RNA; RNA, Messenger; Rabbits; Structure-Activity Relationship
PubMed: 35575378
DOI: 10.1002/chem.202201115 -
Methods in Molecular Biology (Clifton,... 2021Ribosome profiling is a powerful technique that enables researchers to monitor translational events across the transcriptome. It provides a snapshot of ribosome... (Comparative Study)
Comparative Study
Ribosome profiling is a powerful technique that enables researchers to monitor translational events across the transcriptome. It provides a snapshot of ribosome positions and density across the transcriptome at a sub-codon resolution. Here we describe the whole procedure of profiling ribosome footprints in mammalian cells. Two methods for Ribo-seq library construction are introduced, and their advantages and disadvantages are compared. There is a room for further improvement of Ribo-seq in terms of the amount of starting material, the duration of library construction, and the resolution of sequencing results.
Topics: Gene Library; HEK293 Cells; High-Throughput Nucleotide Sequencing; Humans; Poly A; Protein Biosynthesis; RNA, Messenger; Ribosomes; Sequence Analysis, RNA; Software
PubMed: 33765278
DOI: 10.1007/978-1-0716-1150-0_10 -
Biochemistry. Biokhimiia Sep 2021"Would it be possible to analyze molecular mechanisms and structural organisation of polyribosome assemblies using cryo electron tomography?" - we asked through a... (Review)
Review
"Would it be possible to analyze molecular mechanisms and structural organisation of polyribosome assemblies using cryo electron tomography?" - we asked through a longstanding collaboration between my research group and that of Alexander S. Spirin. Indeed, it was: we found that double-row polyribosomes can have both circular and linear arrangements of their mRNA [Afonina, Z. A., et al. (2013) Biochemistry (Moscow)], we figured out how eukaryotic ribosomes assemble on an mRNA to form supramolecular left-handed helices [Myasnikov, A. G., et al. (2014) Nat. Commun.], that the circularization of polyribosomes is poly-A and cap-independent [Afonina, Z. A., et al. (2014) Nucleic Acids Res.], and that intermediary polyribosomes with open structures exist after a transition from a juvenile phase to strongly translating polysomes of medium size [Afonina, Z. A., et al. (2015) Nucleic Acids Res.] until they form densely packed helical structures with reduced activity. Our joint fruitful exchanges, hence, led to major advances in the field, which are reviewed here from a personal and historical perspective in memory of Alexander S. Spirin.
Topics: Cryoelectron Microscopy; Eukaryota; Nucleic Acid Conformation; Poly A; Polyribosomes; RNA Caps; RNA, Messenger; Ribosome Subunits
PubMed: 34565311
DOI: 10.1134/S0006297921090030 -
Methods in Molecular Biology (Clifton,... 2022Polyadenylation and deadenylation of mRNA are major RNA modifications associated with nucleus-to-cytoplasm translocation, mRNA stability, translation efficiency, and...
Polyadenylation and deadenylation of mRNA are major RNA modifications associated with nucleus-to-cytoplasm translocation, mRNA stability, translation efficiency, and mRNA decay pathways. Our current knowledge of polyadenylation and deadenylation has been expanded due to recent advances in transcriptome-wide poly(A) tail length assays. Whereas these methods measure poly(A) length by quantifying the adenine (A) base stretch at the 3' end of mRNA, we developed a more cost-efficient technique that does not rely on A-base counting, called tail-end-displacement sequencing (TED-seq). Through sequencing highly size-selected 3' RNA fragments including the poly(A) tail pieces, TED-seq provides accurate measure of transcriptome-wide poly(A)-tail lengths in high resolution, economically suitable for larger scale analysis under various biologically transitional contexts.
Topics: Genome; Poly A; Polyadenylation; RNA Stability; RNA, Messenger; Sequence Analysis, RNA
PubMed: 34694615
DOI: 10.1007/978-1-0716-1851-6_15 -
ELife Nov 2022Alternative polyadenylation yields many mRNA isoforms whose 3' termini occur disproportionately in clusters within 3' untranslated regions. Previously, we showed that...
Alternative polyadenylation yields many mRNA isoforms whose 3' termini occur disproportionately in clusters within 3' untranslated regions. Previously, we showed that profiles of poly(A) site usage are regulated by the rate of transcriptional elongation by RNA polymerase (Pol) II (Geisberg et al., 2020). Pol II derivatives with slow elongation rates confer an upstream-shifted poly(A) profile, whereas fast Pol II strains confer a downstream-shifted poly(A) profile. Within yeast isoform clusters, these shifts occur steadily from one isoform to the next across nucleotide distances. In contrast, the shift between clusters - from the last isoform of one cluster to the first isoform of the next - is much less pronounced, even over large distances. GC content in a region 13-30 nt downstream from isoform clusters correlates with their sensitivity to Pol II elongation rate. In human cells, the upstream shift caused by a slow Pol II mutant also occurs continuously at single nucleotide resolution within clusters but not between them. Pol II occupancy increases just downstream of poly(A) sites, suggesting a linkage between reduced elongation rate and cluster formation. These observations suggest that (1) Pol II elongation speed affects the nucleotide-level dwell time allowing polyadenylation to occur, (2) poly(A) site clusters are linked to the local elongation rate, and hence do not arise simply by intrinsically imprecise cleavage and polyadenylation of the RNA substrate, (3) DNA sequence elements can affect Pol II elongation and poly(A) profiles, and (4) the cleavage/polyadenylation and Pol II elongation complexes are spatially, and perhaps physically, coupled so that polyadenylation occurs rapidly upon emergence of the nascent RNA from the Pol II elongation complex.
Topics: Humans; Polyadenylation; Nucleotides; RNA Polymerase II; Poly A; Saccharomyces cerevisiae; 3' Untranslated Regions; Transcription, Genetic
PubMed: 36421680
DOI: 10.7554/eLife.83153 -
PloS One 2017RNA-seq reads containing part of the poly(A) tail of transcripts (denoted as poly(A) reads) provide the most direct evidence for the position of poly(A) sites in the...
RNA-seq reads containing part of the poly(A) tail of transcripts (denoted as poly(A) reads) provide the most direct evidence for the position of poly(A) sites in the genome. However, due to reduced coverage of poly(A) tails by reads, poly(A) reads are not routinely identified during RNA-seq mapping. Nevertheless, recent studies for several herpesviruses successfully employed mapping of poly(A) reads to identify herpesvirus poly(A) sites using different strategies and customized programs. To more easily allow such analyses without requiring additional programs, we integrated poly(A) read mapping and prediction of poly(A) sites into our RNA-seq mapping program ContextMap 2. The implemented approach essentially generalizes previously used poly(A) read mapping approaches and combines them with the context-based approach of ContextMap 2 to take into account information provided by other reads aligned to the same location. Poly(A) read mapping using ContextMap 2 was evaluated on real-life data from the ENCODE project and compared against a competing approach based on transcriptome assembly (KLEAT). This showed high positive predictive value for our approach, evidenced also by the presence of poly(A) signals, and considerably lower runtime than KLEAT. Although sensitivity is low for both methods, we show that this is in part due to a high extent of spurious results in the gold standard set derived from RNA-PET data. Sensitivity improves for poly(A) sites of known transcripts or determined with a more specific poly(A) sequencing protocol and increases with read coverage on transcript ends. Finally, we illustrate the usefulness of the approach in a high read coverage scenario by a re-analysis of published data for herpes simplex virus 1. Thus, with current trends towards increasing sequencing depth and read length, poly(A) read mapping will prove to be increasingly useful and can now be performed automatically during RNA-seq mapping with ContextMap 2.
Topics: Animals; Humans; Poly A; RNA, Messenger; Sequence Analysis, RNA; Software; Transcriptome
PubMed: 28135292
DOI: 10.1371/journal.pone.0170914 -
Molekuliarnaia Biologiia 2017Polyadenylation is the non-template addition of adenosine nucleotides at the 3'-end of RNA, which occurs after transcription and generates a poly(A) tail up to 250-300... (Review)
Review
Polyadenylation is the non-template addition of adenosine nucleotides at the 3'-end of RNA, which occurs after transcription and generates a poly(A) tail up to 250-300 nucleotides long. In the first section of our review, we consider the classical process of mRNA 3'-terminus formation, which involves the cleavage of the transcript synthesized by RNA polymerase II and the associated poly(A) tail synthesis by canonical polyadenylate polymerase. Nucleotide sequences needed for mRNA cleavage and poly(A) tail synthesis, in particular the AAUAAA polyadenylation signal, as well as numerous proteins and their complexes involved in mRNA cleavage and polyadenylation, is described in detail. The significance of the poly(A) tail for prolonging mRNA lifetime and stimulating their translation is discussed. Data presented in the second section demonstrate that RNA transcribed by RNA polymerase III from certain SINEs (Short Interspersed Elements) can undergo AAUAAA-dependent polyadenylation. The structural and functional features of RNA polymerase III determine the unusual character of polyadenylation of RNAs synthesized by this enzyme. The history of recent developments in this area of study have been described in greater detail, in particular the discovery of AAUAAA-dependent polyadenylation of RNA synthesized by RNA polymerase III, which has not been discussed previously. Data on AAUAAA-independent polyadenylation catalyzed by noncanonical TRAMP poly(A)-polymerases (Trf4 and Trf5) have been presented in the third section. These enzymes promote rapid degradation of RNAs by adding a short poly(A) tail to them. This mechanism enables the recognition, poly(A)-marking, and elimination of incorrectly folded noncoding transcripts (e.g. ribosomal and transfer RNAs).
Topics: Animals; Humans; Poly A; Polyadenylation; RNA, Messenger
PubMed: 28537233
DOI: 10.7868/S0026898417010189