Review
Cell Biology
Inma Gonzalez, Amandine Molliexa, Pablo Navarro
Summary: As cells undergo mitosis, drastic changes occur in their structure and function, posing a challenge to gene regulatory processes. However, chromatin-associated mechanisms play a crucial role in assisting daughter cells in reestablishing gene activity with greater fidelity post-mitosis.
CURRENT OPINION IN CELL BIOLOGY
(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
Multidisciplinary Sciences
Tatsuya Fukuyama, Lucan Yan, Masahito Tanaka, Megumi Yamaoka, Kei Saito, Shih-Chieh Ti, Chung-Chi Liao, Kuo-Chiang Hsia, Yusuke T. Maeda, Yuta Shimamoto
Summary: The spindle is a dynamic intracellular structure essential for chromosome segregation during cell division. It can exhibit varied shape morphologies through nonrandom, bistable self-organization paths. The emergence of different spindle shapes is influenced by both physical and molecular factors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Genetics & Heredity
Kenji Ito, Kenneth S. Zaret
Summary: During mitosis, gene expression changes occur in cells, but these changes are reversed when cells exit mitosis. Recent studies have shown that many transcription factors can be retained in mitotic chromatin, potentially due to nonspecific binding. Understanding the mechanisms behind mitotic memory and gene expression fidelity is crucial.
ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Yujin Kang, Yea Woon Kim, Jin Kang, AeRi Kim
Summary: Histone H3K4me1 and H3K27ac have reciprocal effects on each other, with H3K4me1 affecting nucleosome eviction and H3K27ac influencing enhancer RNA transcription. The loss of H3K4me1 reduces H3K27ac at enhancers, while H3K27ac is required for eRNA transcription independently of H3K4me1.
Article
Biophysics
Leo S. McCormack, Artem K. Efremov, Jie Yan
Summary: Research has found that proteins on finite-size DNA form oscillatory patterns, influenced by the DNA length and the proteins' binding cooperativity. The geometric characteristics of protein patterns are not significantly affected by small variations in proteins' affinity to DNA due to sequence heterogeneity. Competition between different types of proteins for binding to DNA leads to diverse and complex alternating positioning of the proteins.
BIOPHYSICAL JOURNAL
(2021)
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
Biochemistry & Molecular Biology
Liyun Miao, Yin Tang, Ashley R. Bonneau, Shun Hang Chan, Mina L. Kojima, Mark E. Pownall, Charles E. Vejnar, Feng Gao, Smita Krishnaswamy, Caroline E. Hendry, Antonio J. Giraldez
Summary: This study reveals the function of NPS in chromatin reprogramming and genome activation in zebrafish. NPS individually or redundantly open chromatin, regulate histone acetylation, and the position of nucleosomes is influenced by different transcription factors.
Review
Biochemistry & Molecular Biology
Alicia K. Michael, Nicolas H. Thomae
Summary: Eukaryotic DNA-binding proteins interact with nucleosomal DNA in the context of chromatin. While nucleosomes make a large fraction of the DNA inaccessible to proteins, certain factors can still bind to DNA sites obstructed by chromatin. Various strategies are employed to read DNA sequences on nucleosomes, such as releasing nucleosomal DNA, shifting DNA motifs, and using nucleosome-specific DNA binding modes. Motif location and nucleosome positioning both play a crucial role in determining protein access to DNA for transcription and repair processes.
Article
Biochemistry & Molecular Biology
Imon Goswami, Poorva Sandlesh, Aimee Stablewski, Ilya Toshkov, Alfiya F. Safina, Mikhail Magnitov, Jianmin Wang, Katerina Gurova
Summary: This study highlights the importance of nucleosome maintenance during transcription and suggests that the histone chaperone FACT plays a role in preserving chromatin integrity in mammalian adult stem cells.
Article
Multidisciplinary Sciences
Lauren Cole, Sebastian Kurscheid, Maxim Nekrasov, Renae Domaschenz, Daniel L. Vera, Jonathan H. Dennis, David J. Tremethick
Summary: In this study, the authors present high-depth maps of the position and accessibility of H2A.Z-containing nucleosomes for human Pol II promoters and provide evidence that H2A.Z has multiple and distinct roles in regulating gene expression dependent upon its location in a promoter.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Matthew J. Rossi, Prashant K. Kuntala, William K. M. Lai, Naomi Yamada, Nitika Badjatia, Chitvan Mittal, Guray Kuzu, Kylie Bocklund, Nina P. Farrell, Thomas R. Blanda, Joshua D. Mairose, Ann Basting, Katelyn S. Mistretta, David J. Rocco, Emily S. Perkinson, Gretta D. Kellogg, Shaun Mahony, B. Franklin Pugh
Summary: The study revealed the genome-wide architecture of chromatin-associated proteins and identified 21 meta-assemblages consisting of around 400 different proteins related to various processes such as DNA replication and transcription. Promoters associated with Pol II mostly evolved to have only a core promoter, while a small fraction evolved an architecture for inducibility. Surprisingly, interactions between sequence-specific transcription factors and TFIID were not detected, suggesting a different mechanism for gene regulation.
Article
Biochemistry & Molecular Biology
Christophe Papin, Stephanie Le Gras, Abdulkhaleg Ibrahim, Hatem Salem, Mohammad Mahdi Karimi, Isabelle Stoll, Iva Ugrinova, Maria Schroder, Emeline Fontaine-Pelletier, Ziad Omran, Christian Bronner, Stefan Dimitrov, Ali Hamiche
Summary: Epigenetic modifications and nucleosome positioning are important in gene expression regulation. CpG density, promoter activity, and histone marks accumulation are correlated. CGI boundaries define chromatin promoter regions for epigenetic modifications, while H2A.Z presence is not related to transcriptional control.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Aakash Basu, Dmitriy G. Bobrovnikov, Zan Qureshi, Tunc Kayikcioglu, Thuy T. M. Ngo, Anand Ranjan, Sebastian Eustermann, Basilio Cieza, Michael T. Morgan, Miroslav Hejna, H. Tomas Rube, Karl-Peter Hopfner, Cynthia Wolberger, Jun S. Song, Taekjip Ha
Summary: Mechanical deformations of DNA, such as bending, are common and have been implicated in various cellular functions. A high-throughput assay called 'loop-seq' was developed to measure DNA looping propensity and intrinsic cyclizabilities of DNA fragments across different genomic regions. The study found regions of low bendability in nucleosome-depleted regions, which affects nucleosome sliding and gene transcription. Overall, the study shows that local DNA mechanics have broad functional implications on chromatin organization and transcription.
Review
Plant Sciences
Tomasz Bieluszewski, Sandhan Prakash, Thomas Roule, Doris Wagner
Summary: SWI/SNF class chromatin remodeling complexes play crucial roles in facilitating access of proteins to the genomic DNA and altering chromatin compaction and accessibility. Recent studies have identified different subtypes of SWI/SNF complexes with unique properties and functions. Understanding the complex regulation of SWI/SNF activity and its impact on proper development and response to extrinsic cues is of great importance.
ANNUAL REVIEW OF PLANT BIOLOGY
(2023)
Article
Cell & Tissue Engineering
Richard Patryk Ngondo, Daniel Cirera-Salinas, Jian Yu, Harry Wischnewski, Maxime Bodak, Sandrine Vandormael-Pournin, Anna Geiselmann, Rahel Wettstein, Janina Luitz, Michel Cohen-Tannoudji, Constance Ciaudo
Article
Biochemistry & Molecular Biology
Leonard Jarzebowski, Marie Le Bouteiller, Sabrina Coqueran, Aurelien Raveux, Sandrine Vandormael-Pournin, Alexandre David, Ana Cumano, Michel Cohen-Tannoudji
Article
Cell & Tissue Engineering
Sylvain Bessonnard, Sandrine Vandormael-Pournin, Sabrina Coqueran, Michel Cohen-Tannoudji, Jerome Artus
Article
Multidisciplinary Sciences
Victor Heurtier, Nick Owens, Inma Gonzalez, Florian Mueller, Caroline Proux, Damien Mornico, Philippe Clerc, Agnes Duboisl, Pablo Navarro
NATURE COMMUNICATIONS
(2019)
Article
Biology
Nick Owens, Thaleia Papadopoulou, Nicola Festuccia, Alexandra Tachtsidi, Inma Gonzalez, Agnes Dubois, Sandrine Vandormael-Pournin, Elphege P. Nora, Benoit G. Bruneau, Michel Cohen-Tannoudji, Pablo Navarro
Article
Biochemistry & Molecular Biology
Aurelien Raveux, Aline Stedman, Sabrina Coqueran, Sandrine Vandormael-Pournin, Nick Owens, Beatrice Romagnolo, Michel Cohen-Tannoudji
CELL DEATH AND DIFFERENTIATION
(2020)
Article
Hematology
Giulia Pavani, Anna Fabiano, Marine Laurent, Fatima Amor, Erika Cantelli, Anne Chalumeau, Giulia Maule, Alexandra Tachtsidi, Jean-Paul Concordet, Anna Cereseto, Fulvio Mavilio, Giuliana Ferrari, Annarita Miccio, Mario Amendola
Summary: Beta-thalassemias are blood disorders caused by mutations in the beta-globin gene cluster. A novel strategy using CRISPR/Cas9 to edit the alpha-globin locus in human HSPCs has been developed to correct alpha/beta globin imbalance in thalassemic cells, showing potential for new therapeutic approaches. This approach combines alpha-globin downregulation with beta-globin expression to address the underlying pathology of beta-thalassemias.
Review
Cell Biology
Inma Gonzalez, Amandine Molliexa, Pablo Navarro
Summary: As cells undergo mitosis, drastic changes occur in their structure and function, posing a challenge to gene regulatory processes. However, chromatin-associated mechanisms play a crucial role in assisting daughter cells in reestablishing gene activity with greater fidelity post-mitosis.
CURRENT OPINION IN CELL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Nicolas Allegre, Sabine Chauveau, Cynthia Dennis, Yoan Renaud, Dimitri Meistermann, Lorena Valverde Estrella, Pierre Pouchin, Michel Cohen-Tannoudji, Laurent David, Claire Chazaud
Summary: The initiation and regulation of epiblast lineage specification during embryonic development remains unclear. This study shows that coordinated expression of pluripotency markers is crucial for epiblast identity, and that this process is triggered by NANOG activity in a stochastic manner. The findings suggest that these features are likely conserved in human embryos as well.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Richard Patryk Ngondo, Michel Cohen-Tannoudji, Constance Ciaudo