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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A chromosome-level genome assembly of the giant grouper (Epinephelus lanceolatus) provides insights into its innate immunity and rapid growth.
Zhou Q, Gao H, Zhang Y, Fan G, Xu H, Zhai J, Xu W, Chen Z, Zhang H, Liu S, Niu Y, Li W, Li W, Lin H, Chen S (Mol Ecol Resour. 2019 Jun 22;:)
Giant grouper (Epinephelus lanceolatus) is the largest coral reef teleost, with a native range that spans temperate and tropical-waters in the Pacific and the Indian Oceans. It is artificially cultured and used as a breeding species in aquaculture due to its rapid growth rate. Here we report a giant grouper genome assembled at the chromosome-scale from sequences generated using Illumina HiSeq4000 ......
Specific Contributions of Cohesin-SA1 and Cohesin-SA2 to TADs and Polycomb Domains in Embryonic Stem Cells.
Cuadrado A, Giménez-Llorente D, Kojic A, Rodríguez-Corsino M, Cuartero Y, Martín-Serrano G, Gómez-López G, Marti-Renom MA, Losada A (Cell Rep. 2019 Jun 18;27(12):3500-3510.e4)
Cohesin exists in two variants carrying either STAG/SA1 or SA2. Here we have addressed their specific contributions to the unique spatial organization of the mouse embryonic stem cell genome, which ensures super-enhancer-dependent transcription of pluripotency factors and repression of lineage-specification genes within Polycomb domains. We find that cohesin-SA2 facilitates Polycomb domain compac......
Statistics of chromatin organization during cell differentiation revealed by heterogeneous cross-linked polymers.
Shukron O, Piras V, Noordermeer D, Holcman D (Nat Commun. 2019 Jun 14;10(1):2626)
Chromatin of mammalian nucleus folds into discrete contact enriched regions such as Topologically Associating Domains (TADs). Folding hierarchy and internal organization of TADs is highly dynamic throughout cellular differentiation, and are correlated with gene activation and silencing. To account for multiple interacting TADs, we developed a parsimonious randomly cross-linked (RCL) polymer model ......
The Impact of Centromeres on Spatial Genome Architecture.
Muller H, Gil J, Drinnenberg IA (Trends Genet. 2019 Jun 11;:)
The development of new technologies and experimental techniques is enabling researchers to see what was once unable to be seen. For example, the centromere was first seen as the mediator between spindle fiber and chromosome during mitosis and meiosis. Although this continues to be its most prominent role, we now know that the centromere functions beyond cellular division with important roles in ge......
ZNF143 is a regulator of chromatin loop.
Wen Z, Huang ZT, Zhang R, Peng C (Cell Biol Toxicol. 2018 12;34(6):471-478)
It is known that transcription factor ZNF143 frequently co-binds with CTCF-Cohesin complex in the anchor regions of chromatin loops. However, there is currently no genome-wide experiment to explore the functional roles of ZNF143 in chromatin loops. In this work, we used both computational and experimental analyses to investigate the regulatory effect of ZNF143 on chromatin loops. By jointly analyz......