Article
Genetics & Heredity
Pavel Dvorak, Vojtech Hanicinec, Pavel Soucek
Summary: Evidence shows that introns play a role in regulating the transfer of genetic information, with longer first introns found to be common in eukaryotic gene structure and containing conserved sequences and functional elements. Our study provides more precise information on the position of the longest introns in human protein-coding genes and their possible connection to biological function and gene expression. Results indicate that the longest introns are mainly located in the first and second thirds of introns, with peaks at the middle and last introns, and the median length decreases with increasing distance from the start of the gene.
FRONTIERS IN GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Krishan Gupta, Princey Yadav, Sidrah Maryam, Gaurav Ahuja, Debarka Sengupta
Summary: Aging induces dysregulation of the transcription regulatory machinery, impacting cellular fitness, but evolutionarily conserved pathways have been identified through transcriptomic studies. Further investigation in this area provides crucial insights for observing aging through novel computational methods.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Zhiqing Diao, Qianzhao Ji, Zeming Wu, Weiqi Zhang, Yusheng Cai, Zehua Wang, Jianli Hu, Zunpeng Liu, Qiaoran Wang, Shijia Bi, Daoyuan Huang, Zhejun Ji, Guang-Hui Liu, Si Wang, Moshi Song, Jing Qu
Summary: The expression of SIRT3 is downregulated in senescent human mesenchymal stem cells, and depletion of SIRT3 leads to compromised cellular integrity and accelerated aging. However, reintroduction of SIRT3 can rescue disorganized heterochromatin and senescence phenotypes.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Agriculture, Multidisciplinary
Wang Pei-pei, Wang Zhao-ke, Guan Le, Muhammad Salman Haider, Maazullah Nasim, Yuan Yong-bing, Liu Geng-sen, Leng Xiang-peng
Summary: Nudix hydrolases are widely distributed enzymes that can hydrolyze organic pyrophosphates. In grapevine, the Nudix gene family has been shown to play regulatory roles in growth, development, and stress responses. The spatial and temporal expression patterns of VvNUDX genes suggest their involvement in multiple developmental processes and potential roles in berry development.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2022)
Article
Cell Biology
Se-Ra Park, Seong-Kwan Kim, Soo-Rim Kim, Doojin Kim, Kun-Woo Kim, In-Sun Hong, Hwa-Yong Lee
Summary: Chronic stress negatively impacts female fertility, possibly through the reduction of uterine receptivity by glucocorticoids. These hormones may directly damage endometrial stem cells, affecting endometrial reconstruction and leading to infertility. Additionally, cortisol suppresses beneficial functions of human endometrial stem cells through its receptor, contributing to the decline in fertility.
CELL DEATH & DISEASE
(2021)
Article
Biology
Panjiao Lin, Benjamin T. Gillard, Audrys G. Pauza, Fernando A. Iraizoz, Mahmoud A. Ali, Andre S. Mecawi, Fatma Z. Djazouli Alim, Elena Romanova, Pamela A. Burger, Michael P. Greenwood, Abdu Adem, David Murphy
Summary: This study focuses on the mechanisms of adaptive response to osmotic stress in the camel supraoptic nucleus, aiming to reveal the central control of water homeostasis in camels. By building three-dimensional models and comparing transcriptomic data, we identified unique adaptive genes in camels and common elements in the water deprivation transcriptomic response network.
COMMUNICATIONS BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Xiaona Chen, Jie Yuan, Guang Xue, Silvia Campanario, Di Wang, Wen Wang, Xi Mou, Shiau Wei Liew, Mubarak Ishaq Umar, Joan Isern, Yu Zhao, Liangqiang He, Yuying Li, Christopher J. Mann, Xiaohua Yu, Lei Wang, Eusebio Perdiguero, Wei Chen, Yuanchao Xue, Yoshikuni Nagamine, Chun Kit Kwok, Hao Sun, Pura Munoz-Canoves, Huating Wang
Summary: DHX36 helicase is essential for muscle regeneration by promoting mRNA translation through binding and unwinding rG4 structures during SC activation, thus acting as a crucial post-transcriptional regulator of SC function.
NATURE COMMUNICATIONS
(2021)
Article
Plant Sciences
Xinyi Zhao, Shiyang Guo, Chen Xu, Suyao Li, Yunjin Chen, Jianying Cheng, Qian Wang, Shumiao Jiang, Anyong Hu, Jinbiao Li
Summary: In this study, the interactive effects of aluminum (Al) and cadmium (Cd) in acidic soils were investigated using different wheat cultivars. The results showed that Al could alleviate the root growth inhibition caused by Cd stress in Al-tolerant wheat cultivar, but had no effect on the root growth of Al-sensitive cultivar. Al also decreased the accumulation of Cd in both roots and shoots of the wheat cultivars. The non-invasive micro-test technology confirmed that Al and Cd co-exposure inhibited the net Cd2+ influx into the roots compared to Cd-only stress. The study also found that Al downregulated the expression of certain Cd-related genes responsible for Cd uptake and translocation in wheat roots.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Plant Sciences
Zhennan Zhao, Renren Zhang, Dongjiao Wang, Jing Zhang, Shoujian Zang, Wenhui Zou, Aoyin Feng, Chuihuai You, Yachun Su, Qibin Wu, Youxiong Que
Summary: In this study, 44 SsTGA genes were identified from Saccharum spontaneum and shown to be involved in hormone and stress response. A ScTGA1 gene was also cloned and found to enhance the resistance of Nicotiana benthamiana to bacterial and fungal infections. This research provides important insights into the evolution and function of the SsTGA gene family and has implications for understanding the biotic stress responses in sugarcane.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Mughair Abdul Aziz, Miloofer Sabeem, Sangeeta Kutty Mullath, Faical Brini, Khaled Masmoudi
Summary: Plants have evolved defense mechanisms in response to environmental stresses, including overexpressing stress-responsive genes, among them genes encoding intrinsically disordered proteins (IDPs) like group II LEA proteins. These proteins play vital roles in protecting plant integrity by preventing crystallization of cellular components prior to various stresses, with studies on their distribution, structure, and genomic diversification providing insights into their role in plant stress tolerance mechanisms.
Article
Chemistry, Analytical
Sangamithirai Subramanian Parimalam, Mahmoud Nady Abdelmoez, Arata Tsuchida, Naoyuki Sotta, Mayuki Tanaka, Takashi Kuromori, Toru Fujiwara, Masami Yokota Hirai, Ryuji Yokokawa, Yusuke Oguchi, Hirofumi Shintaku
Summary: Researchers have developed a new microfluidic approach that combines pulsed and DC electric fields to permeabilize cell walls and selectively extract cellular contents from targeted cells, enabling rapid extraction of molecules from intact plant clusters for off-chip analyses.
Article
Biochemistry & Molecular Biology
Nikki Clauss, Kelsey Brass Allen, Katie D. Billings, Mikayla D. M. Tolliver, Ray Garza, Jennifer Byrd-Craven, Polly Campbell
Summary: This study on mouse model demonstrates that prenatal Western-pattern diet can alleviate the impact of maternal stress on dams and offspring, and sheds light on the relationship between pre- and post-natal nutrition, gene expression, and behaviors that lead to long-term health effects.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Fang He, Yu-Jie Shi, Qian Zhao, Kuang-Ji Zhao, Xing-Lei Cui, Liang-Hua Chen, Han-Bo Yang, Fan Zhang, Jia-Xuan Mi, Jin-Liang Huang, Xue-Qin Wan
Summary: This study conducted a genome-wide analysis of the PPO gene family in Populus, identifying 18 PtrPPO genes and revealing their characteristics through analyses of gene structure, phylogeny, chromosomal localization, gene replication, cis-elements, and expression patterns. The study results indicate that the PtrPPO gene family plays a crucial role in stress responses and may have important implications for stress resistance in forest trees.
Article
Plant Sciences
Zhaokui Du, Shixian You, Dang Yang, Yutian Tao, Yunxiao Zhu, Wen Sun, Zhengman Chen, Junmin Li
Summary: This study conducted a genome-wide analysis of NAC genes in the important mangrove species Kandelia obovata for the first time, identifying 79 KoNACs and studying their response to low-temperature stress. The results provide a foundation for understanding the evolution and molecular mechanisms of KoNACs in response to environmental stress.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Kathryn Vaillancourt, Jennie Yang, Gary G. Chen, Volodymyr Yerko, Jean-Francois Theroux, Zahia Aouabed, Alberto Lopez, Kimberly C. Thibeault, Erin S. Calipari, Benoit Labonte, Naguib Mechawar, Carl Ernst, Corina Nagy, Thierry Forne, Eric J. Nestler, Deborah C. Mash, Gustavo Turecki
Summary: The study explored the role of DNA methylation in cocaine dependence and found a correlation between hypomethylation of the IRX2 gene and addiction. The findings suggest that cocaine-related hypomethylation of IRX2 contributes to the development and maintenance of cocaine dependence through alterations in 3D chromatin structure.
MOLECULAR PSYCHIATRY
(2021)
Review
Biochemistry & Molecular Biology
Emily J. Shields, Ana F. Petracovici, Roberto Bonasio
BIOCHEMICAL JOURNAL
(2019)
Article
Genetics & Heredity
David B. Beck, Ana Petracovici, Chongsheng He, Hannah W. Moore, Raymond J. Louie, Muhammad Ansar, Sofia Douzgou, Sivagamy Sithambaram, Trudie Cottrell, Regie Lyn P. Santos-Cortez, Eloise J. Prijoles, Renee Bend, Boris Keren, Cyril Mignot, Marie-Christine Nougues, Katrin Ounap, Tiia Reimand, Sander Pajusalu, Muhammad Zahid, Muhammad Arif Nadeem Saqib, Julien Buratti, Eleanor G. Seaby, Kirsty McWalter, Aida Telegrafi, Dustin Baldridge, Marwan Shinawi, Suzanne M. Leal, G. Bradley Schaefer, Roger E. Stevenson, Siddharth Banka, Roberto Bonasio, Jill A. Fahrner
AMERICAN JOURNAL OF HUMAN GENETICS
(2020)
Review
Biology
Hua Yan, Shadi Jafari, Gregory Pask, Xiaofan Zhou, Danny Reinberg, Claude Desplan
JOURNAL OF EXPERIMENTAL BIOLOGY
(2020)
Article
Multidisciplinary Sciences
Wenqing Ren, Nicole Medeiros, Robert Warneford-Thomson, Phillip Wulfridge, Qingqing Yan, Joyce Bian, Simone Sidoli, Benjamin A. Garcia, Emmanuel Skordalakes, Eric Joyce, Roberto Bonasio, Kavitha Sarma
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Lihong Sheng, Emily J. Shields, Janko Gospocic, Karl M. Glastad, Puttachai Ratchasanmuang, Arjun Raj, Shawn Little, Roberto Bonasio, Shelley L. Berger
Article
Biochemistry & Molecular Biology
Blake A. Caldwell, Monica Yun Liu, Rexxi D. Prasasya, Tong Wang, Jamie E. DeNizio, N. Adrian Leu, Nana Yaa A. Amoh, Christopher Krapp, Yemin Lan, Emily J. Shields, Roberto Bonasio, Christopher J. Lengner, Rahul M. Kohli, Marisa S. Bartolomei
Summary: Active DNA demethylation through TET enzymes is crucial for epigenetic reprogramming in cell state transitions. Biochemically engineered TET mutants that uncouple the oxidation steps of 5mC show distinct roles of 5fC/5caC in somatic cell reprogramming, highlighting their importance in chromatin accessibility changes and DNA demethylation.
Article
Biochemistry & Molecular Biology
Chongsheng He, Julianna Bozler, Kevin A. Janssen, Jeremy E. Wilusz, Benjamin A. Garcia, Andrea J. Schorn, Roberto Bonasio
Summary: TET2 protein promotes the conversion of 5-methylcytosine to 5-hydroxymethylcytosine on tRNAs and affects the processing or stability of different classes of tRNA fragments. The interaction between TET2 and RNA, particularly tRNAs, reveals a new function of TET2 in regulating RNA modifications and small noncoding RNAs.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Ana Petracovici, Roberto Bonasio
Summary: In the process of differentiation from ESCs to NPCs, PRC2 subunits MTF2 and JARID2 play distinct roles in Polycomb silencing, indicating that PRC2.1 and PRC2.2 have unique functions in maintaining and establishing Polycomb repression.
Article
Cell Biology
Jennifer R. Aleman, Terra M. Kuhn, Pau Pascual-Garcia, Janko Gospocic, Yemin Lan, Roberto Bonasio, Shawn C. Little, Maya Capelson
Summary: Dosage compensation in Drosophila melanogaster involves a 2-fold transcriptional upregulation of the male X chromosome, which relies on the X-chromosome-binding male-specific lethal complex. This study shows that the nuclear pore component Mtor plays a key role in regulating the correct transcription levels from the male X chromosome by affecting the function of the MSL complex, rather than through defects in mRNA export. Depletion of Mtor results in selective upregulation of X chromosome target genes beyond the required 2-fold, further highlighting its importance in dosage compensation.
Article
Biology
Emily J. Shields, Masato Sorida, Lihong Sheng, Bogdan Sieriebriennikov, Long Ding, Roberto Bonasio
Summary: The study utilized Iso-Seq to comprehensively annotate the transcriptome of the ant Harpegnathos saltator, resulting in additional splice isoforms and extended 3' untranslated regions for more than 4000 genes. This improved annotation allowed for more accurate identification of cell type markers in the ant brain and discovery of genes differentially expressed across castes in specific cell types. The findings highlight the efficiency and effectiveness of Iso-Seq in enhancing genome annotations and maximizing information obtained from genomic datasets in various organisms.
Article
Biochemistry & Molecular Biology
Janko Gospocic, Karl M. Glastad, Lihong Sheng, Emily J. Shields, Shelley L. Berger, Roberto Bonasio
Summary: Kr-h1 is a transcription factor that maintains distinct brain states in Harpegnathos saltator ants, established in response to socially regulated hormones, influencing the characteristic behaviors between workers and gamergates.
Editorial Material
Genetics & Heredity
Alessandro Scacchetti, Roberto Bonasio
Summary: A new study used CRISPR-Cas9-based base editing to simultaneously mutate all copies of histone H3 genes in mammals, revealing the functional importance of H3K27me3 in Polycomb-mediated gene silencing and the dispensability of H3K27ac in transcriptional activation.
Article
Biochemistry & Molecular Biology
Naihua N. Gong, Hang Ngoc Bao Luong, An H. Dang, Benjamin Mainwaring, Emily Shields, Karl Schmeckpeper, Roberto Bonasio, Matthew S. Kayser
Summary: The study reveals that the transcriptional states of sleep output neurons play a crucial role in the changes in sleep across the lifespan in fruit flies.
Article
Cell Biology
Lihong Sheng, Emily J. J. Shields, Janko Gospocic, Masato Sorida, Linyang Ju, China N. N. Byrns, Faith Carranza, Shelley L. L. Berger, Nancy Bonini, Roberto Bonasio
Summary: By studying the changes in the number and gene expression of ensheathing glia in Drosophila melanogaster brain, it is found that dysregulated ensheathing glia can lead to lipid droplet accumulation, cellular dysfunction, and death, affecting brain health and lifespan. Inhibition of apoptosis can restore the declining number of ensheathing glia with age, improve the neuro-motor performance of aged fruit flies and prolong lifespan. Furthermore, an expanded ensheathing glia population can prevent amyloid-beta accumulation in a fly model of Alzheimer's disease and delay the premature death of diseased animals. These findings highlight the vital role of ensheathing glia in regulating brain health and animal longevity.
Article
Cell Biology
Karl M. Glastad, Julian Roessler, Janko Gospocic, Roberto Bonasio, Shelley L. Berger
Summary: In this study, the researchers investigate the role of heat shock responses mediated by hsalHSF2 in extending the longevity and survival of reproductive gamergate ants. They show that the increased heat stress resilience and life span benefits observed in gamergates can be transferred to fruit flies through the expression of hsalHSF2. The study sheds light on the mechanisms underlying the extended life span of gamergates, highlighting the significance of hsalHSF2 in ant longevity. It also underscores the importance of proteostasis in health and aging, as well as the potential for facultative life span extension in ants.
GENES & DEVELOPMENT
(2023)