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Common fragile sites (CFSs) correspond to chromosomal regions susceptible to present breaks, discontinuities or constrictions in metaphase chromosomes from cells subjected to replication stress. They are considered as genomic regions intrinsically difficult to replicate and they are evolutionary conserved at least in mammals. However, the recent discovery that CFSs are cell-type specific indicates that DNA sequence by itself cannot account for CFS instability. Nevertheless, the large gene FHIT that includes FRA3B, the most highly expressed CFS in human lymphocytes, is commonly deleted in a variety of tumors suggesting a tumor suppressor role for its product. Here, we report that the epicenter of fragility of Fra14A2/Fhit, the mouse ortholog of human FRA3B/FHIT that like its human counterpart is the most highly expressed CFS in mouse lymphocytes, is largely attached to the nuclear matrix compartment in naive B lymphocytes but not in primary hepatocytes or cortical neurons that do not express such a CFS. Our results suggest a structural explanation for the difficult-to-replicate nature of such a region and so for its common fragility in lymphocytes, that is independent of the possible tumor suppressor role of the gene harboring such CFS.

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The aim of this study was to perform a proteomic analysis to isolate and identify proteins from the swine sperm nuclear matrix to contribute to a database of swine sperm nuclear proteins. We used pre-chilled diluted semen from seven boars (19 to 24 week old) from the commercial lineLandrace x Large Whitex Pietran. The semen was processed to separate the sperm heads and extract the chromatin and nuclear matrix for protein quantification and analysis by mass spectrometry, by LTQ Orbitrap ELITE Mass spectrometer (Thermo-Finnigan) coupled to a nanoflow chromatography system (LC-MS/MS). We identified 222 different proteins in the sample; a total of 159 (71.6%) were previously described as present in the somatic or sperm nuclei of other species, 41 (18.5%) did not have a previously reported nuclear presence and 22(9.9%) had not been characterized. The most abundant family of proteins corresponded to ribosomal (13.1%), followed by cytoskeleton (12.2%), uncharacterized (9.9%), histones (5.4%), proteasome subunits (3.6%)and heat shock (1.8%). The other proteins clustered in other families accounted for 54% of the total proteins. The protein isolation of the nuclear matrix of the swine spermatozoa was satisfactory, thus demonstrating that the protocol used was efficient. Several proteins were identified and described. However, it was not possible to identify some protein structures. Therefore,this study helps to establish a starting point for future proteomic studies comparing fertile and sub-fertile animals.

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The aim of this study was to perform a proteomic analysis to isolate and identify proteins from the swine sperm nuclear matrix to contribute to a database of swine sperm nuclear proteins. We used pre-chilled diluted semen from seven boars (19 to 24 week old) from the commercial lineLandrace x Large Whitex Pietran. The semen was processed to separate the sperm heads and extract the chromatin and nuclear matrix for protein quantification and analysis by mass spectrometry, by LTQ Orbitrap ELITE Mass spectrometer (Thermo-Finnigan) coupled to a nanoflow chromatography system (LC-MS/MS). We identified 222 different proteins in the sample; a total of 159 (71.6%) were previously described as present in the somatic or sperm nuclei of other species, 41 (18.5%) did not have a previously reported nuclear presence and 22(9.9%) had not been characterized. The most abundant family of proteins corresponded to ribosomal (13.1%), followed by cytoskeleton (12.2%), uncharacterized (9.9%), histones (5.4%), proteasome subunits (3.6%)and heat shock (1.8%). The other proteins clustered in other families accounted for 54% of the total proteins. The protein isolation of the nuclear matrix of the swine spermatozoa was satisfactory, thus demonstrating that the protocol used was efficient. Several proteins were identified and described. However, it was not possible to identify some protein structures. Therefore,this study helps to establish a starting point for future proteomic studies comparing fertile and sub-fertile animals.(AU)

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Classical observations have shown that during the interphase the chromosomal DNA of metazoans is organized in supercoiled loops attached to a compartment known as the nuclear matrix (NM). Fragments of chromosomal DNA able to bind the isolated NM in vitro are known as matrix associated/attachment/addressed regions or MARs. No specific consensus sequence or motif has been found that may constitute a universal, defining feature of MARs. On the other hand, high-salt resistant DNA-NM interactions in situ define true DNA loop anchorage regions or LARs, that might correspond to a subset of the potential MARs but are not necessarily identical to MARs characterized in vitro, since there are several examples of MARs able to bind the NM in vitro but which are not actually bound to the NM in situ. In the present work we assayed the capacity of two LARs, as well as of shorter fragments within such LARs, for binding to the NM in vitro. Paradoxically the isolated (≈2 kb) LARs cannot bind to the NM in vitro while their shorter (≈300 pb) sub-fragments and other non-related but equally short DNA fragments, bind to the NM in a high-salt resistant fashion. Our results suggest that the ability of a given DNA fragment for binding to the NM in vitro primarily depends on the length of the fragment, suggesting that binding to the NM is modulated by the local topology of the DNA fragment in suspension that it is known to depend on the DNA length. J. Cell. Biochem. 118: 4487-4497, 2017. © 2017 Wiley Periodicals, Inc.

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During the interphase the nuclear DNA of metazoan cells is organized in supercoiled loops anchored to constituents of a nuclear substructure or compartment known as the nuclear matrix. The stable interactions between DNA and the nuclear matrix (NM) correspond to a set of topological relationships that define a nuclear higher-order structure (NHOS). Current evidence suggests that the NHOS is cell-type-specific. Biophysical evidence and theoretical models suggest that thermodynamic and structural constraints drive the actualization of DNA-NM interactions. However, if the topological relationships between DNA and the NM were the subject of any biological constraint with functional significance then they must be adaptive and thus be positively selected by natural selection and they should be reasonably conserved, at least within closely related species. We carried out a coarse-grained, comparative evaluation of the DNA-NM topological relationships in primary hepatocytes from two closely related mammals: rat and mouse, by determining the relative position to the NM of a limited set of target sequences corresponding to highly-conserved genomic regions that also represent a sample of distinct chromosome territories within the interphase nucleus. Our results indicate that the pattern of topological relationships between DNA and the NM is not conserved between the hepatocytes of the two closely related species, suggesting that the NHOS, like the karyotype, is species-specific.

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In metazoans, nuclear DNA is organized during the interphase in negatively supercoiled loops anchored to a compartment or substructure known as the nuclear matrix. The interactions between DNA and the nuclear matrix (NM) are of higher affinity than those between DNA and chromatin proteins since the last ones do not resist the procedures for extracting the NM. The structural interactions DNA-NM constitute a set of topological relationships that define a nuclear higher order structure (NHOS) although there are further higher order levels of organization within the nucleus. So far, the evidence derived from studies with primary hepatocytes and naïve B lymphocytes indicates that the NHOS is cell-type specific at the local and at the large-scale level, and so it has been suggested that such NHOS is primary determined by structural and thermodynamic constraints. We carried out a comparative characterization of the NHOS of postmitotic cortical neurons with that of hepatocytes and naïve B lymphocytes. Our results indicate that the NHOS of neurons is completely different at the large scale and at the local level from that one observed in hepatocytes or in naïve B lymphocytes, confirming on the one hand that the set of structural DNA-NM interactions is cell-type specific and supporting, on the other hand the notion that structural constraints that impinge on chromosomal DNA and the NM are more important for determining this NHOS than functional constraints related to replication and/or transcription. J. Cell. Biochem. 118: 2151-2160, 2017. © 2016 Wiley Periodicals, Inc.

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Dentre os diversos tipos de câncer agressivos, o câncer de mama é o mais comum em mulheres. Mutações hereditárias e adquiridas, assim como alterações epigenéticas atuam em sinergia na carcinogênese mamária e na progressão tumoral. A proteína P53 é uma supressora de tumor e possui uma atuação fundamental na integridade genômica. Apesar do vasto conhecimento sobre o controle da P53 a nível de proteína, ainda pouco se sabe sobre o controle transcricional do gene TP53. A série 21T, uma série de 4 linhagens celulares originadas da mama da mesma paciente, representando diferentes estágios de progressão tumoral mamária, é um eficiente modelo para investigação das alterações epigenéticas e suas influências na expressão gênica ao longo da progressão do câncer de mama. Nós analisamos a organização do domínio do gene TP53 através da técnica de arranjo de DNA, em diversas linhagens celulares de câncer de mama e linhagens controle, e realizamos uma tentativa de caracterizar estes elementos de DNA nas linhagens controle não-tumorais HB2 e MCF10A e nas tumorais MCF-7, MDA-MB-231, T47D, através dos marcadores epigenéticos de eucromatina, H4Ac, e heterocromatina, H3K9me3. Ainda analisamos a ligação de proteínas à região associada à matriz nuclear (MAR), denominada MAR 2, e a possível ligação da proteína ligante à matriz nuclear (MARBP), PARP-1, através de ensaios de gel shift (EMSA). Detectamos que na linhagem controle epitelial mamária, HB2, o gene TP53 está posicionado num domínio de DNA relativamente pequeno, aproximadamente 50 kb, delimitado por dois sítios de fixação à matriz nuclear. Interessantemente, esta estrutura de domínio se apresentou radicalmente diferente nas linhagens de câncer de mama estudadas, MCF7, T47D, MDA-MB-231 e BT474, nos quais o tamanho do domínio estudado estava aumentado e a transcrição do TP53 diminuída...

Breast cancer is the most common aggressive cancer type in women. Inherited and acquired mutations as well as epigenetic alterations act together in breast carcinogenesis and tumor progression. P53 is a tumor suppressor protein critical for genome integrity. Although its control at the protein level is well known, the transcriptional regulation of the TP53 gene is still unclear. The 21T series, a series of 4 breast cell lines originating from the same patient and representative of the breast tumor progression stages, is a suitable model to investigate epigenetic alterations and their influences upon gene expression during breast tumor progression. We have analyzed the organization of the TP53 gene domain using DNA arrays in several breast cancer and control cell lines and we made an attempt to characterize these DNA elements in breast non-cancerous cell lines HB2 and MCF-10, and cancerous MCF-7, MDA-MB-231 and T47D, through the determination of epigenetic markers of euchromatin, H4Ac, and heterochromatin, H3K9me3. We further analyzed the matrix attachment region (MAR), named MAR 2, protein binding, and possible MAR 2 binding of the important MAR binding protein (MARBP), PARP-1, by Electrophoretic mobility Shift Assay (EMSA). We have found that in the control breast epithelial cell line, HB2, the TP53 gene is positioned within a relatively small DNA domain, encompassing 50 kb, delimited by two nuclear matrix attachment sites. Interestingly, this domain structure was found to be radically different in the studied breast cancer cell lines, MCF7, T47D, MDA-MB-231 and BT474, in which the domain size was increased and TP53 transcription was decreased...

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Há algumas décadas, pensava-se que espermatozoides maduros possuíssem uma cromatina não funcional, inerte, sem a capacidade de transcrição. Acreditava-se que a matriz nuclear não existisse e que a presença de histonas no núcleo seria um erro no processo de compactação cromatínica, o que poderia interferir na fertilidade do macho. Hoje se sabe que, entre as estruturas toroidais, unidades básicas da cromatina espermática altamente compactada, há algumas poucas regiões que contêm sequências de nucleossomos, e estas geralmente estão anexadas a uma matriz nuclear proteica. Os espermatozoides possuem cromatina altamente organizada e são condutores metabolicamente funcionais do genoma masculino, carreando RNAs de diferentes tipos, os quais, tanto quanto os nucleossomos, são importantes sinalizadores epigenéticos paternos e, logo,influenciam o desenvolvimento embrionário inicial. Portanto, alterações cromatínicas podem não somente interferir no processo de fecundação, como principalmente no desenvolvimento embrionário, o que reforça a necessidade da análise da cromatina na avaliação de reprodutores machos.

Decades ago, it was thought thatspermatozoa had a chromatin nonfunctional, inert, without the abilityto transcription. It was believed in the absence of nuclear matrix and the presence of the core histones would be an error in the chromatin packaging, which could interfere with male fertility. Today we know that between thetoroidal structures, basic units of highly compacted sperm chromatin, there are a few regions containing nucleosome sequences, these usually being attached to a nuclear protein matrix. The sperm chromatin is highly organized and is metabolically functional carrier of male genome, carrying different RNA types, which, along with the nucleosomes are important paternal epigenetic signaling, and influencing early embryonic development. Therefore, chromatin alterations not only interfere with the fertilization process, but also influencethe embryonic development, which reinforces the need for chromatin analysis in the evaluation of breeding males.

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Há algumas décadas, pensava-se que espermatozoides maduros possuíssem uma cromatina não funcional, inerte, sem a capacidade de transcrição. Acreditava-se que a matriz nuclear não existisse e que a presença de histonas no núcleo seria um erro no processo de compactação cromatínica, o que poderia interferir na fertilidade do macho. Hoje se sabe que, entre as estruturas toroidais, unidades básicas da cromatina espermática altamente compactada, há algumas poucas regiões que contêm sequências de nucleossomos, e estas geralmente estão anexadas a uma matriz nuclear proteica. Os espermatozoides possuem cromatina altamente organizada e são condutores metabolicamente funcionais do genoma masculino, carreando RNAs de diferentes tipos, os quais, tanto quanto os nucleossomos, são importantes sinalizadores epigenéticos paternos e, logo,influenciam o desenvolvimento embrionário inicial. Portanto, alterações cromatínicas podem não somente interferir no processo de fecundação, como principalmente no desenvolvimento embrionário, o que reforça a necessidade da análise da cromatina na avaliação de reprodutores machos.(AU)

Decades ago, it was thought thatspermatozoa had a chromatin nonfunctional, inert, without the abilityto transcription. It was believed in the absence of nuclear matrix and the presence of the core histones would be an error in the chromatin packaging, which could interfere with male fertility. Today we know that between thetoroidal structures, basic units of highly compacted sperm chromatin, there are a few regions containing nucleosome sequences, these usually being attached to a nuclear protein matrix. The sperm chromatin is highly organized and is metabolically functional carrier of male genome, carrying different RNA types, which, along with the nucleosomes are important paternal epigenetic signaling, and influencing early embryonic development. Therefore, chromatin alterations not only interfere with the fertilization process, but also influencethe embryonic development, which reinforces the need for chromatin analysis in the evaluation of breeding males.(AU)

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In the interphase nucleus of metazoan cells DNA is organized in supercoiled loops anchored to a nuclear matrix (NM). DNA loops are operationally classified in structural and facultative. Varied evidence indicates that DNA replication occurs in replication foci organized upon the NM and that structural DNA loops may correspond to the replicons in vivo. In normal rat liver the hepatocytes are arrested in G0 but synchronously re-enter the cell cycle after partial-hepatectomy leading to liver regeneration. Using this model we have previously determined that the DNA loops corresponding to a gene-rich genomic region move in a sequential fashion towards the NM during replication and then return to their original configuration in newly quiescent cells, once liver regeneration has been achieved. In the present work we determined the organization into structural DNA loops of a gene-poor region centered on c-myc and tracked-down its movement at the peak of S phase and after the return to cellular quiescence during and after liver regeneration. The results confirmed that looped DNA moves towards the NM during replication but in this case the configuration of the gene-poor region into DNA loops becomes reorganized and after replication only the loop containing c-myc resembles the original in the control G0 hepatocytes. Our results suggest that the local chromatin configuration around potentially active genes constraints the formation of specific structural DNA loops after DNA replication, while in non-coding regions the structural DNA loops are only loosely determined after DNA replication by structural constraints that modulate the DNA-NM interactions.

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In the interphase nucleus of metazoan cells the DNA is organized in supercoiled loops anchored to a nuclear matrix (NM). The DNA is anchored by non-coding sequences known as MARs, in situ operationally classified in structural-constitutive and transient-functional. We have previously shown that the organization of the multi-gene rat-albumin family locus into structural DNA loops is remarkably different between primary hepatocytes, where such genes are expressed, and naïve B lymphocytes, where such genes are not expressed. These results together with previous observations from other authors suggested that the local organization into structural DNA loops might determine the potential for a gene to be expressed or not. Thus in the present work we determined the organization of the Fyn locus, a single large transcriptional unit, into structural DNA loops in both primary rat hepatocytes and B lymphocytes. Our results indicate that the organization of the Fyn locus in structural DNA loops is cell type-specific and yet the gene is expressed in both cell types, supporting the notion that in vivo the organization of DNA into structural loops is primarily determined by factors independent of transcription but also that transcription adapts to work upon radically different structural DNA loop organizations.

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In the interphase nucleus of metazoan cells the DNA is organized in supercoiled loops anchored to a proteinaceous substructure known as the nuclear matrix (NM). The DNA is anchored to the NM by means of non-coding sequences of variable length known as matrix attachment regions or MARs operationally classified in structural-constitutive, resistant to high-salt extraction and transient-functional, non-resistant to high-salt extraction. The former are also known as true loop attachment regions or LARs that determine structural DNA loops. The DNA-NM interactions define a higher order structure within the cell nucleus (NHOS). We studied in a comparative fashion the NHOS in two primary cell types from the rat: hepatocytes and naive B lymphocytes, by analyzing the topological relationships between the NM and a set of eight short gene sequences located in six separate chromosomes and as such representing a coarse-grained, large-scale sample of the actual organization of nuclear DNA into structural loop domains. Our results indicate that such an organization is cell-type specific since most of the gene sequences studied showed significant differences in their relative position to the NM according to cell type. Such cell-type specific differences in the NHOS have no obvious correlation with the tissue-specific transcriptional activity of the corresponding genes, supporting the notion that permanent, structural DNA loops are different from transient, functional DNA loops that may be associated with transcription.

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Studies of chromatin extensibility have revealed the flow of chromatin and DNA from cell nuclei and chromosomes in response to gravity or mechanical stretch following lysis by hypertonic saline and detergent solutions. Since this phenomenon was first reported, the technical methods by which extended chromatin fibers (ECFs) may be analyzed have been improved. These methods include topochemical assays, fluorescence in situ hybridization, immunofluorescence, electron microscopy, and polarization microscopy. Chromatin and DNA "halos" also have been studied in materials subjected to lysis, especially in a horizontal position or after cytocentrifugation. The analysis of ECF formation is useful not only as a tool for detecting the positioning of certain DNA signals on chromatin filaments, but also for describing diverse DNA-protein associations that may be related to varying transcriptional activities and chromatin supraorganization. A brief review of the methods and applications of ECF formation is presented here. We focus on light microscopy studies of ECF formation in mouse hepatocytes under different chromatin supraorganization and physiological conditions and in sperm cells with different DNA-protein complexes.

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In the mammalian liver the quiescent primary hepatocytes preserve a proliferating potential in vivo, yet natural aging correlates with loss of proliferating potential and progression towards terminal differentiation of the hepatocytes. Thus aged, terminally-differentiated hepatocytes may survive in a de facto post-mitotic state, similarly to early post-mitotic cells, like neurons, suggesting that there might be a common factor linking both cellular states. In the interphase of metazoan cells the nuclear DNA is organized in supercoiled loops anchored to a proteinaceous substructure known as the nuclear matrix (NM). The DNA-NM interactions define a higher-order structure in the cell nucleus (NHOS). Natural aging of the rat liver correlates with a progressive strengthening of the NM framework and the stabilization of the DNA-NM interactions in the hepatocytes indicating that the NHOS becomes highly stable with age. We compared the NHOS of post-mitotic rat neurons with that of aged rat hepatocytes. Our results indicate that a very stable NHOS is a common feature of both aged and post-mitotic cells in vivo.

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Transcribed sequences have been suggested to be associated with the nuclear matrix, differing from non-transcribing sequences, which have been reported to be contained in DNA loops. However, although a dozen of genes have their expression level affected by aging, data on chromatin-nuclear matrix interactions under this physiological condition are still scarce. In the present study, liver imprints from young, adult and old mice were subjected to FISH (fluorescence in situ hybridization) for 45S rDNA and telomeric sequences, with or without a lysis treatment to produce extended chromatin fibres. There was an increased amount of 45S rDNA sequences located in DNA loops as the animals grow older, while telomeric sequences were always observed in DNA loops irrespective of the animal age. We assume that active rRNA genes associate with the nuclear matrix, while DNA loops contain silent sequences. Transcription of each 45S rDNA repeat unit is suggested to be dependent on its interaction with the nuclear matrix.

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NeuN is an antigen detected in the nucleus of neurons in a wide range of vertebrates and so it is widely used as a tool for detecting neuronal cells. NeuN has been recently identified as Fox-3, a new member of the Fox-1 gene family of splicing factors. The predominant localization of NeuN/Fox-3 to neuronal nuclei and its role in splicing pose the question of the nuclear compartmentalization of such a protein. Here we provide evidence that NeuN/Fox-3 is an intrinsic component of the neuronal nuclear matrix and a reliable marker of nuclear speckles in neurons.

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1alpha,25-dihydroxy vitamin D(3) (vitamin D(3)) has an important role during osteoblast differentiation as it directly modulates the expression of key bone-related genes. Vitamin D(3) binds to the vitamin D(3) receptor (VDR), a member of the superfamily of nuclear receptors, which in turn interacts with transcriptional activators to target this regulatory complex to specific sequence elements within gene promoters. Increasing evidence demonstrates that the architectural organization of the genome and regulatory proteins within the eukaryotic nucleus support gene expression in a physiological manner. Previous reports indicated that the VDR exhibits a punctate nuclear distribution that is significantly enhanced in cells grown in the presence of vitamin D(3). Here, we demonstrate that in osteoblastic cells, the VDR binds to the nuclear matrix in a vitamin D(3)-dependent manner. This interaction of VDR with the nuclear matrix occurs rapidly after vitamin D(3) addition and does not require a functional VDR DNA-binding domain. Importantly, nuclear matrix-bound VDR colocalizes with its transcriptional coactivator DRIP205/TRAP220/MED1 which is also matrix bound. Together these results indicate that after ligand stimulation the VDR rapidly enters the nucleus and associates with the nuclear matrix preceding vitamin D(3)-transcriptional upregulation.

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The function of dystrophin Dp71 in neuronal cells remains unknown. To approach this issue, we have selected the PC12 neuronal cell line. These cells express both a Dp71f cytoplasmic variant and a Dp71d nuclear isoform. In this study, we demonstrated by electron and confocal microscopy analyses of in situ nuclear matrices and Western blotting evaluation of cell extracts that Dp71d associates with the nuclear matrix. Interestingly, this binding is modulated during NGF-induced neuronal differentiation of PC12 cells with a twofold increment in the differentiated cells, compared to control cells. Also, distribution of Dp71d along the periphery of the nuclear matrix observed in the undifferentiated cells is replaced by intense fluorescent foci localized in the center of the nucleoskeletal structure. In summary, we revealed that Dp71d is a dynamic component of nuclear matrix that might participate in the nuclear modeling occurring during neuronal differentiation.

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The incorporation of exogenous fatty acids bound to L-FABP into nuclei was studied. Rat liver cell nuclei and nuclear matrices (membrane depleted nuclei) were incubated in vitro with [1-(14)C]18:0 and 20:4n-6 either free or bound to L-FABP, ATP and CoA. FA esterification in whole nuclei and endonuclear lipids was ATP-CoA-dependent, and with specificity regarding fatty acid type and lipid class. 18:0 and 20:4n-6, free or L-FABP bound, showed the same incorporation and esterification pattern in lipids of whole nuclei. Only 20:4n-6 L-FABP bound was less incorporated into TAG with respect to free 20:4n-6. In the nuclear matrix, 18:0 free or L-FABP bound was esterified with a higher specific activity (SA) into: PtdEtn > PtdIns, PtdSer > PtdCho. 20:4n-6 free or L-FABP bound was esterified into: PtdIns > PtdEtn > PtdCho. 20:4n-6:L-FABP was esterified in endonuclear total-PL and PtdIns with a greater SA with respect to free 20:4n-6 and with a minor one as FFA. To summarize, trafficking of FA to nuclei includes esterification of 18:0 and 20:4n-6 either free or L-FABP-bound, into nuclear and endonuclear lipids by an ATP-CoA-dependent pathway. Endonuclear fatty acid esterification was more active than that in whole nuclei, and independent of the nuclear membrane. Esterification patterns of fatty acids L-FABP-bound or free into whole nuclear lipids were the same whereas in the nuclear matrix, L-FABP could play an important role in the mobilization of 20:4n-6 into specific sites of utilization such as the PtdIns pools.

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