Topics

Heterogeneous fluid-like movements of chromatin and their implications to transcription.

08:00 EDT 23rd March 2020 | BioPortfolio

Summary of "Heterogeneous fluid-like movements of chromatin and their implications to transcription."

Eukaryotic chromatin is a complex of genome DNA and associated proteins, and its structure and dynamics play a crucial role in regulating DNA functions. Chromatin takes rather irregular structures in the nucleus and exhibits heterogeneous sub-diffusive movements as polymers fluctuating in a fluid state. Using genome-wide single-nucleosome tracking data, heterogeneity of movements was statistically analyzed, which categorized chromatin into two types: slow chromatin that moves under structurally constrained environments and fast chromatin that moves with less constraints. Interactions of chromatin to various protein factors determine the motional constraints. For example, loss of the cohesin complex that bundles the chromatin chains reduces the motional constraints and increases the population of fast chromatin. Another example is the transcriptional machinery. While it was previously thought that the transcriptional activity is associated with more open and dynamic chromatin structure, recent studies suggested a more nuanced role of transcription in chromatin dynamics: dynamic association/dissociation of active RNA polymerase II (RNAPII) and other transcription factors and Mediators (TF-Meds) transiently bridges transcriptionally active DNA regions, which forms a loose network of chromatin and constrains chromatin movement, enhancing the slow chromatin population. This new view on the dynamical effects of transcription urges a reflection on the traditional model of transcription factories and invites the more recent models of condensates/phase-separated liquid droplets of RNAPII, transcription factors, and Mediators. The combined procedure of genome-wide single-nucleosome tracking and its statistical analysis would unveil heterogeneity in the chromatin movement, which should provide a key to understanding the relations among chromatin dynamics, structure, and function.

Affiliation

Journal Details

This article was published in the following journal.

Name: Biophysical reviews
ISSN: 1867-2450
Pages:

Links

DeepDyve research library

PubMed Articles [10901 Associated PubMed Articles listed on BioPortfolio]

Structural transition of the nucleosome during chromatin remodeling and transcription.

In eukaryotes, the nucleosome is the basic unit of chromatin. Since the genomic DNA is tightly wrapped around the histone octamer in the nucleosome, its function is severely restricted in chromatin. T...

Chromatin dynamics and the transcriptional competence of HSV-1 genomes during lytic infections.

During latent infections with herpes simplex virus 1 (HSV-1), viral transcription is restricted and the genomes are mostly maintained in silenced chromatin, whereas in lytically infected cells all vir...

Chromatin domains in space and their functional implications.

Genome organization displays functional compartmentalization. Many factors, including epigenetic modifications, transcription factors, chromatin remodelers, and RNAs, shape chromatin domains and the t...

The Hsp90 Molecular Chaperone Regulates the Transcription Factor Network Controlling Chromatin Accessibility.

Genomic events including gene regulation and chromatin status are controlled by transcription factors. Here we report that the Hsp90 molecular chaperone broadly regulates the transcription factor prot...

Bon voyage: A transcriptional journey around DNA breaks.

DNA double-strand breaks (DSBs) affect chromatin integrity and impact DNA-dependent processes such as transcription. Several studies revealed that the transcription of genes located in close proximity...

Clinical Trials [3855 Associated Clinical Trials listed on BioPortfolio]

Cerebrospinal Fluid Movements Through Interventricular Foramina in Phase Contrast Magnetic Resonance Imaging (PC-MRI)

Assess the reproductability of PC-MRI for cerebrospinal fluid movements through the interventricular foramina on volunteer subjects.

Effect of Seminal Fluid on the Colon Wall; Implications for HIV Transmission

This research is being done to learn how seminal fluid affects the lining of the colon, and whether this might make it easier for HIV to get into the body and cause infection.

Disturbances of Kynurenine Pathway of Trytophan Metabolism in Schizophrenia: A Quantitative Reverse Transcription Polymerase Chain Reaction (RT-PCR) Study

In this pilot study, the investigators propose to characterize the pattern of activation of the kynurenine pathway of tryptophan metabolism in peripheral macrophages of patients with schiz...

Intraoperative Fluid Therapy for Deceased Donor Renal Transplantation

Delayed graft function (DGF) is defined as requirement for dialysis in the first week following kidney transplantation. DGF is a common complication occurring in 39% of the deceased donor...

Studying Automatic Movements in Patients With Parkinson's Disease

Parkinson's disease patients usually have difficulty making automatic movements. Automatic movements are movements people often make without conscious thought. The purpose of this study ...

Medical and Biotech [MESH] Definitions

A family of histone acetyltransferases that is structurally-related to CREB-BINDING PROTEIN and to E1A-ASSOCIATED P300 PROTEIN. They function as transcriptional coactivators by bridging between DNA-binding TRANSCRIPTION FACTORS and the basal transcription machinery. They also modify transcription factors and CHROMATIN through ACETYLATION.

An E2F transcription factor that represses GENETIC TRANSCRIPTION required for CELL CYCLE entry and DNA synthesis. E2F5 recruits chromatin remodeling factors indirectly to target gene promoters through RETINOBLASTOMA LIKE PROTEIN P130.

An E2F transcription factor that represses GENETIC TRANSCRIPTION required for CELL CYCLE entry and DNA synthesis. E2F6 recruits chromatin remodeling factors directly to target gene promoters and lacks the transactivation domain responsible for binding to the retinoblastoma family of tumor suppressors.

An E2F transcription factor that represses GENETIC TRANSCRIPTION required for CELL CYCLE entry and DNA synthesis. E2F4 recruits chromatin remodeling factors indirectly to target gene PROMOTER REGIONS through RETINOBLASTOMA LIKE PROTEIN P130 and RETINOBLASTOMA LIKE PROTEIN P107.

A retinoblastoma-binding protein that is involved in CHROMATIN REMODELING, histone deacetylation, and transcription repression. Although initially discovered as a retinoblastoma binding protein it has an affinity for core HISTONES and is a subunit of chromatin assembly factor-1 where it plays a role in the deposition of NUCLEOSOMES on newly synthesized DNA.

Quick Search


DeepDyve research library

Relevant Topics

Bioinformatics
Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...

Nutrition
Within medicine, nutrition (the study of food and the effect of its components on the body) has many different roles. Appropriate nutrition can help prevent certain diseases, or treat others. In critically ill patients, artificial feeding by tubes need t...

Polymerase Chain Reaction (PCR)
PCR (Polymerase Chain Reaction) uses the ability of DNA polymerase (enzymes that create DNA molecules by assembling nucleotides, the building blocks of DNA. These enzymes are essential to DNA replication and usually work in pairs to create two ident...


Searches Linking to this Article