Journal articles: 'Chromatin Architectural Proteins'

1

McBryant, Steven J., Valerie H. Adams, and Jeffrey C. Hansen. "Chromatin architectural proteins." Chromosome Research 14, no. 1 (February 2006): 39–51. http://dx.doi.org/10.1007/s10577-006-1025-x.

Full text

APA, Harvard, Vancouver, ISO, and other styles

2

Thakur, Jitendra, and Steven Henikoff. "Architectural RNA in chromatin organization." Biochemical Society Transactions 48, no. 5 (September 8, 2020): 1967–78. http://dx.doi.org/10.1042/bst20191226.

Full text

Abstract:

RNA plays a well-established architectural role in the formation of membraneless interchromatin nuclear bodies. However, a less well-known role of RNA is in organizing chromatin, whereby specific RNAs have been found to recruit chromatin modifier proteins. Whether or not RNA can act as an architectural molecule for chromatin remains unclear, partly because dissecting the architectural role of RNA from its regulatory role remains challenging. Studies that have addressed RNA's architectural role in chromatin organization rely on in situ RNA depletion using Ribonuclease A (RNase A) and suggest that RNA plays a major direct architectural role in chromatin organization. In this review, we will discuss these findings, candidate chromatin architectural long non-coding RNAs and possible mechanisms by which RNA, along with RNA binding proteins might be mediating chromatin organization.

APA, Harvard, Vancouver, ISO, and other styles

3

Grasser, K. "HMG1 and HU proteins: architectural elements in plant chromatin." Trends in Plant Science 3, no. 7 (July 1, 1998): 260–65. http://dx.doi.org/10.1016/s1360-1385(98)01259-x.

Full text

APA, Harvard, Vancouver, ISO, and other styles

4

van Holde, Kensal, and Jordanka Zlatanova. "Chromatin architectural proteins and transcription factors: A structural connection." BioEssays 18, no. 9 (September 1996): 697–700. http://dx.doi.org/10.1002/bies.950180903.

Full text

APA, Harvard, Vancouver, ISO, and other styles

5

Zhao, Bo, Yanpeng Xi, Junghyun Kim, and Sibum Sung. "Chromatin architectural proteins regulate flowering time by precluding gene looping." Science Advances 7, no. 24 (June 2021): eabg3097. http://dx.doi.org/10.1126/sciadv.abg3097.

Full text

Abstract:

Chromatin structure is critical for gene expression and many other cellular processes. In Arabidopsis thaliana, the floral repressor FLC adopts a self-loop chromatin structure via bridging of its flanking regions. This local gene loop is necessary for active FLC expression. However, the molecular mechanism underlying the formation of this class of gene loops is unknown. Here, we report the characterization of a group of linker histone-like proteins, named the GH1-HMGA family in Arabidopsis, which act as chromatin architecture modulators. We demonstrate that these family members redundantly promote the floral transition through the repression of FLC. A genome-wide study revealed that this family preferentially binds to the 5′ and 3′ ends of gene bodies. The loss of this binding increases FLC expression by stabilizing the FLC 5′ to 3′ gene looping. Our study provides mechanistic insights into how a family of evolutionarily conserved proteins regulates the formation of local gene loops.

APA, Harvard, Vancouver, ISO, and other styles

6

Driessen, Rosalie P. C., and Remus Th Dame. "Structure and dynamics of the crenarchaeal nucleoid." Biochemical Society Transactions 41, no. 1 (January 29, 2013): 321–25. http://dx.doi.org/10.1042/bst20120336.

Full text

Abstract:

Crenarchaeal genomes are organized into a compact nucleoid by a set of small chromatin proteins. Although there is little knowledge of chromatin structure in Archaea, similarities between crenarchaeal and bacterial chromatin proteins suggest that organization and regulation could be achieved by similar mechanisms. In the present review, we describe the molecular properties of crenarchaeal chromatin proteins and discuss the possible role of these architectural proteins in organizing the crenarchaeal chromatin and in gene regulation.

APA, Harvard, Vancouver, ISO, and other styles

7

Foulger, Larus E., Connie Goh Then Sin, Q. Q. Zhuang, Hugh Smallman, James M. Nicholson, Stanley J. Lambert, Colin D. Reynolds, et al. "Efficient purification of chromatin architectural proteins: histones, HMGB proteins and FKBP3 (FKBP25) immunophilin." RSC Advances 2, no. 28 (2012): 10598. http://dx.doi.org/10.1039/c2ra21758a.

Full text

APA, Harvard, Vancouver, ISO, and other styles

8

Alpsoy, Aktan, Surbhi Sood, and Emily C. Dykhuizen. "At the Crossroad of Gene Regulation and Genome Organization: Potential Roles for ATP-Dependent Chromatin Remodelers in the Regulation of CTCF-Mediated 3D Architecture." Biology 10, no. 4 (March 27, 2021): 272. http://dx.doi.org/10.3390/biology10040272.

Full text

Abstract:

In higher order organisms, the genome is assembled into a protein-dense structure called chromatin. Chromatin is spatially organized in the nucleus through hierarchical folding, which is tightly regulated both in cycling cells and quiescent cells. Assembly and folding are not one-time events in a cell’s lifetime; rather, they are subject to dynamic shifts to allow changes in transcription, DNA replication, or DNA damage repair. Chromatin is regulated at many levels, and recent tools have permitted the elucidation of specific factors involved in the maintenance and regulation of the three-dimensional (3D) genome organization. In this review/perspective, we aim to cover the potential, but relatively unelucidated, crosstalk between 3D genome architecture and the ATP-dependent chromatin remodelers with a specific focus on how the architectural proteins CTCF and cohesin are regulated by chromatin remodeling.

APA, Harvard, Vancouver, ISO, and other styles

9

Driessen, Rosalie P. C., and Remus Th Dame. "Nucleoid-associated proteins in Crenarchaea." Biochemical Society Transactions 39, no. 1 (January 19, 2011): 116–21. http://dx.doi.org/10.1042/bst0390116.

Full text

Abstract:

Architectural proteins play an important role in compacting and organizing the chromosomal DNA in all three kingdoms of life (Eukarya, Bacteria and Archaea). These proteins are generally not conserved at the amino acid sequence level, but the mechanisms by which they modulate the genome do seem to be functionally conserved across kingdoms. On a generic level, architectural proteins can be classified based on their structural effect as DNA benders, DNA bridgers or DNA wrappers. Although chromatin organization in archaea has not been studied extensively, quite a number of architectural proteins have been identified. In the present paper, we summarize the knowledge currently available on these proteins in Crenarchaea. By the type of architectural proteins available, the crenarchaeal nucleoid shows similarities with that of Bacteria. It relies on the action of a large set of small, abundant and generally basic proteins to compact and organize their genome and to modulate its activity.

APA, Harvard, Vancouver, ISO, and other styles

10

Brzeski, Jan, and Andrzej Jerzmanowski. "Plant chromatin - epigenetics linked to ATP-dependent remodeling and architectural proteins." FEBS Letters 567, no. 1 (April 9, 2004): 15–19. http://dx.doi.org/10.1016/j.febslet.2004.03.068.

Full text

APA, Harvard, Vancouver, ISO, and other styles

11

Llères, David, Yui Imaizumi, and Robert Feil. "Exploring chromatin structural roles of non-coding RNAs at imprinted domains." Biochemical Society Transactions 49, no. 4 (August 2, 2021): 1867–79. http://dx.doi.org/10.1042/bst20210758.

Full text

Abstract:

Different classes of non-coding RNA (ncRNA) influence the organization of chromatin. Imprinted gene domains constitute a paradigm for exploring functional long ncRNAs (lncRNAs). Almost all express an lncRNA in a parent-of-origin dependent manner. The mono-allelic expression of these lncRNAs represses close by and distant protein-coding genes, through diverse mechanisms. Some control genes on other chromosomes as well. Interestingly, several imprinted chromosomal domains show a developmentally regulated, chromatin-based mechanism of imprinting with apparent similarities to X-chromosome inactivation. At these domains, the mono-allelic lncRNAs show a relatively stable, focal accumulation in cis. This facilitates the recruitment of Polycomb repressive complexes, lysine methyltranferases and other nuclear proteins — in part through direct RNA–protein interactions. Recent chromosome conformation capture and microscopy studies indicate that the focal aggregation of lncRNA and interacting proteins could play an architectural role as well, and correlates with close positioning of target genes. Higher-order chromatin structure is strongly influenced by CTCF/cohesin complexes, whose allelic association patterns and actions may be influenced by lncRNAs as well. Here, we review the gene-repressive roles of imprinted non-coding RNAs, particularly of lncRNAs, and discuss emerging links with chromatin architecture.

APA, Harvard, Vancouver, ISO, and other styles

12

Minervini, Angela, Nicoletta Coccaro, Luisa Anelli, Antonella Zagaria, Giorgina Specchia, and Francesco Albano. "HMGA Proteins in Hematological Malignancies." Cancers 12, no. 6 (June 3, 2020): 1456. http://dx.doi.org/10.3390/cancers12061456.

Full text

Abstract:

The high mobility group AT-Hook (HMGA) proteins are a family of nonhistone chromatin remodeling proteins known as “architectural transcriptional factors”. By binding the minor groove of AT-rich DNA sequences, they interact with the transcription apparatus, altering the chromatin modeling and regulating gene expression by either enhancing or suppressing the binding of the more usual transcriptional activators and repressors, although they do not themselves have any transcriptional activity. Their involvement in both benign and malignant neoplasias is well-known and supported by a large volume of studies. In this review, we focus on the role of the HMGA proteins in hematological malignancies, exploring the mechanisms through which they enhance neoplastic transformation and how this knowledge could be exploited to devise tailored therapeutic strategies.

APA, Harvard, Vancouver, ISO, and other styles

13

Adkins, Nicholas L., and Philippe T. Georgel. "MeCP2: structure and functionThis paper is one of a selection of papers published in a Special Issue entitled 31st Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process." Biochemistry and Cell Biology 89, no. 1 (February 2011): 1–11. http://dx.doi.org/10.1139/o10-112.

Full text

Abstract:

Despite a vast body of literature linking chromatin structure to regulation of gene expression, the role of architectural proteins in higher order chromatin transitions required for transcription activation and repression has remained an under-studied field. To demonstrate the current knowledge of the role of such proteins, we have focused our attention on the methylated DNA binding and chromatin-associated protein MeCP2. Structural studies using chromatin assembled in vitro have revealed that MeCP2 can associate with nucleosomes in an N-terminus dependent manner and efficiently condense nucleosome arrays. The present review attempts to match MeCP2 structural domains, or lack thereof, and specific chromatin features needed for the proper recruitment of MeCP2 to its multiple functions as either activator or repressor. We specifically focused on MeCP2’s role in Rett syndrome, a neurological disorder associated with specific MeCP2 mutations.

APA, Harvard, Vancouver, ISO, and other styles

14

Vermunt, Marit W., Di Zhang, and Gerd A. Blobel. "The interdependence of gene-regulatory elements and the 3D genome." Journal of Cell Biology 218, no. 1 (November 15, 2018): 12–26. http://dx.doi.org/10.1083/jcb.201809040.

Full text

Abstract:

Imaging studies, high-resolution chromatin conformation maps, and genome-wide occupancy data of architectural proteins have revealed that genome topology is tightly intertwined with gene expression. Cross-talk between gene-regulatory elements is often organized within insulated neighborhoods, and regulatory cues that induce transcriptional changes can reshape chromatin folding patterns and gene positioning within the nucleus. The cause–consequence relationship of genome architecture and gene expression is intricate, and its molecular mechanisms are under intense investigation. Here, we review the interdependency of transcription and genome organization with emphasis on enhancer–promoter contacts in gene regulation.

APA, Harvard, Vancouver, ISO, and other styles

15

Luijsterburg, Martijn S., Malcolm F. White, Roel van Driel, and Remus Th Dame. "The Major Architects of Chromatin: Architectural Proteins in Bacteria, Archaea and Eukaryotes." Critical Reviews in Biochemistry and Molecular Biology 43, no. 6 (January 2008): 393–418. http://dx.doi.org/10.1080/10409230802528488.

Full text

APA, Harvard, Vancouver, ISO, and other styles

16

Parisi, Silvia, Silvia Piscitelli, Fabiana Passaro, and Tommaso Russo. "HMGA Proteins in Stemness and Differentiation of Embryonic and Adult Stem Cells." International Journal of Molecular Sciences 21, no. 1 (January 6, 2020): 362. http://dx.doi.org/10.3390/ijms21010362.

Full text

Abstract:

HMGA1 and HMGA2 are chromatin architectural proteins that do not have transcriptional activity per se, but are able to modify chromatin structure by interacting with the transcriptional machinery and thus negatively or positively regulate the transcription of several genes. They have been extensively studied in cancer where they are often found to be overexpressed but their functions under physiologic conditions have still not been completely addressed. Hmga1 and Hmga2 are expressed during the early stages of mouse development, whereas they are not detectable in most adult tissues. Hmga overexpression or knockout studies in mouse have pointed to a key function in the development of the embryo and of various tissues. HMGA proteins are expressed in embryonic stem cells and in some adult stem cells and numerous experimental data have indicated that they play a fundamental role in the maintenance of stemness and in the regulation of differentiation. In this review, we discuss available experimental data on HMGA1 and HMGA2 functions in governing embryonic and adult stem cell fate. Moreover, based on the available evidence, we will aim to outline how HMGA expression is regulated in different contexts and how these two proteins contribute to the regulation of gene expression and chromatin architecture in stem cells.

APA, Harvard, Vancouver, ISO, and other styles

17

Cubeñas-Potts, Caelin, M. Jordan Rowley, Xiaowen Lyu, Ge Li, Elissa P. Lei, and Victor G. Corces. "Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture." Nucleic Acids Research 45, no. 4 (November 29, 2016): 1714–30. http://dx.doi.org/10.1093/nar/gkw1114.

Full text

APA, Harvard, Vancouver, ISO, and other styles

18

Valletta, Mariangela, Rosita Russo, Ilaria Baglivo, Veronica Russo, Sara Ragucci, Annamaria Sandomenico, Emanuela Iaccarino, et al. "Exploring the Interaction between the SWI/SNF Chromatin Remodeling Complex and the Zinc Finger Factor CTCF." International Journal of Molecular Sciences 21, no. 23 (November 25, 2020): 8950. http://dx.doi.org/10.3390/ijms21238950.

Full text

Abstract:

The transcription factor CCCTC-binding factor (CTCF) modulates pleiotropic functions mostly related to gene expression regulation. The role of CTCF in large scale genome organization is also well established. A unifying model to explain relationships among many CTCF-mediated activities involves direct or indirect interactions with numerous protein cofactors recruited to specific binding sites. The co-association of CTCF with other architectural proteins such as cohesin, chromodomain helicases, and BRG1, further supports the interplay between master regulators of mammalian genome folding. Here, we report a comprehensive LC-MS/MS mapping of the components of the switch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complex co-associated with CTCF including subunits belonging to the core, signature, and ATPase modules. We further show that the localization patterns of representative SWI/SNF members significantly overlap with CTCF sites on transcriptionally active chromatin regions. Moreover, we provide evidence of a direct binding of the BRK-BRG1 domain to the zinc finger motifs 4–8 of CTCF, thus, suggesting that these domains mediate the interaction of CTCF with the SWI/SNF complex. These findings provide an updated view of the cooperative nature between CTCF and the SWI/SNF ATP-dependent chromatin remodeling complexes, an important step for understanding how these architectural proteins collaborate to shape the genome.

APA, Harvard, Vancouver, ISO, and other styles

19

McBryant, Steven J., Christine Krause, Christopher L. Woodcock, and Jeffrey C. Hansen. "The Silent Information Regulator 3 Protein, SIR3p, Binds to Chromatin Fibers and Assembles a Hypercondensed Chromatin Architecture in the Presence of Salt." Molecular and Cellular Biology 28, no. 11 (March 24, 2008): 3563–72. http://dx.doi.org/10.1128/mcb.01389-07.

Full text

Abstract:

ABSTRACT The telomeres and mating-type loci of budding yeast adopt a condensed, heterochromatin-like state through recruitment of the silent information regulator (SIR) proteins SIR2p, SIR3p, and SIR4p. In this study we characterize the chromatin binding determinants of recombinant SIR3p and identify how SIR3p mediates chromatin fiber condensation in vitro. Purified full-length SIR3p was incubated with naked DNA, nucleosome core particles, or defined nucleosomal arrays, and the resulting complexes were analyzed by electrophoretic shift assays, sedimentation velocity, and electron microscopy. SIR3p bound avidly to all three types of templates. SIR3p loading onto its nucleosomal sites in chromatin produced thickened condensed fibers that retained a beaded morphology. At higher SIR3p concentrations, individual nucleosomal arrays formed oligomeric suprastructures bridged by SIR3p oligomers. When condensed SIR3p-bound chromatin fibers were incubated in Mg2+, they folded and oligomerized even further to produce hypercondensed higher-order chromatin structures. Collectively, these results define how SIR3p may function as a chromatin architectural protein and provide new insight into the interplay between endogenous and protein-mediated chromatin fiber condensation pathways.

APA, Harvard, Vancouver, ISO, and other styles

20

Deng, Tao, Z. Iris Zhu, Shaofei Zhang, Fenfei Leng, Srujana Cherukuri, Loren Hansen, Leonardo Mariño-Ramírez, Eran Meshorer, David Landsman, and Michael Bustin. "HMGN1 Modulates Nucleosome Occupancy and DNase I Hypersensitivity at the CpG Island Promoters of Embryonic Stem Cells." Molecular and Cellular Biology 33, no. 16 (June 17, 2013): 3377–89. http://dx.doi.org/10.1128/mcb.00435-13.

Full text

Abstract:

Chromatin structure plays a key role in regulating gene expression and embryonic differentiation; however, the factors that determine the organization of chromatin around regulatory sites are not fully known. Here we show that HMGN1, a nucleosome-binding protein ubiquitously expressed in vertebrate cells, preferentially binds to CpG island-containing promoters and affects the organization of nucleosomes, DNase I hypersensitivity, and the transcriptional profile of mouse embryonic stem cells and neural progenitors. Loss of HMGN1 alters the organization of an unstable nucleosome at transcription start sites, reduces the number of DNase I-hypersensitive sites genome wide, and decreases the number of nestin-positive neural progenitors in the subventricular zone (SVZ) region of mouse brain. Thus, architectural chromatin-binding proteins affect the transcription profile and chromatin structure during embryonic stem cell differentiation.

APA, Harvard, Vancouver, ISO, and other styles

21

Nalabothula, Narasimharao, Graham McVicker, John Maiorano, Rebecca Martin, Jonathan K. Pritchard, and Yvonne N. Fondufe-Mittendorf. "The chromatin architectural proteins HMGD1 and H1 bind reciprocally and have opposite effects on chromatin structure and gene regulation." BMC Genomics 15, no. 1 (2014): 92. http://dx.doi.org/10.1186/1471-2164-15-92.

Full text

APA, Harvard, Vancouver, ISO, and other styles

22

Kamagata, Kiyoto, Kana Ouchi, Cheng Tan, Eriko Mano, Sridhar Mandali, Yining Wu, Shoji Takada, Satoshi Takahashi, and Reid C. Johnson. "The HMGB chromatin protein Nhp6A can bypass obstacles when traveling on DNA." Nucleic Acids Research 48, no. 19 (September 30, 2020): 10820–31. http://dx.doi.org/10.1093/nar/gkaa799.

Full text

Abstract:

Abstract DNA binding proteins rapidly locate their specific DNA targets through a combination of 3D and 1D diffusion mechanisms, with the 1D search involving bidirectional sliding along DNA. However, even in nucleosome-free regions, chromosomes are highly decorated with associated proteins that may block sliding. Here we investigate the ability of the abundant chromatin-associated HMGB protein Nhp6A from Saccharomyces cerevisiae to travel along DNA in the presence of other architectural DNA binding proteins using single-molecule fluorescence microscopy. We observed that 1D diffusion by Nhp6A molecules is retarded by increasing densities of the bacterial proteins Fis and HU and by Nhp6A, indicating these structurally diverse proteins impede Nhp6A mobility on DNA. However, the average travel distances were larger than the average distances between neighboring proteins, implying Nhp6A is able to bypass each of these obstacles. Together with molecular dynamics simulations, our analyses suggest two binding modes: mobile molecules that can bypass barriers as they seek out DNA targets, and near stationary molecules that are associated with neighboring proteins or preferred DNA structures. The ability of mobile Nhp6A molecules to bypass different obstacles on DNA suggests they do not block 1D searches by other DNA binding proteins.

APA, Harvard, Vancouver, ISO, and other styles

23

Senigagliesi, Beatrice, Carlotta Penzo, Luisa Ulloa Severino, Riccardo Maraspini, Sara Petrosino, Hernan Morales-Navarrete, Enrico Pobega, et al. "The High Mobility Group A1 (HMGA1) Chromatin Architectural Factor Modulates Nuclear Stiffness in Breast Cancer Cells." International Journal of Molecular Sciences 20, no. 11 (June 4, 2019): 2733. http://dx.doi.org/10.3390/ijms20112733.

Full text

Abstract:

Plasticity is an essential condition for cancer cells to invade surrounding tissues. The nucleus is the most rigid cellular organelle and it undergoes substantial deformations to get through environmental constrictions. Nuclear stiffness mostly depends on the nuclear lamina and chromatin, which in turn might be affected by nuclear architectural proteins. Among these is the HMGA1 (High Mobility Group A1) protein, a factor that plays a causal role in neoplastic transformation and that is able to disentangle heterochromatic domains by H1 displacement. Here we made use of atomic force microscopy to analyze the stiffness of breast cancer cellular models in which we modulated HMGA1 expression to investigate its role in regulating nuclear plasticity. Since histone H1 is the main modulator of chromatin structure and HMGA1 is a well-established histone H1 competitor, we correlated HMGA1 expression and cellular stiffness with histone H1 expression level, post-translational modifications, and nuclear distribution. Our results showed that HMGA1 expression level correlates with nuclear stiffness, is associated to histone H1 phosphorylation status, and alters both histone H1 chromatin distribution and expression. These data suggest that HMGA1 might promote chromatin relaxation through a histone H1-mediated mechanism strongly impacting on the invasiveness of cancer cells.

APA, Harvard, Vancouver, ISO, and other styles

24

Tessari, Michela A., Monica Gostissa, Sandro Altamura, Riccardo Sgarra, Alessandra Rustighi, Clio Salvagno, Giuseppina Caretti, et al. "Transcriptional Activation of the Cyclin A Gene by the Architectural Transcription Factor HMGA2." Molecular and Cellular Biology 23, no. 24 (December 15, 2003): 9104–16. http://dx.doi.org/10.1128/mcb.23.24.9104-9116.2003.

Full text

Abstract:

ABSTRACT The HMGA2 protein belongs to the HMGA family of architectural transcription factors, which play an important role in chromatin organization. HMGA proteins are overexpressed in several experimental and human tumors and have been implicated in the process of neoplastic transformation. Hmga2 knockout results in the pygmy phenotype in mice and in a decreased growth rate of embryonic fibroblasts, thus indicating a role for HMGA2 in cell proliferation. Here we show that HMGA2 associates with the E1A-regulated transcriptional repressor p120E4F, interfering with p120E4F binding to the cyclin A promoter. Ectopic expression of HMGA2 results in the activation of the cyclin A promoter and induction of the endogenous cyclin A gene. In addition, chromatin immunoprecipitation experiments show that HMGA2 associates with the cyclin A promoter only when the gene is transcriptionally activated. These data identify the cyclin A gene as a cellular target for HMGA2 and, for the first time, suggest a mechanism for HMGA2-dependent cell cycle regulation.

APA, Harvard, Vancouver, ISO, and other styles

25

Qin, L., A. M. Erkelens, F. Ben Bdira, and R. T. Dame. "The architects of bacterial DNA bridges: a structurally and functionally conserved family of proteins." Open Biology 9, no. 12 (December 2019): 190223. http://dx.doi.org/10.1098/rsob.190223.

Full text

Abstract:

Every organism across the tree of life compacts and organizes its genome with architectural chromatin proteins. While eukaryotes and archaea express histone proteins, the organization of bacterial chromosomes is dependent on nucleoid-associated proteins. In Escherichia coli and other proteobacteria, the histone-like nucleoid structuring protein (H-NS) acts as a global genome organizer and gene regulator. Functional analogues of H-NS have been found in other bacterial species: MvaT in Pseudomonas species, Lsr2 in actinomycetes and Rok in Bacillus species. These proteins complement hns − phenotypes and have similar DNA-binding properties, despite their lack of sequence homology. In this review, we focus on the structural and functional characteristics of these four architectural proteins. They are able to bridge DNA duplexes, which is key to genome compaction, gene regulation and their response to changing conditions in the environment. Structurally the domain organization and charge distribution of these proteins are conserved, which we suggest is at the basis of their conserved environment responsive behaviour. These observations could be used to find and validate new members of this protein family and to predict their response to environmental changes.

APA, Harvard, Vancouver, ISO, and other styles

26

Niu, Longjian, Wei Shen, Zhaoying Shi, Yongjun Tan, Na He, Jing Wan, Jialei Sun, et al. "Three-dimensional folding dynamics of the Xenopus tropicalis genome." Nature Genetics 53, no. 7 (June 7, 2021): 1075–87. http://dx.doi.org/10.1038/s41588-021-00878-z.

Full text

Abstract:

AbstractAnimal interphase chromosomes are organized into topologically associating domains (TADs). How TADs are formed is not fully understood. Here, we combined high-throughput chromosome conformation capture and gene silencing to obtain insights into TAD dynamics in Xenopus tropicalis embryos. First, TAD establishment in X. tropicalis is similar to that in mice and flies and does not depend on zygotic genome transcriptional activation. This process is followed by further refinements in active and repressive chromatin compartments and the appearance of loops and stripes. Second, within TADs, higher self-interaction frequencies at one end of the boundary are associated with higher DNA occupancy of the architectural proteins CTCF and Rad21. Third, the chromatin remodeling factor ISWI is required for de novo TAD formation. Finally, TAD structures are variable in different tissues. Our work shows that X. tropicalis is a powerful model for chromosome architecture analysis and suggests that chromatin remodeling plays an essential role in de novo TAD establishment.

APA, Harvard, Vancouver, ISO, and other styles

27

Chikhirzhina, Elena, Tatyana Starkova, Anton Beljajev, Alexander Polyanichko, and Alexey Tomilin. "Functional Diversity of Non-Histone Chromosomal Protein HmgB1." International Journal of Molecular Sciences 21, no. 21 (October 26, 2020): 7948. http://dx.doi.org/10.3390/ijms21217948.

Full text

Abstract:

The functioning of DNA in the cell nucleus is ensured by a multitude of proteins, whose interactions with DNA as well as with other proteins lead to the formation of a complicated, organized, and quite dynamic system known as chromatin. This review is devoted to the description of properties and structure of the progenitors of the most abundant non-histone protein of the HMGB family—the HmgB1 protein. The proteins of the HMGB family are also known as “architectural factors” of chromatin, which play an important role in gene expression, transcription, DNA replication, and repair. However, as soon as HmgB1 goes outside the nucleus, it acquires completely different functions, post-translational modifications, and change of its redox state. Despite a lot of evidence of the functional activity of HmgB1, there are still many issues to be solved related to the mechanisms of the influence of HmgB1 on the development and treatment of different diseases—from oncological and cardiovascular diseases to pathologies during pregnancy and childbirth. Here, we describe molecular structure of the HmgB1 protein and discuss general mechanisms of its interactions with other proteins and DNA in cell.

APA, Harvard, Vancouver, ISO, and other styles

28

Dunigan, David D., Ronald L. Cerny, Andrew T. Bauman, Jared C. Roach, Leslie C. Lane, Irina V. Agarkova, Kurt Wulser, et al. "Paramecium bursaria Chlorella Virus 1 Proteome Reveals Novel Architectural and Regulatory Features of a Giant Virus." Journal of Virology 86, no. 16 (June 13, 2012): 8821–34. http://dx.doi.org/10.1128/jvi.00907-12.

Full text

Abstract:

The 331-kbp chlorovirusParamecium bursariachlorella virus 1 (PBCV-1) genome was resequenced and annotated to correct errors in the original 15-year-old sequence; 40 codons was considered the minimum protein size of an open reading frame. PBCV-1 has 416 predicted protein-encoding sequences and 11 tRNAs. A proteome analysis was also conducted on highly purified PBCV-1 virions using two mass spectrometry-based protocols. The mass spectrometry-derived data were compared to PBCV-1 and its hostChlorella variabilisNC64A predicted proteomes. Combined, these analyses revealed 148 unique virus-encoded proteins associated with the virion (about 35% of the coding capacity of the virus) and 1 host protein. Some of these proteins appear to be structural/architectural, whereas others have enzymatic, chromatin modification, and signal transduction functions. Most (106) of the proteins have no known function or homologs in the existing gene databases except as orthologs with proteins of other chloroviruses, phycodnaviruses, and nuclear-cytoplasmic large DNA viruses. The genes encoding these proteins are dispersed throughout the virus genome, and most are transcribed late or early-late in the infection cycle, which is consistent with virion morphogenesis.

APA, Harvard, Vancouver, ISO, and other styles

29

Sgarra, Riccardo, Silvia Pegoraro, Daniela D’Angelo, Gloria Ros, Rossella Zanin, Michela Sgubin, Sara Petrosino, Sabrina Battista, and Guidalberto Manfioletti. "High Mobility Group A (HMGA): Chromatin Nodes Controlled by a Knotty miRNA Network." International Journal of Molecular Sciences 21, no. 3 (January 22, 2020): 717. http://dx.doi.org/10.3390/ijms21030717.

Full text

Abstract:

High mobility group A (HMGA) proteins are oncofoetal chromatin architectural factors that are widely involved in regulating gene expression. These proteins are unique, because they are highly expressed in embryonic and cancer cells, where they play a relevant role in cell proliferation, stemness, and the acquisition of aggressive tumour traits, i.e., motility, invasiveness, and metastatic properties. The HMGA protein expression levels and activities are controlled by a connected set of events at the transcriptional, post-transcriptional, and post-translational levels. In fact, microRNA (miRNA)-mediated RNA stability is the most-studied mechanism of HMGA protein expression modulation. In this review, we contribute to a comprehensive overview of HMGA-targeting miRNAs; we provide detailed information regarding HMGA gene structural organization and a comprehensive evaluation and description of HMGA-targeting miRNAs, while focusing on those that are widely involved in HMGA regulation; and, we aim to offer insights into HMGA-miRNA mutual cross-talk from a functional and cancer-related perspective, highlighting possible clinical implications.

APA, Harvard, Vancouver, ISO, and other styles

30

Szerlong, H. "The nuclear actin-related proteins Arp7 and Arp9: a dimeric module that cooperates with architectural proteins for chromatin remodeling." EMBO Journal 22, no. 12 (June 16, 2003): 3175–87. http://dx.doi.org/10.1093/emboj/cdg296.

Full text

APA, Harvard, Vancouver, ISO, and other styles

31

Visone, Valeria, Antonella Vettone, Mario Serpe, Anna Valenti, Giuseppe Perugino, Mosè Rossi, and Maria Ciaramella. "Chromatin Structure and Dynamics in Hot Environments: Architectural Proteins and DNA Topoisomerases of Thermophilic Archaea." International Journal of Molecular Sciences 15, no. 9 (September 25, 2014): 17162–87. http://dx.doi.org/10.3390/ijms150917162.

Full text

APA, Harvard, Vancouver, ISO, and other styles

32

Willemin, Andréa, Lucille Lopez-Delisle, Christopher Chase Bolt, Marie-Laure Gadolini, Denis Duboule, and Eddie Rodriguez-Carballo. "Induction of a chromatin boundary in vivo upon insertion of a TAD border." PLOS Genetics 17, no. 7 (July 22, 2021): e1009691. http://dx.doi.org/10.1371/journal.pgen.1009691.

Full text

Abstract:

Mammalian genomes are partitioned into sub-megabase to megabase-sized units of preferential interactions called topologically associating domains or TADs, which are likely important for the proper implementation of gene regulatory processes. These domains provide structural scaffolds for distant cis regulatory elements to interact with their target genes within the three-dimensional nuclear space and architectural proteins such as CTCF as well as the cohesin complex participate in the formation of the boundaries between them. However, the importance of the genomic context in providing a given DNA sequence the capacity to act as a boundary element remains to be fully investigated. To address this question, we randomly relocated a topological boundary functionally associated with the mouse HoxD gene cluster and show that it can indeed act similarly outside its initial genomic context. In particular, the relocated DNA segment recruited the required architectural proteins and induced a significant depletion of contacts between genomic regions located across the integration site. The host chromatin landscape was re-organized, with the splitting of the TAD wherein the boundary had integrated. These results provide evidence that topological boundaries can function independently of their site of origin, under physiological conditions during mouse development.

APA, Harvard, Vancouver, ISO, and other styles

33

Luijsterburg, Martijn S., Maarten C. Noom, Gijs J. L. Wuite, and Remus Th Dame. "The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: A molecular perspective." Journal of Structural Biology 156, no. 2 (November 2006): 262–72. http://dx.doi.org/10.1016/j.jsb.2006.05.006.

Full text

APA, Harvard, Vancouver, ISO, and other styles

34

Creamer, K. M., and J. B. Lawrence. "XIST RNA: a window into the broader role of RNA in nuclear chromosome architecture." Philosophical Transactions of the Royal Society B: Biological Sciences 372, no. 1733 (September 25, 2017): 20160360. http://dx.doi.org/10.1098/rstb.2016.0360.

Full text

Abstract:

XIST RNA triggers the transformation of an active X chromosome into a condensed, inactive Barr body and therefore provides a unique window into transitions of higher-order chromosome architecture. Despite recent progress, how XIST RNA localizes and interacts with the X chromosome remains poorly understood. Genetic engineering of XIST into a trisomic autosome demonstrates remarkable capacity of XIST RNA to localize and comprehensively silence that autosome. Thus, XIST does not require X chromosome-specific sequences but operates on mechanisms available genome-wide. Prior results suggested XIST localization is controlled by attachment to the insoluble nuclear scaffold. Our recent work affirms that scaffold attachment factor A (SAF-A) is involved in anchoring XIST , but argues against the view that SAF-A provides a unimolecular bridge between RNA and the chromosome. Rather, we suggest that a complex meshwork of architectural proteins interact with XIST RNA. Parallel work studying the territory of actively transcribed chromosomes suggests that repeat-rich RNA ‘coats’ euchromatin and may impact chromosome architecture in a manner opposite of XIST . A model is discussed whereby RNA may not just recruit histone modifications, but more directly impact higher-order chromatin condensation via interaction with architectural proteins of the nucleus. This article is part of the themed issue ‘X-chromosome inactivation: a tribute to Mary Lyon’.

APA, Harvard, Vancouver, ISO, and other styles

35

Pathak, Rashmi U., Nandini Rangaraj, Satish Kallappagoudar, Krishnaveni Mishra, and Rakesh K. Mishra. "Boundary Element-Associated Factor 32B Connects Chromatin Domains to the Nuclear Matrix." Molecular and Cellular Biology 27, no. 13 (May 7, 2007): 4796–806. http://dx.doi.org/10.1128/mcb.00305-07.

Full text

Abstract:

ABSTRACT Chromatin domain boundary elements demarcate independently regulated domains of eukaryotic genomes. While a few such boundary sequences have been studied in detail, only a small number of proteins that interact with them have been identified. One such protein is the boundary element-associated factor (BEAF), which binds to the scs′ boundary element of Drosophila melanogaster. It is not clear, however, how boundary elements function. In this report we show that BEAF is associated with the nuclear matrix and map the domain required for matrix association to the middle region of the protein. This region contains a predicted coiled-coil domain with several potential sites for posttranslational modification. We demonstrate that the DNA sequences that bind to BEAF in vivo are also associated with the nuclear matrix and colocalize with BEAF. These results suggest that boundary elements may function by tethering chromatin to nuclear architectural components and thereby provide a structural basis for compartmentalization of the genome into functionally independent domains.

APA, Harvard, Vancouver, ISO, and other styles

36

Becker, Matthias, Antje Becker, Faiçal Miyara, Zhiming Han, Maki Kihara, David T. Brown, Gordon L. Hager, Keith Latham, Eli Y. Adashi, and Tom Misteli. "Differential In Vivo Binding Dynamics of Somatic and Oocyte-specific Linker Histones in Oocytes and During ES Cell Nuclear Transfer." Molecular Biology of the Cell 16, no. 8 (August 2005): 3887–95. http://dx.doi.org/10.1091/mbc.e05-04-0350.

Full text

Abstract:

The embryonic genome is formed by fusion of a maternal and a paternal genome. To accommodate the resulting diploid genome in the fertilized oocyte dramatic global genome reorganizations must occur. The higher order structure of chromatin in vivo is critically dependent on architectural chromatin proteins, with the family of linker histone proteins among the most critical structural determinants. Although somatic cells contain numerous linker histone variants, only one, H1FOO, is present in mouse oocytes. Upon fertilization H1FOO rapidly populates the introduced paternal genome and replaces sperm-specific histone-like proteins. The same dynamic replacement occurs upon introduction of a nucleus during somatic cell nuclear transfer. To understand the molecular basis of this dynamic histone replacement process, we compared the localization and binding dynamics of somatic H1 and oocyte-specific H1FOO and identified the molecular determinants of binding to either oocyte or somatic chromatin in living cells. We find that although both histones associate readily with chromatin in nuclei of somatic cells, only H1FOO is capable of correct chromatin association in the germinal vesicle stage oocyte nuclei. This specificity is generated by the N-terminal and globular domains of H1FOO. Measurement of in vivo binding properties of the H1 variants suggest that H1FOO binds chromatin more tightly than somatic linker histones. We provide evidence that both the binding properties of linker histones as well as additional, active processes contribute to the replacement of somatic histones with H1FOO during nuclear transfer. These results provide the first mechanistic insights into the crucial step of linker histone replacement as it occurs during fertilization and somatic cell nuclear transfer.

APA, Harvard, Vancouver, ISO, and other styles

37

Cesarini, Elisa, Anna D'Alfonso, and Giorgio Camilloni. "H4K16 acetylation affects recombination and ncRNA transcription at rDNA in Saccharomyces cerevisiae." Molecular Biology of the Cell 23, no. 14 (July 15, 2012): 2770–81. http://dx.doi.org/10.1091/mbc.e12-02-0095.

Full text

Abstract:

Transcription-associated recombination is an important process involved in several aspects of cell physiology. In the ribosomal DNA (rDNA) of Saccharomyces cerevisiae, RNA polymerase II transcription–dependent recombination has been demonstrated among the repeated units. In this study, we investigate the mechanisms controlling this process at the chromatin level. On the basis of a small biased screening, we found that mutants of histone deacetylases and chromatin architectural proteins alter both the amount of Pol II–dependent noncoding transcripts and recombination products at rDNA in a coordinated manner. Of interest, chromatin immunoprecipitation analyses in these mutants revealed a corresponding variation of the histone H4 acetylation along the rDNA repeat, particularly at Lys-16. Here we provide evidence that a single, rapid, and reversible posttranslational modification—the acetylation of the H4K16 residue—is involved in the coordination of transcription and recombination at rDNA.

APA, Harvard, Vancouver, ISO, and other styles

38

Becker, Nicole A., and L. James Maher. "High-resolution mapping of architectural DNA binding protein facilitation of a DNA repression loop in Escherichia coli." Proceedings of the National Academy of Sciences 112, no. 23 (May 26, 2015): 7177–82. http://dx.doi.org/10.1073/pnas.1500412112.

Full text

Abstract:

Double-stranded DNA is a locally inflexible polymer that resists bending and twisting over hundreds of base pairs. Despite this, tight DNA bending is biologically important for DNA packaging in eukaryotic chromatin and tight DNA looping is important for gene repression in prokaryotes. We and others have previously shown that sequence nonspecific DNA kinking proteins, such as Escherichia coli heat unstable and Saccharomyces cerevisiae non-histone chromosomal protein 6A (Nhp6A), facilitate lac repressor (LacI) repression loops in E. coli. It has been unknown if this facilitation involves direct protein binding to the tightly bent DNA loop or an indirect effect promoting global negative supercoiling of DNA. Here we adapt two high-resolution in vivo protein-mapping techniques to demonstrate direct binding of the heterologous Nhp6A protein at a LacI repression loop in living E. coli cells.

APA, Harvard, Vancouver, ISO, and other styles

39

Soler-Vila, Paula, Pol Cuscó, Irene Farabella, Marco Di Stefano, and Marc A. Marti-Renom. "Hierarchical chromatin organization detected by TADpole." Nucleic Acids Research 48, no. 7 (February 21, 2020): e39-e39. http://dx.doi.org/10.1093/nar/gkaa087.

Full text

Abstract:

Abstract The rapid development of Chromosome Conformation Capture (3C-based techniques), as well as imaging together with bioinformatics analyses, has been fundamental for unveiling that chromosomes are organized into the so-called topologically associating domains or TADs. While TADs appear as nested patterns in the 3C-based interaction matrices, the vast majority of available TAD callers are based on the hypothesis that TADs are individual and unrelated chromatin structures. Here we introduce TADpole, a computational tool designed to identify and analyze the entire hierarchy of TADs in intra-chromosomal interaction matrices. TADpole combines principal component analysis and constrained hierarchical clustering to provide a set of significant hierarchical chromatin levels in a genomic region of interest. TADpole is robust to data resolution, normalization strategy and sequencing depth. Domain borders defined by TADpole are enriched in main architectural proteins (CTCF and cohesin complex subunits) and in the histone mark H3K4me3, while their domain bodies, depending on their activation-state, are enriched in either H3K36me3 or H3K27me3, highlighting that TADpole is able to distinguish functional TAD units. Additionally, we demonstrate that TADpole's hierarchical annotation, together with the new DiffT score, allows for detecting significant topological differences on Capture Hi-C maps between wild-type and genetically engineered mouse.

APA, Harvard, Vancouver, ISO, and other styles

40

Bell, P., C. Mais, B. McStay, and U. Scheer. "Association of the nucleolar transcription factor UBF with the transcriptionally inactive rRNA genes of pronuclei and early Xenopus embryos." Journal of Cell Science 110, no. 17 (September 1, 1997): 2053–63. http://dx.doi.org/10.1242/jcs.110.17.2053.

Full text

Abstract:

When nuclei (pronuclei) were assembled from sperm chromatin in Xenopus egg extract and examined by immunofluorescence microscopy, UBF was concentrated at a single intranuclear dot-like or more extended necklace-like structure. These UBF-foci contained rDNA as demonstrated by in situ hybridization and hence represent the chromosomal nucleolus organizing regions (NORs). Besides UBF, other components of the transcription machinery such as the TATA-box binding protein (TBP) and RNA polymerase I (pol I) as well as several nucleolar proteins could not be detected at the NORs. Immuno-depletion experiments indicated the UBF is maternally provided and taken up by the pronuclei. Essentially the same results were obtained when we examined the NORs of early Xenopus embryos up to the midblastula stage. After this stage, when transcription of the rRNA genes has begun, nucleoli developed and the NORs acquired TBP and pol I. Our results support the hypothesis that UBF is an architectural element which converts the rDNA chromatin into a transcriptionally competent form.

APA, Harvard, Vancouver, ISO, and other styles

41

Benavente, R., and G. Krohne. "Involvement of nuclear lamins in postmitotic reorganization of chromatin as demonstrated by microinjection of lamin antibodies." Journal of Cell Biology 103, no. 5 (November 1, 1986): 1847–54. http://dx.doi.org/10.1083/jcb.103.5.1847.

Full text

Abstract:

The nuclear lamins are major components of a proteinaceous polymer that is located at the interface of the nuclear membrane and chromatin; these lamins are solubilized and dispersed throughout the cytoplasm during mitosis. It has been postulated that these proteins, assembled into the lamina, provide an architectural framework for the organization of the cell nucleus. To test this hypothesis we microinjected lamin antibodies into cultured PtK2 cells during mitosis, thereby decreasing the soluble pool of lamins. The antibody injected was identified, together with the lamins, in cytoplasmic aggregates by immunoelectron microscopy. We show that microinjected cells are not able to form normal daughter nuclei, in contrast to cells injected with other immunoglobulins. Although cells injected with lamin antibodies are able to complete cytokinesis, the chromatin of their daughter nuclei remains arrested in a telophase-like configuration, and the telophase-like chromatin remains inactive as judged from its condensed state and by the absence of nucleoli. These results indicate that lamins and the nuclear lamina structure are involved in the functional organization of the interphase chromatin.

APA, Harvard, Vancouver, ISO, and other styles

42

Gosalia, Nehal, Daniel Neems, Jenny L. Kerschner, Steven T. Kosak, and Ann Harris. "Architectural proteins CTCF and cohesin have distinct roles in modulating the higher order structure and expression of the CFTR locus." Nucleic Acids Research 42, no. 15 (July 31, 2014): 9612–22. http://dx.doi.org/10.1093/nar/gku648.

Full text

Abstract:

Abstract Higher order chromatin structures across the genome are maintained in part by the architectural proteins CCCTC binding factor (CTCF) and the cohesin complex, which co-localize at many sites across the genome. Here, we examine the role of these proteins in mediating chromatin structure at the cystic fibrosis transmembrane conductance regulator (CFTR) gene. CFTR encompasses nearly 200 kb flanked by CTCF-binding enhancer-blocking insulator elements and is regulated by cell-type-specific intronic enhancers, which loop to the promoter in the active locus. SiRNA-mediated depletion of CTCF or the cohesin component, RAD21, showed that these two factors have distinct roles in regulating the higher order organization of CFTR. CTCF mediates the interactions between CTCF/cohesin binding sites, some of which have enhancer-blocking insulator activity. Cohesin shares this tethering role, but in addition stabilizes interactions between the promoter and cis-acting intronic elements including enhancers, which are also dependent on the forkhead box A1/A2 (FOXA1/A2) transcription factors (TFs). Disruption of the three-dimensional structure of the CFTR gene by depletion of CTCF or RAD21 increases gene expression, which is accompanied by alterations in histone modifications and TF occupancy across the locus, and causes internalization of the gene from the nuclear periphery.

APA, Harvard, Vancouver, ISO, and other styles

43

Popova, Evgenya Y., Sharon Wald Krauss, Sarah A. Short, Gloria Lee, Jonathan Villalobos, Joan Etzell, Mark J. Koury, Paul A. Ney, Joel Anne Chasis, and Sergei A. Grigoryev. "Chromatin condensation in terminally differentiating mouse erythroblasts does not involve special architectural proteins but depends on histone deacetylation." Chromosome Research 17, no. 1 (January 2009): 47–64. http://dx.doi.org/10.1007/s10577-008-9005-y.

Full text

APA, Harvard, Vancouver, ISO, and other styles

44

Raghuram, Nikhil, Gustavo Carrero, John Th’ng, and Michael J. Hendzel. "Molecular dynamics of histone H1This paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process." Biochemistry and Cell Biology 87, no. 1 (February 2009): 189–206. http://dx.doi.org/10.1139/o08-127.

Full text

Abstract:

The histone H1 family of nucleoproteins represents an important class of structural and architectural proteins that are responsible for maintaining and stabilizing higher-order chromatin structure. Essential for mammalian cell viability, they are responsible for gene-specific regulation of transcription and other DNA-dependent processes. In this review, we focus on the wealth of information gathered on the molecular kinetics of histone H1 molecules using novel imaging techniques, such as fluorescence recovery after photobleaching. These experiments have shed light on the effects of H1 phosphorylation and core histone acetylation in influencing chromatin structure and dynamics. We also delineate important concepts surrounding the C-terminal domain of H1, such as the intrinsic disorder hypothesis, and how it affects H1 function. Finally, we address the biochemical mechanisms behind low-affinity H1 binding.

APA, Harvard, Vancouver, ISO, and other styles

45

Bouallaga, Isabelle, Sébastien Teissier, Moshe Yaniv, and Françoise Thierry. "HMG-I(Y) and the CBP/p300 Coactivator Are Essential for Human Papillomavirus Type 18 Enhanceosome Transcriptional Activity." Molecular and Cellular Biology 23, no. 7 (April 1, 2003): 2329–40. http://dx.doi.org/10.1128/mcb.23.7.2329-2340.2003.

Full text

Abstract:

ABSTRACT A strong epithelial specific enhancer drives transcription of the human papillomavirus type 18 (HPV18) oncogenes. Its activity depends on the formation of a higher-order nucleoprotein complex (enhanceosome) involving the sequence-specific JunB/Fra2 transcription factor and the HMG-I(Y) architectural protein. Here we show that proteins from HeLa cell nuclear extract cover almost all of the HPV18 enhancer sequences and that it contains seven binding sites for the purified HMG-I(Y) protein, providing evidence for a tight nucleoprotein structure. Binding of HMG-I(Y) and the AP1 heterodimer from HeLa nuclear extract to overlapping sites of the core enhanceosome is cooperative. The integrity of this specific HMG-I(Y) binding site is as essential as the AP1 binding site for the enhancer function, indicating the fundamental role played by this architectural protein. We demonstrate that the CBP/p300 coactivator is recruited by the HPV18 enhanceosome and that it is limiting for transcriptional activation, since it is sequestered by the adenovirus E1A protein and by the JunB/Fra2 positive factor in excess. We show the involvement of JunB and p300 in vivo in the HPV18 transcription by chromatin immunoprecipitation of HPV18 sequences in HeLa cells.

APA, Harvard, Vancouver, ISO, and other styles

46

Ritt, Christoph, Rudi Grimm, Silvia Fernandez, Juan C. Alonso, and Klaus D. Grasser. "Four differently chromatin-associated maize HMG domain proteins modulate DNA structure and act as architectural elements in nucleoprotein complexes." Plant Journal 14, no. 5 (June 1998): 623–31. http://dx.doi.org/10.1046/j.1365-313x.1998.00154.x.

Full text

APA, Harvard, Vancouver, ISO, and other styles

47

González-Huici, Víctor, Martín Alcorlo, Margarita Salas, and José M. Hermoso. "Phage φ29 Proteins p1 and p17 Are Required for Efficient Binding of Architectural Protein p6 to Viral DNA In Vivo." Journal of Bacteriology 186, no. 24 (December 15, 2004): 8401–6. http://dx.doi.org/10.1128/jb.186.24.8401-8406.2004.

Full text

Abstract:

ABSTRACT Bacteriophage φ29 protein p6 is a viral architectural protein, which binds along the whole linear φ29 DNA in vivo and is involved in initiation of DNA replication and transcription control. Protein p1 is a membrane-associated viral protein, proposed to attach the viral genome to the cell membrane. Protein p17 is involved in pulling φ29 DNA into the cell during the injection process. We have used chromatin immunoprecipitation and real-time PCR to analyze in vivo p6 binding to DNA in cells infected with φ29 sus1 or sus17 mutants; in both cases p6 binding is significantly decreased all along φ29 DNA. φ29 DNA is topologically constrained in vivo, and p6 binding is highly increased in the presence of novobiocin, a gyrase inhibitor that produces a loss of DNA negative superhelicity. Here we show that, in cells infected with φ29 sus1 or sus17 mutants, the increase of p6 binding by novobiocin is even higher than in cells containing p1 and p17, alleviating the p6 binding deficiency. Therefore, proteins p1 and p17 could be required to restrain the proper topology of φ29 DNA, which would explain the impaired DNA replication observed in cells infected with sus1 or sus17 mutants.

APA, Harvard, Vancouver, ISO, and other styles

48

Scaffidi, Paola, and Marco E. Bianchi. "Spatially Precise DNA Bending Is an Essential Activity of the Sox2 Transcription Factor." Journal of Biological Chemistry 276, no. 50 (October 2, 2001): 47296–302. http://dx.doi.org/10.1074/jbc.m107619200.

Full text

Abstract:

Sox proteins, a subclass of high mobility group box proteins, govern cell fate decisions by acting both as classical transcription factors and architectural components of chromatin. We aimed to demonstrate that the DNA bending activity of Sox proteins is essential to regulate gene expression. We focused on mouse Sox2, which participates in the transactivation of theFgf4(fibroblastgrowthfactor4) gene in the inner cell mass of the blastocyst. We generated six substitutions in the high mobility group box of Sox2. One mutant showed a reduced DNA bending activity on theFgf4enhancer (46° instead of 80°), which resulted in more powerful transactivation compared with the wild type protein. We then selected two single-base mutations in theFgf4enhancer that make the DNA less bendable by the Sox2 protein. Again, a different DNA bend (0° and 42° instead of 80°) resulted in a different activation of transcription, but in this case reduced bending corresponded to decreased transcription. We found that the opposite effect on transcription of similar DNA bending angles is due to a 20° difference in the relative orientation of the DNA bends, proving that a correct three-dimensional geometry of enhanceosome complexes is necessary to promote transcription.

APA, Harvard, Vancouver, ISO, and other styles

49

Agoston, D. v., and A. Dobi. "Complexity of transcriptional control in neuropeptide gene expression; enkephalin gene regulation during neurodevelopment." Biochemical Society Transactions 28, no. 4 (August 1, 2000): 446–51. http://dx.doi.org/10.1042/bst0280446.

Full text

Abstract:

The gene for enkephalin is expressed only in specific subsets of neurons in the mammalian central nervous system (CNS), whereas the large majority of neurons do not express the gene. This restricted expression is the result of a developmental process during which some of the multi-potent neural progenitors express the gene for enkephalin and thereby become enkephalinergic neurons. The regulation of this process is not well understood. We have used a novel approach to identify DNA-protein interactions that regulate the developmental expression of the gene for enkephalin. We have identified four novel DNA regulatory sites and their binding proteins that are expressed in the developing mammalian CNS. These protein-DNA interactions regulate DNA and nuclear structures through DNA bending, DNA sliding, chromatin remodelling and far-distant DNA interactions. The concerted and coordinated interactions of these four DNA elements and their binding proteins contribute to the guiding of multipotent neural progenitors into enkephalinergic neurons. The provided examples suggest an important role for architectural transcriptional regulation during CNS development.

APA, Harvard, Vancouver, ISO, and other styles

50

Guelman, Sebastián, Kenji Kozuka, Yifan Mao, Victoria Pham, Mark J. Solloway, John Wang, Jiansheng Wu, Jennie R. Lill, and Jiping Zha. "The Double-Histone-Acetyltransferase Complex ATAC Is Essential for Mammalian Development." Molecular and Cellular Biology 29, no. 5 (December 22, 2008): 1176–88. http://dx.doi.org/10.1128/mcb.01599-08.

Full text

Abstract:

ABSTRACT Acetylation of the histone tails, catalyzed by histone acetyltransferases (HATs), is a well-studied process that contributes to transcriptionally active chromatin states. Here we report the characterization of a novel mammalian HAT complex, which contains the two acetyltransferases GCN5 and ATAC2 as well as other proteins linked to chromatin metabolism. This multisubunit complex has a similar but distinct subunit composition to that of the Drosophila ADA2A-containing complex (ATAC). Recombinant ATAC2 has a weak HAT activity directed to histone H4. Moreover, depletion of ATAC2 results in the disassembly of the complex, indicating that ATAC2 not only carries out an enzymatic function but also plays an architectural role in the stability of mammalian ATAC. By targeted disruption of the Atac2 locus in mice, we demonstrate for the first time the essential role of the ATAC complex in mammalian development, histone acetylation, cell cycle progression, and prevention of apoptosis during embryogenesis.

APA, Harvard, Vancouver, ISO, and other styles

Journal articles on the topic 'Chromatin Architectural Proteins'

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles