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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
..., a particular gene of interest (GOI) remains a persistent experimental and conceptual challenge. This gene-centric question is complicated by the multilayered regulatory environment in which each gene resides, comprising 3D chromatin structure, enhancer–promoter looping, DNA accessibility, histone modifications...
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Research: Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains
- Sergey V. Ulianov,
- Ekaterina E. Khrameeva,
- Alexey A. Gavrilov,
- Ilya M. Flyamer,
- Pavel Kos,
- Elena A. Mikhaleva,
- Aleksey A. Penin,
- Maria D. Logacheva,
- Maxim V. Imakaev,
- Alexander Chertovich,
- Mikhail S. Gelfand,
- Yuri Y. Shevelyov,
- and Sergey V. Razin
Genome Res. January 2016 26: 70-84; Published in Advance October 30, 2015, doi:10.1101/gr.196006.115
....v.razin@usa.net ↵ 12 These authors contributed equally to this work. Abstract Recent advances enabled by the Hi-C technique have unraveled many principles of chromosomal folding that were subsequently linked to disease and gene regulation. In particular, Hi-C revealed that chromosomes of animals...
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ARTICLE: Characterization of the 55-kb mouse histone gene cluster on chromosome 3.
- Z F Wang,
- R Tisovec,
- R W Debry,
- M R Frey,
- A G Matera,
- and W F Marzluff
Genome Res. August 1996 6: 702-714; doi:10.1101/gr.6.8.702
...genes map to multiple chromosomes. Proc. Natl. Acad. Sci. 83 : 3185 – 3188 . Wang Z.-F., Krasikov, T. Frey, M.R. Wang, J. Matera, A.G. and Marzluff. W.F. 1996 . Characterization of the mouse histone gene cluster on chromosome 13: 45 histone genes in three patches spread over 1 Mb. Genome Res. (this...
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Research: Evolution of a genomic regulatory domain: The role of gene co-option and gene duplication in the Enhancer of split complex
- Elizabeth J. Duncan and
- Peter K. Dearden
Genome Res. July 2010 20: 917-928; Published in Advance May 10, 2010, doi:10.1101/gr.104794.109
...into the Notch signaling cascade. [Supplemental material is available online at http://www..org.] The Enhancer of split complex [E(spl)-C] ofDrosophilamelanogaster is a well characterized genetic locus containing 12 genes on chromosome 3R, most of which are to be effectors or modulators of Notch signaling. The E...
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Research: Expanding heterochromatin reveals discrete subtelomeric domains delimited by chromatin landscape transitions
- Antoine Hocher,
- Myriam Ruault,
- Petra Kaferle,
- Marc Descrimes,
- Mickaël Garnier,
- Antonin Morillon,
- and Angela Taddei
Genome Res. December 2018 28: 1867-1881; Published in Advance October 24, 2018, doi:10.1101/gr.236554.118
...is overexpressed (Supplemental Fig. S6C).H3K79 methylation protects euchromatin from the spread of silencingTo identify H3 and H4 histone residues involved in the limitation of Sir3 spreading, we set a genetic screen based on the Synthetic Gene Array (Dai and Boeke 2012). H3K79R was the sole histone point mutant...
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Research: Active retrotransposons help maintain pericentromeric heterochromatin required for faithful cell division
- Yajing Hao,
- Dongpeng Wang,
- Shuheng Wu,
- Xiao Li,
- Changwei Shao,
- Peng Zhang,
- Jia-Yu Chen,
- Do-Hwan Lim,
- Xiang-Dong Fu,
- Runsheng Chen,
- and Shunmin He
Genome Res. November 2020 30: 1570-1582; Published in Advance October 15, 2020, doi:10.1101/gr.256131.119
...repeat-derived endo-siRNA mimics are sufficient to rescue Dcr-2-deficiency-induced defects in heterochromatin formation in interphase and chromosome segregation during mitosis, demonstrating that active retrotransposons are required for stable genetic inheritance.Eukaryotic s contain both gene...
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Research: H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction
- Gillian C.A. Taylor,
- Ragnhild Eskeland,
- Betül Hekimoglu-Balkan,
- Madapura M. Pradeepa,
- and Wendy A. Bickmore
Genome Res. December 2013 23: 2053-2065; Published in Advance August 29, 2013, doi:10.1101/gr.155028.113
...of almost equal height centered over the +1 and 1 nucleosomes, whereas H3K4me3 peaks asymmetrically over the +1 position. H4K16ac also spreads further into the gene body compared with H3K4me3, but its distribution differs from that of H3K36me3, a histone modification associated with the elongation...
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LETTER: Controlled exchange of chromosomal arms reveals principles driving telomere interactions in yeast
- Heiko Schober,
- Véronique Kalck,
- Miguel A. Vega-Palas,
- Griet Van Houwe,
- Daniel Sage,
- Michael Unser,
- Marc R. Gartenberg,
- and Susan M. Gasser
Genome Res. February 2008 18: 261-271; Published in Advance December 20, 2007, doi:10.1101/gr.6687808
...arm length drive telomere clustering An analysis of subtelomeric sequences of yeast chromosomes indicated that they fall into seven subgroups reflecting the presence of subtelomeric gene families (Supplemental Fig. 3; see also www.nottingham.ac.uk/genetics/louis ). Given that this number agreed...
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Research: Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis
- Ozren Bogdanović,
- Steven W. Long,
- Simon J. van Heeringen,
- Arie B. Brinkman,
- Jose Luis Gómez-Skarmeta,
- Hendrik G. Stunnenberg,
- Peter L. Jones,
- and Gert Jan C. Veenstra
Genome Res. August 2011 21: 1313-1327; Published in Advance June 2, 2011, doi:10.1101/gr.114843.110
...genes. Histone H3 lysine 4 trimethylation (H3K4me3) is enriched at the 59 ends of active genes. Clusters 1 and 3 correspond to methylated CpGis with different methylation profiles between stages. A few of these are located in introns of actively transcribed genes (RNAPII-positive, RNA...
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Research: A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci
- Elisabeth J. van Bree,
- Rita L.F.P. Guimarães,
- Mischa Lundberg,
- Elena R. Blujdea,
- Jimi L. Rosenkrantz,
- Fred T.G. White,
- Josse Poppinga,
- Paula Ferrer-Raventós,
- Anne-Fleur E. Schneider,
- Isabella Clayton,
- David Haussler,
- Marcel J.T. Reinders,
- Henne Holstege,
- Adam D. Ewing,
- Colette Moses,
- and Frank M.J. Jacobs
Genome Res. April 2022 32: 656-670; Published in Advance March 24, 2022, doi:10.1101/gr.275515.121
...-VNTR-Alu) families can still actively spread through the , and new insertions cause variation between individuals in the form of presence/absence TE-insertional polymorphisms (Kazazian et al. 1988; Batzer et al. 1991; Brouha et al. 2003; Ostertag et al. 2003). TEs can alter gene regulation in the locus in which...
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