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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3C and 3C-based techniques: the powerful tools for spatial genome organization deciphering.
Han J, Zhang Z, Wang K (Mol Cytogenet. 2018;11:21)
It is well known that the chromosomes are organized in the nucleus and this spatial arrangement of genome play a crucial role in gene regulation and genome stability. Different techniques have been developed and applied to uncover the intrinsic mechanism of genome architecture, especially the chromosome conformation capture (3C) and 3C-derived methods. 3C and 3C-derived techniques provide us appro......
Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci.
Amaral PP, Leonardi T, Han N, Viré E, Gascoigne DK, Arias-Carrasco R, Büscher M, Pandolfini L, Zhang A, Pluchino S, Maracaja-Coutinho V, Nakaya HI, Hemberg M, Shiekhattar R, Enright AJ, Kouzar... (Genome Biol. 2018 Mar 15;19(1):32)
BACKGROUND: The mammalian genome is transcribed into large numbers of long noncoding RNAs (lncRNAs), but the definition of functional lncRNA groups has proven difficult, partly due to their low sequence conservation and lack of identified shared properties. Here we consider promoter conservation and positional conservation as indicators of functional commonality....
Protein-mediated loops in supercoiled DNA create large topological domains.
Yan Y, Ding Y, Leng F, Dunlap D, Finzi L (Nucleic Acids Res. 2018 Mar 10;:)
Supercoiling can alter the form and base pairing of the double helix and directly impact protein binding. More indirectly, changes in protein binding and the stress of supercoiling also influence the thermodynamic stability of regulatory, protein-mediated loops and shift the equilibria of fundamental DNA/chromatin transactions. For example, supercoiling affects the hierarchical organization and fu......
Evidence for a second ankylosing spondylitis-associated RUNX3 regulatory polymorphism.
Vecellio M, Cortes A, Roberts AR, Ellis J, Cohen CJ, Knight JC, Brown MA, Bowness P, Wordsworth BP (RMD Open. 2018;4(1):e000628)
Objectives: To explore the functions of RUNX3 single nucleotide polymorphisms (SNPs) associated with ankylosing spondylitis (AS)....
Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries.
Gong Y, Lazaris C, Sakellaropoulos T, Lozano A, Kambadur P, Ntziachristos P, Aifantis I, Tsirigos A (Nat Commun. 2018 02 07;9(1):542)
The metazoan genome is compartmentalized in areas of highly interacting chromatin known as topologically associating domains (TADs). TADs are demarcated by boundaries mostly conserved across cell types and even across species. However, a genome-wide characterization of TAD boundary strength in mammals is still lacking. In this study, we first use fused two-dimensional lasso as a machine learning m......