Article
Cell Biology
Lauren Winkler, Maria Jimenez, Joshua T. Zimmer, Adam Williams, Matthew D. Simon, Nadya Dimitrova
Summary: The study shows that the full transcription, splicing, and accumulation of lincRNA-p21 are not crucial for gene regulation, but the production of lincRNA-p21 through specific exon regions can promote cis-activation of the gene.
Review
Cell Biology
Umer Farooq, Dimple Notani
Summary: 9p21 locus is a highly reproducible region in genome-wide association studies (GWAS) and is associated with various diseases and cancers. The genes within this region, including CDKN2A/B genes, play critical roles in cell cycle regulation and are linked to cellular regeneration, stemness, aging, and cancers. Understanding the regulation of these genes through promoter-driven and distal mechanisms could provide insights for targeting this locus in pathologies and aging.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Binyuan Jiang, Yeqin Yuan, Ting Yi, Wei Dang
Summary: Antisense long noncoding RNA (as-lncRNA) is a reverse transcription product that is partially or completely complementary to the corresponding sense protein-coding or noncoding genes. As-lncRNAs, also known as natural antisense transcripts (NATs), can regulate the expression of adjacent sense genes through various mechanisms, influencing cellular activities and participating in the development of various tumors. This study aims to explore the functional roles of as-lncRNAs in cis-regulating protein-coding sense genes and provide a theoretical basis for lncRNA-targeted tumor therapy by comprehensively understanding the occurrence and development of malignant tumors.
Article
Cell Biology
Ana Rita Amandio, Leonardo Beccari, Lucille Lopez-Delisle, Benedicte Mascrez, Jozsef Zakany, Sandra Gitto, Denis Duboule
Summary: Understanding the diverse functions of CTCF sites within the Hox gene clusters is crucial for the formation of TAD borders and maintaining gene expression, showing significant evolutionary conservation.
GENES & DEVELOPMENT
(2021)
Article
Cell Biology
Tian-Tian Liu, Feiya Ou, Julia A. Belk, Prachi Bagadia, David A. Anderson III, Vivek Durai, Winnie Yao, Ansuman T. Satpathy, Theresa L. Murphy, Kenneth M. Murphy
Summary: In this study, the researchers found that different elements within the Irf8 superenhancer have cooperative or temporal effects on dendritic cell development. They discovered that the +41-kb enhancer is required for pre-cDC1 specification, while the +32-kb enhancer is necessary for cDC1 maturation. They also demonstrated that the +32-kb enhancer is dependent on the +41-kb enhancer, and that the activation of the +32-kb enhancer is controlled by chromatin accessibility and transcription factor binding.
GENES & DEVELOPMENT
(2023)
Review
Biochemistry & Molecular Biology
Chong Tong, Yafei Yin
Summary: The subcellular localization of RNA is crucial for its function and regulation, with different RNAs being retained in the nucleus or exported to the cytoplasm based on their types and functions. While the mechanisms controlling RNA export have been well studied, the mechanisms governing RNA nuclear retention, especially for noncoding RNAs, are still relatively unexplored. Future research will focus on uncovering the general principles of RNA nuclear retention and exploring potential areas for investigation.
Review
Biochemistry & Molecular Biology
Robert J. Schmitz, Erich Grotewold, Maike Stam
Summary: This review discusses the characteristics, identification technologies, and role of cis-regulatory sequences in plant biology. Despite advances in sequence assembly and genome annotation, there are still challenges in identifying and understanding cis-regulatory modules.
Article
Multidisciplinary Sciences
Xukang Shen, Siliang Song, Chuan Li, Jianzhi Zhang
Summary: Synonymous mutations in protein-coding genes are not neutral and often result in reduced fitness and disturbed mRNA expression levels. Non-synonymous mutations have greater fitness variations across environments, which may explain the lower substitution rates compared to synonymous mutations.
Review
Ecology
David C. Culver, Johanna E. Kowalko, Tanja Pipan
Summary: Subterranean organisms often show reductions or losses of eyes and pigment, which can be explained by the accumulation of selectively neutral mutations or by direct selection and pleiotropy. However, these explanations are often one-sided and fail to consider the role of migration and epigenetic effects in cave evolution.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Article
Plant Sciences
Xiaomin Zheng, Yanjun Chen, Yifan Zhou, Keke Shi, Xiao Hu, Danyang Li, Hanzhe Ye, Yu Zhou, Kun Wang
Summary: The study integrated multiple RNA sequencing technologies to identify 9,240 lncRNAs in the diploid cotton Gossypium arboreum. It revealed the widespread alternative usage of transcription start and termination sites in lncRNAs during plant growth, and discovered that many lncRNAs act in cis to regulate adjacent protein-coding genes.
Article
Biology
Loic Mangnier, Charles Joly-Beauparlant, Arnaud Droit, Steve Bilodeau, Alexandre Bureau
Summary: The 3D conformation of chromatin plays a vital role in gene regulation, especially in complex diseases. This study discovered functional interactions within cis-regulatory hubs (CRHs) in neurons, providing insights into the epigenetic mechanisms involved in diseases such as schizophrenia. CRHs highlighted significant enrichments in schizophrenia-associated genes, SNPs, and heritability, and also exhibited a higher proportion of differentially expressed genes in schizophrenia compared to other regulatory structures. Therefore, CRHs serve as 3D models to study dysregulation of gene expression in complex diseases.
LIFE SCIENCE ALLIANCE
(2022)
Article
Multidisciplinary Sciences
Xingjie Ren, Mengchi Wang, Bingkun Li, Kirsty Jamieson, Lina Zheng, Ian R. Jones, Bin Li, Maya Asami Takagi, Jerry Lee, Lenka Maliskova, Tsz Wai Tam, Miao Yu, Rong Hu, Lindsay Lee, Armen Abnousi, Gang Li, Yun Li, Ming Hu, Bing Ren, Wei Wang, Yin Shen
Summary: The study introduces a screening strategy called CRISPRpath for characterizing CREs of genes linked to the same biological pathway and converging phenotypes in parallel. It demonstrates the ability of CRISPRpath to identify functional enhancers of six genes in the 6-thioguanine-induced DNA mismatch repair pathway simultaneously.
Article
Endocrinology & Metabolism
Ya Wang, Li Lu, Yajing Niu, Qiongdan Zhang, Chen Cheng, Han Huang, Xinyao Huang, Qingyang Huang
Summary: The study identified four enhancer SNPs as potential causal SNPs for osteoporosis, including rs9820407 which showed the strongest enhancer activity and could modulate CTNNB1 gene expression. The research provided insight into how the noncoding enhancer SNP rs9820407 distally regulates CTNNB1 expression and modulates osteoporosis risk.
Article
Genetics & Heredity
Tingyi Cao, Marcella E. O'Reilly, Caitlin Selvaggi, Esther Cynn, Heidi Lumish, Chenyi Xue, Anjali Jha, Muredach P. Reilly, Andrea S. Foulkes
Summary: The genetically regulated expression of non-conserved lincRNAs shows similar rates of association with complex cardiometabolic traits as conserved lincRNAs, challenging the conventional notion of conservation and highlighting the need for comprehensive strategies to study non-conserved lincRNAs in human disease.
JOURNAL OF HUMAN GENETICS
(2022)
Review
Plant Sciences
Yue Cui, Qiao Cao, Yongpeng Li, Mingqi He, Xigang Liu
Summary: Transcriptional regulation is critical for controlling gene expression, and involves the interaction between cis-acting elements and trans-acting factors to determine expression patterns and levels. While many studies have focused on trans-acting factors, such as enhancers and silencers, cis-acting elements and natural variations in the genome also play important roles in gene expression regulation. The use of CRISPR/Cas9-mediated gene editing techniques can harness these elements for improving crop quality and yield, and this review discusses the current understanding and advancements in this field for major crops.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Genetics & Heredity
Santiago Naranjo, Justin D. Smith, Carlo G. Artieri, Mian Zhang, Yiqi Zhou, Michael E. Palmer, Hunter B. Fraser
Article
Biochemistry & Molecular Biology
Becky X. H. Fu, Robert P. St. Onge, Andrew Z. Fire, Justin D. Smith
NUCLEIC ACIDS RESEARCH
(2016)
Article
Biochemistry & Molecular Biology
Albi Celaj, Ulrich Schlecht, Justin D. Smith, Weihong Xu, Sundari Suresh, Molly Miranda, Ana Maria Aparicio, Michael Proctor, Ronald W. Davis, Frederick P. Roth, Robert P. St. Onge
MOLECULAR SYSTEMS BIOLOGY
(2017)
Article
Biochemistry & Molecular Biology
Justin D. Smith, Ulrich Schlecht, Weihong Xu, Sundari Suresh, Joe Horecka, Michael J. Proctor, Raeka S. Aiyar, Richard A. O. Bennett, Angela Chu, Yong Fuga Li, Kevin Roy, Ronald W. Davis, Lars M. Steinmetz, Richard W. Hyman, Sasha F. Levy, Robert P. St Onge
MOLECULAR SYSTEMS BIOLOGY
(2017)
Article
Biotechnology & Applied Microbiology
Kevin R. Roy, Justin D. Smith, Sibylle C. Vonesch, Gen Lin, Chelsea Szu Tu, Alex R. Lederer, Angela Chu, Sundari Suresh, Michelle Nguyen, Joe Horecka, Ashutosh Tripathi, Wallace T. Burnett, Maddison A. Morgan, Julia Schulz, Kevin M. Orsley, Wu Wei, Raeka S. Aiyar, Ronald W. Davis, Vytas A. Bankaitis, James E. Haber, Marc L. Salit, Robert P. St Onge, Lars M. Steinmetz
NATURE BIOTECHNOLOGY
(2018)
Article
Multidisciplinary Sciences
Hinco J. Gierman, Kristen Fortney, Jared C. Roach, Natalie S. Coles, Hong Li, Gustavo Glusman, Glenn J. Markov, Justin D. Smith, Leroy Hood, L. Stephen Coles, Stuart K. Kim
Article
Biochemistry & Molecular Biology
Mia Jaffe, Adam Dziulko, Justin D. Smith, Robert P. St Onge, Sasha F. Levy, Gavin Sherlock
Article
Microbiology
Becky Xu Hua Fu, Justin D. Smith, Ryan T. Fuchs, Megumu Mabuchis, Jennifer Curcuru, G. Brett Robb, Andrew Z. Fire
NATURE MICROBIOLOGY
(2019)
Article
Cell Biology
Sandra Backes, Yury S. Bykov, Tamara Flohr, Markus Raeschle, Jialin Zhou, Svenja Lenhard, Lena Kraemer, Timo Muehlhaus, Chen Bibi, Cosimo Jann, Justin D. Smith, Lars M. Steinmetz, Doron Rapaport, Zuzana Storchova, Maya Schuldiner, Felix Boos, Johannes M. Herrmann
Summary: Tom70 protein functions at the interface of cytosol and mitochondria, recruiting cytosolic chaperones to the outer mitochondrial membrane to reduce proteotoxicity of mitochondrial precursor proteins.
Editorial Material
Education, Scientific Disciplines
Saumya M. Sankaran, Justin D. Smith, Kevin R. Roy
JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION
(2021)
Article
Biotechnology & Applied Microbiology
Justin D. Smith, Sundari Suresh, Ulrich Schlecht, Manhong Wu, Omar Wagih, Gary Peltz, Ronald W. Davis, Lars M. Steinmetz, Leopold Parts, Robert P. St Onge
Article
Biochemistry & Molecular Biology
Russll M. Gordley, Justin D. Smith, Torbjorn Graslund, Carlos F. Barbas
JOURNAL OF MOLECULAR BIOLOGY
(2007)