Article
Genetics & Heredity
Randall H. Morse
Summary: Chromatin-mediated transcriptional regulation is regulated by post-translational modifications of core histones, particularly the H3 and H4 tails. In yeast, the H3 and H4 tails can be deacetylated by Rpd3 to repress target genes, and hypoacetylated histones can facilitate the recruitment of the Tup1-Ssn6 complex to effect gene repression. This study used a chromatin modifier compendium of yeast strains mutated for chromatin-related genes to analyze the effect of these mutations on gene repression mediated by the histone tails and/or by Rpd3.
Review
Biochemistry & Molecular Biology
Ashish Kumar Singh, Felix Mueller-Planitz
Summary: Eukaryotes form nucleosome particles by associating their genomes with histone proteins, which regulate and protect genetic information. These nucleosomes often assemble into evenly spaced arrays, covering significant portions of the genome, with a high degree of conservation throughout the eukaryotic domain. Various factors like transcription, nucleosome remodelers, DNA sequence, and histone density play roles in the formation of these arrays, with unanswered questions remaining about their biogenesis and cellular functions.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Peter R. Eriksson, David J. Clark
Summary: Research reveals that ISW1b primarily regulates nucleosome spacing and resolution of closely packed dinucleosomes, with ISW1a playing a minor role. ISW1b and Chd1 make additive contributions to dinucleosome resolution. Set2-mediated H3-K36 trimethylation contributes to ISW1b-mediated dinucleosome separation.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Colleen E. Quaas, Baicheng Lin, David T. Long
Summary: Modification of histones, especially histone acetylation, plays a crucial role in regulating chromatin structure and DNA access. Defects in histone acetylation patterns are associated with various human diseases. In this study, Xenopus egg extracts are used to investigate the impact of histone acetylation changes on gene transcription. The findings reveal that inhibiting histone deacetylase 1 and 2 (HDAC1/2) counteracts transcription suppression by preventing chromatin compaction and deacetylation of specific histone residues. HDAC1 is identified as the primary driver of transcription suppression through the Sin3 histone deacetylase complex.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Eunhye Lee, Chanshin Kang, Pasi Purhonen, Hans Hebert, Karim Bouazoune, Sungchul Hohng, Ji-Joon Song
Summary: CHD7 is a crucial chromatin remodeler, and its N-CRD region is essential for its ATPase stimulation and nucleosome remodeling activity. Mutations in this region can lead to defects in CHD7 function, affecting remodeling activity.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Simon Obermeyer, Richard Stoeckl, Tobias Schnekenburger, Henna Kapoor, Thomas Stempfl, Uwe Schwartz, Klaus D. Grasser
Summary: In addition to transcriptional initiation, mRNA production is regulated during elongation, and various transcript elongation factors modulate the synthesis of mRNAs by RNA polymerase II (RNAPII) in the chromatin context. TFIIS is an elongation factor that stimulates the transcript cleavage activity of RNAPII, and its deficiency in Arabidopsis plants leads to increased sensitivity to heat stress and decreased expression of heat-induced genes. Further analysis reveals that TFIIS is required for proper RNAPII accumulation at specific nucleosomes and plays a role in reprogramming gene expression for establishing plant thermotolerance.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Guoqing Liu, Zhi Zhang, Biyu Dong, Jia Liu
Summary: This study used a DNA deformation energy model to investigate the nucleosome organization in different chromatin states in mouse ESCs. The results showed that active genes have higher nucleosome occupancy around their TSS and TTS, and there is no nucleosome-depleted region at the TTS. An improved model was developed to predict rotational positioning and nucleosome occupancy. The model successfully predicted nucleosome occupancy around the binding sites of developmentally important transcription factors and captured the difference in nucleosome occupancy between CpG-rich and CpG-poor promoters.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Silvia Dyson, Joana Segura, Belen Martinez-Garcia, Antonio Valdes, Joaquim Roca
Summary: Recent studies in budding yeast have shown that there is a mechanism that minimizes the probability of DNA knotting. Experimental results demonstrate that the low knotting probability of DNA is not dependent on the capacity of topoisomerase II or the activities of cohesin or Smc5/6 complexes. However, inactivation of condensin increases the occurrence of DNA knots throughout the cell cycle.
Article
Biology
Roman Jaksik, David A. A. Wheeler, Marek Kimmel
Summary: This study proposes a method of detecting ORI based on somatic mutation patterns caused by the mutator phenotype of damaged DNA polymerase epsilon (POLE), and identifies shared ORI locations in tumors through accumulated mutations. The study also compares the results from multiple detection methods and defines a consensus set of ORI. The results demonstrate the viability of mutation-based detection in determining ORI location and associated sequence features.
Article
Biochemistry & Molecular Biology
Fabrizio Cleri, Stefano Giordano, Ralf Blossey
Summary: This study investigates the mechanical response of chromatin to applied stress at the molecular level using a trinucleosome array as a model. The results show that DNA linkers between nucleosome pairs play a major role in accommodating compressive stress and storing elastic energy. Different mechanical instabilities can cause deformation of the DNA structure, and the histone tails assist in this deformation. Compressive stress leads to plastic deformation and localized defects in the nucleosome assembly, potentially impacting DNA transcription, signaling pathways, gene expression regulation, and DNA repair.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Review
Physics, Condensed Matter
Helmut Schiessel
Summary: DNA molecules with a length of two meters contain genetic information in every cell. Cells use sophisticated physical mechanisms to control gene access, organize spatial structure, duplicate and separate genetic material. Base pair sequences multiplex information, chromatin remodelers mobilize nucleosomes, loop extruders organize chromatin spatially, and biomolecular condensates concentrate molecules in specialized compartments. This review discusses the understanding of these mechanisms in genetic material organization.
ANNUAL REVIEW OF CONDENSED MATTER PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Astrid Lancrey, Alexandra Joubert, Evelyne Duvernois-Berthet, Etienne Routhier, Saurabh Raj, Agnes Thierry, Marta Sigarteu, Loic Ponger, Vincent Croquette, Julien Mozziconacci, Jean-Baptiste Boule
Summary: The artificial 601 DNA sequence is effective in positioning nucleosomes in vitro, but its application in vivo is limited and depends on the chromosomal context.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Review
Genetics & Heredity
Jeremy Barbier, Cedric Vaillant, Jean-Nicolas Volff, Frederic G. Brunet, Benjamin Audit
Summary: The nucleosome plays a critical role in regulating DNA accessibility and cell processes. DNA sequence and factors like ATP-dependent remodelers affect nucleosome positioning on genomes and influence accessibility. Sequence-encoded nucleosome positioning has functional impacts on cell processes and can be selected or counter-selected during evolution.
Review
Biochemistry & Molecular Biology
Maria Theresia Watzlowik, Sujaan Das, Markus Meissner, Gernot Laengst
Summary: The gene transcription regulation of the human malaria parasite Plasmodium falciparum is governed by complex epigenetic mechanisms involving chromatin structure and dynamics. The high AT-content of the parasite genome and sequence divergence of chromatin-related proteins suggest significant differences in chromatin-dependent regulation compared to other eukaryotes. Specialized chromatin remodeling enzymes play an essential role in gene regulation in P. falciparum.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Jonna Heldrich, Carolyn R. Milano, Tovah E. Markowitz, Sarah N. Ur, Luis A. Vale-Silva, Kevin D. Corbett, Andreas Hochwagen
Summary: Successful meiotic recombination requires conserved axis proteins, which distribute on chromosomes through two independent pathways: a cohesin-dependent pathway and a cohesin-independent pathway. These pathways result in a stereotypic distribution pattern and the formation of chromatin islands that influence chromosome structure.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biophysics
Davood Norouzi, Victor B. Zhurkin
BIOPHYSICAL JOURNAL
(2015)
Article
Biophysics
Maryam Ghahremani Nasab, Leila Hassani, Sara Mohammadi Nejad, Davood Norouzi
JOURNAL OF BIOLOGICAL PHYSICS
(2017)
Article
Materials Science, Biomaterials
Zhila Niknezhad, Leila Hassani, Davood Norouzi
MATERIALS SCIENCE & ENGINEERING C-MATERIALS FOR BIOLOGICAL APPLICATIONS
(2016)
Article
Biochemistry & Molecular Biology
Jenna M. Buckwalter, Davood Norouzi, Anna Harutyunyan, Victor B. Zhurkin, Sergei A. Grigoryev
NUCLEIC ACIDS RESEARCH
(2017)
Article
Biochemistry & Molecular Biology
Bing-Rui Zhou, Jiansheng Jiang, Rodolfo Ghirlando, Davood Norouzi, K. N. Sathish Yadav, Hanqiao Feng, Rui Wang, Ping Zhang, Victor Zhurkin, Yawen Bai
JOURNAL OF MOLECULAR BIOLOGY
(2018)
Article
Biophysics
Davood Norouzi, Victor B. Zhurkin
BIOPHYSICAL JOURNAL
(2018)
Article
Biochemistry & Molecular Biology
Davood Norouzi, Farshid Mohammad-Rafiee
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2014)
Article
Physics, Fluids & Plasmas
Weria Pezeshkian, Narges Nikoofard, Davood Norouzi, Farshid Mohammad-Rafiee, Hossein Fazli
Article
Physics, Multidisciplinary
Davood Norouzi, Farshid Mohammad-Rafiee, Ramin Golestanian
PHYSICAL REVIEW LETTERS
(2008)
Article
Biochemistry & Molecular Biology
Filipe Tavares-Cadete, Davood Norouzi, Bastiaan Dekker, Yu Liu, Job Dekker
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2020)
Article
Physics, Fluids & Plasmas
Davood Norouzi, Martin Michael Mueller, Markus Deserno
Article
Biophysics
Davood Norouzi, Ataur Katebi, Feng Cui, Victor B. Zhurkin