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Series GSE182204 Query DataSets for GSE182204
Status Public on Jul 21, 2023
Title Acetyl-methyllysine marks chromatin at active transcription start sites
Organisms Drosophila melanogaster; Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Lysine residues in histones and other proteins can be modified by post-translational modifications (PTMs) that encode regulatory information. Acetylation and methylation of histone lysine residues are especially important for regulating chromatin and gene expression. Pathways involving these PTMs are targets for clinically approved therapeutics to treat human diseases. Lysine methylation and acetylation are generally assumed to be mutually exclusive at the same residue. Here, we report the discovery of cellular lysine residues that are both methylated and acetylated on the same sidechain to form acetyl-methyllysine (Kacme). We show that Kacme is found on histone H4 across a range of species and across mammalian tissues. Kacme is associated with marks of active chromatin and is regulated in response to biological signals. Analysis of nascent transcription and promoter-proximal pausing in human cells demonstrates that higher levels of Kacme are associated with higher levels of initiation and transcription. H4Kacme can be installed by enzymatic acetylation of monomethylated lysine peptides and is resistant to deacetylation by some HDACs in vitro. Further, Kacme can be bound by chromatin proteins that recognize modified lysine residues as we demonstrate with the crystal structure of acetyllysine-binding protein BRD2 bound to a histone H4Kacme peptide. These results establish Kacme as a new cellular PTM with the potential to encode information distinct from methylation and acetylation alone and demonstrate that Kacme has all the hallmarks of a PTM with fundamental importance to chromatin biology.
 
Overall design ChIP-seq with Kacme and H4Kac antibodies in S2 cells +/- heatshock, ChIP-seq with Kacme and H4Kac antibodies in K562 and HEK 293T cells, ChIP-seq with H4Kacme antibodies in HEK 293T cells, and CUT&RUN with Kacme and H4Kac antibodies in K562 cells. TT-TL-seq and STL-seq performed in HEK 293T cells. TT-TL-seq performed in HEK 293T cells treated with TSA (400 nM) or DMSO for 15 hours. All experiments performed in duplicate. Inputs included.
 
Contributor(s) Lu-Culligan WJ, Connor LJ, Xie Y, Ekundayo BE, Rose BT, Pintado-Urbanc AP, Machyna M, Zimmer JT, Vock IW, Bhanu NV, King MC, Garcia BA, Bleichert F, Simon MD
Citation(s) 37731000
Submission date Aug 16, 2021
Last update date Oct 06, 2023
Contact name Matthew Simon
E-mail(s) matthew.simon@yale.edu
Organization name Yale University
Department Molecular Biophysics and Biochemistry
Street address 100 West Campus Drive, Ste MIC 231
City Orange
State/province CT
ZIP/Postal code 06477
Country USA
 
Platforms (2)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
GPL25244 Illumina NovaSeq 6000 (Drosophila melanogaster)
Samples (68)
GSM5520524 Input_S2
GSM6578672 Kacme_S2_1
GSM6578673 Kacme_S2_2
Relations
BioProject PRJNA755299
SRA SRP332720

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Supplementary file Size Download File type/resource
GSE182204_RAW.tar 37.8 Gb (http)(custom) TAR (of BIGWIG, NARROWPEAK, TDF)
GSE182204_STL_293T_data.csv.gz 174.8 Kb (ftp)(http) CSV
GSE182204_TT_TL_293T_data.csv.gz 295.3 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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