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PRC2 binds active promoters and contacts nascent RNAs in embryonic stem cells

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TLDR
Using in vivo RNA-protein cross-linking, it is shown that EZH2 directly binds the 5′ region of nascent RNAs transcribed from a subset of these promoters and that these binding events correlate with decreased H3K27me3.
Abstract
Polycomb repressive complex 2 (PRC2) acts as an epigenetic repressor by depositing repressive H3K27me3 marks, but how it is regulated and directed to specific genes remains unknown PRC2 is now found to bind at low levels to many gene promoters, including active ones devoid of H3K27me3, and the EZH2 catalytic subunit binds directly to nascent transcripts

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RNA-binding proteins in pluripotency, differentiation, and reprogramming

TL;DR: This work reviews the current studies on RBPs and focuses on those that have functional implications in pluripotency, differentiation, and/or reprogramming in both the human and mouse systems.
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Methylome-wide Sequencing Detects DNA Hypermethylation Distinguishing Indolent from Aggressive Prostate Cancer

TL;DR: This compendium of methylation changes reveals crucial molecular distinctions between indolent and aggressive prostate cancer, and extensive, focal hypermethylation regions unique to high-grade disease.
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'Oming in on RNA-protein interactions.

TL;DR: With recent advances in technology, together with powerful combined experimental and computational developments, the authors have witnessed unprecedented new insights into the diverse and dynamic interactions that occur between RNA and proteins.
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Long non-coding RNAs in hematological malignancies: translating basic techniques into diagnostic and therapeutic strategies.

TL;DR: The utility and advancement of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system as gene-editing tools are envisioned to facilitate the molecular dissection of lncRNAs via different knock-in/out strategies.
References
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Journal ArticleDOI

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.

TL;DR: By following this protocol, investigators are able to gain an in-depth understanding of the biological themes in lists of genes that are enriched in genome-scale studies.
Journal ArticleDOI

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

TL;DR: Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches and can be used simultaneously to achieve even greater alignment speeds.
Journal ArticleDOI

Model-based Analysis of ChIP-Seq (MACS)

TL;DR: This work presents Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer, and uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions.
Journal ArticleDOI

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

TL;DR: It is demonstrated in macrophages and B cells that collaborative interactions of the common factor PU.1 with small sets of macrophage- or B cell lineage-determining transcription factors establish cell-specific binding sites that are associated with the majority of promoter-distal H3K4me1-marked genomic regions.
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