1,720,968 research outputs found
Regulation of microRNA biogenesis
No full textMicroRNAs (miRNAs)
are small non-coding RNAs that function as guide molecules
in RNA silencing. Targeting most protein-coding transcripts, miRNAs
are involved in nearly all
developmental and pathological processes in animals. The biogenesis of miRNAs
is under
tight temporal and spatial control, and their dysregulation is associated with many human
diseases, particularly cancer. In animals, miRNAs
are ~22 nucleotides in length, and they are
produced by two RNase III proteins — Drosha and Dicer. miRNA biogenesis is regulated at
multiple levels, including at the level of miRNA transcription; its processing by Drosha and
Dicer in the nucleus and cytoplasm, respectively; its modification by RNA editing, RNA
methylation, uridylation and adenylation; Argonaute loading; and RNA decay. Non-canonical
pathways for miRNA biogenesis, including those that are independent of Drosha or Dicer,
are also emerging.1135614331sciescopu
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
TUT7 controls the fate of precursor microRNAs by using three different uridylation mechanisms
No full textTerminal uridylyl transferases (TUTs) function as integral regulators of microRNA (miRNA) biogenesis. Using biochemistry, single-molecule, and deep sequencing techniques, we here investigate the mechanism by which human TUT7 (also known as ZCCHC6) recognizes and uridylates precursor miRNAs (pre-miRNAs) in the absence of Lin28. We find that the overhang of a pre-miRNA is the key structural element that is recognized by TUT7 and its paralogues, TUT4 (ZCCHC11) and TUT2 (GLD2/PAPD4). For group II pre-miRNAs, which have a 1-nt 3′ overhang, TUT7 restores the canonical end structure (2-nt 3′ overhang) through mono-uridylation, thereby promoting miRNA biogenesis. For pre-miRNAs where the 3′ end is further recessed into the stem (as in 3′ trimmed pre-miRNAs), TUT7 generates an oligo-U tail that leads to degradation. In contrast to Lin28-stimulated oligo-uridylation, which is processive, a distributive mode is employed by TUT7 for both mono- and oligo-uridylation in the absence of Lin28. The overhang length dictates the frequency (but not duration) of the TUT7-RNA interaction, thus explaining how TUT7 differentiates pre-miRNA species with different overhangs. Our study reveals dual roles and mechanisms of uridylation in repair and removal of defective pre-miRNAs. Synopsis Uridylation of miRNA precursors can either stimulate processing or trigger RNA degradation. This study shows how RNA overhang structure and the mode of TUTase binding facilitate differential uridylation of specific precursor types. Terminal uridylyl transferases (TUTs) exert multiple roles in miRNA biogenesis by uridylating precursor miRNAs, thereby determining their fates. For group II pre-miRNAs, which carry a 1-nt 3′ overhang, TUT7/4/2 restore the canonical end structure through mono-uridylation, promoting miRNA biogenesis. For 3′ trimmed pre-miRNAs, TUT7/4 distributively generate an oligo-U tail that triggers degradation. TUT7 distinguishes pre-miRNA species at the binding step and shows distinct binding frequency to different RNA substrates. Uridylation of miRNA precursors can either stimulate processing or trigger RNA degradation. This study shows how RNA overhang structure and the mode of TUTase binding facilitate differential uridylation of specific precursor types. © 2015 The Authors. Published under the terms of the CC BY 4.0 license122251sciescopu
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
LIN28A Is a Suppressor of ER-Associated Translation in Embryonic Stem Cells
No full textLIN28 plays a critical role in developmental transition, glucose metabolism, and tumorigenesis. At the molecular level, LIN28 is known to repress maturation of let-7 microRNAs and enhance translation of certain mRNAs. In this study, we obtain a genome-wide view of the molecular function of LIN28A in mouse embryonic stem cells by carrying out RNA crosslinking-immunoprecipitation-sequencing (CLIP-seq) and ribosome footprinting. We find that, in addition to let-7 precursors, LIN28A binds to a large number of spliced mRNAs. LIN28A recognizes AAGNNG, AAGNG, and less frequently UGUG, which are located in the terminal loop of a small hairpin. LIN28A is localized to the periendo-plasmic reticulum (ER) area and inhibits translation of mRNAs that are destined for the ER, reducing the synthesis of transmembrane proteins, ER or Golgi lumen proteins, and secretory proteins. Our study suggests a selective regulatory mechanism for ER-associated translation and reveals an unexpected role of LIN28A as a global suppressor of genes in the secretory pathway.11211111sciescopu
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
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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