Article
Multidisciplinary Sciences
Nicholas J. Fuda, Katjusa Brejc, William S. Kruesi, Edward J. Ralston, Rachel Bigley, Aram Shin, Miki Okada, Barbara J. Meyer
Summary: The study identifies critical X-sequence motifs in Caenorhabditis elegans that act synergistically in hermaphrodites to direct X-specific recruitment of the dosage compensation complex (DCC), a condensin complex. The findings reveal that synergy in DCC binding via combinatorial clustering of motifs triggers DCC assembly specifically on X chromosomes.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biology
Qiming Yang, Te-Wen Lo, Katjusa Brejc, Caitlin Schartner, Edward J. Ralston, Denise M. Lapidus, Barbara J. Meyer
Summary: An evolutionary perspective reveals that the genetic regulatory hierarchy controlling sex determination and X-chromosome dosage compensation is conserved but with divergent mechanisms between Caenorhabditis briggsae and Caenorhabditis elegans. While the binding of the specialized condensin dosage compensation complex (DCC) to recruitment sites in Cbr is additive, DCC binding to Cel recruitment sites is synergistic. Rapid divergence of DCC target specificity, determined by motifs, has played a crucial role in establishing reproductive isolation between nematode species.
Review
Biochemistry & Molecular Biology
Yuri Y. Shevelyov, Sergey Ulianov, Mikhail S. Gelfand, Stepan N. Belyakin, Sergey Razin
Summary: Dosage compensation ensures equal gene expression between a single male X chromosome and the pairs of autosomes and female X chromosomes. In fruit flies, canonical dosage compensation is achieved through the action of the male-specific lethal (MSL) complex in all male somatic cells. This complex contains the acetyl transferase males absent on the first (MOF), which specifically hyperacetylates H4K16 on the male X chromosome, promoting transcription of X-linked genes. Additionally, there is growing evidence for the existence of non-canonical dosage compensation mechanisms in somatic and germline cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Genetics & Heredity
Barbara J. Meyer
Summary: Abnormalities in chromosome number can disrupt gene expression balance and decrease fitness. The difference in X-chromosome dose used to determine sexual fate is well tolerated across species. The nematode Caenorhabditis elegans provides insights into the chromosome counting and dosage compensation mechanisms and how small quantitative differences in signals can lead to different fates. Understanding X-chromosome dosage compensation reveals the interplay between chromatin modification and chromosome structure in regulating gene expression.
Article
Multidisciplinary Sciences
Leah F. Rosin, Dahong Chen, Yang Chen, Elissa P. Lei
Summary: Research on the chromatin structure in the silkmoth, Bombyx mori, reveals that the two male sex chromosomes are equally downregulated after dosage compensation (DC) is established. In females, the Z chromosome chromatin becomes more accessible and repositions towards the nuclear center during the early stages of DC. This study also uncovers intriguing similarities between DC mechanisms in B. mori and C. elegans, despite having evolutionarily distinct sex chromosomes, suggesting a possible role for holocentricity in DC mechanisms.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Ryoma Ota, Makoto Hayashi, Shumpei Morita, Hiroki Miura, Satoru Kobayashi
Summary: Dosage compensation equalizes sex chromosome gene expression between the sexes in Drosophila, achieved by the male-specific lethal (MSL) complex in somatic cells. However, it remains unclear whether dosage compensation occurs in germline cells. Transcriptome analysis showed higher expression of X-linked genes in female primordial germ cells (PGCs) compared to males, with absence of H4K16ac due to failure of MSL complex formation in male PGCs.
SCIENTIFIC REPORTS
(2021)
Article
Biotechnology & Applied Microbiology
Irene Talon, Adrian Janiszewski, Bart Theeuwes, Thomas Lefevre, Juan Song, Greet Bervoets, Lotte Vanheer, Natalie De Geest, Suresh Poovathingal, Ryan Allsop, Jean-Christophe Marine, Florian Rambow, Thierry Voet, Vincent Pasque
Summary: Our study reveals that intrinsic compensatory mechanisms exist in mammalian cells, involving modulation of chromatin accessibility to counteract imbalances in gene dosage between the X chromosome and autosomes caused by evolutionary changes or X chromosome inactivation in vitro. Through genome-wide approaches, allele-specific ATAC-seq, and single-cell RNA-seq, we demonstrate increased chromatin accessibility on the upregulated active X chromosome compared to autosomes in female embryonic fibroblasts and during reprogramming to pluripotency. Additionally, our data show that ZFP42/REX1, a gene associated with pluripotency that evolved specifically in placental mammals, targets multiple X-linked genes, suggesting an evolutionary link between ZFP42/REX1, X chromosome reactivation, and pluripotency.
Article
Genetics & Heredity
Bhavana Ragipani, Sarah Elizabeth Albritton, Ana Karina Morao, Diogo Mesquita, Maxwell Kramer, Sevinc Ercan
Summary: This study found that Caenorhabditis elegans can tolerate increased gene dosage, but lacks a genome-wide dosage compensation mechanism at the mRNA level. Different genes within chromosomal duplications show variable levels of mRNA increase, indicating feedback regulation. Somatic dosage compensation and germline repression reduce the mRNA increase from X chromosomal duplications.
G3-GENES GENOMES GENETICS
(2022)
Article
Biotechnology & Applied Microbiology
Pallavi Chauhan, Janne Swaegers, Rosa A. Sanchez-Guillen, Erik Svensson, Maren Wellenreuther, Bengt Hansson
Summary: This study reveals the conservation of sex chromosome synteny and balanced expression of X-linked genes between sexes in Ischnura elegans, as well as the presence of sex-biased gene expression in the sex-determining pathway. Furthermore, the study shows the independent evolution of dosage compensation among insect orders separated by millions of years of evolutionary history.
Review
Genetics & Heredity
M. Felicia Basilicata, Claudia Isabelle Keller Valsecchi
Summary: Gene dosage changes play a significant role at the intersection of evolutionary advantage and pathogenicity, providing a common ground for understanding developmental disorders caused by copy number alterations.
Article
Multidisciplinary Sciences
Shuai Zhang, Haizhu Qi, Cheng Huang, Lijia Yuan, Ludan Zhang, Ruixue Wang, Yu Tian, Lin Sun
Summary: The study demonstrates that the inverse dosage effect caused by chromosome number variations has global consequences in genomic imbalance, including sexual dimorphism and an X chromosome-specific response. Over-expression of MSL2 and analysis of different transcriptomes revealed that the de novo MSL complex assembled on the X chromosomes in females further reduces global gene expression levels through epigenetic modulations.
SCIENTIFIC REPORTS
(2021)
Review
Biochemistry & Molecular Biology
Patrycja Juchniewicz, Ewa Piotrowska, Anna Kloska, Magdalena Podlacha, Jagoda Mantej, Grzegorz Wegrzyn, Stefan Tukaj, Joanna Jakobkiewicz-Banecka
Summary: Advancements in genomic and metabolomic technologies are rapidly increasing our understanding of the molecular and biochemical causes of genetic disorders, with an emphasis on the varying phenotypes. Dosage compensation through lyonization helps balance gene expression on heteromorphic sex chromosomes, greatly impacting the manifestation of X-linked disorders in females. This review summarizes clinical and genetic findings in female carriers of pathogenic variants in selected X-linked genes that result in metabolic disorders.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Immunology
Lorenzo Brusini, Simon D'Archivio, Jennifer McDonald, Bill Wickstead
Summary: Kinetochores play a crucial role in eukaryotes, binding chromosomes to the mitotic spindle. While the composition of kinetochores varies greatly among extant eukaryotes, a stable 9-protein kinetoplastid outer kinetochore complex has been identified in trypanosomes. This complex incorporates proteins from other nuclear processes and bridges inner- and outer-kinetochore components, suggesting design parallels in organisms with diverse kinetochore composition.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yuka Sakata, Hong Zhang, Akiko Sugiyama, Nami Motosugi, Hiroshi Kimura, Yosuke Okamura, Atsushi Fukuda
Summary: High-resolution imaging analysis is essential for studying cell functions, but culturing cells on glass substrates often leads to cell instability. In this study, we coated the glass substrate with a nanosheet composed of hydrophobic polystyrene and Matrigel, which significantly improved the viability of human pluripotent stem cells (hPSCs). The nanosheet coating did not affect the transcriptome status of hPSC and allowed for high-resolution imaging assay. Our findings demonstrate that the nanosheet coating is beneficial for sensitive cells cultured on glass substrates.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Editorial Material
Biochemistry & Molecular Biology
Joanna W. W. Jachowicz
Summary: Unlike autosomal genes, X-linked genes are expressed from only one copy in both male and female mammals. How cells increase X-linked gene expression to match autosomal levels is unclear. New evidence suggests that lower levels of RNA modifications on X chromosome-derived transcripts critically regulate mRNA stability and help to balance X-to-autosome gene expression levels.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2023)
Article
Cell Biology
Daniel J. McKay, Stephen Klusza, Taylor J. R. Penke, Michael P. Meers, Kaitlin P. Curry, Stephen L. McDaniel, Pamela Y. Malek, Stephen W. Cooper, Deirdre C. Tatomer, Jason D. Lieb, Brian D. Strahl, Robert J. Duronio, A. Gregory Matera
DEVELOPMENTAL CELL
(2015)
Article
Cell Biology
Jinchuan Hu, Sheera Adar, Christopher P. Selby, Jason D. Lieb, Aziz Sancar
GENES & DEVELOPMENT
(2015)
Editorial Material
Genetics & Heredity
Sebastian Pott, Jason D. Lieb
Article
Genetics & Heredity
Joseph D. Fleming, Paul G. Giresi, Marianne Lindahl-Allen, Elsa B. Krall, Jason D. Lieb, Kevin Struhl
EPIGENETICS & CHROMATIN
(2015)
Article
Cell Biology
Vincent J. Lynch, Mauris C. Nnamani, Aurelie Kapusta, Kathryn Brayer, Silvia L. Plaza, Erik C. Mazur, Deena Emera, Shehzad Z. Sheikh, Frank Gruetzner, Stefan Bauersachs, Alexander Graf, Steven L. Young, Jason D. Lieb, Francesco J. DeMayo, Cedric Feschotte, Guenter P. Wagner
Article
Developmental Biology
Joseph C. Pearson, Daniel J. McKay, Jason D. Lieb, Stephen T. Crews
Article
Cell Biology
Sophia C. Tintori, Erin Osborne Nishimura, Patrick Golden, Jason D. Lieb, Bob Goldstein
DEVELOPMENTAL CELL
(2016)
Article
Immunology
Jeremy M. Simon, James P. Davis, Saangyoung E. Lee, Matthew R. Schaner, Gregory R. Gipson, Matthew Weiser, R. Balfour Sartor, Hans H. Herfarth, Reza Rahbar, Timothy S. Sadiq, Mark J. Koruda, Dermot P. McGovern, Jason D. Lieb, Karen L. Mohlke, Terrence S. Furey, Shehzad Z. Sheikh
EUROPEAN JOURNAL OF IMMUNOLOGY
(2016)
Article
Multidisciplinary Sciences
Jinchuan Hu, Jason D. Lieb, Aziz Sancar, Sheera Adar
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2016)
Article
Biochemistry & Molecular Biology
Jennifer W. Israel, Grace A. Chappell, Jeremy M. Simon, Sebastian Pott, Alexias Safi, Lauren Lewis, Paul Cotney, Hala S. Boulos, Wanda Bodnar, Jason D. Lieb, Gregory E. Crawford, Terrence S. Furey, Ivan Rusyn
Article
Multidisciplinary Sciences
Joshua W. K. Ho, Youngsook L. June, Tao Liu, Burak H. Alver, Soohyun Lee, Kohta Ikegami, Kyung-Ah Sohn, Aki Minoda, Michael Y. Tolstorukov, Alex Appert, Stephen C. J. Parker, Tingting Gu, Anshul Kundaje, Nicole C. Riddle, Eric Bishop, Thea A. Egelhofer, Sheng'en Shawn Hu, Artyom A. Alekseyenko, Andreas Rechtsteiner, Dalal Asker, Jason A. Belsky, Sarah K. Bowmanm, Q. Brent Chens, Ron A. -J. Chen, Daniel S. Day, Yan Dong, Andrea C. Dose, Xikun Duan, Charles B. Epstein, Sevinc Ercan, Elise A. Feingold, Francesco Ferrari, Jacob M. Garrigues, Nils Gehlenborg, Peter J. Good, Psalm Haseley, Daniel He, Moritz Herrmann, Michael M. Hoffman, Tess E. Jeffers, Peter V. Kharchenko, Paulina Kolasinska-Zwierz, Chitra V. Kotwaliwale, Nischay Kumar, Sasha A. Langley, Erica N. Larschan, Isabel Latorre, Maxwell W. Libbrecht, Xueqiu Lin, Richard Park, Michael J. Pazin, Hoang N. Pham, Annette Plachetka, Bo Qin, Yuri B. Schwartz, Noam Shoresh, Przemyslaw Stempor, Anne Vielle, Chengyang Wang, Christina M. Whittle, Huiling Xue, Robert E. Kingstonm, Ju Han Kim, Bradley E. Bernstein, Abby F. Dernburg, Vincenzo Pirrotta, Mitzi I. Kuroda, William S. Noble, Thomas D. Tullius, Manolis Kellis, David M. MacAlpine, Susan Strome, Sarah C. R. Elgin, Xiaole Shirley Liu, Jason D. Lieb, Julie Ahringer, Gary H. Karpen, Peter J. Park
Correction
Biochemical Research Methods
Jeremy M. Simon, Paul G. Giresi, Ian J. Davis, Jason D. Lieb
Article
Multidisciplinary Sciences
Manolis Kellis, Barbara Wold, Michael P. Snyder, Bradley E. Bernstein, Anshul Kundaje, Georgi K. Marinov, Lucas D. Ward, Ewan Birney, Gregory E. Crawford, Job Dekker, Ian Dunham, Laura L. Elnitski, Peggy J. Farnham, Elise A. Feingold, Mark Gerstein, Morgan C. Giddings, David M. Gilbert, Thomas R. Gingeras, Eric D. Green, Roderic Guigo, Tim Hubbard, Jim Kent, Jason D. Lieb, Richard M. Myers, Michael J. Pazin, Bing Ren, John A. Stamatoyannopoulos, Zhiping Weng, Kevin P. White, Ross C. Hardison
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2014)
Editorial Material
Biotechnology & Applied Microbiology
Sebastian Pott, Jason D. Lieb
Meeting Abstract
Biochemistry & Molecular Biology
J. Hu, O. Adebali, J. Lieb, A. Sancar, S. Adar