The increasing availability of high-throughput datasets allows amalgamating research information across a large body of genome regulation studies. Given the recent success of meta-analyses on transcriptional regulators, epigenetic marks, and enhancer:gene associations, we expect that such surveys will continue to provide novel and reproducible insights. However, meta-analyses are severely hampered by the diversity of available data, concurring protocols, an eclectic amount of bioinformatics tools, and myriads of conceivable parameter combinations. Such factors can easily bar life scientists from synthesizing omics data and substantially curb their interpretability. Despite statistical challenges of the method, we would like to emphasize the advantages of joining data from different sources through vote-counting and showcase examples that achieve a simple but highly intuitive data integration.
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http://dx.doi.org/10.1016/j.tig.2022.06.012 | DOI Listing |
Proc Natl Acad Sci U S A
February 2025
Molecular Genetics, Institute of Biology, Faculty of Life Sciences, Humboldt Universität zu Berlin, Berlin 10115, Germany.
The chloroplast genome encodes key components of the photosynthetic light reaction machinery as well as the large subunit of the enzyme central for carbon fixation, Ribulose-1,5-bisphosphat-carboxylase/-oxygenase (RuBisCo). Its expression is predominantly regulated posttranscriptionally, with nuclear-encoded RNA-binding proteins (RBPs) playing a key role. Mutants of chloroplast gene expression factors often exhibit impaired chloroplast biogenesis, especially in cold conditions.
View Article and Find Full Text PDFJ Vis Exp
January 2025
Institute of Biochemistry and Molecular Biology, Hengyang Medical School, University of South China; National Health Commission Key Laboratory of Birth Defect Research and Preventio, Hunan Provincial Maternal and Child Health Care Hospital;
Both DNA replication and RNA transcription utilize genomic DNA as their template, necessitating spatial and temporal separation of these processes. Conflicts between the replication and transcription machinery, termed transcription-replication conflicts (TRCs), pose a considerable risk to genome stability, a critical factor in cancer development. While several factors regulating these collisions have been identified, pinpointing primary causes remains difficult due to limited tools for direct visualization and clear interpretation.
View Article and Find Full Text PDFRice (N Y)
January 2025
College of Agronomy, Anhui Agricultural University, Hefei, 230000, China.
Panicle elongation length (PEL), which determines panicle exsertion, is an important outcrossing-related trait. Mining genes controlling PEL in rice (Oryza sativa L.) has great practical significance in breeding cytoplasmic male sterility (CMS) lines with increased PEL and simplified, high-efficiency seed production.
View Article and Find Full Text PDFJ Cancer Res Clin Oncol
January 2025
Key Laboratory of Laboratory Medicine, Ministry of Education of China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
Purpose: Growing evidence suggests that the tyrosine phosphatase SHP2 is pivotal for tumor progression. Triple-negative breast cancer (TNBC) is the most lethal subtype of breast cancer, characterized by its high recurrence rate, aggressive metastasis, and resistance to chemotherapy. Understanding the mechanisms of tumorigenesis and the underlying molecular pathways in TNBC could aid in identifying new therapeutic targets.
View Article and Find Full Text PDFMar Biotechnol (NY)
January 2025
Marine Ecology Research Center, Ministry of Natural Resources, First Institute of Oceanography, Qingdao, 266061, China.
Planiliza haematocheilus, a teleostan species noted for its ecological adaptability and economic significance, thrives in both freshwater and marine environments. This study presents a novel chromosome-level genome assembly through Hi-C, PacBio CCS, and Illumina sequencing methods. The assembled genome has a final size of 651.
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