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Research: Xist upstream deletion leads to dysregulation of Xist and autosomal gene expression
- Sudeshna Majumdar,
- Lakshmi Sowjanya Bammidi,
- Hemant C. Naik,
- Avinchal Manhas,
- Runumi Baro,
- Akash Kalita,
- Amlan Jyoti Naskar,
- Sundarraj Nidharshan,
- Girija S. Bariha,
- Dimple Notani,
- and Srimonta Gayen
Genome Res. September 2025 35: 1992-2010; Published in Advance August 6, 2025, doi:10.1101/gr.279822.124
...) lying between Tsix and Jpx in the regulation of Xist and XCI in mouse extra-embryonic endoderm stem cells (XEN), which represent the maintenance phase of imprinted XCI. Here, we show that the deletion of this Xist upstream sequence in the inactive X leads to the upregulation of Xist expression...
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Research: Multiple paralogs and recombination mechanisms contribute to the high incidence of 22q11.2 deletion syndrome
- Lisanne Vervoort,
- Nicolas Dierckxsens,
- Marta Sousa Santos,
- Senne Meynants,
- Erika Souche,
- Ruben Cools,
- Tracy Heung,
- Koen Devriendt,
- Hilde Peeters,
- Donna M. McDonald-McGinn,
- Ann Swillen,
- Jeroen Breckpot,
- Beverly S. Emanuel,
- Hilde Van Esch,
- Anne S. Bassett,
- and Joris R. Vermeesch
Genome Res. April 2025 35: 786-797; Published in Advance November 13, 2024, doi:10.1101/gr.279331.124
...is that two consecutive PATRR-mediated events created an LCR22-A/B inversion and a deletion allele in the patient from family AB002 (Fig. 4C).DiscussionDue to the limitations of short- and standard long-read sequencing methods and the absence of an accurate reference , the exact positions...
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Research: Deciphering D4Z4 CpG methylation gradients in fascioscapulohumeral muscular dystrophy using nanopore sequencing
- Russell J. Butterfield,
- Diane M. Dunn,
- Brett Duval,
- Sarah Moldt,
- and Robert B. Weiss
Genome Res. September 2023 33: 1439-1454; Published in Advance October 5, 2023, doi:10.1101/gr.277871.123
..., Salt Lake City, Utah 84112, USA Corresponding author: russell.butterfield@hsc.utah.eduAbstractFascioscapulohumeral muscular dystrophy (FSHD) is caused by a unique genetic mechanism that relies on contraction and hypomethylation of the D4Z4 macrosatellite array on the Chromosome 4q telomere allowing...
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Research: Transcriptomic and proteomic effects of gene deletion are not evolutionarily conserved
- Yang Li and
- Jianzhi Zhang
Genome Res. March 2025 35: 512-521; Published in Advance February 18, 2025, doi:10.1101/gr.280008.124
.../or understanding gene function, pleiotropy, and biological complexity.The current gold standard of inferring the function of a gene requires measuring the phenotypic effect of deleting the gene or mutating the gene in such a way that its function is completely abolished (Alberts et al. 2002). For an essential gene...
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Research: Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging
- Amy R. Vandiver,
- Allen Herbst,
- Paul Stothard,
- and Jonathan Wanagat
Genome Res. January 2025 35: 55-65; Published in Advance November 27, 2024, doi:10.1101/gr.279072.124
...Chimeric mitochondrial RNA transcripts predict mitochondrial deletion mutations in mitochondrial genetic diseases and aging Amy R. Vandiver1,2, Allen Herbst3,5, Paul Stothard3 and Jonathan Wanagat2,4 1Department of Medicine, Division of Dermatology, University of California, Los Angeles, Los...
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Research: Single-cell spatial transcriptomics reveals a dystrophic trajectory following a developmental bifurcation of myoblast cell fates in facioscapulohumeral muscular dystrophy
- Lujia Chen,
- Xiangduo Kong,
- Kevin G. Johnston,
- Ali Mortazavi,
- Todd C. Holmes,
- Zhiqun Tan,
- Kyoko Yokomori,
- and Xiangmin Xu
Genome Res. May 2024 34: 665-679; Published in Advance May 22, 2024, doi:10.1101/gr.278717.123
...92697, USA ↵8 These authors contributed equally to this work. Corresponding authors: tanz@hs.uci.edu, kyokomor@uci.edu, xiangmix@uci.eduAbstractFacioscapulohumeral muscular dystrophy (FSHD) is linked to abnormal derepression of the transcription activator DUX4. This effect is localized to a low...
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Method: Enhancing CRISPR deletion via pharmacological delay of DNA-PKcs
- Núria Bosch-Guiteras,
- Tina Uroda,
- Hugo A. Guillen-Ramirez,
- Rahel Riedo,
- Amiq Gazdhar,
- Roberta Esposito,
- Carlos Pulido-Quetglas,
- Yitzhak Zimmer,
- Michaela Medová,
- and Rory Johnson
Genome Res. March 2021 31: 461-471; Published in Advance February 11, 2021, doi:10.1101/gr.265736.120
...with sgRNAs delivered by standard low-MOI lentiviral infection. In initial experiments, M3814 was added to cell media at the same time of lentiviral transduction, but almost no improvement in deletion efficiency was observed (Supplemental Fig. S9A). This is explained by the fact that lentiviruses require...
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Research: ZNF91 deletion in human embryonic stem cells leads to ectopic activation of SVA retrotransposons and up-regulation of KRAB zinc finger gene clusters
- Nina L. Haring,
- Elisabeth J. van Bree,
- Whitney S. Jordaan,
- Judith R.E. Roels,
- Gonzalo Congrains Sotomayor,
- Tiziana M. Hey,
- Fred T.G. White,
- Marc D. Galland,
- Marten P. Smidt,
- and Frank M.J. Jacobs
Genome Res. April 2021 31: 551-563; Published in Advance March 15, 2021, doi:10.1101/gr.265348.120
...elusive. We analyzed the -wide binding profile for ZNF91 in human cells and found that ZNF91 interacts with the VNTR region of SVAs. Through CRISPR-Cas9-mediated deletion of ZNF91 in human embryonic stem cells, we established that loss of ZNF91 results in increased transcriptional activity of SVAs...
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Research: Listeria monocytogenes genes supporting growth under standard laboratory cultivation conditions and during macrophage infection
- Martin A. Fischer,
- Tim Engelgeh,
- Patricia Rothe,
- Stephan Fuchs,
- Andrea Thürmer,
- and Sven Halbedel
Genome Res. September 2022 32: 1711-1726; Published in Advance September 16, 2022, doi:10.1101/gr.276747.122
...processes that maintain pathogen growth inside and outside the host. Here, we have applied transposon insertion sequencing (Tn-Seq) to L. monocytogenes for the identification of such processes on a -wide scale. Our approach identified 394 open reading frames that are required for growth under standard...
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Research: 4q-D4Z4 chromatin architecture regulates the transcription of muscle atrophic genes in facioscapulohumeral muscular dystrophy
- Alice Cortesi,
- Matthieu Pesant,
- Shruti Sinha,
- Federica Marasca,
- Eleonora Sala,
- Francesco Gregoretti,
- Laura Antonelli,
- Gennaro Oliva,
- Chiara Chiereghin,
- Giulia Soldà,
- and Beatrice Bodega
Genome Res. June 2019 29: 883-895; Published in Advance May 16, 2019, doi:10.1101/gr.233288.117
...to this work. Corresponding author: bodega@ingm.orgAbstractDespite increasing insights in structure organization, the role of DNA repetitive elements, accounting for more than two thirds of the human , remains elusive. Facioscapulohumeral muscular dystrophy (FSHD) is associated with deletion of D4Z4 repeat...
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