Article
Biochemistry & Molecular Biology
Tom Aharon Hait, Ran Elkon, Ron Shamir
Summary: In this study, we introduce the CT-FOCS method, which uses linear mixed effect models to infer enhancer-promoter links that are specifically active in certain cell types. The results show that CT-FOCS accurately predicts these links compared to other methods, and it reveals that strictly cell type-specific EP links are rare in the human genome.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Ravi Maisuria, Andrew Norton, Cynthia Shao, Elizabeth W. Bradley, Kim Mansky
Summary: This study aims to determine the role of MEF2C in osteoclast differentiation and analyze the skeletal phenotype of Mef2c-cKO mice. The results suggest that MEF2C is critical for osteoclastogenesis and its dysregulation leads to a sex-specific osteopenic phenotype.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Plant Sciences
Lucia Strader, Dolf Weijers, Doris Wagner
Summary: This article reviews new findings on the function of plant transcription factors and their role in shaping transcription in the context of chromatin.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Wenjie Wang, Yuchao Yu, Nancy P. Keller, Pinmei Wang
Summary: Fungal secondary metabolites are both toxic and valuable sources of drugs, regulated by pathway specific transcription factors (PSTFs) in biosynthetic gene clusters (BGCs). The size of BGCs can predict the presence of PSTFs, and the number and relative location of PSTFs can affect their regulation of gene clusters.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Siqian Feng, Richard S. Mann
Summary: Chromatin immunoprecipitation (ChIP) is a crucial technique for studying protein-DNA interactions, but lacks cell type-specificity in complex tissues. SpyChIP overcomes this limitation by utilizing a specific isopeptide bond to identify cell type-specific transcription factor (TF) binding sites, offering insights into TF mechanisms in different cell types.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Tiebin Wang, Nathan Tague, Stephen A. Whelan, Mary J. Dunlop
Summary: Transcription factor decoys can effectively regulate gene expression, with tunability through changes in copy number or modifications to the DNA decoy site sequence. Introducing the decoy system can significantly increase arginine production in metabolic flux steering, without affecting growth compared to wild type strains.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Eugeniya I. Bondar, Maxim E. Troukhan, Konstantin V. Krutovsky, Tatiana V. Tatarinova
Summary: This study utilized computational approaches to predict genome-wide TSS in four conifer species, laying the groundwork for future research on gene regulatory regions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Joan Frigola, Radhakrishnan Sabarinathan, Abel Gonzalez-Perez, Nuria Lopez-Bigas
Summary: An abnormally high rate of UV-light related mutations is observed at transcription factor binding sites (TFBS) across melanomas, with certain TFs impairing the repair of UV-induced lesions and increasing the rate of lesion generation at their binding sites. Through nucleotide-resolution data, it is found that mutation rate increase in TFBS is mainly due to decreased repair efficiency, rather than the rate of lesion formation.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Shilu Zhang, Saptarshi Pyne, Stefan Pietrzak, Spencer Halberg, Sunnie Grace McCalla, Alireza Fotuhi Siahpirani, Rupa Sridharan, Sushmita Roy
Summary: The authors developed a method called single-cell Multi-Task Network Inference (scMTNI) to accurately infer the dynamics of cell type-specific Gene Regulatory Networks (GRNs) from scRNA-seq and scATAC-seq datasets. This method can identify key regulators and accurately model network dynamics for diverse processes such as cellular reprogramming and differentiation.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Sara Lago, Matteo Nadai, Filippo M. Cernilogar, Maryam Kazerani, Helena Dominiguez Moreno, Gunnar Schotta, Sara N. Richter
Summary: G-quadruplex structures play complex roles linked to transcription regulation. Here the authors, by comparing G4 location and transcript levels in liposarcoma and keratinocyte cells, reveal that G4s cooperate with transcription factors to determine cell-specific transcriptional programs.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Elizabeth D. Larson, Hideyuki Komori, Tyler J. Gibson, Cyrina M. Ostgaard, Danielle C. Hamm, Jack M. Schnell, Cheng-Yu Lee, Melissa M. Harrison
Summary: The pioneer transcription factor Zelda plays a crucial role in reprogramming germ cells during early Drosophila embryo development. Research further demonstrates that Zelda promotes undifferentiated stem-cell fate in the larval brain, and its ability to define cis-regulatory regions is influenced by cell-type-specific chromatin architecture. It is proposed that Zelda regulates essential transitions in neuroblasts and embryos through a shared gene-regulatory network driven by cell-type-specific enhancers.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Warren Winick-Ng, Alexander Kukalev, Izabela Harabula, Luna Zea-Redondo, Dominik Szabo, Mandy Meijer, Leonid Serebreni, Yingnan Zhang, Simona Bianco, Andrea M. Chiariello, Ibai Irastorza-Azcarate, Christoph J. Thieme, Thomas M. Sparks, Silvia Carvalho, Luca Fiorillo, Francesco Musella, Ehsan Irani, Elena Torlai Triglia, Aleksandra A. Kolodziejczyk, Andreas Abentung, Galina Apostolova, Eleanor J. Paul, Vedran Franke, Rieke Kempfer, Altuna Akalin, Sarah A. Teichmann, Georg Dechant, Mark A. Ungless, Mario Nicodemi, Lonnie Welch, Goncalo Castelo-Branco, Ana Pombo
Summary: The 3D structure of chromatin is crucial for gene regulation and cell function. A new method called immunoGAM has been developed to map 3D chromatin topology in specific brain cell types at a genome-wide scale. The results show that highly specific chromatin conformations in brain cells are closely related to gene regulation mechanisms and specialized functions.
Article
Biotechnology & Applied Microbiology
Pengyu Ni, David Wilson, Zhengchang Su
Summary: This study integrated ChIP-seq datasets of approximately 9,000 transcription factors (TFs) to construct a candidate set of cis-regulatory modules (CRMs) in the mouse genome, covering approximately 55.5% of the mappable genome. These CRMCs were under strong evolutionary constraints and were likely authentic regulatory elements.
Article
Biochemical Research Methods
Yongqing Zhang, Zixuan Wang, Yuanqi Zeng, Jiliu Zhou, Quan Zou
Summary: Research has shown that deep learning models can predict TFBSs at the base-pair level, but there is a need for improvement to integrate information more effectively for increased accuracy.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Computer Science, Artificial Intelligence
Shushan Toneyan, Ziqi Tang, Peter K. Koo
Summary: This study introduces a unified evaluation framework and uses it to compare different binary and quantitative models for predicting chromatin accessibility data. The results show that quantitative modeling improves the generalizability and interpretability of the models, and a robustness metric is introduced to enhance model selection and variant effect predictions.
NATURE MACHINE INTELLIGENCE
(2022)