SummaryAs the premier model organism in biomedical research, the laboratory mouse shares the majority of protein-coding genes with humans, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications, and replication domains throughout the mouse genome in diverse cell and tissue types. By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of other sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization. Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases.

Summary The three-dimensional configuration of DNA is integral to all nuclear processes in eukaryotes, yet our knowledge of the chromosome architecture is still limited. Genome-wide chromosome conformation capture studies have uncovered features of chromatin organization in cultured cells, but genome architecture in human tissues has yet to be explored. Here, we report the most comprehensive survey to date of chromatin organization in human tissues. Through integrative analysis of chromatin contact maps in 21 primary human tissues and cell types, we found topologically associating domains highly conserved in different tissues. We also discover genomic regions that exhibit unusually high levels of local chromatin interactions. These frequently interacting regions (FIREs) are enriched for super-enhancers and are near tissue-specifically expressed genes. They display strong tissue-specificity in local chromatin interactions. Additionally, FIRE formation is partially dependent on CTCF and the Cohesin complex. We further show that FIREs can help annotate function of non-coding sequence variants.

SummaryUnderstanding the diversity of human tissues is fundamental to disease and requires linking genetic information, which is identical in most of an individual’s cells, with epigenetic mechanisms that could play tissue-specific roles. Surveys of DNA methylation in human tissues have established a complex landscape including both tissue-specific and invariant methylation patterns1,2. Here we report high coverage methylomes that catalogue cytosine methylation in all contexts for the major human organ systems, integrated with matched transcriptomes and genomic sequence. By combining these diverse data types with each individuals’ phased genome3, we identified widespread tissue-specific differential CG methylation (mCG), partially methylated domains, allele-specific methylation and transcription, and the unexpected presence of non-CG methylation (mCH) in almost all human tissues. mCH correlated with tissue-specific functions, and using this mark, we made novel predictions of genes that escape X-chromosome inactivation in specific tissues. Overall, DNA methylation in multiple genomic contexts varies substantially among human tissues.

In Drosophila, the neuropeptide pigment-dispersing factor (PDF) is required to maintain behavioral rhythms under constant conditions. To understand how PDF exerts its influence, we performed time-series immunostainings for the PERIOD protein in normal and pdf mutant flies over 9 d of constant conditions. Without pdf, pacemaker neurons that normally express PDF maintained two markers of rhythms: that of PERIOD nuclear translocation and its protein staining intensity. As a group, however, they displayed a gradual dispersion in their phasing of nuclear translocation. A separate group of non-PDF circadian pacemakers also maintained PERIOD nuclear translocation rhythms without pdf but exhibited altered phase and amplitude of PERIOD staining intensity. Therefore, pdf is not required to maintain circadian protein oscillations under constant conditions; however, it is required to coordinate the phase and amplitude of such rhythms among the diverse pacemakers. These observations begin to outline the hierarchy of circadian pacemaker circuitry in the Drosophila brain.Key words: pigment-dispersing factor; circadian rhythm; Drosophila; lateral neurons; nuclear accumulation; period IntroductionThe organizing principles for the neuronal networks underlying circadian oscillations are essentially unknown. Which cells are the critical oscillators for particular output functions, what is their hierarchical organization, and how are synchronizing signals coordinated among pacemaker groups to provide coherent circadian output? In the Drosophila brain, ϳ100 pacemaker neurons are defined by expression of period ( per) and other genes essential for circadian rhythmicity (Kaneko and Hall, 2000). These clock cells are divided into the lateral (LN) and dorsal (DN) neural groups (Helfrich-Förster, 2003). Mosaic analysis suggests that LNs, but not DNs, are necessary to establish locomotor rhythms (Frisch et al., 1994;Vosshall and Young, 1995). LNs are segregated into distinct dorsal (LN d ) and ventral (LN v ) groups; the latter is divided into small and large subgroups. The LN v clock neurons express the neuropeptide pigment-dispersing factor ( pdf ) (Helfrich-Förster, 1998). Genetic ablation of the entire LN v group produces a syndrome similar to that observed in pdf 01 mutant flies (Renn et al., 1999). Such flies anticipate light-to-dark transition events but are phase advanced; in constant darkness, ϳ70% lose their locomotor rhythms, and the remainder display only weak rhythms.The rhythmic nature of single pacemaker cells has traditionally been ascribed to individual cell properties (Michel et al., 1993;Welsh et al., 1995;Liu et al., 1997;Herzog et al., 1998). Recent evidence, however, suggests that interneuronal communication may be required to sustain basic molecular rhythms.Manipulations that alter pacemaker membrane excitability or disrupt transmitter signaling between pacemakers result in severe dampening of molecular rhythms (Harmar et al., 2002;Nitabach et al., 2002;Colwell et al., 2003;Lee et al., 2003). Likewise, Peng et al. (...

Although the similarities between humans and mice are typically highlighted, morphologically and genetically, there are many differences. To better understand these two species on a molecular level, we performed a comparison of the expression profiles of 15 tissues by deep RNA sequencing and examined the similarities and differences in the transcriptome for both protein-coding and -noncoding transcripts. Although commonalities are evident in the expression of tissue-specific genes between the two species, the expression for many sets of genes was found to be more similar in different tissues within the same species than between species. These findings were further corroborated by associated epigenetic histone mark analyses. We also find that many noncoding transcripts are expressed at a low level and are not detectable at appreciable levels across individuals. Moreover, the majority lack obvious sequence homologs between species, even when we restrict our attention to those which are most highly reproducible across biological replicates. Overall, our results indicate that there is considerable RNA expression diversity between humans and mice, well beyond what was described previously, likely reflecting the fundamental physiological differences between these two organisms.transcriptome | epigenome | species comparison | noncoding transcripts T he mouse has served as a valuable model organism for human biology and disease. It is widely assumed that biochemical, cellular, and developmental pathways in the mouse are highly conserved with humans and that many processes are clearly preserved at a molecular and genetic level. Moreover, recent detailed studies have examined gene expression in a limited number of tissues in humans and mice. These studies have indicated that gene expression is often conserved and is more similar between the comparable tissues of different organisms rather than within tissues of the same organism. In contrast, the transcript isoform repertoire was found to be markedly different between species (1, 2). Gene Expression Is More Similar Among Tissues Within a Species Than Between Corresponding Tissues of the Two SpeciesTo examine the similarities between humans and mice in much greater detail, we produced RNA-seq data from 13 human tissues [as part of the Encyclopedia Of DNA Elements (ENCODE)], another 11 human tissues [as part of the Roadmap Epigenomics Mapping Consortium (REMC) (3)], and 13 mouse tissues (for mouse ENCODE). We also included in our analysis other data from mouse ENCODE and the Illumina Human BodyMap 2.0 (HBM) (SI Materials and Methods). Sequencing was performed to a depth of 11,313,824-166,188,101 mappable reads (median of 68,399,538 with and an interquartile range of 31,557,836,199). In total, our analysis used 93 datasets encompassing the most tissue-diverse RNA-seq dataset to date spanning several major projects. Thirteen of the mouse and human orthologous datasets were produced by the same laboratory. For our analysis regarding noncoding transcripts, we incorporated an ad...