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Open AccessJournal ArticleDOI

Nuclear m(6)A Reader YTHDC1 Regulates mRNA Splicing.

TLDR
The findings provide the direct evidence that m(6)A reader YTHDC1 regulates mRNA splicing through recruiting and modulating pre-mRNA splicing factors for their access to the binding regions of targeted mRNAs.
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This article is published in Molecular Cell.The article was published on 2016-02-18 and is currently open access. It has received 1244 citations till now. The article focuses on the topics: RNA Splicing Factors & Exonic splicing enhancer.

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Citations
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Dynamic RNA Modifications in Gene Expression Regulation

TL;DR: Roles for mRNA modification in nearly every aspect of the mRNA life cycle, as well as in various cellular, developmental, and disease processes are revealed.
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Post-transcriptional gene regulation by mRNA modifications

TL;DR: N6-adenosine methylation directs mRNAs to distinct fates by grouping them for differential processing, translation and decay in processes such as cell differentiation, embryonic development and stress responses.
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Reading, writing and erasing mRNA methylation.

TL;DR: New and emerging methods to characterize and quantify the epitranscriptome are reviewed, and new concepts — in some cases, controversies — are discussed regarding the authors' understanding of the mechanisms and functions of m6A readers, writers and erasers are discussed.
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m 6 A RNA methylation promotes XIST -mediated transcriptional repression

TL;DR: The long non-coding RNA X-inactive specific transcript (XIST) mediates the transcriptional silencing of genes on the X chromosome and is highly methylated with at least 78 N6-methyladenosine (m6A) residues, revealing a pathway of m6A formation and recognition required for XIST-mediated transcriptional repression.
References
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Journal ArticleDOI

Fast and accurate short read alignment with Burrows–Wheeler transform

TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
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Trimmomatic: a flexible trimmer for Illumina sequence data

TL;DR: Timmomatic is developed as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data and is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested.
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Cutadapt removes adapter sequences from high-throughput sequencing reads

TL;DR: The command-line tool cutadapt is developed, which supports 454, Illumina and SOLiD (color space) data, offers two adapter trimming algorithms, and has other useful features.
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BEDTools: a flexible suite of utilities for comparing genomic features

TL;DR: A new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format, which allows the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks.
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HTSeq—a Python framework to work with high-throughput sequencing data

TL;DR: This work presents HTSeq, a Python library to facilitate the rapid development of custom scripts for high-throughput sequencing data analysis, and presents htseq-count, a tool developed with HTSequ that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes.
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