BORIS/CTCFL epigenetically reprograms clustered CTCF binding sites into alternative transcriptional start sites
Pervasive usage of alternative promoters leads to the deregulation of gene expression in carcinogenesis and may drive the emergence of new genes in spermatogenesis. However, little is known regarding the mecha... (Source: Genome Biology)
Source: Genome Biology - January 31, 2024 Category: Genetics & Stem Cells Authors: Elena M. Pugacheva, Dharmendra Nath Bhatt, Samuel Rivero-Hinojosa, Md Tajmul, Liron Fedida, Emma Price, Yon Ji, Dmitri Loukinov, Alexander V. Strunnikov, Bing Ren and Victor V. Lobanenkov Tags: Research Source Type: research
deMULTIplex2: robust sample demultiplexing for scRNA-seq
Sample multiplexing enables pooled analysis during single-cell RNA sequencing workflows, thereby increasing throughput and reducing batch effects. A challenge for all multiplexing techniques is to link sample-... (Source: Genome Biology)
Source: Genome Biology - January 30, 2024 Category: Genetics & Stem Cells Authors: Qin Zhu, Daniel N. Conrad and Zev J. Gartner Tags: Method Source Type: research
Mosaic loss of Y chromosome is associated with aging and epithelial injury in chronic kidney disease
Mosaic loss of Y chromosome (LOY) is the most common chromosomal alteration in aging men. Here, we use single-cell RNA and ATAC sequencing to show that LOY is present in the kidney and increases with age and c... (Source: Genome Biology)
Source: Genome Biology - January 29, 2024 Category: Genetics & Stem Cells Authors: Parker C. Wilson, Amit Verma, Yasuhiro Yoshimura, Yoshiharu Muto, Haikuo Li, Nicole P. Malvin, Eryn E. Dixon and Benjamin D. Humphreys Tags: Research Source Type: research
Gene panel selection for targeted spatial transcriptomics
Targeted spatial transcriptomics hold particular promise in analyzing complex tissues. Most such methods, however, measure only a limited panel of transcripts, which need to be selected in advance to inform on... (Source: Genome Biology)
Source: Genome Biology - January 25, 2024 Category: Genetics & Stem Cells Authors: Yida Zhang, Viktor Petukhov, Evan Biederstedt, Richard Que, Kun Zhang and Peter V. Kharchenko Tags: Method Source Type: research
The unusual gene architecture of polyubiquitin is created by dual-specific splice sites
The removal of introns occurs through the splicing of a 5 ′ splice site (5′ss) with a 3′ splice site (3′ss). These two elements are recognized by distinct components of the spliceosome. However, introns in high... (Source: Genome Biology)
Source: Genome Biology - January 24, 2024 Category: Genetics & Stem Cells Authors: Chaorui Duan, Truman Mooney, Luke Buerer, Cory Bowers, Stephen Rong, Seong Won Kim, Alger M. Fredericks, Sean F. Monaghan and William G. Fairbrother Tags: Research Source Type: research
Quartet metabolite reference materials for inter-laboratory proficiency test and data integration of metabolomics profiling
Various laboratory-developed metabolomic methods lead to big challenges in inter-laboratory comparability and effective integration of diverse datasets. (Source: Genome Biology)
Source: Genome Biology - January 24, 2024 Category: Genetics & Stem Cells Authors: Naixin Zhang, Qiaochu Chen, Peipei Zhang, Kejun Zhou, Yaqing Liu, Haiyan Wang, Shumeng Duan, Yongming Xie, Wenxiang Yu, Ziqing Kong, Luyao Ren, Wanwan Hou, Jingcheng Yang, Xiaoyun Gong, Lianhua Dong, Xiang Fang & hellip; Tags: Research Source Type: research
FMRP-mediated spatial regulation of physiologic NMD targets in neuronal cells
In non-polarized cells, nonsense-mediated mRNA decay (NMD) generally begins during the translation of newly synthesized mRNAs after the mRNAs are exported to the cytoplasm. Binding of the FMRP translational re... (Source: Genome Biology)
Source: Genome Biology - January 23, 2024 Category: Genetics & Stem Cells Authors: Tatsuaki Kurosaki, Xavier Rambout and Lynne E. Maquat Tags: Review Source Type: research
Unraveling the phylogenomic diversity of Methanomassiliicoccales and implications for mitigating ruminant methane emissions
Methanomassiliicoccales are a recently identified order of methanogens that are diverse across global environments particularly the gastrointestinal tracts of animals; however, their metabolic capacities are d... (Source: Genome Biology)
Source: Genome Biology - January 23, 2024 Category: Genetics & Stem Cells Authors: Fei Xie, Shengwei Zhao, Xiaoxiu Zhan, Yang Zhou, Yin Li, Weiyun Zhu, Phillip B. Pope, Graeme T. Attwood, Wei Jin and Shengyong Mao Tags: Research Source Type: research
SURGE: uncovering context-specific genetic-regulation of gene expression from single-cell RNA sequencing using latent-factor models
Genetic regulation of gene expression is a complex process, with genetic effects known to vary across cellular contexts such as cell types and environmental conditions. We developed SURGE, a method for unsuper... (Source: Genome Biology)
Source: Genome Biology - January 22, 2024 Category: Genetics & Stem Cells Authors: Benjamin J. Strober, Karl Tayeb, Joshua Popp, Guanghao Qi, M. Grace Gordon, Richard Perez, Chun Jimmie Ye and Alexis Battle Tags: Method Source Type: research
PICALO: principal interaction component analysis for the identification of discrete technical, cell-type, and environmental factors that mediate eQTLs
Expression quantitative trait loci (eQTL) offer insights into the regulatory mechanisms of trait-associated variants, but their effects often rely on contexts that are unknown or unmeasured. We introduce PICAL... (Source: Genome Biology)
Source: Genome Biology - January 22, 2024 Category: Genetics & Stem Cells Authors: Martijn Vochteloo, Patrick Deelen, Britt Vink, Ellen A. Tsai, Heiko Runz, Sergio Andreu-S ánchez, Jingyuan Fu, Alexandra Zhernakova, Harm-Jan Westra and Lude Franke Tags: Method Source Type: research
Structural variation and DNA methylation shape the centromere-proximal meiotic crossover landscape in Arabidopsis
Centromeres load kinetochore complexes onto chromosomes, which mediate spindle attachment and allow segregation during cell division. Although centromeres perform a conserved cellular function, their underlyin... (Source: Genome Biology)
Source: Genome Biology - January 22, 2024 Category: Genetics & Stem Cells Authors: Joiselle B. Fernandes, Matthew Naish, Qichao Lian, Robin Burns, Andrew J. Tock, Fernando A. Rabanal, Piotr Wlodzimierz, Anette Habring, Robert E. Nicholas, Detlef Weigel, Raphael Mercier and Ian R. Henderson Tags: Research Source Type: research
DeepVelo: deep learning extends RNA velocity to multi-lineage systems with cell-specific kinetics
Existing RNA velocity estimation methods strongly rely on predefined dynamics and cell-agnostic constant transcriptional kinetic rates, assumptions often violated in complex and heterogeneous single-cell RNA s... (Source: Genome Biology)
Source: Genome Biology - January 19, 2024 Category: Genetics & Stem Cells Authors: Haotian Cui, Hassaan Maan, Maria C. Vladoiu, Jiao Zhang, Michael D. Taylor and Bo Wang Tags: Method Source Type: research
Compact CRISPR genetic screens enabled by improved guide RNA library cloning
CRISPR genome editing approaches theoretically enable researchers to define the function of each human gene in specific cell types, but challenges remain to efficiently perform genetic perturbations in relevan... (Source: Genome Biology)
Source: Genome Biology - January 19, 2024 Category: Genetics & Stem Cells Authors: Seok-Jin Heo, Lauren D. Enriquez, Scot Federman, Amy Y. Chang, Rachel Mace, Kaivalya Shevade, Phuong Nguyen, Adam J. Litterman, Shawn Shafer, Laralynne Przybyla and Eric D. Chow Tags: Method Source Type: research
Haplotype-resolved assembly of a tetraploid potato genome using long reads and low-depth offspring data
Potato is one of the world ’s major staple crops, and like many important crop plants, it has a polyploid genome. Polyploid haplotype assembly poses a major computational challenge. We introduce a novel strateg... (Source: Genome Biology)
Source: Genome Biology - January 19, 2024 Category: Genetics & Stem Cells Authors: Rebecca Serra Mari, Sven Schrinner, Richard Finkers, Freya Maria Rosemarie Ziegler, Paul Arens, Maximilian H.-W. Schmidt, Bj örn Usadel, Gunnar W. Klau and Tobias Marschall Tags: Method Source Type: research
Structure-primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference
Modeling of gene regulatory networks (GRNs) is limited due to a lack of direct measurements of genome-wide transcription factor activity (TFA) making it difficult to separate covariance and regulatory interact... (Source: Genome Biology)
Source: Genome Biology - January 18, 2024 Category: Genetics & Stem Cells Authors: Andreas Tj ärnberg, Maggie Beheler-Amass, Christopher A. Jackson, Lionel A. Christiaen, David Gresham and Richard Bonneau Tags: Research Source Type: research
