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Repetitive sequences and chromatin accessibility can confound scoring of chromatin immunoprecipitation data generated by high–throughput sequencing. Using data sets they produce for human RNA polymerase II and the transcription factor STAT1, Rozowsky et al. compensate for these biases by correcting for 'mappability' and normalizing the data against an input–DNA control.

This overview of the ENCODE project outlines the data accumulated so far, revealing that 80% of the human genome now has at least one biochemical function assigned to it; the newly identified functional elements should aid the interpretation of results of genome-wide association studies, as many correspond to sites of association with human disease.

Using variants from the 1000 Genomes Project, RNA-seq and ChIP-seq data from related projects, this study describes a resource and survey of allele-specific binding and gene expression. A catalogue of allelic SNPs and annotation elements is available as an online resource at alleledb.gersteinlab.org.

The authors summarize the data produced by phase III of the Encyclopedia of DNA Elements (ENCODE) project, a resource for better understanding of the human and mouse genomes.

The next step after sequencing a genome is to figure out how the cell actually uses it as an instruction manual. A large international consortium has examined 1% of the genome for what part is transcribed, where proteins are bound, what the chromatin structure looks like, and how the sequence compares to that of other organisms.

A description is given of the ENCODE consortium’s efforts to examine the principles of human transcriptional regulatory networks; the results are integrated with other genomic information to form a hierarchical meta-network where different levels have distinct properties.

A description is given of the ENCODE effort to provide a complete catalogue of primary and processed RNAs found either in specific subcellular compartments or throughout the cell, revealing that three-quarters of the human genome can be transcribed, and providing a wealth of information on the range and levels of expression, localization, processing fates and modifications of known and previously unannotated RNAs.

Uniform processing and detailed annotation of human, worm and fly RNA-sequencing data reveal ancient, conserved features of the transcriptome, shared co-expression modules (many enriched in developmental genes), matched expression patterns across development and similar extent of non-canonical, non-coding transcription; furthermore, the data are used to create a single, universal model to predict gene-expression levels for all three organisms from chromatin features at the promoter.

Supervised machine-learning models trained using Drosophila epigenetic and STARR-seq data can be transferred to predict mouse and human enhancers.

ENCODE is a resource comprising thousands of functional genomic datasets. Here, the authors present custom annotation within ENCODE for cancer, highlighting a workflow that can help prioritise key elements in oncogenesis.

Extracellular miRNAs are present in a variety of bodily fluids. Here, Freedman et al. analysed plasma-derived RNA by RNA-seq from 40 people followed by targeted RT-qPCR in an additional 2,763 people, and report over 1,000 extracellular RNAs including microRNAs, piwi-interacting RNA and small nucleolar RNAs.

A genome-wide association study including over 76,000 individuals with schizophrenia and over 243,000 control individuals identifies common variant associations at 287 genomic loci, and further fine-mapping analyses highlight the importance of genes involved in synaptic processes.

Most of the human genome consists of non-protein-coding DNA. This article describes the progress made in annotating this non-coding portion of the genome by combining data from comparative and functional genomics analyses.

A map of genome-wide binding locations of 165 human, 93 worm and 52 fly transcription-regulatory factors (almost 50% presented for the first time) from diverse cell types, developmental stages, or conditions reveals that gene-regulatory properties previously observed for individual factors may be general principles of metazoan regulation that are well preserved.

A full understanding of the biology and function of the numerous cell types that comprise the nervous system requires analysis of their transcriptional and translational profiles. In this Review article, the authors discuss the methods for overcoming the challenges that accompany the collection of large proteomic datasets and their integration with other data modalities.

The Impact of Genomic Variation on Function Consortium is combining single-cell mapping, genomic perturbations and predictive modelling to investigate relationships between human genomic variation, genome function and phenotypes and will provide an open resource to the community.

The authors summarize the history of the ENCODE Project, the achievements of ENCODE 1 and ENCODE 2, and how the new data generated and analysed in ENCODE 3 complement the previous phases.

The RGASP consortium compared 25 RNA-seq analysis programs in their ability to identify exons, reconstruct transcripts and quantify expression levels. Assembly of isoforms and their expression levels in higher eukaryotes remains a challenge.