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Title: The Genomic Sequences Bound to Special AT-rich Sequence-binding Protein 1 (SATB1) In Vivo in Jurkat T Cells Are Tightly Associated with the Nuclear Matrix at the Bases of the Chromatin Loops

Journal Article · · Journal of Cell Biology
 [1];  [1];  [1]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Life Science Division
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Special AT-rich sequence-binding protein 1 (SATB1), a DNA-binding protein expressed predominantly in thymocytes, recognizes an ATC sequence context that consists of a cluster of sequence stretches with well-mixed A's, T's, and C's without G's on one strand. Such regions confer a high propensity for stable base unpairing. Using an in vivo cross-linking strategy, specialized genomic sequences (0.1–1.1 kbp) that bind to SATB1 in human lymphoblastic cell line Jurkat cells were individually isolated and characterized. All in vivo SATB1-binding sequences examined contained typical ATC sequence contexts, with some exhibiting homology to autonomously replicating sequences from the yeast Saccharomyces cerevisiae that function as replication origins in yeast cells. In addition, LINE 1 elements, satellite 2 sequences, and CpG island–containing DNA were identified. To examine the higher-order packaging of these in vivo SATB1-binding sequences, high-resolution in situ fluorescence hybridization was performed with both nuclear “halos” with distended loops and the nuclear matrix after the majority of DNA had been removed by nuclease digestion. In vivo SATB1-binding sequences hybridized to genomic DNA as single spots within the residual nucleus circumscribed by the halo of DNA and remained as single spots in the nuclear matrix, indicating that these sequences are localized at the base of chromatin loops. In human breast cancer SK-BR-3 cells that do not express SATB1, at least one such sequence was found not anchored onto the nuclear matrix. These findings provide the first evidence that a cell type–specific factor such as SATB1 binds to the base of chromatin loops in vivo and suggests that a specific chromatin loop domain structure is involved in T cell–specific gene regulation.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1625109
Journal Information:
Journal of Cell Biology, Vol. 141, Issue 2; ISSN 0021-9525
Publisher:
Rockefeller University PressCopyright Statement
Country of Publication:
United States
Language:
English

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Cited By (24)

Tissue-specific nuclear architecture and gene expession regulated by SATB1 journal April 2003
ALK4 coordinates extracellular and intrinsic signals to regulate development of cortical somatostatin interneurons journal November 2019
Cis -regulation of microRNA expression by scaffold/matrix-attachment regions journal May 2011
Chromatin looping and organization at developmentally regulated gene loci: Chromatin looping and organization during development journal January 2013
15q11-13 GABAA receptor genes are normally biallelically expressed in brain yet are subject to epigenetic dysregulation in autism-spectrum disorders journal March 2007
SATB family chromatin organizers as master regulators of tumor progression journal November 2018
Expression of nuclear matrix proteins binding matrix attachment regions in prostate cancer. PARP-1: New player in tumor progression: MAR-Binding Proteins in Prostate Cancer journal April 2015
Linkages between changes in the 3D organization of the genome and transcription during myotube differentiation in vitro journal April 2017
SATB1 packages densely looped, transcriptionally active chromatin for coordinated expression of cytokine genes journal October 2006
SATB1 targets chromatin remodelling to regulate genes over long distances journal October 2002
ConteXt of change—X inactivation and disease journal December 2009
Satb2 Is a Postmitotic Determinant for Upper-Layer Neuron Specification in the Neocortex journal February 2008
Association of Chromosome Territories with the Nuclear Matrix journal August 1999
PDZ domain-mediated dimerization and homeodomain-directed specificity are required for high-affinity DNA binding by SATB1 journal January 2008
The Scaffold attachment factor b1 (Safb1) regulates myogenic differentiation by facilitating the transition of myogenic gene chromatin from a repressed to an activated state journal April 2013
Loss of Special AT-Rich Binding Protein 1 Expression is a Marker of Poor Survival in Lung Cancer journal July 2011
A comparative study of S/MAR prediction tools journal March 2007
Strand bias structure in mouse DNA gives a glimpse of how chromatin structure affects gene expression journal January 2008
Identification of novel Y chromosome encoded transcripts by testis transcriptome analysis of mice with deletions of the Y chromosome long arm journal December 2005
Correction to: Identification of novel Y chromosome encoded transcripts by testis transcriptome analysis of mice with deletions of the Y chromosome long arm journal August 2019
A Histone Map of Human Chromosome 20q13.12 journal February 2009
Regulation of DNA Replication Timing on Human Chromosome by a Cell-Type Specific DNA Binding Protein SATB1 journal August 2012
Involvement of the SATB1/F-actin complex in chromatin reorganization during active cell death journal March 2014
SATB1 collaborates with loss of p16 in cellular transformation text January 2013

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59 BASIC BIOLOGICAL SCIENCES
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