Article
Biochemistry & Molecular Biology
Ran Brosh, Camil Coedho, Andre M. Ribeiro-dos-Santos, Gwen Ellis, Megan S. Hogan, Hannah J. Ashe, Nicolette Somogyi, Raquel Ordonez, Raven D. Luther, Emily Huang, Jef D. Booke, Matthew T. Maurano
Summary: The expression of Sox2 gene in mouse embryonic stem cells (mESCs) relies on a cluster of distal DNase I hypersensitive sites (DHSs), but the individual contributions and the degree of interdependence between these DHSs are still unknown. Through the use of Big-IN technology, we found that two DHSs were sufficient to activate Sox2 gene expression over long distances, while three nearby DHSs were entirely context dependent and showed no activity alone, but significantly enhanced the activity of autonomous DHSs. Our study highlights the role of context in modulating genomic regulatory element function, and our synthetic regulatory genomics approach provides a roadmap for dissecting other genomic loci.
Article
Biochemistry & Molecular Biology
Ryan Loker, Richard S. Mann
Summary: Gene duplication and the duplication of enhancers are important contributors to genome evolution and biological complexity. This study investigated the regulation and function of the paralogous nubbin/pdm2 genes during wing development in Drosophila melanogaster. The researchers found that these genes have redundant roles in the wing and rely on a shared enhancer for their expression. However, the two genes have different abilities to respond to this enhancer, with one gene featuring a specific silencer element that leads to expression divergence.
Article
Multidisciplinary Sciences
Ravneet Jaura, Ssu-Yu Yeh, Kaitlin N. Montanera, Alyssa Ialongo, Zobia Anwar, Yiming Lu, Kavindu Puwakdandawa, Ho Sung Rhee
Summary: This study reveals that extended intergenic regions play a role in tissue-specific gene expression, particularly in neural tissues. These intergenic regions contain more active enhancers and are associated with co-expression of neighboring neural genes. Generic neural genes expressed in multiple tissues have longer intergenic regions and contain tissue-specific enhancers.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Iris Zhu, David Landsman
Summary: Housekeeping genes are regulated by cell type-specific enhancers, and most transcription factors bind cell type-specifically. TF binding at regulatory sites is cell type-specific and is related to the collective TF recruitment, as each cell type has a unique repertoire of TFs. The top TF-enriched regulatory sites in HepG2 cells can be predicted from the binding profile of as few as 30 TFs.
Article
Multidisciplinary Sciences
Zachary T. Olmsted, Janet L. Paluh
Summary: Researchers have successfully studied the co-development of the central and peripheral nervous systems with trunk mesendoderm in elongating multi-lineage organized (EMLO) gastruloids. They identified NCCs that differentiate to form peripheral neurons integrated with an upstream spinal cord region after day 8.
NATURE COMMUNICATIONS
(2021)
Article
Plant Sciences
Evgeny A. Elisafenko, Elena V. Evtushenko, Alexander V. Vershinin
Summary: The duplication of CENH3 in cereals led to changes in the exon-intron structure of the beta CENH3 paralog. The general trend towards the expansion of the CENH3 locus reveals the diverse ways different species implement the scenario described in this paper.
Article
Cell Biology
Miriam Pagin, Mattias Pernebrink, Mattia Pitasi, Federica Malighetti, Chew-Yee Ngan, Sergio Ottolenghi, Giulio Pavesi, Claudio Cantu, Silvia K. Nicolis
Summary: The transcription factor SOX2 is crucial for brain development and neural stem cell maintenance. Study shows that FOS, a SOX2 transcriptional target, can rescue defects in neuronal production caused by Sox2 deletion.
Article
Medicine, General & Internal
Shang-Xin Liu, Chong Wang, Ruo-Bin Lin, Wei-Yue Ding, Gaurab Roy, Hong-Bo Wang, Ting Yang, Qian Liu, Yi-Ling Luo, Shui-Lin Jin, Mu-Sheng Zeng, Bo Zhao, Qian Zhong
Summary: This study revealed the critical role of super-enhancers associated with SOX2 in the tumorigenesis of nasopharyngeal carcinoma (NPC). High expression of SOX2 was correlated with poor prognosis. Inhibition of SOX2 suppressed tumor growth, highlighting the potential of SOX2 as a therapeutic target for NPC patients.
Article
Ecology
Tatsuki Nagasawa, Mari Kawaguchi, Kohki Nishi, Shigeki Yasumasu
Summary: In this study, the molecular evolution of C6astacin genes in vertebrates was described in detail, revealing the presence of these genes in basal animals and large-scale gene duplication in amphibians. This study provides important insights into the molecular evolution of vertebrate C6astacin genes, hatching enzymes, and their paralogous genes.
BMC ECOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Dia A. Ghose, Kaitlyn E. Przydzial, Emily M. Mahoney, Amy E. Keating, Michael T. Laub
Summary: The evolution of novel functions in biology relies on gene duplication and divergence, creating large paralogous protein families. However, the specificity of these paralogs to their interaction partners can be sensitive to mutation. Through deep mutational scanning, it was demonstrated that a family of bacterial signaling proteins exhibits marginal specificity, with individual substitutions leading to substantial cross-talk between pathways. These findings suggest that the evolution of bacterial signaling proteins is constrained by sequence space crowding, and that evolution selects for good enough rather than optimized phenotypes in paralogs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Wouter Steyaert, Lonneke Haer-Wigman, Rolph Pfundt, Debby Hellebrekers, Marloes Steehouwer, Juliet Hampstead, Elke de Boer, Alexander Stegmann, Helger Yntema, Erik-Jan Kamsteeg, Han Brunner, Alexander Hoischen, Christian Gilissen
Summary: This paper presents a method called "Chameleolyser" that accurately identifies variants in duplicated genomic regions. Application of this method to a large cohort of exome samples led to the identification of a significant number of rare variants, including those that resulted in direct molecular diagnoses for previously undiagnosed patients.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Dou Ye, Fang Du, Qingxiu Hu, Yajie Zou, Xue Bai
Summary: This study compared the primordium expression profiles of Pleurotus eryngii under blue-light stimulation, red-light stimulation, and darkness using high-throughput sequencing. A large number of differentially expressed genes (DEGs) related to light stimulation and amino acid biosynthesis were identified. The MAPK signaling pathway, oxidative phosphorylation pathway, and RNA transport were shown to be most active during primordium differentiation. The blue-light photoreceptor WC-1 and Deoxyribodipyrimidine photolyase PHR were predicted to play important roles in the primordium differentiation of P. eryngii. The results of this study provide a speculative mechanism for light-induced primordium differentiation and a foundation for further research on fruiting body development in P. eryngii.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Zhong Wu, Jin Zhou, Xiaoyang Zhang, Zhouwei Zhang, Yingtian Xie, Jie bin Liu, Zandra Ho, Arpit Panda, Xintao Qiu, Paloma Cejas, Israel Canadas, Fahire Goknur Akarca, James M. McFarland, Ankur K. Nagaraja, Louisa B. Goss, Nikolas Kesten, Longlong Si, Klothilda Lim, Yanli Liu, Yanxi Zhang, Ji Yeon Baek, Yang Liu, Deepa T. Patil, Jonathan P. Katz, Josephine Hai, Chunyang Bao, Matthew Stachler, Jun Qi, Jeffrey J. Ishizuka, Hiroshi Nakagawa, Anil K. Rustgi, Kwok-Kin Wong, Matthew Meyerson, David A. Barbie, Myles Brown, Henry Long, Adam J. Bass
Summary: The transition from normal esophageal tissue to squamous carcinoma is characterized by an altered SOX2 cistrome, leading to transcriptional reprogramming that activates endogenous retroviruses and double-stranded RNA expression, creating a dependency on the RNA editing enzyme ADAR1.
Article
Developmental Biology
Ivelisse Cajigas, Abhijit Chakraborty, Madison Lynam, Kelsey R. Swyter, Monique Bastidas, Linden Collens, Hao Luo, Ferhat Ay, Jhumku D. Kohtz
Summary: The study reveals that Evf2 interacts with factors like Sox2 to regulate gene expression on chromosome 6 in mice. The interactions between Evf2 and Sox2 influence the activity of Dlx5/6UCE, ultimately affecting gene expression.
Article
Plant Sciences
Jiajun Liu, Xi'an Shi, Tianhui Zhong, Wanrong Jie, Ruihan Xu, Yanfeng Ding, Chengqiang Ding
Summary: Auxin transporter proteins PINOID, PIN-FORMED1c, and PIN-FORMED1d play essential roles in leaf development in rice. Mutant lines lacking these proteins exhibit severe defects in leaf morphology, including drooping and semi-drooping blades, thickened sheath and lamina joint, and fused leaves with absent ligules and auricles. RNA sequencing analysis of the triple mutant further reveals altered gene expression essential for leaf development. This study enhances our understanding of auxin transport in monocot rice leaf development.
PLANT AND CELL PHYSIOLOGY
(2023)
Article
Developmental Biology
Makiko Iwafuchi-Doi, Kenneth S. Zaret
Article
Biochemistry & Molecular Biology
Kenneth S. Zaret, Jonathan Lerner, Makiko Iwafuchi-Doi
Article
Biochemistry & Molecular Biology
Makiko Iwafuchi-Doi, Greg Donahue, Akshay Kakumanu, Jason A. Watts, Shaun Mahony, B. Franklin Pugh, Dolim Lee, Klaus H. Kaestner, Kenneth S. Zaret
Review
Medicine, Research & Experimental
Makiko Iwafuchi-Doi
WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE
(2019)
Article
Biochemistry & Molecular Biology
Isao Kobayashi, Katsura Kojima, Keiro Uchino, Hideki Sezutsu, Tetsuya Iizuka, Ken-Ichiro Tatematsu, Naoyuki Yonemura, Hiromitsu Tanaka, Minoru Yamakawa, Eri Ogura, Yusuke Kamachi, Toshiki Tamura
ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY
(2011)
Article
Developmental Biology
Makiko Iwafuchi-Doi, Kazunari Matsuda, Kazuhiro Murakami, Hitoshi Niwa, Paul J. Tesar, Jun Aruga, Isao Matsuo, Hisato Kondoh
Review
Cell Biology
Masanori Uchikawa, Megumi Yoshida, Makiko Iwafuchi-Doi, Kazunari Matsuda, Yoshiko Ishida, Tatsuya Takemoto, Hisato Kondoh
DEVELOPMENT GROWTH & DIFFERENTIATION
(2011)
Article
Developmental Biology
Makiko Iwafuchi-Doi, Yuzo Yoshida, Daria Onichtchouk, Manuel Leichsenring, Wolfgang Driever, Tatsuya Takemoto, Masanori Uchikawa, Yusuke Kamachi, Hisato Kondoh
DEVELOPMENTAL BIOLOGY
(2011)
Review
Cell Biology
Makiko Iwafuchi-Doi, Kenneth S. Zaret
GENES & DEVELOPMENT
(2014)
Article
Neurosciences
Ritsuko Ohtani-Kaneko, Makiko Iwafuchi, Takashi Iwakura, Daisuke Muraoka, Makoto Yokosuka, Takashi Shiga, Chiho Watanabe
NEUROSCIENCE RESEARCH
(2010)
Article
Multidisciplinary Sciences
Deshani C. Ranawakage, Takuya Takada, Yusuke Kamachi
SCIENTIFIC REPORTS
(2019)
Article
Genetics & Heredity
Makiko Iwafuchi, Isabel Cuesta, Greg Donahue, Naomi Takenaka, Anna B. Osipovich, Mark A. Magnuson, Heinrich Roder, Steven H. Seeholzer, Pilar Santisteban, Kenneth S. Zaret
Article
Cell Biology
Deshani C. Ranawakage, Keita Okada, Kota Sugio, Yuya Kawaguchi, Yuki Kuninobu-Bonkohara, Takuya Takada, Yusuke Kamachi
Summary: This study successfully demonstrated precise gene knock-ins with composite tags in the zebrafish genome using CRISPR-Cas9 technology, highlighting the importance of the structural and sequence characteristics of the donor templates for efficient knock-in.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Keita Okada, Kanae Aoki, Teruyuki Tabei, Kota Sugio, Katsunori Imai, Yuki Bonkohara, Yusuke Kamachi
Summary: This study investigated the gRNA sequence features of a CRISPR-Cas9 ribonucleoprotein (RNP) complex composed of crRNA and tracrRNA, and identified novel mononucleotide features that are relevant to cleavage efficiency. The overall features of wild-type Cas9 resembled those of HiFi Cas9, but specific differences were also observed. Mutational analysis confirmed the relevance of mononucleotide features to cleavage efficiency. In addition, a mononucleotide feature-based score correlated well with gRNA efficiencies in zebrafish RNP injection experiments and independently tested crRNAs in RNP format, but not with Cas9 mRNA co-injection.
NUCLEIC ACIDS RESEARCH
(2022)