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Research: MYT1L is required for suppressing earlier neuronal development programs in the adult mouse brain
- Jiayang Chen,
- Nicole A. Fuhler,
- Kevin K. Noguchi,
- and Joseph D. Dougherty
Genome Res. April 2023 33: 541-556; Published in Advance April 26, 2023, doi:10.1101/gr.277413.122
....CUT&RUN identifies MYT1L binding targets in the mouse embryonic cortexTo understand how MYT1L regulates the DL/UL neuron ratio, as well as the altered transcriptional profile we previously observed (Chen et al. 2021), we next investigated MYT1L genomic binding targets in vivo. MYT1L has peak protein expression...
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Research: Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer
- Milad Razavi-Mohseni,
- Weitai Huang,
- Yu A. Guo,
- Dustin Shigaki,
- Shamaine Wei Ting Ho,
- Patrick Tan,
- Anders J. Skanderup,
- and Michael A. Beer
Genome Res. May 2024 34: 680-695; Published in Advance May 22, 2024, doi:10.1101/gr.278565.123
...of Mes-like TFs and their target genes is predictive of disease severity and suggests both prognostic and therapeutic utility.Taken together, we identified altered regulatory programs in GC along with their distinct transcriptional responses driven by differential enhancer activity. We identify CN DNA...
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Research: Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary
- Satyam P. Srivastav,
- Cédric Feschotte,
- and Andrew G. Clark
Genome Res. May 2024 34: 711-724; Published in Advance May 15, 2024, doi:10.1101/gr.278062.123
...in Drosophila melanogaster, much less is known about the origin and evolution of piCs in this or any other species. To investigate piC origin and evolution, we use a population genomic approach to compare piC activity and sequence composition across eight geographically distant strains of D. melanogaster...
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Research: Long read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation
- Alexander Ritter,
- Jolene M Draper,
- Christopher Vollmers,
- and Jeremy Sanford
Genome Res. June 5, 2024 gr.279170.124; Published in Advance June 5, 2024, doi:10.1101/gr.279170.124
...-459-1822; Fax: 831-459-3139 Email: 12 jsanfor2@ucsc.edu 13 14 ABSTRACT 15 Alternative splicing (AS) alters the cis-regulatory landscape of mRNA isoforms leading to transcripts with 16 distinct localization, stability and translational efficiency. To rigorously investigate mRNA isoform-17 specific ribosome...
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Research: tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis
- Junling Shi,
- Jiaqi Xu,
- Jun Ma,
- and Feng He
Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
...RNA-mRNA interaction that can best explain our mRNA-seq data in response to sponge perturbations. These software had been used to predict the post-transcriptional regulation of specific tsRNAs on putative target genes in human and Drosophila cells (Luo et al. 2018; Chen et al. 2022; Tu et al. 2023). We note...
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Method: Power-law behavior of transcriptional bursting regulated by enhancer–promoter communication
- Zihao Wang,
- Zhenquan Zhang,
- Songhao Luo,
- Tianshou Zhou,
- and Jiajun Zhang
Genome Res. January 2024 34: 106-118; Published in Advance January 3, 2024, doi:10.1101/gr.278631.123
...is believed to increase the local concentrations of transcription factors (TFs) and coactivators, seems necessary for cells to execute correct gene-transcription programs in living Drosophila embryos (Chen et al. 2018; Lim et al. 2018). To understand the mechanism of transcriptional bursting theoretically...
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Research: Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single-cell resolution
- Justyna A. Resztak,
- Julong Wei,
- Samuele Zilioli,
- Edward Sendler,
- Adnan Alazizi,
- Henriette E. Mair-Meijers,
- Peijun Wu,
- Xiaoquan Wen,
- Richard B. Slatcher,
- Xiang Zhou,
- Francesca Luca,
- and Roger Pique-Regi
Genome Res. June 2023 33: 839-856; Published in Advance July 13, 2023, doi:10.1101/gr.276765.122
...to this work. Corresponding authors: fluca@wayne.edu, rpique@wayne.eduAbstractSynthetic glucocorticoids, such as dexamethasone, have been used as a treatment for many immune conditions, such as asthma and, more recently, severe COVID-19. Single-cell data can capture more fine-grained details on transcriptional...
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Resource: A limited set of transcriptional programs define major cell types
- Alessandra Breschi,
- Manuel Muñoz-Aguirre,
- Valentin Wucher,
- Carrie A. Davis,
- Diego Garrido-Martín,
- Sarah Djebali,
- Jesse Gillis,
- Dmitri D. Pervouchine,
- Anna Vlasova,
- Alexander Dobin,
- Chris Zaleski,
- Jorg Drenkow,
- Cassidy Danyko,
- Alexandra Scavelli,
- Ferran Reverter,
- Michael P. Snyder,
- Thomas R. Gingeras,
- and Roderic Guigó
Genome Res. July 2020 30: 1047-1059; Published in Advance July 29, 2020, doi:10.1101/gr.263186.120
...from different locations in the human body. The clustering of these primary cells reveals that most cells in the human body share a few broad transcriptional programs, which define five major cell types: epithelial, endothelial, mesenchymal, neural, and blood cells. These act as basic components...
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Research: Genomic origin, fragmentomics, and transcriptional properties of long cell-free DNA molecules in human plasma
- Huiwen Che,
- Peiyong Jiang,
- L.Y. Lois Choy,
- Suk Hang Cheng,
- Wenlei Peng,
- Rebecca W.Y. Chan,
- Jing Liu,
- Qing Zhou,
- W.K. Jacky Lam,
- Stephanie C.Y. Yu,
- So Ling Lau,
- Tak Y. Leung,
- John Wong,
- Vincent Wai-Sun Wong,
- Grace L.H. Wong,
- Stephen L. Chan,
- K.C. Allen Chan,
- and Y.M. Dennis Lo
Genome Res. February 2024 34: 189-200; Published in Advance February 26, 2024, doi:10.1101/gr.278556.123
...carcinoma (HCC) from non-HCC subjects (AUC = 0.87). We also investigated knockout mice in which selected nuclease genes had been inactivated in comparison with wild-type mice. The proportion of long molecules originating from transcription start sites are lower in Dffb-deficient mice but higher in Dnase1l3...
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Resource: The Drosophila brain on cocaine at single-cell resolution
- Brandon M. Baker,
- Sneha S. Mokashi,
- Vijay Shankar,
- Jeffrey S. Hatfield,
- Rachel C. Hannah,
- Trudy F.C. Mackay,
- and Robert R.H. Anholt
Genome Res. October 2021 31: 1927-1937; Published in Advance May 25, 2021, doi:10.1101/gr.268037.120
...glia, act as the blood-brain barrier (DeSalvo et al. 2014; Kremer et al. 2017) and mediate the innate immune response (Kounatidis and Chtarbanova 2018). Genes associated with the blood-brain barrier in Drosophila are also up-regulated in response to cocaine. This includes ogre, which regulates gap...
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