Article
Biology
Alexandre P. Thiery, Ailin Leticia Buzzi, Eva Hamrud, Chris Cheshire, Nicholas M. Luscombe, James Briscoe, Andrea Streit
Summary: The vertebrate neural plate border is a transient territory that contains precursors for all ectodermal derivatives. Through single cell RNA sequencing, this study explores the diversity and heterogeneity of cells in the neural plate border and reveals the dynamic expression patterns and fate enrichment of genes previously classified as neural plate border specifiers. Furthermore, the study suggests that individual cells in the neural plate border co-express competing transcriptional programs, indicating their undecided fate.
Article
Biology
Ruth M. Williams, Martyna Lukoseviciute, Tatjana Sauka-Spengler, Marianne E. Bronner
Summary: This study generates a single-cell atlas of the developing chick epiblast and focuses on the transcriptional changes at the neural plate border. The results reveal the heterogeneity of cells at the neural plate border before early neurulation, suggesting a later onset of lineage segregation compared to previous predictions.
Article
Multidisciplinary Sciences
Marta Losa, Iros Barozzi, Marco Osterwalder, Viviana Hermosilla-Aguayo, Angela Morabito, Brandon H. Chacon, Peyman Zarrineh, Ausra Girdziusaite, Jean Denis Benazet, Jianjian Zhu, Susan Mackem, Terence D. Capellini, Diane Dickel, Nicoletta Bobola, Aimee Zuniga, Axel Visel, Rolf Zeller, Licia Selleri
Summary: This study investigates how transcription factors with widespread distribution in vertebrate embryos can perform tissue-specific functions. The researchers demonstrate that PBX TALE homeoproteins interact with the transcriptional regulator HAND2 to regulate a gene regulatory network (GRN) in subsets of hindlimb mesenchymal cells, revealing principles of cooperation between promiscuous and tissue-specific regulators in developmental programs.
NATURE COMMUNICATIONS
(2023)
Article
Oncology
Vito Alessandro Lasorsa, Annalaura Montella, Sueva Cantalupo, Matilde Tirelli, Carmen de Torres, Sanja Aveic, Gian Paolo Tonini, Achille Iolascon, Mario Capasso
Summary: This study focuses on noncoding cis-regulatory variants in neuroblastoma and identifies somatic mutations in regulatory elements that play a role in tumorigenesis. The findings highlight the importance of assessing these variants and long-range interactions in understanding the drivers of neuroblastoma.
Article
Biology
Zhanying Feng, Zhana Duren, Ziyi Xiong, Sijia Wang, Fan Liu, Wing Hung Wong, Yong Wang
Summary: Cranial Neural Crest Cells (CNCC) originate from different regions of the brain and differentiate into multiple cell types in the craniofacial region. The regulatory network hReg-CNCC integrates gene expression and chromatin accessibility data to predict high-quality regulations associated with neural plate border, specification, and migration functions. This network can help interpret genetic variants related to craniofacial development and connect them to cis-regulatory sequences, GWAS SNPs, disease risk loci, and evolutionarily-conserved regions of the genome.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Bahareh Nikparvar, Margarita Andreevskaya, Ilhan C. Duru, Florentina I. Bucur, Leontina Grigore-Gurgu, Daniela Borda, Anca I. Nicolau, Christian U. Riedel, Petri Auvinen, Nadav Bar
Summary: The pathogen Listeria (L.) monocytogenes exhibits different gene regulation modes in response to high pressure processing, including survival mode, repair mode, and re-growth mode. This allows for the timely activation of transcription factors associated with immediate stress response, followed by repair and re-growth to survive and recover from extreme conditions. The findings provide insights for potential design of specific strategies to target genes or mechanisms to prevent L. monocytogenes recovery during food storage under high pressure conditions.
Article
Developmental Biology
Makoto Abe, Timothy C. Cox, Anthony B. Firulli, Stanley M. Kanai, Jacob Dahlka, Kim-Chew Lim, James Douglas Engel, David E. Clouthier
Summary: Neural crest cells in the mandibular and maxillary prominences initially respond to signals from both regions, with GATA3 playing a crucial role in separating the upper and lower jaw domains during development by influencing BMP4 and FGF8 gene regulatory networks.
Article
Biochemical Research Methods
Lirong Zhang, Yanchao Yang, Lu Chai, Qianzhong Li, Junjie Liu, Hao Lin, Li Liu
Summary: This study quantitatively analyzed the correlation between transcription factors (TFs) and gene expression and identified TF modules associated with gene expression. A convolutional neural network model, TFCNN, was constructed to predict gene expression levels based on the enrichment characteristics of TFs. Results showed that TFCNN achieved high prediction performance and outperformed other models by better extracting combinatorial interactions among TFs.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Cell Biology
Nagif Alata Jimenez, Pablo H. Strobl-Mazzulla
Summary: This study reveals the impact of folate deficiency on the specification and territorial restriction of progenitor cells during early embryonic development. The findings suggest that folate deficiency induces methylation changes in specific genomic regions, leading to a dysregulation of signaling pathways in the neural plate and NPB territories.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Junguang Liao, Yuping Huang, Qiang Wang, Sisi Chen, Chenyang Zhang, Dan Wang, Zhengbing Lv, Xingen Zhang, Mengrui Wu, Guiqian Chen
Summary: This article summarizes the important role of the cranial neural crest (CNC) in calvarial bone development, including discussing the potential cell fate of CNC and the gene regulatory network that controls this potential. Furthermore, the study has found a close correlation between CNC patterning disorders and clinical birth defects and diseases. The article emphasizes the potential regenerative alternative based on CNC patterning and genetic molecules for treating clinical disorders.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Genetics & Heredity
Dabin Jeong, Sangsoo Lim, Sangseon Lee, Minsik Oh, Changyun Cho, Hyeju Seong, Woosuk Jung, Sun Kim
Summary: This paper presents a novel computational method for constructing condition-specific transcriptional networks, focusing on the complex multiple-to-multiple regulatory interactions between transcription factors and target genes. By applying kernel canonical correlation analysis, the method identifies these relationships and was demonstrated on responses to high fat diet in humans and cold/heat stress in arabidopsis. The method not only detected known regulatory interactions but also uncovered novel TF-TG relations in response to specific stress.
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
Yesid Cuesta-Astroz, Guilherme Gischkow Rucatti, Leandro Murgas, Carol D. SanMartin, Mario Sanhueza, Alberto J. M. Martin
Summary: Gene Regulatory Networks (GRNs) are useful for studying gene expression regulation of whole genomes, but assigning Transcription Factors (TFs) to specific genes is still challenging and expensive. ChIP-Seq allows the determination of TF Binding Sites (TFBSs) but is costly and requires replicates. This study introduces a two-step methodology using Drosophila melanogaster as a case study to address these challenges in TF-gene regulation assignment.
FRONTIERS IN GENETICS
(2021)
Article
Cell Biology
Steven L. Klein, Andre L. P. Tavares, Meredith Peterson, Charles H. Sullivan, Sally A. Moody
Summary: The formation of the embryonic ectoderm domains involves a series of signaling factor gradients. Early cell autonomous repressive transcription factor interactions within individual cells are followed by non-cell autonomous signaling between cells contributing to the separation of the domains.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Pharmacology & Pharmacy
Guangyu Xu, Yanbo Feng, Han Li, Cong Chen, He Li, Chunmei Wang, Jianguang Chen, Jinghui Sun
Summary: This study explored the molecular mechanism of SA's regulatory effect on the immune function of cyclophosphamide-induced immunosuppressive mice through screening different genes and constructing a transcription factor target gene regulatory network. The results showed that SA alleviated the immunosuppression induced by cyclophosphamide in mice by regulating multiple genes and their transcription factors.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Plant Sciences
Gerardo Nunez-Lillo, Jose Zabala, Victoria Lillo-Carmona, Jose Miguel Alvarez, Romina Pedreschi, Claudio Meneses
Summary: Fruit development is a complex process that involves the interplay of different biological processes. The NAC072 transcription factor has been identified as a key regulatory element in the slow ripening phenotype of peaches. By using transcriptomic analysis, a regulatory network for NAC072 was constructed and potential elements related to peach fruit development were identified.
JOURNAL OF PLANT GROWTH REGULATION
(2023)
Article
Developmental Biology
Ruth M. Williams, Upeka Senanayake, Mara Artibani, Gunes Taylor, Daniel Wells, Ahmed Ashour Ahmed, Tatjana Sauka-Spengler
Article
Cell Biology
Amy Kenyon, Daria Gavriouchkina, Jernej Zorman, Vanessa Chong-Morrison, Giorgio Napolitani, Vincenzo Cerundolo, Tatjana Sauka-Spengler
DISEASE MODELS & MECHANISMS
(2018)
Article
Biochemical Research Methods
Le A. Trinh, Vanessa Chong-Morrison, Tatjana Sauka-Spengler
Article
Cell Biology
Martyna Lukoseviciute, Daria Gavriouchkina, Ruth M. Williams, Tatiana Hochgreb-Hagele, Upeka Senanayake, Vanessa Chong-Morrison, Supat Thongjuea, Emmanouela Repapi, Adam Mead, Tatjana Sauka-Spengler
DEVELOPMENTAL CELL
(2018)
Article
Biochemistry & Molecular Biology
Kerstin Pinkwart, Falk Schneider, Martyna Lukoseviciute, Tatjana Sauka-Spengler, Edward Lyman, Christian Eggeling, Erdinc Sezgin
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Article
Cell Biology
Irving T. C. Ling, Tatjana Sauka-Spengler
NATURE CELL BIOLOGY
(2019)
Article
Biology
Mohammad KaramiNejadRanjbar, Sahand Sharifzadeh, Nina C. Wietek, Mara Artibani, Salma El-Sahhar, Tatjana Sauka-Spengler, Christopher Yau, Volker Tresp, Ahmed A. Ahmed
Article
Multidisciplinary Sciences
Lu Cui, Shih-Yu Chen, Tristan Lerbs, Jin-Wook Lee, Pablo Domizi, Sydney Gordon, Yong-hun Kim, Garry Nolan, Paola Betancur, Gerlinde Wernig
NATURE COMMUNICATIONS
(2020)
Article
Neurosciences
Surangi N. Perera, Ruth M. Williams, Rachel Lyne, Oliver Stubbs, Dennis P. Buehler, Tatjana Sauka-Spengler, Masaharu Noda, Gos Micklem, E. Michelle Southard-Smith, Clare V. H. Baker
Article
Multidisciplinary Sciences
Gi Fay Mok, Leighton Folkes, Shannon A. Weldon, Eirini Maniou, Victor Martinez-Heredia, Alice M. Godden, Ruth M. Williams, Tatjana Sauka-Spengler, Grant N. Wheeler, Simon Moxon, Andrea E. Muensterberg
Summary: This study used ATAC-seq and RNA-seq to analyze the spatiotemporal dynamics along the chick embryonic axis, identifying differential binding site coverage for key transcription factors and connecting accessible chromatin with nearby expressed genes. The authors determined cis-regulatory elements for TCF15 and MEOX1, investigated their spatiotemporal activity and evolutionary conservation, and disrupted their expression through epigenome silencing to recapitulate phenotypic abnormalities of anterior-posterior axis extension. This integrated approach allows for dissection of paraxial mesoderm regulatory circuits in vivo and has implications for investigating gene regulatory networks.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Fei Xu, Ferdinand Marletaz, Daria Gavriouchkina, Xiao Liu, Tatjana Sauka-Spengler, Guofan Zhang, Peter W. H. Holland
Summary: The article discusses the similar expression patterns of Hox and ParaHox genes encoding transcription factors in divergent animals, highlighting the regulatory role of the Pdx gene on the insulin gene in Pacific oysters. The study shows that cgILP gene is co-expressed with cgPdx in oyster digestive tissue, indicating this gene interaction dates back to the origin of Bilateria.
NATURE COMMUNICATIONS
(2021)
Article
Oncology
Carolina Di Benedetto, Justin Oh, Zainab Choudhery, Weiquan Shi, Gilmer Valdes, Paola Betancur
Summary: This study identified two novel super-enhancer dysregulated genes highly associated with poor prognosis and negative response to treatment in breast cancer patients. Modulating the transcript levels of one of these genes could improve patients' response to chemotherapy, consequently improving disease outcome.
Review
Genetics & Heredity
Oana Pelea, Tudor A. A. Fulga, Tatjana Sauka-Spengler
Summary: CRISPR-Cas9 has become a major tool for genome manipulation. Recent studies have shown that the activity of CRISPR can be controlled by sensing the expression levels of endogenous transcripts, which is of great significance for studying cell types, disease states, and environmental challenges.
Article
Oncology
Carolina Di Benedetto, Taimoor Khan, Santiago Serrano-Saenz, Anthony Rodriguez-Lemus, Chananat Klomsiri, Tim-Mathis Beutel, Alysia Thach, Henning Walczak, Paola Betancur
Summary: We discovered a novel gene regulatory mechanism involving enhancer clusters that explains the high levels of TRAIL expression in cancer cells. Interferon stimulation leads to the upregulation of TRAIL, but instead of being secreted, it accumulates intracellularly and is unable to induce apoptosis. Our study provides insights into the mechanism behind TRAIL upregulation and its intracellular accumulation in cancer cells, suggesting a potential role in apoptosis resistance.
Article
Biology
Vanessa Chong-Morrison, Sarah Mayes, Filipa C. Simoes, Upeka Senanayake, Dervla S. Carroll, Paul R. Riley, Stephen W. Wilson, Tatjana Sauka-Spengler
Summary: Due to its genetic amenability coupled with advances in genome editing, zebrafish is an excellent model to examine the function of (epi)genomic elements. We repurposed the Ac/Ds maize transposition system to efficiently characterise zebrafish cis-regulated elements, also known as enhancers, in F0-microinjected embryos. We used the system to stably express guide RNAs enabling CRISPR/dCas9-interference (CRISPRi) perturbation of enhancers without disrupting the underlying genetic sequence. In addition, we probed the phenomenon of antisense transcription at two neural crest gene loci. Our study highlights the utility of Ac/Ds transposition as a new tool for transient epigenome modulation in zebrafish.