Structure, activity and function of the lysine methyltransferase SETD5

Li, Mingyang; Hou, Yanan; Zhang, Ziwei; Zhang, Bowen; Huang, Ting; Sun, Aixin; Shao, Gang; Lin, Qian

doi:10.3389/fendo.2023.1089527

Cited by 6 publications

(1 citation statement)

References 61 publications

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“…Among these are the SET domain-containing 5 ( Setd5 ) promoter (Fig. 5b ) 43 , the Phosphoglucokinase ( Pgk1 ) promoter (Fig. 5c ) 44 , which are also from the PDGFB-driven tumor and normal comparison, displaying clear differences between the tumors.…”

Section: Resultsmentioning

confidence: 99%

Epigenomic analysis of formalin-fixed paraffin-embedded samples by CUT&Tag

Henikoff,

Ahmad

et al. 2023

Nat Commun

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For more than a century, formalin-fixed paraffin-embedded (FFPE) sample preparation has been the preferred method for long-term preservation of biological material. However, the use of FFPE samples for epigenomic studies has been difficult because of chromatin damage from long exposure to high concentrations of formaldehyde. Previously, we introduced Cleavage Under Targeted Accessible Chromatin (CUTAC), an antibody-targeted chromatin accessibility mapping protocol based on CUT&Tag. Here we show that simple modifications of our CUTAC protocol either in single tubes or directly on slides produce high-resolution maps of paused RNA Polymerase II at enhancers and promoters using FFPE samples. We find that transcriptional regulatory element differences produced by FFPE-CUTAC distinguish between mouse brain tumors and identify and map regulatory element markers with high confidence and precision, including microRNAs not detectable by RNA-seq. Our simple workflows make possible affordable epigenomic profiling of archived biological samples for biomarker identification, clinical applications and retrospective studies.

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Section: Resultsmentioning

confidence: 99%

Epigenomic analysis of formalin-fixed paraffin-embedded samples by CUT&Tag

Henikoff,

Ahmad

et al. 2023

Nat Commun

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Knockdown of SETD5 Inhibits Colorectal Cancer Cell Growth and Stemness by Regulating PI3K/AKT/mTOR Pathway

Zhou,

Chen,

Zhuang

et al. 2024

Biochem Genet

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The chromatin factors SET-26 and HCF-1 oppose the histone deacetylase HDA-1 in longevity and gene regulation in C. elegans

Emerson,

Chiu,

Lin

et al. 2024

Nat Commun

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SET-26, HCF-1, and HDA-1 are highly conserved chromatin factors with key roles in development and aging. Here we present mechanistic insights into how these factors regulate gene expression and modulate longevity in C. elegans. We show that SET-26 and HCF-1 cooperate to regulate a common set of genes, and both antagonize the histone deacetylase HDA-1 to limit longevity. HCF-1 localization at chromatin is largely dependent on functional SET-26, whereas SET-26 is only minorly affected by loss of HCF-1, suggesting that SET-26 could recruit HCF-1 to chromatin. HDA-1 opposes SET-26 and HCF-1 on the regulation of a subset of their common target genes and in longevity. Our findings suggest that SET-26, HCF-1, and HDA-1 comprise a mechanism to fine-tune gene expression and longevity and likely have important implications for the mechanistic understanding of how these factors function in diverse organisms, particularly in aging biology.

show abstract

Structure, activity and function of the lysine methyltransferase SETD5

Cited by 6 publications

References 61 publications

Epigenomic analysis of formalin-fixed paraffin-embedded samples by CUT&Tag

Epigenomic analysis of formalin-fixed paraffin-embedded samples by CUT&Tag

Knockdown of SETD5 Inhibits Colorectal Cancer Cell Growth and Stemness by Regulating PI3K/AKT/mTOR Pathway

The chromatin factors SET-26 and HCF-1 oppose the histone deacetylase HDA-1 in longevity and gene regulation in C. elegans

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