Article
Biochemistry & Molecular Biology
Corinna Lieleg, Ana Novacic, Sanja Musladin, Andrea Schmid, Goezde Gueclueler Akpinar, Slobodan Barbaric, Philipp Korber
Summary: Chromatin remodeling by ATP-dependent enzymes is crucial for genomic processes. The recruitment of remodelers, such as the SWI/SNF complex, in the removal of nucleosomes in yeast PHO gene induction is specific and may affect the outcome of remodeling.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Fei He, Qi Yu, Min Wang, Rongsha Wang, Xuanyunjing Gong, Feng Ge, Xilan Yu, Shanshan Li
Summary: This study reveals the inhibitory effect of H3pT11 on H3K79me3 and uncovers the histone crosstalk regulating autophagy and telomere silencing. It is also discovered that Reb1 recruits the SESAME complex to telomere regions to prevent the invasion of H3K79me3 into heterochromatin, maintaining telomere silencing.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Sarah G. Swygert, Dejun Lin, Stephanie Portillo-Ledesma, Po-Yen Lin, Dakota R. Hunt, Cheng-Fu Kao, Tamar Schlick, William S. Noble, Toshio Tsukiyama
Summary: The study found that an increase in the range of local inter-nucleosomal contacts in quiescent yeast drives genome-wide compaction of chromatin fibers, leading to global repression of transcription. Unlike actively dividing cells, inter-nucleosomal interactions in quiescent cells require a specific basic patch in the histone H4 tail.
Article
Biochemistry & Molecular Biology
Toby Barnes, Philipp Korber
Summary: In vivo nucleosome depletion over poly(dA:dT) tracts is not universal, with weak depletion observed in S. pombe. The energy penalty for incorporating these tracts into nucleosomes is modest compared to the ATP hydrolysis energy expended by chromatin remodelers. Nucleosome depletion over poly(dA:dT) tracts is stronger in vivo compared to in vitro, and it is actively maintained in vivo.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Ryota Yamamoto, Genki Sato, Takamitsu Amai, Mitsuyoshi Ueda, Kouichi Kuroda
Summary: In this study, a novel technology for inducing chromatin loosening in target regions of Saccharomyces cerevisiae was established through nucleosomal histone acetylation. The system successfully increased euchromatic DNA at the target locus, suggesting the potential of inducing euchromatic state in a target locus using this developed method.
Article
Biochemistry & Molecular Biology
Myriam Ruault, Vittore F. Scolari, Luciana Lazar-Stefanita, Antoine Hocher, Isabelle Loiodice, Romain Koszul, Angela Taddei
Summary: The study reveals that in budding yeast, telomere clustering is functionally linked to heterochromatin formation, with Sir3 directly promoting long-range contacts between distant regions. Additionally, Sir3 is shown to promote rDNA compaction independently of its known partners, suggesting it acts as a molecular bridge stabilizing long-range interactions.
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)
Article
Multidisciplinary Sciences
Emily Nischwitz, Vivien A. C. Schoonenberg, Albert Fradera-Sola, Mario Dejung, Olga Vydzhak, Michal Levin, Brian Luke, Falk Butter, Marion Scheibe
Summary: By using quantitative mass spectrometry, we identified 337 binding proteins in 11 species that are involved in DNA repair. Through bioinformatics analysis, we discovered 44 previously uncharacterized proteins associated with DNA repair and provided a resource for studying the crosstalk and evolutionary conservation of DNA damage repair across different domains of life.
Article
Biochemistry & Molecular Biology
Julien Soudet, Nissrine Beyrouthy, Anna Marta Pastucha, Andrea Maffioletti, Dario Menendez, Zahra Bakir, Francoise Stutz
Summary: In this study, the researchers developed a genetic screen to identify new factors involved in Antisense-Mediated Transcription Interference (AMTI). They found that the HIR histone chaperone complex is involved in repressing the promoters of SAGA-dependent genes through antisense non-coding transcription. However, the presence of antisense transcription at gene promoters is not sufficient to determine the mode of gene regulation.
NUCLEIC ACIDS RESEARCH
(2022)
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
Biochemical Research Methods
David G. Nickens, Matthew L. Bochman
Summary: DNA helicases play a crucial role in nucleic acid transactions and genome integrity. Research has shown that the PIF1 (Pif1 and Rrm3) and RecQ (Hrq1 and Sgs1) family helicases exhibit genetic and biochemical interactions in vivo, affecting genome integrity pathways and telomerase activity.
Article
Cell Biology
Magdalena Murawska, R. A. Greenstein, Tamas Schauer, Karl C. F. Olsen, Henry Ng, Andreas G. Ladurner, Bassem Al-Sady, Sigurd Braun
Summary: The formation of heterochromatin involves nucleation, self-propagation, and maintenance steps, with the histone chaperone FACT playing a crucial role in promoting heterochromatin spreading by repressing heterochromatic histone turnover in fission yeast. This study sheds light on the mechanisms underlying the involvement of FACT in heterochromatin silencing.
Article
Biochemistry & Molecular Biology
Audrey Paille, Francois Peyresaubes, Thomas Gardrat, Carlos Zeledon, Antonio Conconi
Summary: UV radiation leads to the formation of pyrimidine dimers (PDs), which are repaired through Transcription-coupled nucleotide excision repair (TC-NER) and Global Genome nucleotide excision repair (GG-NER). In TC-NER, RNA polymerase-I is involved in the repair process, while GG-NER removes PDs in the absence of RNA polymerase-I. Repair efficiency in the transcribed strand is influenced by the density of RNA polymerase-I and varies along the gene. In the non-transcribed strand, GG-NER is solely responsible for removing UV-induced DNA lesions.
Article
Biology
Zhi Yang Tan, Shujun Cai, Alex J. Noble, Jon K. Chen, Jian Shi, Lu Gan
Summary: Research has found that the diversity of nucleosome structures in budding yeast cells far exceeds the canonical structure determined in vitro, and the DNA of nucleosomes is partially detached in situ.
Article
Cell Biology
Natalya Maluchenko, Darya Koshkina, Anna Korovina, Vasily Studitsky, Alexey Feofanov
Summary: The cytotoxicity of poly(ADP-ribose-)polymerase-1 (PARP1) inhibitors (PARPi) in antitumor therapy is correlated with their trapping efficiency in cell chromatin. The interactions of PARP1-nucleosome complexes with PARPi were studied, and it was found that the efficiency of PARP1 trapping on nucleosomes is affected by the chromatin structure.