MBL-1 and EEL-1 affect the splicing and protein levels of MEC-3 to control dendrite complexity
by Jianxin Xie, Wei Zou, Madina Tugizova, Kang Shen, Xiangming Wang
Transcription factors (TFs) play critical roles in specifying many aspects of neuronal cell fate including dendritic morphology. How TFs are accurately regulated during neuronal morphogenesis is not fully understood. Here, we show that LIM homeodomain protein MEC-3, the key TF forC.elegans PVD dendrite morphogenesis, is regulated by both alternative splicing and an E3 ubiquitin ligase. Themec-3 gene generates several transcripts by alternative splicing. We find thatmbl-1, the orthologue of the muscular dystrophy disease gene muscleblind-like (MBNL), is re...
Source: PLoS Genetics - September 20, 2023 Category: Genetics & Stem Cells Authors: Jianxin Xie Source Type: research
Expression of Concern: PHYTOCHROME C regulation of photoperiodic flowering via < i > PHOTOPERIOD1 < /i > is mediated by < i > EARLY FLOWERING 3 < /i > in < i > Brachypodium distachyon < /i >
by The PLOS Genetics Editors (Source: PLoS Genetics)
Source: PLoS Genetics - September 19, 2023 Category: Genetics & Stem Cells Authors: The PLOS Genetics Editors Source Type: research
Expression of Concern: MiR172 < i > -APETALA2-like < /i > genes integrate vernalization and plant age to control flowering time in wheat
by The PLOS Genetics Editors (Source: PLoS Genetics)
Source: PLoS Genetics - September 19, 2023 Category: Genetics & Stem Cells Authors: The PLOS Genetics Editors Source Type: research
Review and further developments in statistical corrections for Winner ’s Curse in genetic association studies
by Amanda Forde, Gibran Hemani, John Ferguson
Genome-wide association studies (GWAS) are commonly used to identify genomic variants that are associated with complex traits, and estimate the magnitude of this association for each variant. However, it has been widely observed that the association estimates of variants tend to be lower in a replication study than in the study that discovered those associations. A phenomenon known asWinner ’s Curse is responsible for this upward bias present in association estimates of significant variants in the discovery study. We review existingWinner ’s Curse correction methods which ...
Source: PLoS Genetics - September 18, 2023 Category: Genetics & Stem Cells Authors: Amanda Forde Source Type: research
eQTL Catalogue 2023: New datasets, X chromosome QTLs, and improved detection and visualisation of transcript-level QTLs
by Nurlan Kerimov, Ralf Tambets, James D. Hayhurst, Ida Rahu, Peep Kolberg, Uku Raudvere, Ivan Kuzmin, Anshika Chowdhary, Andreas Vija, Hans J. Teras, Masahiro Kanai, Jacob Ulirsch, Mina Ryten, John Hardy, Sebastian Guelfi, Daniah Trabzuni, Sarah Kim-Hellmuth, William Rayner, Hilary Finucane, Hedi Peterson, Abayomi Mosaku, Helen Parkinson, Kaur Alasoo
The eQTL Catalogue is an open database of uniformly processed human molecular quantitative trait loci (QTLs). We are continuously updating the resource to further increase its utility for interpreting genetic associations with complex traits. Over the past two years, we have...
Source: PLoS Genetics - September 18, 2023 Category: Genetics & Stem Cells Authors: Nurlan Kerimov Source Type: research
Neuronal mTORC1 inhibition promotes longevity without suppressing anabolic growth and reproduction in < i > C < /i > . < i > elegans < /i >
by Hannah J. Smith, Anne Lanjuin, Arpit Sharma, Aditi Prabhakar, Ewelina Nowak, Peter G. Stine, Rohan Sehgal, Klement Stojanovski, Benjamin D. Towbin, William B. Mair
mTORC1 (mechanistic target of rapamycin complex 1) is a metabolic sensor that promotes growth when nutrients are abundant. Ubiquitous inhibition of mTORC1 extends lifespan in multiple organisms but also disrupts several anabolic processes resulting in stunted growth, slowed development, reduced fertility, and disrupted metabolism. However, it is unclear if these pleotropic effects of mTORC1 inhibition can be uncoupled from longevity. Here, we utilize the aux...
Source: PLoS Genetics - September 18, 2023 Category: Genetics & Stem Cells Authors: Hannah J. Smith Source Type: research
The proprotein convertase BLI-4 promotes collagen secretion prior to assembly of the < i > Caenorhabditis elegans < /i > cuticle
by Susanna K. Birnbaum, Jennifer D. Cohen, Alexandra Belfi, John I. Murray, Jennifer R. G. Adams, Andrew D. Chisholm, Meera V. Sundaram
Some types of collagens, including transmembrane MACIT collagens andC.elegans cuticle collagens, are N-terminally cleaved at a dibasic site that resembles the consensus for furin or other proprotein convertases of the subtilisin/kexin (PCSK) family. Such cleavage may release transmembrane collagens from the plasma membrane and affect extracellular matrix assembly or structure. However, the functional consequences of such cleavage are unclear and evidence for the role of specific PCSKs is ...
Source: PLoS Genetics - September 18, 2023 Category: Genetics & Stem Cells Authors: Susanna K. Birnbaum Source Type: research
Genome-wide circadian gating of a cold temperature response in bread wheat
by Calum A. Graham, Pirita Paajanen, Keith J. Edwards, Antony N. Dodd
Circadian rhythms coordinate the responses of organisms to their daily fluctuating environments, by establishing a temporal program of gene expression. This schedules aspects of metabolism, physiology, development and behaviour according to the time of day. Circadian regulation in plants is extremely pervasive, and is important because it underpins both productivity and seasonal reproduction. Circadian regulation extends to the control of environmental responses through a regulatory process known as circadian gating. Circadian gating is the process wher...
Source: PLoS Genetics - September 18, 2023 Category: Genetics & Stem Cells Authors: Calum A. Graham Source Type: research
Saturation genome editing of 11 codons and exon 13 of < i > BRCA2 < /i > coupled with chemotherapeutic drug response accurately determines pathogenicity of variants
by Sounak Sahu, Teresa L. Sullivan, Alexander Y. Mitrophanov, M élissa Galloux, Darryl Nousome, Eileen Southon, Dylan Caylor, Arun Prakash Mishra, Christine N. Evans, Michelle E. Clapp, Sandra Burkett, Tyler Malys, Raj Chari, Kajal Biswas, Shyam K. Sharan
The unknown pathogenicity of a significant number of variants found in cancer-related genes is attributed to limited epidemiological data, resulting in their classification as variant of uncertain significance (VUS). To date, Breast Cancer gene-2(BRCA2) has the highest number of VUSs, which has necessitated the development of several robust functional assays to determin...
Source: PLoS Genetics - September 15, 2023 Category: Genetics & Stem Cells Authors: Sounak Sahu Source Type: research
Rescue of < i > bmp15 < /i > deficiency in zebrafish by mutation of < i > inha < /i > reveals mechanisms of BMP15 regulation of folliculogenesis
by Yue Zhai, Xin Zhang, Cheng Zhao, Ruijing Geng, Kun Wu, Mingzhe Yuan, Nana Ai, Wei Ge
As an oocyte-specific growth factor, bone morphogenetic protein 15 (BMP15) plays a critical role in controlling folliculogenesis. However, the mechanism of BMP15 action remains elusive. Using zebrafish as the model, we created abmp15 mutant using CRISPR/Cas9 and demonstrated thatbmp15 deficiency caused a significant delay in follicle activation and puberty onset followed by a complete arrest of follicle development at previtellogenic (PV) stage without yolk accumulation. The mutant females eventually underwent female-to-male sex revers...
Source: PLoS Genetics - September 15, 2023 Category: Genetics & Stem Cells Authors: Yue Zhai Source Type: research
Non < i > -O < /i > ABO blood group genotypes differ in their associations with < i > Plasmodium falciparum < /i > rosetting and severe malaria
by D. Herbert Opi, Carolyne M. Ndila, Sophie Uyoga, Alex W. Macharia, Clare Fennell, Lucy B. Ochola, Gideon Nyutu, Bethseba R. Siddondo, John Ojal, Mohammed Shebe, Kennedy O. Awuondo, Neema Mturi, Norbert Peshu, Benjamin Tsofa, Gavin Band, Kathryn Maitland, Dominic P. Kwiatkowski, Kirk A. Rockett, Thomas N. Williams, J. Alexandra Rowe
Blood group O is associated with protection against severe malaria and reduced size and stability ofP.falciparum-host red blood cell (RBC) rosettes compared to non-O blood groups. Whether the non-O blood groups encoded by the specificABO genotypesAO,BO,AA,BB andAB differ in their association...
Source: PLoS Genetics - September 14, 2023 Category: Genetics & Stem Cells Authors: D. Herbert Opi Source Type: research
A detoxification pathway initiated by a nuclear receptor TcHR96h in < i > Tetranychus cinnabarinus < /i > (Boisduval)
by Xiang Wen, Kaiyang Feng, Juan Qin, Peng Wei, Peng Cao, Youjun Zhang, Zhiguang Yuchi, Lin He
Understanding the mechanism of detoxification initiation in arthropods after pesticide exposure is crucial. Although the identity of transcription factors that induce and regulate the expression of detoxification genes in response to pesticides is beginning to emerge, whether transcription factors directly interact with xenobiotics is unclear. The findings of this study revealed that a nuclear hormone receptor,Tetranychus cinnabarinus hormone receptor (HR)TcHR96h, regulates the overexpression of the detoxification geneTcGSTm02, ...
Source: PLoS Genetics - September 14, 2023 Category: Genetics & Stem Cells Authors: Xiang Wen Source Type: research
Correction: A novel nematode species from the Siberian permafrost shares adaptive mechanisms for cryptobiotic survival with < i > C < /i > . < i > elegans < /i > dauer larva
by The PLOS Genetics Staff (Source: PLoS Genetics)
Source: PLoS Genetics - September 14, 2023 Category: Genetics & Stem Cells Authors: The PLOS Genetics Staff Source Type: research
Histone methylation regulates reproductive diapause in < i > Drosophila melanogaster < /i >
This study reveals chromatin determinants of phenotypic plasticity and suggests that these determinants may be genotype-dependent, offering new insight into how organisms may exploit and evolve epigenetic mechanisms to persist in fluctuating environments. (Source: PLoS Genetics)
Source: PLoS Genetics - September 13, 2023 Category: Genetics & Stem Cells Authors: Abigail DiVito Evans Source Type: research
Inferring gene regulatory network from single-cell transcriptomes with graph autoencoder model
by Jiacheng Wang, Yaojia Chen, Quan Zou
The gene regulatory structure of cells involves not only the regulatory relationship between two genes, but also the cooperative associations of multiple genes. However, most gene regulatory network inference methods for single cell only focus on and infer the regulatory relationships of pairs of genes, ignoring the global regulatory structure which is crucial to identify the regulations in the complex biological systems. Here, we proposed a graph-based Deep learning model for Regulatory networks Inference among Genes (DeepRIG) from single-cell RNA-seq data. To learn the global regu...
Source: PLoS Genetics - September 13, 2023 Category: Genetics & Stem Cells Authors: Jiacheng Wang Source Type: research
