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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
...of transcriptional regulation whereby approximately 200 mammalian genes are expressed monoallelically according to their parental origin. This crucial developmental process is primarily controlled by discrete cis-regulatory elements known as imprinting control regions (ICRs), which play essential roles in directing...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...@tamu.edu, jje@uci.eduAbstractMany essential functions of organisms are encoded in highly repetitive genomic regions, including histones involved in DNA packaging, centromeres that are core components of chromosome segregation, ribosomal RNA comprising the protein translation machinery, telomeres that ensure...
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Research: SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells
- A. Rasim Barutcu,
- Bryan R. Lajoie,
- Andrew J. Fritz,
- Rachel P. McCord,
- Jeffrey A. Nickerson,
- Andre J. van Wijnen,
- Jane B. Lian,
- Janet L. Stein,
- Job Dekker,
- Gary S. Stein,
- and Anthony N. Imbalzano
Genome Res. September 2016 26: 1188-1201; Published in Advance July 19, 2016, doi:10.1101/gr.201624.115
...in higher-order genome organization. SMARCA4 knockdown in human mammary epithelial MCF-10A cells resulted in 176 up-regulated genes, including many related to lipid and calcium metabolism, and 1292 down-regulated genes, some of which encode extracellular matrix (ECM) components that can exert mechanical...
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Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
- Bertille Montibus,
- James A. Cain,
- Rocio T. Martinez-Nunez,
- and Rebecca J. Oakey
Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
...to deal with these constraints while enhancing their evolutionary stability because a mutation in an overlapping pair would affect more than one gene (Simon-Loriere et al. 2013). Higher-order organisms, on the other hand, contain vast amount of intergenic space for genes to occupy, do not have...
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Method: Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories
- Borislav Hrisimirov Hristov,
- William Stafford Noble,
- and Alessandro Bertero
Genome Res. October 2024 34: 1610-1623; Published in Advance September 25, 2024, doi:10.1101/gr.278327.123
.... 2D; Supplemental Fig. S1B).Identification of Greek islands regulating the expression of mouse olfactory receptor genesTo further validate trans-C, we turned to the mouse and its larger diploid nuclear . In mouse olfactory sensory neurons (mOSNs), chromatin regions associated to olfactory receptor...
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Research: Identification of a transcriptional signature found in multiple models of ASD and related disorders
- Samuel Thudium,
- Katherine Palozola,
- Éloïse L'Her,
- and Erica Korb
Genome Res. September 2022 32: 1642-1654; Published in Advance September 14, 2022, doi:10.1101/gr.276591.122
...with this as the main control condition for subsequent analysis.We next examined all higher-order intersections between these gene sets to determine which genes are commonly disrupted in response to knockdown of multiple ID/ASD-linked chromatin modifiers (Fig. 2B,C). Only six genes were common between all data sets...
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Research: Identification of FMR1-regulated molecular networks in human neurodevelopment
- Meng Li,
- Junha Shin,
- Ryan D. Risgaard,
- Molly J. Parries,
- Jianyi Wang,
- Deborah Chasman,
- Shuang Liu,
- Sushmita Roy,
- Anita Bhattacharyya,
- and Xinyu Zhao
Genome Res. March 2020 30: 361-374; Published in Advance March 16, 2020, doi:10.1101/gr.251405.119
...–Madison, Madison, WI 53715, USA Corresponding authors: Xinyu.zhao@wisc.edu, bhattacharyy@waisman.wisc.edu, sroy@biostat.wisc.eduAbstractRNA-binding proteins (RNA-BPs) play critical roles in development and disease to regulate gene expression. However, -wide identification of their targets in primary human cells...
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Perspective: What does our genome encode?
- John A. Stamatoyannopoulos
Genome Res. September 2012 22: 1602-1611; doi:10.1101/gr.146506.112
...findings. Although the gene has conventionally been viewed as the fundamental unit of genomic organization, on the basis of ENCODE data it is now compellingly argued that this unit is not the gene but rather the transcript (Washietl et al. 2007; Djebali et al. 2012a). On this view, genes represent a higher-order...
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Method: Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay
- Jennifer Hammelman,
- Konstantin Krismer,
- Budhaditya Banerjee,
- David K. Gifford,
- and Richard I. Sherwood
Genome Res. October 2020 30: 1468-1480; Published in Advance September 24, 2020, doi:10.1101/gr.263228.120
...Identification of determinants of differential chromatin accessibility through a massively parallel -integrated reporter assay Jennifer Hammelman1,2, Konstantin Krismer2,3, Budhaditya Banerjee4, David K. Gifford2,3,5 and Richard I. Sherwood4,6 1Computational and Systems Biology, Massachusetts...
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Research: Deep learning of the regulatory grammar of yeast 5′ untranslated regions from 500,000 random sequences
- Josh T. Cuperus,
- Benjamin Groves,
- Anna Kuchina,
- Alexander B. Rosenberg,
- Nebojsa Jojic,
- Stanley Fields,
- and Georg Seelig
Genome Res. December 2017 27: 2015-2024; Published in Advance November 2, 2017, doi:10.1101/gr.224964.117
...effect on expression (Supplemental Fig. S3D).Native 5′ UTRs may contain a higher density of motifs or higher order motifs not captured using a random library. We therefore asked whether the model could predict protein expression from native S. cerevisiae 5′ UTRs (Park et al. 2014). We constructed...

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