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Research: Gene by environment interaction mouse model reveals a functional role for 5-hydroxymethylcytosine in neurodevelopmental disorders
- Ligia A. Papale,
- Andy Madrid,
- Qi Zhang,
- Kailei Chen,
- Lara Sak,
- Sündüz Keleş,
- and Reid S. Alisch
Genome Res. February 2022 32: 266-279; Published in Advance December 23, 2021, doi:10.1101/gr.276137.121
.... Genomic profiling revealed disruptions in hippocampal and striatal 5hmC levels that are correlated to altered transcript levels of genes linked to these phenotypes (e.g., Reln, Dst, Trio, and Epha5). Chromatin immunoprecipitation coupled with high-throughput sequencing and hippocampal nuclear lysate pull...
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Method: Identification of the shortest species-specific oligonucleotide sequences
- Ioannis Mouratidis,
- Maxwell A. Konnaris,
- Nikol Chantzi,
- Candace S.Y. Chan,
- Michail Patsakis,
- Kimonas Provatas,
- Austin Montgomery,
- Fotis A. Baltoumas,
- Congzhou M. Sha,
- Manvita Mareboina,
- Georgios A. Pavlopoulos,
- Dionysios V. Chartoumpekis,
- and Ilias Georgakopoulos-Soares
Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
....View larger version: In this window In a new window Figure 4. Taxonomic nucleic quasi-prime sequences. (A) Density of human quasi-primes across genic regions. (B) Density of human quasi-primes across cis-regulatory elements. (C) Gene expression of human quasi-primes across tissues. (D–F) GO term analysis...
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Research: Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock
- Akanksha Bafna,
- Gareth Banks,
- Michael H. Hastings,
- and Patrick M. Nolan
Genome Res. May 2023 33: 673-688; Published in Advance May 8, 2023, doi:10.1101/gr.277581.122
...and BMAL1 recruitment to support local circadian gene expression (Koike et al. 2012; Sobel et al. 2017). Additionally, advances in sequencing technologies have highlighted the occurrence of rhythmic modulation in chromatin topology that facilitates proximal and distal circadian gene expression (Aguilar...
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LETTER: Gene Conversion and the Evolution of Protocadherin Gene Cluster Diversity
- James P. Noonan,
- Jane Grimwood,
- Jeremy Schmutz,
- Mark Dickson,
- and Richard M. Myers
Genome Res. March 2004 14: 354-366; doi:10.1101/gr.2133704
...to provide a molecular code involved in the generation of synaptic complexity in the developing brain. Variation in copy number and sequence content of protocadherin cluster genes among vertebrate species could reflect adaptive differences in protocadherin function. We have completed an analysis of zebrafish...
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LETTER: The Contribution of Exon-Skipping Events on Chromosome 22 to Protein Coding Diversity
- Winston A. Hide,
- Vladimir N. Babenko,
- Peter A. van Heusden,
- Cathal Seoighe,
- and Janet F. Kelso
Genome Res. November 1, 2001 11: 1848-1853; Published in Advance October 15, 2001, doi:10.1101/gr.188001
...sequence. Relative expression levels of transcripts are estimated from EST database representation. The rigorous in silico method accurately identifies exon skipping using verified genome sequence. 545 genes have been studied in this first hand-curated assessment of exon skipping on chromosome 22...
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LETTER: Biased clustered substitutions in the human genome: The footprints of male-driven biased gene conversion
- Timothy R. Dreszer,
- Gregory D. Wall,
- David Haussler,
- and Katherine S. Pollard
Genome Res. October 2007 17: 1420-1430; Published in Advance September 4, 2007, doi:10.1101/gr.6395807
...signal on chromosome X. These observations support the hypothesis that biased gene conversion (BGC), specifically in the male germline, played a significant role in the evolution of the human . With the sequencing of the chimpanzee ( Chimpanzee Sequencing and Analysis Consortium 2005 ), detailed analysis...
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LETTER: Changes in Gene Expression Profiles in Developing B Cells of Murine Bone Marrow
- Reinhard Hoffmann,
- Thomas Seidl,
- Martin Neeb,
- Antonius Rolink,
- and Fritz Melchers
Genome Res. January 1, 2002 12: 98-111; doi:10.1101/gr.201501
...submitted to the Gene Expression Omnibus (GEO) at the National Center for Biotechnology Information (NCBI) under accession number GSE13. Online supplementary material available at www..org .] Mouse B-lymphocytes develop from progenitors and precursors in bone marrow in a sequence that can be ordered...
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Method: bigSCale: an analytical framework for big-scale single-cell data
- Giovanni Iacono,
- Elisabetta Mereu,
- Amy Guillaumet-Adkins,
- Roser Corominas,
- Ivon Cuscó,
- Gustavo Rodríguez-Esteban,
- Marta Gut,
- Luis Alberto Pérez-Jurado,
- Ivo Gut,
- and Holger Heyn
Genome Res. June 2018 28: 878-890; Published in Advance May 3, 2018, doi:10.1101/gr.230771.117
..., respectively, of 1.5–1.8 Mb at the chromosome band 7q11.23. This region is flanked by segmental duplicationswith high sequence identity that canmediate nonhomologous recombination with the consequent loss or gain of 26– 30 contiguous genes, whose transcriptional levels vary in linewith their allele dosage...
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PERSPECTIVE: Impact of genomics on research in the rat
- Jozef Lazar,
- Carol Moreno,
- Howard J. Jacob,
- and Anne E. Kwitek
Genome Res. December 2005 15: 1717-1728; doi:10.1101/gr.3744005
...disease gene discovery. Genetic mapping and positional cloning QTL mapping Quantitative trait locus (QTL) mapping is a proven useful resource to assign the biology of the rat onto the genomic sequence by identifying chromosomal regions that contain genes affecting complex phenotypes. While a QTL...

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