TITLE

CTCF-mediated functional chromatin interactome in pluripotent cells

AUTHOR(S)
Handoko, Lusy; Han Xu; Guoliang Li; Chew Yee Ngan; Chew, Elaine; Schnapp, Marie; Lee, Charlie Wah Heng; Chaopeng Ye; Ping, Joanne Lim Hui; Mulawadi, Fabianus; Wong, Eleanor; Jianpeng Sheng; Yubo Zhang; Poh, Thompson; Chee Seng Chan; Kunarso, Galih; Shahab, Atif; Bourque, Guillaume; Cacheux-Rataboul, Valere; Wing-Kin Sung
PUB. DATE
July 2011
SOURCE
Nature Genetics;Jul2011, Vol. 43 Issue 7, p630
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Mammalian genomes are viewed as functional organizations that orchestrate spatial and temporal gene regulation. CTCF, the most characterized insulator-binding protein, has been implicated as a key genome organizer. However, little is known about CTCF-associated higher-order chromatin structures at a global scale. Here we applied chromatin interaction analysis by paired-end tag (ChIA-PET) sequencing to elucidate the CTCF-chromatin interactome in pluripotent cells. From this analysis, we identified 1,480 cis- and 336 trans-interacting loci with high reproducibility and precision. Associating these chromatin interaction loci with their underlying epigenetic states, promoter activities, enhancer binding and nuclear lamina occupancy, we uncovered five distinct chromatin domains that suggest potential new models of CTCF function in chromatin organization and transcriptional control. Specifically, CTCF interactions demarcate chromatin-nuclear membrane attachments and influence proper gene expression through extensive cross-talk between promoters and regulatory elements. This highly complex nuclear organization offers insights toward the unifying principles that govern genome plasticity and function.
ACCESSION #
61898357

 

Related Articles

  • The pluripotent genome in three dimensions is shaped around pluripotency factors. de Wit, Elzo; Bouwman, Britta A. M.; Zhu, Yun; Klous, Petra; Splinter, Erik; Verstegen, Marjon J. A. M.; Krijger, Peter H. L.; Festuccia, Nicola; Nora, Elphège P.; Welling, Maaike; Heard, Edith; Geijsen, Niels; Poot, Raymond A.; Chambers, Ian; de Laat, Wouter // Nature;9/12/2013, Vol. 501 Issue 7466, p227 

    It is becoming increasingly clear that the shape of the genome importantly influences transcription regulation. Pluripotent stem cells such as embryonic stem cells were recently shown to organize their chromosomes into topological domains that are largely invariant between cell types. Here we...

  • In this issue.  // Nature Biotechnology;Aug2011, Vol. 29 Issue 8, pvii 

    The article discusses various reports published within this issue including one on the isolation of pancreatic cell types, one on the assembling of genomic structural variation, and one on genome editing in pluripotent cells.

  • Navigating the epigenetic landscape of pluripotent stem cells. Li, Mo; Liu, Guang-Hui; Belmonte, Juan Carlos Izpisua // Nature Reviews Molecular Cell Biology;Aug2012, Vol. 13 Issue 8, p524 

    Pluripotent stem cells, which include embryonic stem cells and induced pluripotent stem cells, use a complex network of genetic and epigenetic pathways to maintain a delicate balance between self-renewal and multilineage differentiation. Recently developed high-throughput genomic tools greatly...

  • Systematically dissecting the global mechanism of miRNA functions in mouse pluripotent stem cells. Anyou Wang; Qianchuan He; Yan Zhong // BMC Genomics;Jul2015, Vol. 16 Issue 1, p1 

    Background: MicroRNAs (miRNAs) critically modulate stem cell properties like pluripotency, but the fundamental mechanism remains largely unknown. Method: This study systematically analyzes multiple-omics data and builds a systems physical network including genome-wide interactions between miRNAs...

  • Charting histone modifications and the functional organization of mammalian genomes. Zhou, Vicky W.; Goren, Alon; Bernstein, Bradley E. // Nature Reviews Genetics;Jan2011, Vol. 12 Issue 1, p7 

    A succession of technological advances over the past decade have enabled researchers to chart maps of histone modifications and related chromatin structures with increasing accuracy, comprehensiveness and throughput. The resulting data sets highlight the interplay between chromatin and genome...

  • Chromatin Dynamics in Lineage Commitment and Cellular Reprogramming. Shchuka, Virlana M.; Malek-Gilani, Nakisa; Singh, Gurdeep; Langroudi, Lida; Dhaliwal, Navroop K.; Moorthy, Sakthi D.; Davidson, Scott; Macpherson, Neil N.; Mitchell, Jennifer A. // Genes;2015, Vol. 6 Issue 3, p641 

    Dynamic structural properties of chromatin play an essential role in defining cell identity and function. Transcription factors and chromatin modifiers establish and maintain cell states through alteration of DNA accessibility and histone modifications. This activity is focused at both...

  • Stem cells: Chimpanzee induced pluripotent stem cells. Waldron, Denise // Nature Reviews Genetics;Aug2015, Vol. 16 Issue 8, p439 

    The article discusses research being done on pluripotent stem cells from chimpanzees, which reference the study "A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics," by I. G. Romero in the 2015 issue.

  • Tracking the mechanical dynamics of human embryonic stem cell chromatin. Hinde, Elizabeth; Cardarelli, Francesco; Chen, Aaron; Khine, Michelle; Gratton, Enrico // Epigenetics & Chromatin;2012, Vol. 5 Issue 1, p1 

    Background: A plastic chromatin structure has emerged as fundamental to the self-renewal and pluripotent capacity of embryonic stem (ES) cells. Direct measurement of chromatin dynamics in vivo is, however, challenging as high spatiotemporal resolution is required. Here, we present a new...

  • iPSCs: A Minireview from Bench to Bed, including Organoids and the CRISPR System. Orqueda, Andrés Javier; Giménez, Carla Alejandra; Pereyra-Bonnet, Federico // Stem Cells International;1/6/2016, p1 

    When Dolly the sheep was born, the first probe into an adult mammalian genome traveling back in time and generating a whole new animal appeared. Ten years later, the reprogramming process became a defined method of producing induced pluripotent stem cells (iPSCs) through the overexpression of...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics