The novel SAR‐binding domain of scaffold attachment factor A (SAF‐A) is a target in apoptotic nuclear breakdown

The scaffold attachment factor A (SAF‐A) is an abundant component of the nuclear scaffold and of chromatin, and also occurs in heterogeneous nuclear ribonucleoprotein (hnRNP) complexes. Evidence from previous experiments had suggested that SAF‐A most likely has at least two different functions, being involved both in nuclear architecture and RNA metabolism. We now show that the protein has a novel scaffold‐associated region (SAR)‐specific bipartite DNA‐binding domain which is independent from the previously identified RNA‐binding domain, the RGG box. During apoptosis, but not during necrosis, SAF‐A is cleaved in a caspase‐dependent way. Cleavage occurs within the bipartite DNA‐binding domain, resulting in a loss of DNA‐binding activity and a concomitant detachment of SAF–A from nuclear structural sites. On the other hand, cleavage does not compromise the association of SAF‐A with hnRNP complexes, indicating that the function of SAF‐A in RNA metabolism is not affected in apoptosis. Our results suggest that detachment of SAF–A from SARs, caused by apoptotic proteolysis of its DNA‐binding domain, is linked to the formation of oligonucleosomal‐sized DNA fragments and could therefore contribute to nuclear breakdown in apoptotic cells.

[1]  P. Angeli,et al.  Hepatitis C virus related cirrhosis decreased as indication to liver transplantation since the introduction of direct-acting antivirals: A single-center study , 2018, World journal of gastroenterology.

[2]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[3]  F. O. Fackelmayer,et al.  The scaffold/matrix attachment region binding protein hnRNP-U (SAF-A) is directly bound to chromosomal DNA in vivo: a chemical cross-linking study. , 1997, Biochemistry.

[4]  P. Nicotera,et al.  Intracellular Adenosine Triphosphate (ATP) Concentration: A Switch in the Decision Between Apoptosis and Necrosis , 1997, The Journal of experimental medicine.

[5]  R. van Driel,et al.  Major internal nuclear matrix proteins are common to different human cell types , 1997, Journal of cellular biochemistry.

[6]  P. Krammer,et al.  The CD95 system and the death of a lymphocyte. , 1997, Seminars in immunology.

[7]  A. Martelli,et al.  Association of nuclear matrix proteins with granular and threaded nuclear bodies in cell lines undergoing apoptosis. , 1997, Experimental cell research.

[8]  T. Jenuwein,et al.  Extension of chromatin accessibility by nuclear matrix attachment regions , 1997, Nature.

[9]  E. Alnemri,et al.  Heteronuclear Ribonucleoproteins C1 and C2, Components of the Spliceosome, Are Specific Targets of Interleukin 1β-converting Enzyme-like Proteases in Apoptosis* , 1996, The Journal of Biological Chemistry.

[10]  T. Nakajima,et al.  Degradation of Topoisomerase IIα during Adenovirus E1A-induced Apoptosis Is Mediated by the Activation of the Ubiquitin Proteolysis System* , 1996, The Journal of Biological Chemistry.

[11]  B. Humbel,et al.  hnRNP proteins and B23 are the major proteins of the internal nuclear matrix of HeLa S3 cells , 1996, Journal of cellular biochemistry.

[12]  Malmqvist,et al.  Epitope Mapping by Label-Free Biomolecular Interaction Analysis , 1996, Methods.

[13]  D. Agard,et al.  Specific interactions of chromatin with the nuclear envelope: positional determination within the nucleus in Drosophila melanogaster. , 1996, Molecular biology of the cell.

[14]  H. Hsu,et al.  Dynamic changes of NuMA during the cell cycle and possible appearance of a truncated form of NuMA during apoptosis. , 1996, Journal of cell science.

[15]  J. Yanagisawa,et al.  A matrix attachment region (MAR)-binding activity due to a p114 kilodalton protein is found only in human breast carcinomas and not in normal and benign breast disease tissues. , 1996, Cancer research.

[16]  U. K. Laemmli,et al.  SARs are cis DNA elements of chromosome dynamics: Synthesis of a SAR repressor protein , 1995, Cell.

[17]  S. Orrenius,et al.  Cellular events in Fas/APO-1-mediated apoptosis in JURKAT T lymphocytes. , 1995, Experimental cell research.

[18]  Y. Lazebnik,et al.  Characterization of the execution phase of apoptosis in vitro using extracts from condemned-phase cells , 1995, Journal of Cell Science.

[19]  T. Kohwi-Shigematsu,et al.  Nucleolin is a matrix attachment region DNA-binding protein that specifically recognizes a region with high base-unpairing potential , 1995, Molecular and cellular biology.

[20]  F. O. Fackelmayer,et al.  Purification of two isoforms of hnRNP-U and characterization of their nucleic acid binding activity. , 1994, Biochemistry.

[21]  F. Buck,et al.  Chicken MAR binding protein p120 is identical to human heterogeneous nuclear ribonucleoprotein (hnRNP) U. , 1994, Nucleic acids research.

[22]  F. O. Fackelmayer,et al.  Nucleic-acid-binding properties of hnRNP-U/SAF-A, a nuclear-matrix protein which binds DNA and RNA in vivo and in vitro. , 1994, European journal of biochemistry.

[23]  M. S. Patil,et al.  Characterisation of two intronic nuclear-matrix-attachment regions in the human DNA topoisomerase I gene. , 1994, European journal of biochemistry.

[24]  U. K. Laemmli,et al.  Metaphase chromosome structure: Bands arise from a differential folding path of the highly AT-rich scaffold , 1994, Cell.

[25]  X. M. Sun,et al.  Changes in nuclear chromatin precede internucleosomal DNA cleavage in the induction of apoptosis by etoposide. , 1994, Biochemical pharmacology.

[26]  K. Zhao,et al.  SAR‐dependent mobilization of histone H1 by HMG‐I/Y in vitro: HMG‐I/Y is enriched in H1‐depleted chromatin. , 1993, The EMBO journal.

[27]  T. Yasuda,et al.  Identification and characterization of a nuclear scaffold protein that binds the matrix attachment region DNA. , 1993, The Journal of biological chemistry.

[28]  J. Lawrence,et al.  Higher level organization of individual gene transcription and RNA splicing. , 1993, Science.

[29]  L. Jong,et al.  Binding of matrix attachment regions to lamin B1 , 1992, Cell.

[30]  F. O. Fackelmayer,et al.  Characterization of SAF‐A, a novel nuclear DNA binding protein from HeLa cells with high affinity for nuclear matrix/scaffold attachment DNA elements. , 1992, The EMBO journal.

[31]  X. M. Sun,et al.  Key morphological features of apoptosis may occur in the absence of internucleosomal DNA fragmentation. , 1992, The Biochemical journal.

[32]  Y. Kohwi,et al.  A tissue-specific MAR SAR DNA-binding protein with unusual binding site recognition , 1992, Cell.

[33]  G. Dreyfuss,et al.  Primary structure and binding activity of the hnRNP U protein: binding RNA through RGG box. , 1992, The EMBO journal.

[34]  U. K. Laemmli,et al.  In vivo topoisomerase II cleavage of the Drosophila histone and satellite III repeats: DNA sequence and structural characteristics. , 1992, The EMBO journal.

[35]  R. Berezney,et al.  A comprehensive study on the isolation and characterization of the HeLa S3 nuclear matrix. , 1991, Journal of cell science.

[36]  S. Adam,et al.  Nuclear protein import in permeabilized mammalian cells requires soluble cytoplasmic factors , 1990, The Journal of cell biology.

[37]  C. Got,et al.  Supragenic loop organization: mapping in Drosophila embryos, of scaffold-associated regions on a 800 kilobase DNA continuum cloned from the 14B-15B first chromosome region , 1990, Nucleic Acids Res..

[38]  P. Walker,et al.  Periodicity of DNA folding in higher order chromatin structures. , 1990, The EMBO journal.

[39]  J. Nickerson,et al.  Core filaments of the nuclear matrix , 1990, The Journal of cell biology.

[40]  U. K. Laemmli,et al.  Highly preferential nucleation of histone H1 assembly on scaffold-associated regions. , 1989, Journal of molecular biology.

[41]  U. K. Laemmli,et al.  Preferential, cooperative binding of DNA topoisomerase II to scaffold‐associated regions. , 1989, The EMBO journal.

[42]  A. E. Sippel,et al.  A nuclear DNA attachment element mediates elevated and position-independent gene activity , 1989, Nature.

[43]  U. K. Laemmli,et al.  The metaphase scaffold is helically folded: Sister chromatids have predominantly opposite helical handedness , 1988, Cell.

[44]  E. Zuckerkandl,et al.  Generation of high specificity of effect through low‐specificity binding of proteins to DNA , 1988, FEBS letters.

[45]  U. K. Laemmli,et al.  Cohabitation of scaffold binding regions with upstream/enhancer elements of three developmentally regulated genes of D. melanogaster , 1986, Cell.

[46]  S. Penman,et al.  The nonchromatin substructures of the nucleus: the ribonucleoprotein (RNP)-containing and RNP-depleted matrices analyzed by sequential fractionation and resinless section electron microscopy , 1986, The Journal of cell biology.

[47]  P. Cockerill,et al.  Chromosomal loop anchorage of the kappa immunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites , 1986, Cell.

[48]  G. Dreyfuss,et al.  Isolation of the heterogeneous nuclear RNA-ribonucleoprotein complex (hnRNP): a unique supramolecular assembly. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[49]  U. K. Laemmli,et al.  Organization of the higher-order chromatin loop: specific DNA attachment sites on nuclear scaffold , 1984, Cell.

[50]  G. Dreyfuss,et al.  Characterization of heterogeneous nuclear RNA-protein complexes in vivo with monoclonal antibodies , 1984, Molecular and cellular biology.

[51]  D. Wessel,et al.  A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. , 1984, Analytical biochemistry.

[52]  B. Vogelstein,et al.  Supercoiled loops and eucaryotic DNA replication , 1980, Cell.

[53]  H. Towbin,et al.  Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: procedure and some applications. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[54]  R. Hancock.  Interphase chromosomal deoxyribonucleoprotein isolated as a discrete structure from cultured cells. , 1974, Journal of molecular biology.

[55]  U. K. Laemmli,et al.  Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4 , 1970, Nature.

[56]  F. O. Fackelmayer,et al.  Purification and molecular cloning of the scaffold attachment factor B (SAF-B), a novel human nuclear protein that specifically binds to S/MAR-DNA. , 1996, Nucleic acids research.

[57]  T. Schlake,et al.  Scaffold/matrix-attached regions: topological switches with multiple regulatory functions. , 1996, Critical reviews in eukaryotic gene expression.

[58]  P. Walker,et al.  Degradation of nuclear matrix and DNA cleavage in apoptotic thymocytes. , 1996, Journal of cell science.

[59]  B. Rost.  PHD: predicting one-dimensional protein structure by profile-based neural networks. , 1996, Methods in enzymology.

[60]  R. Berezney,et al.  The nuclear matrix: a structural milieu for genomic function. , 1995, International review of cytology.

[61]  B. Blencowe,et al.  The architectural organization of nuclear metabolism. , 1995, International review of cytology.

[62]  C. Burd,et al.  hnRNP proteins and the biogenesis of mRNA. , 1993, Annual review of biochemistry.

[63]  U. K. Laemmli,et al.  Scaffold-associated regions: cis-acting determinants of chromatin structural loops and functional domains. , 1992, Current opinion in genetics & development.

[64]  W. Garrard.  Chromosomal Loop Organization in Eukaryotic Genomes , 1990 .

[65]  E. Harlow,et al.  Antibodies: A Laboratory Manual , 1988 .

[66]  M. Uhlén,et al.  A gene fusion system for generating antibodies against short peptides. , 1987, Gene.

[67]  Susan M. Gasser,et al.  A glimpse at chromosomal order , 1987 .