Searching journal content for articles similar to Pundhir et al. 33 (3): 332.

Displaying results 1-10 of 6182

For checked items

view abstracts
download to citation manager

Select this article
Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
- Haiyue Liu and
- Lea H. Gregersen
Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
...(Saponaro et al. 2014). Factors involved in cotranscriptional RNA processing have also been shown to impact elongation rate. The splicing regulator SRSF2 (also known as SC35) promotes transcription elongation in a gene-specific manner (Lin et al. 2008), and U1 small nuclear ribonucleoprotein (U1 sn...
OPEN ACCESS ARTICLE
Select this article
Research: Intergenic accumulation of RNA polymerase II maintains the potential for swift transcriptional restart upon release from quiescence
- Manuela Baquero Pérez,
- Gertjan Laenen,
- Isabelle Loïodice,
- Mickaël Garnier,
- Ugo Szachnowski,
- Antonin Morillon,
- Myriam Ruault,
- and Angela Taddei
Genome Res. October 2025 35: 2226-2239; Published in Advance August 12, 2025, doi:10.1101/gr.279874.124
...down, 3% of coding genes remain active. Furthermore, RNA polymerase II (RNAPII) accumulates at one-third of gene promoters. The corresponding genes are highly enriched among those showing a high level of transcription and high frequency of expression in individual cells, shortly after cells are refed...
Select this article
Research: ACTB methylation regulates SMARCA4 genomic occupancy to promote translation and reduce adhesion in colorectal cancer cells
- Elina Abaev-Schneiderman,
- Linh Nguyen,
- Raz Shalev,
- Tzofit Elbaz Biton,
- Anand Chopra,
- Giritharan Jagadeesan,
- Daniel Sevilla-Sanchez,
- Nili Tickotsky Moskovitz,
- Liron Levin,
- Michal Feldman,
- Capucine Van Rechem,
- and Dan Levy
Genome Res. March 25, 2026 ; Published in Advance March 25, 2026, doi:10.1101/gr.280534.125
.... Specifically, we demonstrate that SETD3-mediated ACTB methylation is required for the colocalization of SMARCA4, a subunit of the SWI/SNF BAF complex, at specific genomic loci. Genomic analyses further show that this colocalization enables the coordinated occupancy of SMARCA4 and H73-methylated ACTB at genes...
Select this article
Research: Distinct roles for RSC and SWI/SNF chromatin remodelers in genomic excision repair
- Kaitlynne A. Bohm,
- Amelia J. Hodges,
- Wioletta Czaja,
- Kathiresan Selvam,
- Michael J. Smerdon,
- Peng Mao,
- and John J. Wyrick
Genome Res. June 2021 31: 1047-1059; Published in Advance May 17, 2021, doi:10.1101/gr.274373.120
...that SWI/SNF is largely dispensable for NER across the but does promote NER at specific genes, including those encoding ribosomal proteins. In contrast, our data indicate that RSC has a general role in promoting NER across the , being required for both the GG-NER and TC-NER subpathways. RSC not only...
Select this article
Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
...with the impact of the total RNA level of the gene transcript (P < 0.00001, slope = 0.659). The interaction term of the regression is negligible. A comparable effect is observed in the other studied samples (Supplemental Table 2). In conclusion, although the half-life of transcripts does have a significant effect...
Select this article
Research: Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy
- Hadi Rahmaninejad,
- Yao Xiao,
- Maxime M.C. Tortora,
- and Geoffrey Fudenberg
Genome Res. August 2025 35: 1745-1757; Published in Advance July 8, 2025, doi:10.1101/gr.280108.124
...times and occupancy (Ramani et al. 2019; Sönmezer et al. 2021), as well as site-specific unbound times. Site-specific unbound times could arise from factors ranging from facilitated diffusion and clustering of sites (Zabet and Adryan 2013) to CTCF-RNA associations (Hansen et al. 2020) that alter CTCF...
OPEN ACCESS ARTICLE
Select this article
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
...with identifying the TSS, the RNA polymerase recruitment point. TF binding sites near the TSS form the promoter, whereas more distant ones are typically called enhancers (Bateman and Johnson 2022). Some genes have multiple functional TSSs, which complicates regulatory analysis, so alternative promoters must...
OPEN ACCESS ARTICLE
Select this article
Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
..., in which the expression of the mutation was confirmed in the TRACERx cohort by RNA-seq (Supplemental Table 5; Frankell et al. 2023). Positive CESs were observed in FIEs in a majority of these functional families (n = 24/28 families) in TCGA pancancer (Supplemental Fig. 17), with somewhat larger effects...
OPEN ACCESS ARTICLE
Select this article
Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
- Prashanthi Ravichandran,
- Princy Parsana,
- Rebecca Keener,
- Kasper D. Hansen,
- and Alexis Battle
Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
...and AI Institute, Johns Hopkins University, Baltimore, Maryland 21218, USA Corresponding author: ajbattle@jhu.eduAbstractGene coexpression networks (GCNs) describe relationships among genes that maintain cellular identity and homeostasis. However, typical RNA-seq experiments often lack sufficient sample...
OPEN ACCESS ARTICLE
Select this article
Research: Histone deacetylases maintain expression of the pluripotent gene network via recruitment of RNA polymerase II to coding and noncoding loci
- Richard D.W. Kelly,
- Kristy R. Stengel,
- Aditya Chandru,
- Lyndsey C. Johnson,
- Scott W. Hiebert,
- and Shaun M. Cowley
Genome Res. January 2024 34: 34-46; Published in Advance January 30, 2024, doi:10.1101/gr.278050.123
.... Among the 18 HDAC enzymes present within mammalian cells, HDAC1, HDAC2, and HDAC3 (class I HDACs) have well-described roles in regulating gene expression as the catalytic core of seven multiprotein complexes: SIN3, NuRD, CoREST, MiDAC, MIER and RERE (HDAC1 and HDAC2), and NCoR (HDAC3) (Millard et al...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Pundhir et al. 33 (3): 332.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: