scholarly journals Comprehensive analysis of mRNA poly(A) tail reveals complex and conserved regulation

2021 ◽  
Author(s):  
Yusheng Liu ◽  
Hu Nie ◽  
Yiwei Zhang ◽  
Falong Lu ◽  
Jiaqiang Wang
Keyword(s):  
Transcriptional Regulation ◽  
Mammalian Cells ◽  
Tail Length ◽  
Comprehensive Analysis ◽  
Full Length ◽  
New Method ◽  
Full Length Cdna ◽  
Simultaneous Evaluation ◽  
Eukaryotic Species ◽  
Post Transcriptional Regulation

Non-templated poly(A) tails are added to the 3′-end of most mRNAs, which have important roles in post-transcriptional regulation. Recent studies have revealed that poly(A) tails are not composed purely of A residues, but also contain U, C and G residues internally and at their 3′-ends, revealing new levels of complexity. However, no method is able to analyze these internal and terminal non-A residues simultaneously. Here, we developed a new method called PAIso-seq2 which captures RNA 3′-ends by direct 3′ adaptor ligation and rRNA removal by CRISPR/Cas9. This method allows simultaneous evaluation of the poly(A) tail length and 5′-end, internal, and 3′-end non-A residues together with the full-length cDNA for a transcript. Applying this method, we achieved the first complete transcriptome-wide 3′ tail map of mRNA within the nuclear and cytoplasmic compartments of mammalian cells, uncovering differences in poly(A) tail length and non-A residues between these two mRNA populations. A survey of diverse eukaryotic species revealed the conservation of a subset of poly(A) tails containing consecutive U residues in the internal positions, whereas those with consecutive C or G residues were of much lower abundance. Together, we established the first method to be able to comprehensively analyze poly(A) tail 5′-end, internal and 3′-end non-A residues in addition to the length simultaneously, and reveal the first complete mRNA 3′ tail map, providing rich insights into the regulatory roles of poly(A) tails.

Rhythmic post-transcriptional regulation of the circadian clock protein mPER2 in mammalian cells: A real-time analysis

2006 ◽  
Vol 401 (1-2) ◽  
pp. 44-48 ◽  
Author(s):  
Keigo Nishii ◽  
Iori Yamanaka ◽  
Maya Yasuda ◽  
Yota B. Kiyohara ◽  
Yoko Kitayama ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Circadian Clock ◽  
Real Time ◽  
Mammalian Cells ◽  
Time Analysis ◽  
Real Time Analysis ◽  
Post Transcriptional Regulation ◽  
Clock Protein

scholarly journals Post-transcriptional regulation of the content of spermidine/spermine N1-acetyltransferase by N1N12-bis(ethyl)spermine

1995 ◽  
Vol 305 (2) ◽  
pp. 451-458 ◽  
Author(s):  
L Parry ◽  
R Balaña Fouce ◽  
A E Pegg
Keyword(s):  
Transcriptional Regulation ◽  
Half Life ◽  
Mammalian Cells ◽  
Significant Proportion ◽  
Untranslated Regions ◽  
Translation Regulation ◽  
Polyamine Analogues ◽  
Post Transcriptional Regulation ◽  
Rate Limiting ◽  
Ssat Activity

Spermidine/spermine N1-acetyltransferase (SSAT) is the rate-limiting enzyme for the degradation and excretion of polyamines in mammalian cells, and its activity is known to be increased enormously on exposure to polyamines and polyamine analogues. The mechanism by which such an analogue, BESM [N1N12-bis(ethyl)spermine], increases the content of SSAT was investigated by transfecting COS-7 cells with plasmids containing SSAT cDNA in the pEUK expression vector. Despite a large increase in mRNA production, there was only a very small increase in SSAT activity in the transfected cells. When BESM was added at 36 h after transfection, there was a large and very rapid increase in SSAT protein amounting to 380-fold in 12 h without any increase in the mRNA. SSAT protein turned over very rapidly, with a half-life of about 20 min. In the presence of BESM, this turnover was greatly reduced, and the half-life increased to more than 13 h. However, this increase was not sufficient to account for all of the increase in SSAT protein, suggesting that there is also regulation of the translation of the mRNA by BESM. Further evidence for such translation regulation was obtained by studying the polysomal distribution of the SSAT mRNA. In the absence of BESM, most of the mRNA was present in fractions which sedimented more slowly than the monoribosome peak. In BESM-treated cells, a significant proportion of the SSAT mRNA was moved into the small-polysome region of the gradient. The expression of SSAT and the effects of BESM on the polysomal distribution of SSAT mRNA were not affected by the 5′- or 3′-untranslated regions of the mRNA, since constructs which lacked all of these regions gave similar results to constructs containing the entire mRNA sequence. These results show that the increased transcription of the SSAT gene that occurs in the presence of polyamine analogues such as BESM is not sufficient for SSAT expression and that post-transcriptional regulation is critical for the control of SSAT content.

scholarly journals Poly(A) tail length is a major regulator of maternal gene expression during the mammalian oocyte-to-embryo transition

2021 ◽  
Author(s):  
Yusheng Liu ◽  
Hu Nie ◽  
Chuanxin Zhang ◽  
Zhenzhen Hou ◽  
Jiaqiang Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Tail Length ◽  
Human Embryos ◽  
Molecular Evidence ◽  
Translational Efficiency ◽  
Mammalian Oocyte ◽  
Maternal Mrna ◽  
Polyadenylation Sites ◽  
Post Transcriptional Regulation

AbstractTranscription is silent during the mammalian oocyte-to-embryo transition (OET) until zygotic genome activation (ZGA). Therefore, the OET relies on post-transcriptional regulation of maternal mRNA, among which poly(A) tail lengths have been found to regulate translation for a small number of genes1–3. However, transcriptome-wide poly(A) tail length dynamics and their role in gene expression during the mammalian OET remain unknown. Here, we quantified transcriptome-wide mRNA poly(A) tail length dynamics during the mammalian OET using PAIso-seq1 and PAIso-seq24,5, two methods with different underlying principles that preserve the poly(A) tail information. We revealed that poly(A) tail length was highly dynamic during the mouse OET, and Btg4 is responsible for global maternal mRNA deadenylation. We found that the poly(A) tail length positively associated with translational efficiency transcriptome-wide in mouse oocytes. In addition, genes with different alternative polyadenylation isoforms show longer poly(A) tails for isoforms with distal polyadenylation sites compared to those with proximal polyadenylation sites in mouse, rat, pig and human oocytes after meiotic resumption, which is not seen in cultured cell lines. Surprisingly, mammalian embryos, namely mouse, rat, pig, and human embryos, all experience highly conserved global mRNA re-polyadenylation after fertilization, providing molecular evidence that the early embryo development before ZGA is driven by re-polyadenylated maternal mRNAs rather than newly transcribed mRNAs. Together, our study reveals the conserved mRNA poly(A) tail length landscape. This resource can be used for exploring spatiotemporal post-transcriptional regulation throughout the mammalian OET.

scholarly journals Abundant non-A residues in the poly(A) tail orchestrate the mouse oocyte-to-embryo transition

2021 ◽  
Author(s):  
Yusheng Liu ◽  
Hu Nie ◽  
Le-Yun Wang ◽  
Shuang Wu ◽  
Wei Li ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
General Pattern ◽  
Mrna Translation ◽  
Tail Length ◽  
Maternal Rna ◽  
Rna Transcripts ◽  
Maternal Mrna ◽  
Genome Wide ◽  
Post Transcriptional Regulation ◽  
Genome Activation

Non-A (U, G, and C) residues can be added to the 5-end, internal, and 3-end positions of poly(A) tails of RNA transcripts, and some of these have been shown to regulate mRNA stability. The mammalian oocyte-to-embryo transition (OET) relies on post-transcriptional regulation of maternal RNA, because transcription is silent during this process until the point of zygotic genome activation (ZGA). Although the regulation of mRNA translation by poly(A) tail length plays an important role in the mammalian OET, the dynamics and functions of non-A residues in poly(A) tails are completely unknown. In this study, we profiled the genome-wide presence, abundance, and roles of non-A residues during the OET in mice using PAIso-seq1 and PAIso-seq, two complementary methods of poly(A) tail analysis. We found that non-A residues are highly dynamic in maternal mRNA, following a general pattern of beginning to increase at the MII stage, becoming highly abundant after fertilization with U residues in about half of poly(A) tails in 1-cell embryos, and declining in 2-cell embryos. We revealed that Btg4-mediated global maternal mRNA deadenylation created the substrates for U residue addition by Tut4/7 at their 3-ends and further re-polyadenylation. In addition, G residues can be added by Tent4a/b. Finally, we demonstrate that G residues stabilize the modified mRNA, while the U residues mark maternal RNA for faster degradation in 2-cell mouse embryos. Taken together, these findings demonstrate that non-A residues are abundant and re-sculpt the maternal transcriptome to initiate zygotic development, which reveals the functional importance of the post-transcriptional regulation mediated by non-A residues in mRNA poly(A) tails.

scholarly journals Comprehensive Analysis of Wound-inducible Genes from the Nicotiana glutinosa Leaves Using a Full-length cDNA Microarray

10.5109/4677 ◽  
2005 ◽  
Vol 50 (2) ◽  
pp. 635-648
Author(s):  
Yoshiaki Kouzuma ◽  
Yusuke Tsutsumi ◽  
Masumi Abe ◽  
Takeshi Hayashi ◽  
Kazumasa Hada ◽  
...  
Keyword(s):  
Cdna Microarray ◽  
Comprehensive Analysis ◽  
Full Length ◽  
Nicotiana Glutinosa ◽  
Full Length Cdna ◽  
Inducible Genes

scholarly journals Dysregulation of Alternative Splicing was Associated with the Pathogenesis of Ulcerative Colitis

2021 ◽  
Author(s):  
Daowei Li ◽  
Yue Tan
Keyword(s):  
Gene Expression ◽  
Ulcerative Colitis ◽  
Immune Response ◽  
Transcriptional Regulation ◽  
Alternative Splicing ◽  
Comprehensive Analysis ◽  
Tissue Samples ◽  
Aberrant Gene Expression ◽  
Post Transcriptional Regulation ◽  
Aberrant Gene

Abstract Background: Although numerous risk loci of Ulcerative Colitis (UC) in the human genome have been identified, the pathogenesis of UC remains not fully understood. Recently, multiple transcriptomic analyses have shown that aberrant gene expression in UC patients’ colon tissues were associated with the disease progressing. A pioneer study also demonstrated that altered post-transcriptional regulation may be involved in the progression of UC. Methods: Herein, we provided a comprehensive analysis of alternative splicing (AS) signature on UC patients. We analyzed three datasets, which include 74 tissue samples from UC patients in total, and identified over 2,000 significant AS events in these datasets. Results: Skipped Exon (SE) and Alternative first exon (AFE) were found to be the top two significantly altered AS events. Immune response related pathways were significantly enriched. Genes that showed significantly AS events were more likely to be dysregulated at the expression level.Conclusion: Overall, these results suggested that alteration of AS may play crucial roles in the pathogenesis of UC.

scholarly journals Alternative Splicing Regulation of Anthocyanin Biosynthesis in Camellia sinensis var. assamica Unveiled by PacBio Iso-Seq

2020 ◽  
Vol 10 (8) ◽  
pp. 2713-2723
Author(s):  
Lijiao Chen ◽  
Xingyun Shi ◽  
Bo Nian ◽  
Shuangmei Duan ◽  
Bin Jiang ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Alternative Splicing ◽  
Camellia Sinensis ◽  
Anthocyanin Biosynthesis ◽  
Average Length ◽  
Full Length ◽  
Normal Green ◽  
Regulation Mechanisms ◽  
Tea Plants ◽  
Post Transcriptional Regulation

Although the pathway and transcription factor regulation of anthocyanin biosynthesis in tea plants [Camellia sinensis (L.) O. Ktze] are known, post-transcriptional regulation mechanisms involved in anthocyanin accumulation have not been comprehensively studied. We obtained the full-length transcriptome of a purple cultivar (‘Zijuan’) and a normal green cultivar (‘Yunkang 10#) of C. sinensis var. asssamica (Masters) showing different accumulation of anthocyanins and catechins through PacBio isoform sequencing (Iso-Seq). In total, 577,557 mapped full-length cDNAs were obtained, and 2,600 average-length gene isoforms were identified in both cultivars. After gene annotations and pathway predictions, we found that 98 key genes in anthocyanin biosynthesis pathways could have undergone alternative splicing (AS) events, and identified a total of 238 isoforms involved in anthocyanin biosynthesis. We verified expression of the C4H, CHS, FLS, CCOM, F3′5’H, LAR, PAL, CCR, CYP73A13, UDP75L12, UDP78A15/UFGT, UDP94P1, GL3, MYB113, ANR, ANS, F3H, 4CL1, CYP98A3/C3H, CHI, DFR genes and their AS transcripts using qRT-PCR. Correlation analysis of anthocyanin biosynthesis and gene expression results revealed that C4H1, FLS1, PAL2, CCR2, UDP75L122 and MYB113-1 are crucial AS transcripts for regulating anthocyanin biosynthesis in C. sinensis var. assamica. Our results reveal post-transcriptional regulation of anthocyanin biosynthesis in tea plants, and provide more new insights into the regulation of secondary metabolism.

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