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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
..., hinging on the precise binding of transcription factors (TFs) and cofactors to gene regulatory elements such as promoters and enhancers. Although it is relatively routine to profile -wide DNA binding landscapes of proteins, identifying the specific proteins that bind to, and regulate the transcription of...
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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
...assessed the role of ZNF91 in repressing SVAs by mapping its binding sites and creating a genetic deletion of ZNF91 in human embryonic stem cells. The data described here elucidate the gene-regulatory role of SVAs under conditions in which epigenetic repression is lost. Furthermore, our findings strengthen...
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Research: Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates
- Étienne Fafard-Couture,
- Pierre-Étienne Jacques,
- and Michelle S. Scott
Genome Res. April 2023 33: 525-540; Published in Advance April 18, 2023, doi:10.1101/gr.277483.122
...-seq data sets that were recently generated in mouse (Mus musculus) embryonic stem cells (mESCs) (McCann et al. 2020). Because these data sets contained only small RNAs, we used an independent RNA-seq data set from 19 different mouse tissues (Shen et al. 2012) to define host gene expression status...
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Research: Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing
- Alaaddin Bulak Arpat,
- Angélica Liechti,
- Mara De Matos,
- René Dreos,
- Peggy Janich,
- and David Gatfield
Genome Res. July 2020 30: 985-999; Published in Advance July 23, 2020, doi:10.1101/gr.257741.119
...ribosomal collisions transcriptome-wide in mouse liver. We uncover that the stacking of an elongating onto a paused ribosome occurs frequently and scales with translation rate, trapping ∼10% of translating ribosomes in the disome state. A distinct class of pause sites is indicative of deterministic pausing...
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Research: Hydroxycarbamide effects on DNA methylation and gene expression in myeloproliferative neoplasms
- Stephania Contreras Castillo,
- Bertille Montibus,
- Azucena Rocha,
- Will Duke,
- Ferdinand von Meyenn,
- Donal McLornan,
- Claire Harrison,
- Ann Mullally,
- Reiner Schulz,
- and Rebecca J. Oakey
Genome Res. August 2021 31: 1381-1394; Published in Advance July 9, 2021, doi:10.1101/gr.270066.120
...in a murine MPN model. This study was replicated in MPN patients by profiling -wide gene expression and DNA methylation using patient blood samples collected longitudinally, before and following HC exposure. The effects of HC on the transcriptome were not only associated with cell cycle interruption but also...
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Method: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification
- Manuel Tardaguila,
- Lorena de la Fuente,
- Cristina Marti,
- Cécile Pereira,
- Francisco Jose Pardo-Palacios,
- Hector del Risco,
- Marc Ferrell,
- Maravillas Mellado,
- Marissa Macchietto,
- Kenneth Verheggen,
- Mariola Edelmann,
- Iakes Ezkurdia,
- Jesus Vazquez,
- Michael Tress,
- Ali Mortazavi,
- Lennart Martens,
- Susana Rodriguez-Navarro,
- Victoria Moreno-Manzano,
- and Ana Conesa
Genome Res. March 2018 28: 396-411; Published in Advance February 9, 2018, doi:10.1101/gr.222976.117
...Bio pipeline (Gordon et al. 2015) obtains auto-clusters of FL and non-FL RoIs and then computes a consensus transcript sequence where errors are significantly reduced. In all cases, comparison to the reference gene models serves to call known and novel transcripts.All PacBio transcriptome papers discover...
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Research: Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome
- Gilad D. Evrony,
- Dwight R. Cordero,
- Jun Shen,
- Jennifer N. Partlow,
- Timothy W. Yu,
- Rachel E. Rodin,
- R. Sean Hill,
- Michael E. Coulter,
- Anh-Thu N. Lam,
- Divya Jayaraman,
- Dianne Gerrelli,
- Diana G. Diaz,
- Chloe Santos,
- Victoria Morrison,
- Antonella Galli,
- Ulrich Tschulena,
- Stefan Wiemann,
- M. Jocelyne Martel,
- Betty Spooner,
- Steven C. Ryu,
- Princess C. Elhosary,
- Jillian M. Richardson,
- Danielle Tierney,
- Christopher A. Robinson,
- Rajni Chibbar,
- Dana Diudea,
- Rebecca Folkerth,
- Sheldon Wiebe,
- A. James Barkovich,
- Ganeshwaran H. Mochida,
- James Irvine,
- Edmond G. Lemire,
- Patricia Blakley,
- and Christopher A. Walsh
Genome Res. August 2017 27: 1323-1335; Published in Advance June 19, 2017, doi:10.1101/gr.219899.116
...gene whose complete loss of function we predict would otherwise be embryonic-lethal—was facilitated by a genomic plus transcriptomic integrated approach that serves as a model for discovering causes of other Mendelian diseases for which sequencing alone has been unsuccessful. A transcriptomic approach...
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Methods: Cross-species de novo identification of cis-regulatory modules with GibbsModule: Application to gene regulation in embryonic stem cells
- Dan Xie,
- Jun Cai,
- Na-Yu Chia,
- Huck H. Ng,
- and Sheng Zhong
Genome Res. August 2008 18: 1325-1335; Published in Advance May 15, 2008, doi:10.1101/gr.072769.107
...Cross-species de novo identification of cis -regulatory modules with GibbsModule: Application to gene regulation in embryonic stem cells Dan Xie 1 , Jun Cai 1 , Na-Yu Chia 2 , Huck H. Ng 2 , 3 , and Sheng Zhong 1 , 4 , 5 , 6 , 7...
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Research: Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome
- Tim R. Mercer,
- Marcel E. Dinger,
- Cameron P. Bracken,
- Gabriel Kolle,
- Jan M. Szubert,
- Darren J. Korbie,
- Marjan E. Askarian-Amiri,
- Brooke B. Gardiner,
- Gregory J. Goodall,
- Sean M. Grimmond,
- and John S. Mattick
Genome Res. December 2010 20: 1639-1650; Published in Advance November 2, 2010, doi:10.1101/gr.112128.110
...-stageand tissue-specific manner. By deep-sequencing size-fractionated pools of human embryonic stem cell RNA, we show that the cleavage pathway has significant impact in remodeling the transcriptome. We conclude that post-transcriptional RNA cleavage is a common mechanism that, alongside transcription initiation...
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Research: Gene duplication and neofunctionalization: POLR3G and POLR3GL
- Marianne Renaud,
- Viviane Praz,
- Erwann Vieu,
- Laurence Florens,
- Michael P. Washburn,
- Philippe l'Hôte,
- and Nouria Hernandez
Genome Res. January 2014 24: 37-51; Published in Advance October 9, 2013, doi:10.1101/gr.161570.113
...to POLR3GL (Haurie et al. 2010). Indeed, POLR3G is one of the most highly up-regulated genes in undifferentiated human stem cells relative to differentiated cells (Enver et al. 2005), and decreasing its levels results in loss of pluripotency (Wong et al. 2011). Suppression of each isoform by si...
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