Previous research efforts have advanced our understanding of specific chromosomal events, such as DNA transcription,replication, recombination, partitioning, and epigenetic modification. One of the major future challenges in chromosome biology will be to provide an overall framework of how these individual activities are orchestrated and coordinated to maximize their effects in a variety of biological processes that evolve over time.
OpenLooper (OLP) collects genome-wide data on chromatin structures investigated by various high-throughput experimental assays, such as Hi-C, ChIA-PET, ChIP-seq, and RNA-seq. Simultaneously, OLP provides a platform that supports opening and sharing high-throughput sequencing datasets.
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Nuclear receptor HNF4A transrepresses CLOCK:BMAL1 and modulates tissue-specific circadian networks.
Qu M, Duffy T, Hirota T, Kay SA (Proc Natl Acad Sci U S A. 2018 Dec 10;:)
Either expression level or transcriptional activity of various nuclear receptors (NRs) have been demonstrated to be under circadian control. With a few exceptions, little is known about the roles of NRs as direct regulators of the circadian circuitry. Here we show that the nuclear receptor HNF4A strongly transrepresses the transcriptional activity of the CLOCK:BMAL1 heterodimer. We define a centra......
Dense neural networks for predicting chromatin conformation.
Farré P, Heurteau A, Cuvier O, Emberly E (BMC Bioinformatics. 2018 Oct 11;19(1):372)
BACKGROUND: DNA inside eukaryotic cells wraps around histones to form the 11nm chromatin fiber that can further fold into higher-order DNA loops, which may depend on the binding of architectural factors. Predicting how the DNA will fold given a distribution of bound factors, here viewed as a type of sequence, is currently an unsolved problem and several heterogeneous polymer models have shown that......
GrapHi-C: graph-based visualization of Hi-C datasets.
MacKay K, Kusalik A, Eskiw CH (BMC Res Notes. 2018 Jun 29;11(1):418)
OBJECTIVES: Hi-C is a proximity-based ligation reaction used to detect regions of the genome that are close in 3D space (or "interacting"). Typically, results from Hi-C experiments (contact maps) are visualized as heatmaps or Circos plots. While informative, these visualizations do not directly represent genomic structure and folding, making the interpretation of the underlying 3D genomic organiza......
Integration of human adipocyte chromosomal interactions with adipose gene expression prioritizes obesity-related genes from GWAS.
Pan DZ, Garske KM, Alvarez M, Bhagat YV, Boocock J, Nikkola E, Miao Z, Raulerson CK, Cantor RM, Civelek M, Glastonbury CA, Small KS, Boehnke M, Lusis AJ, Sinsheimer JS, Mohlke KL, Laakso M, Paju... (Nat Commun. 2018 04 17;9(1):1512)
Increased adiposity is a hallmark of obesity and overweight, which affect 2.2 billion people world-wide. Understanding the genetic and molecular mechanisms that underlie obesity-related phenotypes can help to improve treatment options and drug development. Here we perform promoter Capture Hi-C in human adipocytes to investigate interactions between gene promoters and distal elements as a transcrip......
A comprehensive map coupling histone modifications with gene regulation in adult dopaminergic and serotonergic neurons.
Södersten E, Toskas K, Rraklli V, Tiklova K, Björklund ÅK, Ringnér M, Perlmann T, Holmberg J (Nat Commun. 2018 03 26;9(1):1226)
The brain is composed of hundreds of different neuronal subtypes, which largely retain their identity throughout the lifespan of the organism. The mechanisms governing this stability are not fully understood, partly due to the diversity and limited size of clinically relevant neuronal populations, which constitute a technical challenge for analysis. Here, using a strategy that allows for ChIP-seq ......