Correction
Biochemical Research Methods
M. Grace Gordon, Fumitaka Inoue, Beth Martin, Max Schubach, Vikram Agarwal, Sean Whalen, Shiyun Feng, Jingjing Zhao, Tal Ashuach, Ryan Ziffra, Anat Kreimer, Ilias Georgakopoulos-Soares, Nir Yosef, Chun Jimmie Ye, Katherine S. Pollard, Jay Shendure, Martin Kircher, Nadav Ahituv
Summary: The paper has a published amendment which can be accessed through a link at the top of the paper.
Article
Biochemistry & Molecular Biology
Adi X. Mukund, Josh Tycko, Sage J. Allen, Stephanie A. Robinson, Cecelia Andrews, Joydeb Sinha, Connor H. Ludwig, Kaitlyn Spees, Michael C. Bassik, Lacramioara Bintu
Summary: This study measures the transcriptional activity of 8,400 effector domain combinations and reveals that weak and moderate activation domains synergize to drive strong gene expression, while combining strong activators often results in weaker activation. In contrast, repressor domains combine linearly and produce full gene silencing.
Article
Biochemical Research Methods
Jimin Park, Sung Sun Yim, Harris H. Wang
Summary: Recent efforts have identified numerous Biosynthetic Gene Clusters (BGCs) in bacteria, with genes within BGCs typically being transcriptionally silent. This study used high-throughput DNA synthesis and multiplexed reporter assays to build and characterize a library of BGC-derived regulatory sequences, measuring transcription levels in the Actinobacteria Streptomyces albidoflavus J1074 to identify key features associated with expression. It was also demonstrated that transcription levels could be modulated through coexpression of global regulatory proteins, providing insights into the regulatory landscape of BGCs.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Cristina Vieitez, Bede P. Busby, David Ochoa, Andre Mateus, Danish Memon, Marco Galardini, Umut Yildiz, Matteo Trovato, Areeb Jawed, Alexander G. Geiger, Michaela Oborska-Oplova, Clement M. Potel, Sibylle C. Vonesch, Chelsea Szu Tu, Mohammed Shahraz, Frank Stein, Lars M. Steinmetz, Vikram G. Panse, Kyung-Min Noh, Mikhail M. Savitski, Athanasios Typas, Pedro Beltrao
Summary: Phosphorylation plays a critical role in regulating various cellular processes, but functional annotations for the majority of discovered phosphosites are lacking. A chemical genetic approach was used to study the functional relevance of phosphosites in yeast, revealing potential functional significance for 42% of the sites. This high-throughput method allows for the functional characterization of individual phosphosites at scale.
NATURE BIOTECHNOLOGY
(2022)
Article
Genetics & Heredity
Steven K. Reilly, Sager J. Gosai, Alan Gutierrez, Ava Mackay-Smith, Jacob C. Ulirsch, Masahiro Kanai, Kousuke Mouri, Daniel Berenzy, Susan Kales, Gina M. Butler, Adrianne Gladden-Young, Redwan M. Bhuiyan, Michael L. Stitzel, Hilary K. Finucane, Pardis C. Sabeti, Ryan Tewhey
Summary: HCR-FlowFISH is a new approach for characterizing CRISPR-perturbed cis-regulatory elements (CREs) by accurately quantifying native transcripts and using CASA for analysis. The study found that CREs can regulate multiple genes and exhibit activating and/or silencing effects. At the FADS locus, endogenous screens combined with reporter assays successfully identified target genes for multiple genome-wide association signals.
Article
Biochemistry & Molecular Biology
Marzia Rossato, Luca Marcolungo, Luca De Antoni, Giulia Lopatriello, Elisa Bellucci, Gaia Cortinovis, Giulia Frascarelli, Laura Nanni, Elena Bitocchi, Valerio Di Vittori, Leonardo Vincenzi, Filippo Lucchini, Kirstin E. Bett, Larissa Ramsay, David James Konkin, Massimo Delledonne, Roberto Papa
Summary: High-throughput genotyping allows for the analysis of genetic diversity in large populations and genome-wide association studies. In this study, the researchers used CRISPR-Cas9 technology to remove repetitive elements in the lentil genome, thus focusing the sequencing data on coding and regulatory regions. This method significantly increased genotyping accuracy and the number of genotyped bases compared to non-depleted libraries.
Article
Multidisciplinary Sciences
Mingyi Yang, Omer Ali, Magnar Bjoras, Junbai Wang
Summary: In this article, a non-coding SNVs analysis tool called bpb3 is proposed to identify functional mutation blocks (FMBs) by integrating genome sequencing and transcriptome data. A two-level Bayesian approach with a biophysical model is implemented to compute TF-DNA binding affinity changes based on clustered position weight matrices (PWMs) from over 1700 TF-motifs. By testing datasets from follicular lymphoma and melanoma, bpb3 automatically and robustly identifies FMBs, providing insights into patho-mechanisms and therapeutic targets.
Article
Biochemistry & Molecular Biology
Xi Chen, Jian Zhou, Ran Zhang, Aaron K. Wong, Christopher Y. Park, Chandra L. Theesfeld, Olga G. Troyanskaya
Summary: The FENRIR framework integrates diverse epigenetic and functional genomics datasets to infer tissue-specific functional relationships between enhancers and identify disease-associated enhancers accurately. In a case study on autism, FENRIR effectively prioritized enhancers with pathogenic signals and experimentally validated their differential regulatory potential. FENRIR provides an accurate and effective approach to study tissue-specific enhancers and their role in diseases.
Article
Plant Sciences
Yifan Yu, Zhen Ouyang, Juan Guo, Wen Zeng, Yujun Zhao, Luqi Huang
Summary: The complete chloroplast genome of Erigeron breviscapus was reported, providing valuable information for future studies on chloroplast genome transformation in E. breviscapus.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Multidisciplinary Sciences
Omri Sharabi, Yariv Greenshpan, Noa Ofir, Aner Ottolenghi, Tamar Levi, Leonid Olender, Zachor Adler-Agmon, Angel Porgador, Roi Gazit
Summary: This study presents a method of fine-tuning synthetic promoters for cancer immunotherapy by using factors in the tumor microenvironment. Through screening and validation, two optimized virus vectors with lower background and higher induction were identified.
SCIENTIFIC REPORTS
(2022)
Article
Food Science & Technology
Wenrui Ma, Xiaojie Geng, Fuchen Jia, Xiaomeng Zhang, Yuhong Zhang, Jie Xue
Summary: The microbial composition and function of Zangqu, a saccharifying starter used in the production of highland barley wine, were studied using high throughput sequencing technology. The analysis revealed predominant presence of four fungal and six bacterial phyla in Zangqu samples. Rhizopus oryzae M12 had the highest saccharifying ability, while Bacillus amyloliquefaciens Q4 had the highest protease activity among the isolated strains. This research aims to support the establishment of a microbial database and screening of functional microorganisms for Zangqu production.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Qiang Zhang, Sai Ma, Zhengzhi Liu, Bohan Zhu, Zirui Zhou, Gaoshan Li, J. Javier Meana, Javier Gonzalez-Maeso, Chang Lu
Summary: The genome-wide DNA methylation profile is important for regulating gene activities and cell fate. Existing single-cell methylomic technologies are not easily scalable for a large number of cells. The authors introduce Drop-BS, a droplet-based method, for preparing single-cell bisulfite sequencing libraries and offer a promising solution for examining a large cell population in single-cell methylomic studies.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Ruth Nichols, Brendan L. O'Connell, Ryan M. Mulqueen, Jerushah Thomas, Ashley R. Woodfin, Sonia Acharya, Gail Mandel, Dmitry Pokholok, Frank J. Steemers, Andrew C. Adey
Summary: DNA methylation is an important epigenetic property that plays a key role in gene regulation. Existing single-cell sequencing methods for studying DNA methylation are costly and low throughput. This study presents an improved sequencing technique that allows for high-coverage profiles with minimal contamination. The results obtained from primary human cortex demonstrate the ability to identify different cell types using this improved method, and the data can be integrated with other datasets.
NATURE COMMUNICATIONS
(2022)
Article
Plant Sciences
Aleksandra Suhorukova, Alexander A. Tyurin, Olga S. Pavlenko, Orkhan N. Mustafayev, Igor G. Sinelnikov, Irina Goldenkova-Pavlova
Summary: This study presents a new vector system for quantitative analysis of the contribution of regulatory elements to gene expression in plants. The system quantifies the effect of tested regulatory elements on expression by evaluating the enzyme activities of reporter proteins and taking into account the transcription of their genes.
Article
Biochemical Research Methods
Xiangtao Li, Shaochuan Li, Lei Huang, Shixiong Zhang, Ka-chun Wong
Summary: The article introduces a method called SEDIM, which automatically designs deep neural network architectures for imputing gene expression levels. It improves computational efficiency by constructing an offline surrogate model. Experimental results show that SEDIM significantly improves imputation and clustering performance, and also performs well in other contexts and platforms.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Philip Kleinert, Martin Kircher
Summary: In this study, the authors introduce CADD-SV, a method that uses a wide set of annotations to predict the effects of structural variants (SVs). They overcome previous limitations of supervised learning approaches by using a surrogate training objective and show that CADD-SV can effectively predict pathogenic and rare population variants.
Article
Biotechnology & Applied Microbiology
Junhong Choi, Wei Chen, Chase C. Suiter, Choli Lee, Florence M. Chardon, Wei Yang, Anh Leith, Riza M. Daza, Beth Martin, Jay Shendure
Summary: The PRIME-Del method induces deletions with high precision using a pair of prime editing sgRNAs, outperforming CRISPR-Cas9 and sgRNA pairs in programming deletions up to 10 kb. This method can be broadly useful for precise, flexible programming of genomic deletions and potentially other rearrangements.
NATURE BIOTECHNOLOGY
(2022)
Article
Hematology
Jill M. Johnsen, Shelley N. Fletcher, Angela Dove, Haley McCracken, Beth K. Martin, Martin Kircher, Neil C. Josephson, Jay Shendure, Sarah E. Ruuska, Leonard A. Valentino, Glenn F. Pierce, Crystal Watson, Dunlei Cheng, Michael Recht, Barbara A. Konkle
Summary: The findings of this study report the results of the largest hemophilia genotyping project performed to date. The results support the importance of comprehensive genetic approaches in hemophilia and contribute to a better understanding of variation in the F8 and F9 genes and the risks of inhibitor formation.
JOURNAL OF THROMBOSIS AND HAEMOSTASIS
(2022)
Article
Biochemical Research Methods
Beth K. Martin, Chengxiang Qiu, Eva Nichols, Melissa Phung, Rula Green-Gladden, Sanjay Srivatsan, Ronnie Blecher-Gonen, Brian J. Beliveau, Cole Trapnell, Junyue Cao, Jay Shendure
Summary: Single-cell combinatorial indexing RNA sequencing (sci-RNA-seq) is a powerful method for gene expression analysis at the single-cell level. In this study, a simplified and optimized sci-RNA-seq protocol is presented, which offers improved speed, robustness, sensitivity, and cost-effectiveness compared to the original method. The protocol allows for RNA profiling of various tissue types and challenging samples, such as older mouse embryos or adult tissues. The optimized protocol is demonstrated by analyzing a large number of nuclei from an E16.5 mouse embryo in a single experiment, and a low-input protocol called 'Tiny-Sci' is introduced for experiments with limited materials.
Article
Biochemical Research Methods
Luca Cappelletti, Alessandro Petrini, Jessica Gliozzo, Elena Casiraghi, Max Schubach, Martin Kircher, Giorgio Valentini
Summary: CRRs play a central role in regulating transcription under physiological and pathological conditions. Accurately identifying CRRs and their tissue-specific activity status using machine learning methods is essential for studying the impact of genetic variants on human diseases.
BMC BIOINFORMATICS
(2022)
Article
Neurosciences
Sean Whalen, Fumitaka Inoue, Hane Ryu, Tyler Fair, Eirene Markenscoff-Papadimitriou, Kathleen Keough, Martin Kircher, Beth Martin, Beatriz Alvarado, Orry Elor, Dianne Laboy Cintron, Alex Williams, Abul Hassan Samee, Sean Thomas, Robert Krencik, Erik M. Ullian, Arnold Kriegstein, John L. Rubenstein, Jay Shendure, Alex A. Pollen, Nadav Ahituv, Katherine S. Pollard
Summary: Using ML, the study examined the effects of human-chimpanzee genetic variants on chromatin state and neurodevelopmental enhancer activity in 2,645 human accelerated regions (HARs). The analysis revealed that 43% of HARs had variants with opposing effects on chromatin state, and 14% had effects on neurodevelopmental enhancer activity. This pattern, indicative of compensatory evolution, was confirmed through experimental assays in chimpanzee and human neural progenitor cells.
Article
Biochemistry & Molecular Biology
Justin Koesterich, Joon-Yong An, Fumitaka Inoue, Ajuni Sohota, Nadav Ahituv, Stephan J. Sanders, Anat Kreimer
Summary: Autism spectrum disorder (ASD) is influenced by both common and rare genetic variations, with disruptive rare variants in protein-coding regions having a clear impact on symptoms. However, the role of rare non-coding variants, including promoters, remains unclear. In this study, the functional impact of de novo mutations in promoter regions in ASD cases and controls was analyzed using massively parallel reporter assays. Although certain functionally high confidence de novo variants were identified, no differences in functional impact based on ASD diagnostic status were found.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Martin A. Mensah, Henri Niskanen, Alexandre P. Magalhaes, Shaon Basu, Martin Kircher, Henrike L. Sczakiel, Alisa M. V. Reiter, Jonas Elsner, Peter Meinecke, Saskia Biskup, Brian H. Y. Chung, Gregor Dombrowsky, Christel Eckmann-Scholz, Marc Phillip Hitz, Alexander Hoischen, Paul-Martin Holterhus, Wiebke Huelsemann, Kimia Kahrizi, Vera M. Kalscheuer, Anita Kan, Mandy Krumbiegel, Ingo Kurth, Jonas Leubner, Ann Carolin Longardt, Joerg D. Moritz, Hossein Najmabadi, Karolina Skipalova, Lot Snijders Blok, Andreas Tzschach, Eberhard Wiedersberg, Martin Zenker, Carla Garcia-Cabau, Rene Buschow, Xavier Salvatella, Matthew L. Kraushar, Stefan Mundlos, Almuth Caliebe, Malte Spielmann, Denise Horn, Denes Hnisz
Summary: A study found that thousands of genetic variants in protein-coding genes are associated with diseases. However, the functional impact of these variants is largely unknown because they occur in poorly defined functional regions of intrinsically disordered proteins. It was discovered that certain disease-associated variants in intrinsically disordered regions alter phase separation, causing misplacement in the nucleolus and disrupting nucleolar function.
Article
Multidisciplinary Sciences
Kathleen C. Keough, Sean Whalen, Fumitaka Inoue, Pawel F. Przytycki, Tyler Fair, Chengyu Deng, Marilyn Steyert, Hane Ryu, Kerstin Lindblad-Toh, Elinor Karlsson, Tomasz Nowakowski, Nadav Ahituv, Alex Pollen, Katherine S. Pollard
Summary: Human accelerated regions (HARs) are conserved genomic loci that evolved faster in humans compared to other species, potentially contributing to human-specific traits. Using a combination of automated pipeline and genome alignment, HARs and chimpanzee accelerated regions were identified. Through deep learning and chromatin capture experiments, it was found that HARs are significantly enriched in topologically associating domains that contain human-specific genomic variants which affect three-dimensional genome organization. Differential gene expression between humans and chimpanzees at these loci suggest that HARs have rewired regulatory interactions with neurodevelopmental genes, potentially explaining their rapid evolution.
Article
Multidisciplinary Sciences
Ilias Georgakopoulos-Soares, Chengyu Deng, Vikram Agarwal, Candace S. Y. Chan, Jingjing Zhao, Fumitaka Inoue, Nadav Ahituv
Summary: The grammar of gene regulation is challenging to understand, which hinders our ability to connect genotype with phenotype. In this study, the researchers used massively parallel reporter assays to examine over 200,000 synthetic sequences, revealing that the order and orientation of transcription factor binding sites (TFBS) significantly impact gene regulatory activity.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Max Schubach, Lusine Nazaretyan, Martin Kircher
Summary: This study updates the ReMM score for prioritizing noncoding variants in individuals with rare Mendelian disease. The updated version achieves good performance and better coverage of features. A website and API are provided for easy score lookup.
Article
Biochemical Research Methods
Axel Schmidt, Sebastian Roener, Karola Mai, Hannah Klinkhammer, Martin Kircher, Kerstin U. Ludwig
Summary: The use of AlphaFold2-predicted protein structures improves the accuracy of computational pathogenicity prediction for missense variants. A novel pathogenicity prediction score called AlphScore was developed by engineering features from the AlphaFold2-predicted structures. Combining AlphScore with existing scores enhances the prediction performance for missense variant pathogenicity.
Meeting Abstract
Biochemistry & Molecular Biology
Sebastian Roener, Martin Kircher
EUROPEAN JOURNAL OF HUMAN GENETICS
(2022)
