Replicating chromatin: a tale of histonesThis 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.

2009 ◽  
Vol 87 (1) ◽  
pp. 51-63 ◽  
Author(s):  
Anja Groth
Keyword(s):  
Gene Expression ◽  
Genome Stability ◽  
Peer Review Process ◽  
Replication Forks ◽  
Chromatin Dynamics ◽  
Functional Roles ◽  
Structural Framework ◽  
Dna Strands ◽  
Gain Access ◽  
Selection Of

Chromatin serves structural and functional roles crucial for genome stability and correct gene expression. This organization must be reproduced on daughter strands during replication to maintain proper overlay of epigenetic fabric onto genetic sequence. Nucleosomes constitute the structural framework of chromatin and carry information to specify higher-order organization and gene expression. When replication forks traverse the chromosomes, nucleosomes are transiently disrupted, allowing the replication machinery to gain access to DNA. Histone recycling, together with new deposition, ensures reassembly on nascent DNA strands. The aim of this review is to discuss how histones — new and old — are handled at the replication fork, highlighting new mechanistic insights and revisiting old paradigms.

Transcriptional and epigenetic functions of histone variant H2A.ZThis 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.

2009 ◽  
Vol 87 (1) ◽  
pp. 19-25 ◽  
Author(s):  
Ryan Draker ◽  
Peter Cheung
Keyword(s):  
Gene Expression ◽  
Peer Review Process ◽  
Regulation Of Gene Expression ◽  
Histone Variants ◽  
Histone Variant ◽  
Post Translational Modifications ◽  
Chromatin Dynamics ◽  
Transcription Process ◽  
A Genome ◽  
Selection Of

The chromatin organization of a genome ultimately dictates the gene expression profile of the cell. It is now well recognized that key mechanisms that regulate chromatin structure include post-translational modifications of histones and the incorporation of histone variants at strategic sites within the genome. H2A.Z is a variant of H2A that is localized to the 5′ end of many genes and is required for proper regulation of gene expression. However, its precise function in the transcription process is not yet well defined. In this review, we discuss some of the recent findings related to this histone variant, how it associates with other histone epigenetic marks, and how post-translational modifications of H2A.Z further define its function.

Regulation of gene expression and cellular proliferation by histone H2A.ZThis 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.

2009 ◽  
Vol 87 (1) ◽  
pp. 179-188 ◽  
Author(s):  
Amy Svotelis ◽  
Nicolas Gévry ◽  
Luc Gaudreau
Keyword(s):  
Gene Expression ◽  
Transcriptional Activation ◽  
Mammalian Cells ◽  
Cellular Proliferation ◽  
Replicative Senescence ◽  
Peer Review Process ◽  
Regulation Of Gene Expression ◽  
Histone Variants ◽  
Chromatin Dynamics ◽  
Cycle Arrest

The mammalian genome is organized into a structure of DNA and proteins known as chromatin. In general, chromatin presents a barrier to gene expression that is regulated by several pathways, namely by the incorporation of histone variants into the nucleosome. In yeast, H2A.Z is an H2A histone variant that is incorporated into nucleosomes as an H2A.Z/H2B dimer by the Swr1 complex and by the SRCAP and p400/Tip60 complexes in mammalian cells. H2A.Z has been associated with the poising of genes for transcriptional activation in the yeast model system, and is essential for development in higher eukaryotes. Recent studies in our laboratory have demonstrated a p400-dependent deposition of H2A.Z at the promoter of p21WAF1/CIP1, a consequence that prevents the activation of the gene by p53, thereby inhibiting p53-dependent replicative senescence, a form of cell-cycle arrest crucial in the prevention of carcinogenic transformation of cells. Moreover, H2A.Z is overexpressed in several different types of cancers, and its overexpression has been associated functionally with the proliferation state of cells. Therefore, we suggest that H2A.Z is an important regulator of gene expression, and its deregulation may lead to the increased proliferation of mammalian cells.

Src kinase Hck association with the WASp and mDia1 cytoskeletal regulators promotes chemoattractant-induced Hck membrane targeting and activation in neutrophilsThis 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.

2009 ◽  
Vol 87 (1) ◽  
pp. 207-216 ◽  
Author(s):  
Yongquan Shi ◽  
Baoxia Dong ◽  
Helen Miliotis ◽  
Junye Liu ◽  
Arthur S. Alberts ◽  
...  
Keyword(s):  
Tyrosine Phosphorylation ◽  
Actin Polymerization ◽  
Peer Review Process ◽  
Leading Edge ◽  
Membrane Targeting ◽  
Chromatin Dynamics ◽  
Severe Impairment ◽  
Syndrome Protein ◽  
Proline Rich Region ◽  
Selection Of

The haemopoietic cell kinase (Hck) plays an important but poorly understood role in coupling chemoattractant stimuli to the actin cytoskeletal rearrangement required for neutrophil polarization and chemotaxis. Here, we show that Hck coimmunoprecipitates with the cytoskeletal regulatory Wiskott–Aldrich syndrome protein (WASp) and mammalian diaphanous-related formin 1 (mDia1) in chemoattractant-stimulated neutrophils, and that the 3 proteins inducibly colocalize with one another at the leading edge of chemotaxing cells. Hck interaction with WASp was found to be mediated by the Hck SH3 domain binding to the WASp proline-rich region, while Hck interaction with mDia1 was indirect but was required for binding to WASp. In contrast to wild-type cells, both WASp- and mDia1-deficient neutrophils showed severe impairment of chemokine-induced Hck membrane translocation and induction of Hck binding to WASp, and Hck activation and WASp tyrosine phosphorylation were impaired in mDia1−/− cells. Thus, chemotactic stimulation appears to induce an mDia1/Hck/WASp complex required for Hck membrane targeting and for induction of the Hck-mediated WASp tyrosine phosphorylation thought to be required for WASp-driven actin polymerization. These findings reveal that Hck functions in neutrophils to be realized, at least in part, via its interaction with mDia1 and WASp, and identifies the mDia1/Hck/WASp axis as a cytoskeletal signaling interface linking tyrosine phosphorylation to chemotactic and, possibly, other actin-based neutrophil responses.

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.

2009 ◽  
Vol 87 (1) ◽  
pp. 189-206 ◽  
Author(s):  
Nikhil Raghuram ◽  
Gustavo Carrero ◽  
John Th’ng ◽  
Michael J. Hendzel
Keyword(s):  
Chromatin Structure ◽  
Peer Review Process ◽  
Imaging Techniques ◽  
Histone H1 ◽  
Regulation Of Transcription ◽  
Chromatin Dynamics ◽  
Biochemical Mechanisms ◽  
Specific Regulation ◽  
Kinetics Of ◽  
Selection Of

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.

YEATS domain proteins: a diverse family with many links to chromatin modification and transcriptionThis 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.

2009 ◽  
Vol 87 (1) ◽  
pp. 65-75 ◽  
Author(s):  
Julia M. Schulze ◽  
Alice Y. Wang ◽  
Michael S. Kobor
Keyword(s):  
Review Process ◽  
Protein Complexes ◽  
Peer Review Process ◽  
Chromatin Modification ◽  
Biological Processes ◽  
Chromatin Modifications ◽  
Domain Family ◽  
Chromatin Dynamics ◽  
Eukaryotic Species ◽  
Selection Of

Chromatin modifications play crucial roles in various biological processes. An increasing number of conserved protein domains, often found in multisubunit protein complexes, are involved in establishing and recognizing different chromatin modifications. The YEATS domain is one of these domains, and its role in chromatin modifications and transcription is just beginning to be appreciated. The YEATS domain family of proteins, conserved from yeast to human, contains over 100 members in more than 70 eukaryotic species. Yaf9, Taf14, and Sas5 are the only YEATS domain proteins in Saccharomyces cerevisiae. Human YEATS domain family members, such as GAS41, ENL, and AF9, have a strong link to cancer. GAS41 is amplified in glioblastomas and astrocytomas; ENL and AF9 are among the most frequent translocation partners of the mixed lineage leukemia (MLL) gene. This review will focus on the best characterized YEATS proteins, discuss their diverse roles, and reflect potential functions of the YEATS domain.

Regulatory noncoding RNAs at Hox lociThis 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.

2009 ◽  
Vol 87 (1) ◽  
pp. 27-34 ◽  
Author(s):  
Hugh W. Brock ◽  
Jacob W. Hodgson ◽  
Svetlana Petruk ◽  
Alexander Mazo
Keyword(s):  
Gene Expression ◽  
Hox Genes ◽  
Peer Review Process ◽  
Regulation Of Gene Expression ◽  
Chromatin Dynamics ◽  
Spatial Regulation ◽  
Positional Identity ◽  
In Trans ◽  
In Cis

There is growing awareness of the importance of noncoding (nc)RNAs in the regulation of gene expression during pattern formation in development. Spatial regulation of Hox gene expression in development controls positional identity along the antero–posterior axis. In this review, we will focus on the role of short ncRNAs that repress Hox genes in Drosophila and mammals by RNA interference (RNAi), on long ncRNAs that may repress a Hox in cis in Drosophila by transcriptional interference, and on a novel long ncRNA that functions in trans to regulate Hox genes mammals.

New developments in post-translational modifications and functions of histone H2A variantsThis 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.

2009 ◽  
Vol 87 (1) ◽  
pp. 7-17 ◽  
Author(s):  
Anita A. Thambirajah ◽  
Andra Li ◽  
Toyotaka Ishibashi ◽  
Juan Ausió
Keyword(s):  
Review Process ◽  
Peer Review Process ◽  
Histone Variants ◽  
Histone H2a ◽  
Post Translational Modifications ◽  
New Developments ◽  
Chromatin Dynamics ◽  
Recent Developments ◽  
The Individual ◽  
Selection Of

Structural variability within histone families, such as H2A, can be achieved through 2 primary mechanisms: the expression of histone variants and the incorporation of chemical modifications. The histone H2A family contains several variants in addition to the canonical H2A forms. In this review, recent developments in the study of the heteromorphous variants H2A.X, H2A.Z, and macroH2A will be discussed. Particular focus will be given to the post-translational modifications (PTMs) of these variants, including phosphorylation, ubiquitination, acetylation, and methylation. The combination of the newly identified N- and C-terminal tail PTMs expands the multiplicity of roles that the individual H2A variants can perform. It is of additional interest that analogous sites within these different histone variants can be similarly modified. Whether this is a redundant function or a finely tuned one, designed to meet specific needs, remains to be elucidated.

scholarly journals Transcription-factor-mediated epigenetic control of cell fate and lineage commitmentThis 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.

2009 ◽  
Vol 87 (1) ◽  
pp. 1-6 ◽  
Author(s):  
Gary S. Stein ◽  
Sayyed K. Zaidi ◽  
Janet L. Stein ◽  
Jane B. Lian ◽  
Andre J. van Wijnen ◽  
...  
Keyword(s):  
Cell Fate ◽  
Target Gene ◽  
Peer Review Process ◽  
Regulatory Proteins ◽  
Chromatin Dynamics ◽  
Epigenetic Control ◽  
Regulatory Machinery ◽  
Transcriptional Regulatory ◽  
Proliferation And Differentiation ◽  
Selection Of

Epigenetic control is required to maintain competency for the activation and suppression of genes during cell division. The association between regulatory proteins and target gene loci during mitosis is a parameter of the epigenetic control that sustains the transcriptional regulatory machinery that perpetuates gene-expression signatures in progeny cells. The mitotic retention of phenotypic regulatory factors with cell cycle, cell fate, and tissue-specific genes supports the coordinated control that governs the proliferation and differentiation of cell fate and lineage commitment.

Structure and function of histone methylation binding proteinsThis 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.

2009 ◽  
Vol 87 (1) ◽  
pp. 93-105 ◽  
Author(s):  
Melanie A. Adams-Cioaba ◽  
Jinrong Min
Keyword(s):  
Histone Methylation ◽  
Review Process ◽  
Current Knowledge ◽  
Peer Review Process ◽  
Covalent Modification ◽  
Chromatin Dynamics ◽  
Plant Homeodomain ◽  
And Function ◽  
Histone Exchange ◽  
Selection Of

Chromatin structure is regulated by chromatin remodeling factors, histone exchange, linker histone association, and histone modification. Covalent modification of histones is an important factor in the regulation of the associated processes. The implementation and removal of various histone modifications have been implicated in DNA replication, repair, recombination, and transcription, and in RNA processing. In recent years, histone methylation has emerged as one of the key modifications regulating chromatin function. However, the mechanisms involved are complex and not well understood. A large volume of structural and biochemical information has been recently amassed for the Tudor, plant homeodomain (PHD), and malignant brain tumor (MBT) protein families. This review summarizes current knowledge of the structures and modes of recognition employed by the PHD, Tudor, and MBT domains in their interactions with target histone peptides.

Selection of reliable reference genes for analysis of gene expression in the rat placenta

2021 ◽  
Author(s):  
Caiyun Ge ◽  
Pengxia Yu ◽  
Man Fang ◽  
Hui Wang ◽  
Yuanzhen Zhang
Keyword(s):  
Gene Expression ◽  
Reference Genes ◽  
Selection Of
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