The basic structure of chromatin

2019 ◽  
pp. 7-16
Author(s):  
John C. Lucchesi
Keyword(s):  
Dna Replication ◽  
Chromatin Remodeling ◽  
Functional State ◽  
Basic Structure ◽  
Chromatin Fiber ◽  
Damage Repair ◽  
Core Histones ◽  
Chromatin Remodeling Complexes ◽  
Degree Of Condensation ◽  
Active Genes

In cells, DNA is associated with histones, non-histone proteins and RNA in a complex referred to as chromatin. Four different types of histones form octamers (nucleosomes), around which DNA is wrapped yielding a chromatin fiber with the configuration of “beads on a string.” Disassembly, followed by reassembly, of this structure occurs during DNA replication, damage repair and transcription. Core histones are replication-coupled; variants are replication-independent. Positioning of nucleosomes on the chromatin fiber is mediated by chromatin remodeling complexes and reflects the functional state of various regions along the fiber. Various biophysical methods have been utilized to study the physical association of nucleosomes and DNA. Chromatin can be differentiated on the basis of the activity of the genes that are present in a given region. Heterochromatin represents repressed or inactive regions of the genome and exhibits a greater degree of condensation than euchromatin, which refers to more unwound regions where active genes are located. The two types of chromatin are present in different nuclear locations.

scholarly journals Chromatin remodeler Fft3 plays a dual role at blocked DNA replication forks

2019 ◽  
Vol 2 (5) ◽  
pp. e201900433 ◽  
Author(s):  
Anissia Ait-Saada ◽  
Olga Khorosjutina ◽  
Jiang Chen ◽  
Karol Kramarz ◽  
Vladimir Maksimov ◽  
...  
Keyword(s):  
Dna Damage ◽  
Dna Replication ◽  
Fission Yeast ◽  
Chromatin Remodeling ◽  
Replication Fork ◽  
Strand Break ◽  
Replication Forks ◽  
Damage Repair ◽  
Single Strand Annealing ◽  
Strand Annealing

Here, we investigate the function of fission yeast Fun30/Smarcad1 family of SNF2 ATPase-dependent chromatin remodeling enzymes in DNA damage repair. There are three Fun30 homologues in fission yeast, Fft1, Fft2, and Fft3. We find that only Fft3 has a function in DNA repair and it is needed for single-strand annealing of an induced double-strand break. Furthermore, we use an inducible replication fork barrier system to show that Fft3 has two distinct roles at blocked DNA replication forks. First, Fft3 is needed for the resection of nascent strands, and second, it is required to restart the blocked forks. The latter function is independent of its ATPase activity.

scholarly journals SWR1 Chromatin Remodeling Complex: A Key Transcriptional Regulator in Plants

Cells ◽  
2019 ◽  
Vol 8 (12) ◽  
pp. 1621 ◽  
Author(s):  
Mohammad Aslam ◽  
Beenish Fakher ◽  
Bello Hassan Jakada ◽  
Shijiang Cao ◽  
Yuan Qin
Keyword(s):  
Chromatin Remodeling ◽  
Dna Accessibility ◽  
Physiological Processes ◽  
Chromatin Remodeling Complex ◽  
Damage Repair ◽  
Eukaryotic Chromatin ◽  
Chromatin Remodeling Complexes ◽  
Cellular Machinery ◽  
Environmental Responses

The nucleosome is the structural and fundamental unit of eukaryotic chromatin. The chromatin remodeling complexes change nucleosome composition, packaging and positioning to regulate DNA accessibility for cellular machinery. SWI2/SNF2-Related 1 Chromatin Remodeling Complex (SWR1-C) belongs to the INO80 chromatin remodeling family and mainly catalyzes the exchange of H2A-H2B with the H2A.Z-H2B dimer. The replacement of H2A.Z into nucleosomes affects nucleosome stability and chromatin structure. Incorporation of H2A.Z into the chromatin and its physiochemical properties play a key role in transcriptional regulation during developmental and environmental responses. In Arabidopsis, various studies have uncovered several pivotal roles of SWR1-C. Recently, notable progress has been achieved in understanding the role of SWR1-C in plant developmental and physiological processes such as DNA damage repair, stress tolerance, and flowering time. The present article introduces the SWR1-C and comprehensively reviews recent discoveries made in understanding the function of the SWR1 complex in plants.

Chromatin remodeling complexes: ATP-dependent machines in action

2005 ◽  
Vol 83 (4) ◽  
pp. 405-417 ◽  
Author(s):  
Cotteka N Johnson ◽  
Nicholas L Adkins ◽  
Philippe Georgel
Keyword(s):  
Chromatin Remodeling ◽  
Atp Hydrolysis ◽  
Nucleosome Remodeling ◽  
Core Histones ◽  
Associated Proteins ◽  
Chromatin Template ◽  
Chromatin Remodeling Complexes ◽  
The Individual ◽  
Insight Into

Since the initial characterization of chromatin remodeling as an ATP-dependent process, many studies have given us insight into how nucleosome-remodeling complexes can affect various nuclear functions. However, the multistep DNA-histone remodeling process has not been completely elucidated. Although new studies are published on a nearly weekly basis, the nature and roles of interactions of the individual SWI/SNF- and ISWI-based remodeling complexes and DNA, core histones, and other chromatin-associated proteins are not fully understood. In addition, the potential changes associated with ATP recruitment and its subsequent hydrolysis have not been fully characterized. This review explores possible mechanisms by which chromatin-remodeling complexes are recruited to specific loci, use ATP hydrolysis to achieve actual remodeling through disruption of DNA-histone interactions, and are released from their chromatin template. We propose possible roles for ATP hydrolysis in a chromatin-release/target-scanning process that offer an alternative to or complement the often overlooked function of delivering the energy required for sliding or dislodging specific subsets of core histones.Key words: chromatin remodeling, SWI/SNF, ISWI, APT hydrolysis.

Rvb1–Rvb2: essential ATP-dependent helicases for critical complexesThis paper is one of a selection of papers published in this special issue entitled 8th International Conference on AAA Proteins and has undergone the Journal's usual peer review process.

2010 ◽  
Vol 88 (1) ◽  
pp. 29-40 ◽  
Author(s):  
Jennifer Huen ◽  
Yoshito Kakihara ◽  
Francisca Ugwu ◽  
Kevin L. Y. Cheung ◽  
Joaquin Ortega ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Homo Sapiens ◽  
Peer Review Process ◽  
Cellular Processes ◽  
Damage Repair ◽  
Wide Range ◽  
Chromatin Remodeling Complexes ◽  
Polycomb Repressive Complex 1 ◽  
Brahma Complex ◽  
Regulation Of Growth

Rvb1 and Rvb2 are highly conserved, essential AAA+ helicases found in a wide range of eukaryotes. The versatility of these helicases and their central role in the biology of the cell is evident from their involvement in a wide array of critical cellular complexes. Rvb1 and Rvb2 are components of the chromatin-remodeling complexes INO80, Swr-C, and BAF. They are also members of the histone acetyltransferase Tip60 complex, and the recently identified R2TP complex present in Saccharomyces cerevisiae and Homo sapiens; a complex that is involved in small nucleolar ribonucleoprotein (snoRNP) assembly. Furthermore, in humans, Rvb1 and Rvb2 have been identified in the URI prefoldin-like complex. In Drosophila, the Polycomb Repressive complex 1 contains Rvb2, but not Rvb1, and the Brahma complex contains Rvb1 and not Rvb2. Both of these complexes are involved in the regulation of growth and development genes in Drosophila. Rvbs are therefore crucial factors in various cellular processes. Their importance in chromatin remodeling, transcription regulation, DNA damage repair, telomerase assembly, mitotic spindle formation, and snoRNP biogenesis is discussed in this review.

scholarly journals Roles of the INO80 and SWR1 Chromatin Remodeling Complexes in Plants

2019 ◽  
Vol 20 (18) ◽  
pp. 4591 ◽  
Author(s):  
Jianhao Wang ◽  
Sujuan Gao ◽  
Xiuling Peng ◽  
Keqiang Wu ◽  
Songguang Yang
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Gene Regulation ◽  
Dna Replication ◽  
Chromatin Remodeling ◽  
Eukaryotic Genes ◽  
Eukaryotic Gene ◽  
Chromatin Remodeling Complexes ◽  
Eukaryotic Gene Regulation ◽  
Environmental Responses

Eukaryotic genes are packed into a dynamic but stable nucleoprotein structure called chromatin. Chromatin-remodeling and modifying complexes generate a dynamic chromatin environment that ensures appropriate DNA processing and metabolism in various processes such as gene expression, as well as DNA replication, repair, and recombination. The INO80 and SWR1 chromatin remodeling complexes (INO80-c and SWR1-c) are ATP-dependent complexes that modulate the incorporation of the histone variant H2A.Z into nucleosomes, which is a critical step in eukaryotic gene regulation. Although SWR1-c has been identified in plants, plant INO80-c has not been successfully isolated and characterized. In this review, we will focus on the functions of the SWR1-c and putative INO80-c (SWR1/INO80-c) multi-subunits and multifunctional complexes in Arabidopsis thaliana. We will describe the subunit compositions of the SWR1/INO80-c and the recent findings from the standpoint of each subunit and discuss their involvement in regulating development and environmental responses in Arabidopsis.

scholarly journals ARID1A regulates R-loop associated DNA replication stress

PLoS Genetics ◽  
2021 ◽  
Vol 17 (4) ◽  
pp. e1009238
Author(s):  
Shuhe Tsai ◽  
Louis-Alexandre Fournier ◽  
Emily Yun-chia Chang ◽  
James P. Wells ◽  
Sean W. Minaker ◽  
...  
Keyword(s):  
Dna Replication ◽  
Chromatin Remodeling ◽  
Genome Stability ◽  
Replication Stress ◽  
Clear Cell Ovarian Carcinoma ◽  
Chromatin Remodeling Complexes ◽  
Dna Replication Stress ◽  
Cancer Types ◽  
The Impact ◽  
Transcription And Replication

ARID1A is a core DNA-binding subunit of the BAF chromatin remodeling complex, and is lost in up to 7% of all cancers. The frequency of ARID1A loss increases in certain cancer types, such as clear cell ovarian carcinoma where ARID1A protein is lost in about 50% of cases. While the impact of ARID1A loss on the function of the BAF chromatin remodeling complexes is likely to drive oncogenic gene expression programs in specific contexts, ARID1A also binds genome stability regulators such as ATR and TOP2. Here we show that ARID1A loss leads to DNA replication stress associated with R-loops and transcription-replication conflicts in human cells. These effects correlate with altered transcription and replication dynamics in ARID1A knockout cells and to reduced TOP2A binding at R-loop sites. Together this work extends mechanisms of replication stress in ARID1A deficient cells with implications for targeting ARID1A deficient cancers.

scholarly journals Plasmodium falciparum Histone Acetyltransferase, a Yeast GCN5 Homologue Involved in Chromatin Remodeling

2004 ◽  
Vol 3 (2) ◽  
pp. 264-276 ◽  
Author(s):  
Qi Fan ◽  
Lijia An ◽  
Liwang Cui
Keyword(s):  
Plasmodium Falciparum ◽  
Chromatin Remodeling ◽  
Transcriptional Activation ◽  
Histone Acetyltransferase ◽  
Northern Analysis ◽  
Binding Assays ◽  
Core Histones ◽  
Chromatin Remodeling Complexes

ABSTRACT The yeast transcriptional coactivator GCN5 (yGCN5), a histone acetyltransferase (HAT), is part of large multimeric complexes that are required for chromatin remodeling and transcriptional activation. Like other eukaryotes, the malaria parasite DNA is organized into nucleosomes and the genome encodes components of chromatin-remodeling complexes. Here we show that GCN5 is conserved in Plasmodium species and that the most homologous regions are within the HAT domain and the bromodomain. The Plasmodium falciparum GCN5 homologue (PfGCN5) is spliced with three introns, encoding a protein of 1,464 residues. Mapping of the ends of the PfGCN5 transcript suggests that the mRNA is 5.2 to 5.4 kb, consistent with the result from Northern analysis. Using free core histones, we determined that recombinant PfGCN5 proteins have conserved HAT activity with a substrate preference for histone H3. Using substrate-specific antibodies, we determined that both Lys-8 and -14 of H3 were acetylated by the recombinant PfGCN5. In eukaryotes, GCN5 homologues interact with yeast ADA2 homologues and form large multiprotein HAT complexes. We have identified an ADA2 homologue in P. falciparum, PfADA2. Yeast two-hybrid and in vitro binding assays verified the interactions between PfGCN5 and PfADA2, suggesting that they may be associated with each other in vivo. The conserved function of the HAT domain in PfGCN5 was further illustrated with yeast complementation experiments, which showed that the PfGCN5 region corresponding to the full-length yGCN5 could partially complement the yGCN5 deletion mutation. Furthermore, a chimera comprising the PfGCN5 HAT domain fused to the remainder of yeast GCN5 (yGCN5) fully rescued the yGCN5 deletion mutant. These data demonstrate that PfGCN5 is an authentic GCN5 family member and may exist in chromatin-remodeling complexes to regulate gene expression in P. falciparum.

scholarly journals p300-Mediated acetylation facilitates the transfer of histone H2A–H2B dimers from nucleosomes to a histone chaperone

2000 ◽  
Vol 14 (15) ◽  
pp. 1899-1907 ◽  
Author(s):  
Takashi Ito ◽  
Tsuyoshi Ikehara ◽  
Takeya Nakagawa ◽  
W. Lee Kraus ◽  
Masami Muramatsu
Keyword(s):  
Histone Acetylation ◽  
Chromatin Remodeling ◽  
Transcriptional Activator ◽  
Histone Chaperone ◽  
Assembly System ◽  
Transcriptional Activators ◽  
Histone H2a ◽  
Nucleosome Structure ◽  
Core Histones ◽  
Chromatin Remodeling Complexes

We have used a purified recombinant chromatin assembly system, including ACF (Acf-1 + ISWI) and NAP-1, to examine the role of histone acetylation in ATP-dependent chromatin remodeling. The binding of a transcriptional activator (Gal4–VP16) to chromatin assembled using this recombinant assembly system dramatically enhances the acetylation of nucleosomal core histones by the histone acetyltransferase p300. This effect requires both the presence of Gal4-binding sites in the template and the VP16-activation domain. Order-of-addition experiments indicate that prior activator-meditated, ATP-dependent chromatin remodeling by ACF is required for the acetylation of nucleosomal histones by p300. Thus, chromatin remodeling, which requires a transcriptional activator, ACF and ATP, is an early step in the transcriptional process that regulates subsequent core histone acetylation. Glycerol gradient sedimentation and immunoprecipitation assays demonstrate that the acetylation of histones by p300 facilitates the transfer of H2A–H2B from nucleosomes to NAP-1. The results from these biochemical experiments suggest that (1) transcriptional activators (e.g., Gal4–VP16) and chromatin remodeling complexes (e.g., ACF) induce chromatin remodeling in the absence of histone acetylation; (2) transcriptional activators recruit histone acetyltransferases (e.g., p300) to promoters after chromatin remodeling has occurred; and (3) histone acetylation is important for a step subsequent to chromatin remodeling and results in the transfer of histone H2A–H2B dimers from nucleosomes to a histone chaperone such as NAP-1. Our results indicate a precise role for histone acetylation, namely to alter the structure of nucleosomes (e.g., facilitate the loss of H2A–H2B dimers) that have been remodeled previously by the action of ATP-dependent chromatin remodeling complexes. Thus, transcription from chromatin templates is ordered and sequential, with precise timing and roles for ATP-dependent chromatin remodeling, subsequent histone acetylation, and alterations in nucleosome structure.

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