1,720,969 research outputs found
TAIL-seq: Genome-wide determination of poly(A) tail length and 3' end modifications
No full textGlobal investigation of the 30 extremity of mRNA (30-terminome), despite its importance in gene regulation,has not been feasible due to technical challenges associated with homopolymeric sequences
and relative paucity of mRNA. We here develop a method, TAIL-seq, to sequence the very end of
mRNA molecules. TAIL-seq allows us to measure poly(A) tail length at the genomic scale. Median poly(A) length is 50–100 nt in HeLa and NIH 3T3 cells. Poly(A) length correlates with mRNA half-life,
but not with translational efficiency. Surprisingly, we discover widespread uridylation and guanylation at the downstream of poly(A) tail. The U tails are generally attached to short poly(A) tails (40 nt), implicating their generic roles in mRNA stability control. TAIL-seq is a potent tool to dissect dynamic control of mRNA turnover and translational control, and to discover unforeseen features of RNA cleavage and tailing.11011101sciescopu
Mixed tailing by TENT4A and TENT4B shields mRNA from rapid deadlation
No full textRNA tails play integral roles in the regulation of messenger RNA (mRNA) translation and decay. Guanylation of the poly(A) tail was discovered recently, yet the enzymology and function remain obscure. Here we identify TENT4A (PAPD7) and TENT4B (PAPD5) as the enzymes responsible for mRNA guanylation. Purified TENT4 proteins generate amixed poly(A) tail with intermittent non-adenosine residues, the most common of which is guanosine. A single guanosine residue is sufficient to impede the deadenylase CCR4-NOT complex, which trims the tail and exposes guanosine at the 3' end. Consistently, depletion of TENT4A and TENT4B leads to a decrease in mRNA half-life and abundance in cells. Thus, TENT4A and TENT4B produce a mixed tail that shields mRNA from rapid deadenylation. Our study unveils the role of mixed tailing and expands the complexity of posttranscriptional gene regulation
MTAIL-seq reveals dynamic poly(A) tail regulation in oocyte-to-embryo development
No full textEukaryotic mRNAs are subject to multiple types of tailing that critically influence mRNA stability and translatability. To investigate RNA tails at the genomic scale, we previously developed TAIL-seq, but its low sensitivity precluded its application to biological materials of minute quantity. In this study, we report a new version of TAIL-seq (mRNA TAIL-seq [mTAIL-seq]) with enhanced sequencing depth for mRNAs (by ~1000-fold compared with the previous version). The improved method allows us to investigate the regulation of poly(A) tails in Drosophila oocytes and embryos. We found that maternal mRNAs are polyadenylated mainly during late oogenesis, prior to fertilization, and that further modulation occurs upon egg activation. Wispy, a noncanonical poly(A) polymerase, adenylates the vast majority of maternal mRNAs, with a few intriguing exceptions such as ribosomal protein transcripts. By comparing mTAIL-seq data with ribosome profiling data, we found a strong coupling between poly(A) tail length and translational efficiency during egg activation. Our data suggest that regulation of poly(A) tails in oocytes shapes the translatomic landscape of embryos, thereby directing the onset of animal development. By virtue of the high sensitivity, low cost, technical robustness, and broad accessibility, mTAIL-seq will be a potent tool to improve our understanding of mRNA tailing in diverse biological systems. © 2016 Lim et al122221sciescopu
Uridylation by TUT4 and TUT7 marks mRNA for degradation
No full textUridylation occurs pervasively on mRNAs, yet its
mechanism and significance remain unknown. By
applying TAIL-seq, we identify TUT4 and TUT7
(TUT4/7), also known as ZCCHC11 and ZCCHC6,
respectively, as mRNA uridylation enzymes. Uridylation
readily occurs on deadenylated mRNAs in cells.
Consistently, purified TUT4/7 selectively recognize
and uridylate RNAs with short A-tails (less than
25 nt) in vitro. PABPC1 antagonizes uridylation of
polyadenylated mRNAs, contributing to the specificity
for short A-tails. In cells depleted of TUT4/7,
the vast majority of mRNAs lose the oligo-U-tails,
and their half-lives are extended. Suppression of
mRNA decay factors leads to the accumulation of
oligo-uridylated mRNAs. In line with this, microRNA
induces uridylation of its targets, and TUT4/7 are
required for enhanced decay of microRNA targets.
Our study explains the mechanism underlying
selective uridylation of deadenylated mRNAs and
demonstrates a fundamental role of oligo-U-tail as
a molecular mark for global mRNA decay.170701sciescopu
Mono-Uridylation of Pre-MicroRNA as a Key Step in the Biogenesis of Group II let-7 MicroRNAs
No full textRNase III Drosha initiates microRNA (miRNA) maturation by cleaving a primary miRNA transcript and releasing a pre-miRNA with a 2 nt 3` overhang. Dicer recognizes the 2 nt 3` overhang structure to selectively process pre-miRNAs. Here, we find that, unlike prototypic pre-miRNAs #group I#, group II pre-miRNAs acquire a shorter #1 nt# 3` overhang from Drosha processing and therefore require a 3`-end mono-uridylation for Dicer processing. The majority of let-7 and miR-105 belong to group II. We identify TUT7/ZCCHC6, TUT4/ZCCHC11, and TUT2/PAPD4/GLD2 as the terminal uridylyl transferases responsible for pre-miRNA mono-uridylation. The TUTs act specifically on dsRNAs with a 1 nt 3` overhang, thereby creating a 2 nt 3` overhang. Depletion of TUTs reduces let-7 levels and disrupts let-7 function. Although the let-7 suppressor, Lin28, induces inhibitory oligo-uridylation in embryonic stem cells, mono-uridylation occurs in somatic cells lacking Lin28 to promote let-7 biogenesis. Our study reveals functional duality of uridylation and introduces TUT7/4/2 as components of the miRNA biogenesis pathway.12812911sciescopu
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
진핵생물의 전령RNA 꼬리에 관한 전사체 수준의 연구
Full text link학위논문 (박사)-- 서울대학교 대학원 : 생명과학부, 2016. 8. 김빛내리.Eukaryotic mRNA is subject to intensive post-transcriptional modifications, which critically influences mRNA stability and translatability. Newly synthesized mRNA acquires a 7-methlyguanosine cap at the 5′ end and polyadenosine tail at the 3′ end. In addition to such canonical modifications, recent studies have revealed untemplated nucleotide additions such as U-tail and G-tail, base modifications including N6-methyladenosine and pseudouridylation, and A-to-I editing, as epitranscriptomic signatures of mRNA.
To investigate RNA tailing at the genomic scale, I recently developed a method called TAIL-seq which accurately measures poly(A) tail length and 3′ end modifications. Interestingly, I discovered that mammalian cells carried median 50–100 nt of poly(A) tail and widespread uridylation and guanylation at the downstream of poly(A) tail. Moreover, U-tails were mainly found on short poly(A) tails (<~25 nt), implicating its role in mRNA turnover.
Uridylation has been observed on mRNAs in various species, yet its mechanism and significance remained unknown. By applying TAIL-seq, I identify TUT4 and TUT7 (TUT4/7), also known as ZCCHC11 and ZCCHC6, respectively, as mRNA uridylation enzymes in mammals. Uridylation readily occurs on deadenylated mRNAs in cells. Consistently, purified TUT4/7 selectively recognize and uridylate RNAs with short A tails (<~25 nt) in vitro. Moreover, PABPC1 antagonizes uridylation of polyadenylated mRNAs, contributing to the specificity for short A. In cells depleted of TUT4/7, the vast majority of mRNAs lose the oligo-U tails, and their half-lives are extended. Suppression of mRNA decay factors leads to the accumulation of oligo-uridylated mRNAs. In line with this, microRNA induces uridylation of its targets, and TUT4/7 are required for enhanced decay of microRNA targets. My study explains the mechanism underlying selective uridylation of deadenylated mRNAs, and demonstrates a fundamental role of oligo-U-tail as a molecular mark for global mRNA decay.
Next, I report a new version of TAIL-seq (mRNA TAIL-seq or mTAIL-seq), which increases sequencing depth for mRNAs by ~1,000 fold compared to the previous version. Original version of TAIL-seq provided a various information, but its low sensitivity precluded its application to minute amounts of biological materials. With the improved method, I investigate the regulation of poly(A) tail in Drosophila oocytes and embryos. I find that maternal mRNAs are polyadenylated mainly during late oogenesis, prior to fertilization, and further modulated upon egg activation. Wispy, a noncanonical poly(A) polymerase, adenylates most maternal mRNAs with a few intriguing exceptions such as ribosomal protein transcripts. By comparing mTAIL-seq data to ribosome profiling data, I further find a strong coupling between poly(A) tail length and translational efficiency during egg activation. My data suggest that regulation of poly(A) tail in oocytes shapes the translatomic landscape of embryos, thereby directing the onset of animal development. By virtue of the high sensitivity, low cost, technical robustness, and broad accessibility, mTAIL-seq will be a potent tool to improve our understanding of mRNA tailing.
Taken together, I investigated mRNA tailings in eukaryotes by using sequencing methods that I developed, TAIL-seq and mTAIL-seq, and found their roles in the control of mRNA stability and translation.1 Introduction 1
1.1 Life cycle of mRNA 1
1.2 mRNA tailing in eukaryotes 1
1.3 TAIL-seq: Transcriptome-wide determination of poly(A) tail length and 3′ end modification 4
2 Uridylation marks mRNA for degradation 9
2.1 Background 9
2.2 Results 12
2.2.1 TUT4 and TUT7 catalyze mRNA uridylation 12
2.2.2 TUT4/7 selectively oligo-uridylate mRNAs with short A tails in vivo and in vitro 21
2.2.3 PABP suppresses uridylation of poly(A)+mRNA 29
2.2.4 Uridylation facilitates global mRNA decay 29
2.2.5 Uridylation is involved in miRNA-induced gene silencing 34
2.2.6 mRNA decay factors remove uridylated mRNAs 39
2.3 Discussion 44
2.4 Methods and Materials 48
3 In-depth profiling of poly(A) tail length by mTAIL-seq 99
3.1 Background 99
3.2 Results 101
3.2.1 mTAIL-seq: a solution for limited materials 101
3.2.2 Global poly(A) tail length measurement in Drosophila 111
3.2.3 Distinct patterns of poly(A) tail regulation 121
3.2.4 Correlation between poly(A) tail length and translational efficiency 131
3.3 Discussion 136
3.4 Methods and Materials 139
4 Conclusion 157
Summary (in Korean) 159
Bibliography 161Docto
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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