PRO-IP-seq: Pol II CTD code at nt-resolution in human K562 cells
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA823909 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18653100.fastq.gz | Fastqsanger.gz | |||
| SRR18653101.fastq.gz | Fastqsanger.gz | |||
| SRR18653102.fastq.gz | Fastqsanger.gz | |||
| SRR18653103.fastq.gz | Fastqsanger.gz | |||
| SRR18653104.fastq.gz | Fastqsanger.gz |
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Project description:Active sites of transcription were labelled with biotinylated nucleotide during a run-on reacation, where after an immunoprecipitation with antibodies that target Pol II CTD was conducted. This PRO-IP-seq protocol was conducted in human K562 erythroleukemia cells. The K562 cells were either untreated (NHS) or treated with 30 minutes of heat shock at 42°C (HS).
2023-02-24 | GSE200269 | GEO
Project description:The primary structure and phosphorylation pattern of the tandem YSPTSPS repeats of the RNA polymerase II CTD comprise an informational code that coordinates transcription, chromatin modification, and RNA processing. To gauge the contributions of individual CTD coding “letters” to gene expression, we analyzed the poly(A)+ transcriptomes of fission yeast mutants that lack each of the four inessential CTD phosphoacceptors: Tyr1, Ser2, Thr4, and Ser7. There was a hierarchy of CTD mutational effects with respect to the number of dysregulated protein-coding RNAs, with S2A (n=227) >> Y1F (n=71) > S7A (n=58) >> T4A (n=7). The majority of the protein-coding RNAs affected in Y1F cells were coordinately affected by S2A, suggesting that Tyr1-Ser2 constitutes a two-letter code “word”. Y1F and S2A elicited increased expression of genes encoding proteins involved in iron uptake (Frp1, Fip1, Fio1, Str3, Str1, Sib1), without affecting the expression of the genes that repress the iron regulon, implying that Tyr1-Ser2 transduces a repressive signal. Y1F and S2A cells had increased levels of ferric reductase activity and were hypersensitive to phleomycin, indicative of elevated intracellular iron. The T4A and S7A mutations had opposing effects on the phosphate response pathway. T4A reduced the expression of two genes encoding proteins involved in phosphate acquisition (the Pho1 acid phosphatase and the phosphate transporter SPBC8E4.01c), without affecting the expression of known genes that regulate the phosphate response pathway, while S7A increased pho1+ expression. Meiotic genes were enriched among those up-regulated in S7A cells. These results highlight specific cellular gene expression programs that are responsive to distinct CTD cues.
2014-03-13 | GSE52370 | GEO
Project description:The primary structure and phosphorylation pattern of the tandem YSPTSPS repeats of the RNA polymerase II CTD comprise an informational code that coordinates transcription, chromatin modification, and RNA processing. To gauge the contributions of individual CTD coding M-bM-^@M-^\lettersM-bM-^@M-^] to gene expression, we analyzed the poly(A)+ transcriptomes of fission yeast mutants that lack each of the four inessential CTD phosphoacceptors: Tyr1, Ser2, Thr4, and Ser7. There was a hierarchy of CTD mutational effects with respect to the number of dysregulated protein-coding RNAs, with S2A (n=227) >> Y1F (n=71) > S7A (n=58) >> T4A (n=7). The majority of the protein-coding RNAs affected in Y1F cells were coordinately affected by S2A, suggesting that Tyr1-Ser2 constitutes a two-letter code M-bM-^@M-^\wordM-bM-^@M-^]. Y1F and S2A elicited increased expression of genes encoding proteins involved in iron uptake (Frp1, Fip1, Fio1, Str3, Str1, Sib1), without affecting the expression of the genes that repress the iron regulon, implying that Tyr1-Ser2 transduces a repressive signal. Y1F and S2A cells had increased levels of ferric reductase activity and were hypersensitive to phleomycin, indicative of elevated intracellular iron. The T4A and S7A mutations had opposing effects on the phosphate response pathway. T4A reduced the expression of two genes encoding proteins involved in phosphate acquisition (the Pho1 acid phosphatase and the phosphate transporter SPBC8E4.01c), without affecting the expression of known genes that regulate the phosphate response pathway, while S7A increased pho1+ expression. Meiotic genes were enriched among those up-regulated in S7A cells. These results highlight specific cellular gene expression programs that are responsive to distinct CTD cues. Interrogation of the S. pombe transcriptome using polyA+ strand specific RNA sequencing (Illumina HiSeq 2000) in cultures. A total of 16 samples were analysed: two biological repeates of each WT, Y1F, S2A, T4A, S7A,Y1F-S7A, S2A-S7A and T4A-S7A strains
2014-03-13 | E-GEOD-52370 | biostudies-arrayexpress
Project description:Dynamic post-translational modification of RNA polymerase II (RNAPII) coordinates the co-transcriptional recruitment of enzymatic complexes that regulate chromatin states and co-transcriptional processing of nascent RNA. Extensive phosphorylation of serine residues occurs at the structurally-disordered C-terminal domain (CTD) of the largest RNAPII subunit, which is composed of multiple heptapeptide repeats with consensus sequence Y1-S2-P3-T4-S5-P6-S7. Serine-5 and Serine-7 phosphorylation mark transcription initiation, whereas Serine-2 phosphorylation coincides with productive elongation. In vertebrates, the CTD has eight non-canonical substitutions of Serine-7 into Lysine-7, which can be acetylated (K7ac). Here, we describe for the first time mono- and di-methylation of CTD Lysine-7 residues (K7me1 and K7me2). K7me1 and K7me2 are observed during the earliest transcription stages and precede or accompany Serine-5 and Serine-7 phosphorylation. Genome wide mapping of 2 novel RNAPII post-translational modifications (CTD-K7me1 and CTD-K7me2) in mouse ES cells.
2015-12-22 | E-GEOD-72876 | biostudies-arrayexpress
Project description:ChIP-chip was performed to identify the genomic binding locations for the termination factors Nrd1, and Rtt103, and for RNA polymerase (Pol) II phosphorylated at the tyrosine 1 and threonine 4 position of its C-terminal domain (CTD). In different phases of the transcription cycle, Pol II recruits different factors via its CTD, which consists of heptapeptide repeats with the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. Here we show that the CTD of transcribing yeast Pol II is phosphorylated at Tyr1, and that this impairs recruitment of termination factors. Tyr1 phosphorylation levels rise downstream of the transcription start site (TSS), and decrease before the polyadenylation (pA) site. Tyr1-phosphorylated gene bodies are depleted of CTD-binding termination factors Nrd1, Pcf11, and Rtt103. Tyr1 phosphorylation blocks CTD binding by these termination factors, but stimulates binding of elongation factor Spt6. These results show that CTD modifications can not only stimulate but also block factor recruitment, and lead to an extended CTD code for transcription cycle coordination.
2012-06-29 | E-MTAB-1060 | biostudies-arrayexpress
Project description:Dynamic post-translational modification of RNA polymerase II (RNAPII) coordinates the co-transcriptional recruitment of enzymatic complexes that regulate chromatin states and co-transcriptional processing of nascent RNA. Extensive phosphorylation of serine residues occurs at the structurally-disordered C-terminal domain (CTD) of the largest RNAPII subunit, which is composed of multiple heptapeptide repeats with consensus sequence Y1-S2-P3-T4-S5-P6-S7. Serine-5 and Serine-7 phosphorylation mark transcription initiation, whereas Serine-2 phosphorylation coincides with productive elongation. In vertebrates, the CTD has eight non-canonical substitutions of Serine-7 into Lysine-7, which can be acetylated (K7ac). Here, we describe for the first time mono- and di-methylation of CTD Lysine-7 residues (K7me1 and K7me2). K7me1 and K7me2 are observed during the earliest transcription stages and precede or accompany Serine-5 and Serine-7 phosphorylation.
2015-12-22 | GSE72876 | GEO
Project description:Beauveria bassiana strain:NT | isolate:sp | breed:NT | cultivar:NT Transcriptome or Gene expression
| PRJNA450457 | ENA
Project description:The modification of Ser 5 is important for the relocalization of RNAP II upon NaCl stress. The CTD14 strains harbors a plasmid expressing RPB1 with 14 wild-type CTD repeats. The 5A strain carries a plasmid expressing a chimeric RPB1 in which the CTD was composed of 5 repeats of CTD-serine 5 substituted with alanine followed by 7 wild-type-sequenced repeats. Two-color fluorescence arrays reporting on Rpb3 localization abundance in strains (input vs. IP) before and at 20 min after a shock with 0.7M NaCl
2014-12-03 | E-GEOD-60707 | biostudies-arrayexpress
Project description:Dynamic modification of the carboxy-terminal domain (CTD) of RNA polymerase II (RNAPII) regulates transcription-coupled processes in eukaryotes. The CTD in mammals is composed of 52 heptad-repeats with the consensus sequence Y1-S2-P3-T4-S5-P6-S7. Repeats in the distal part of CTD deviate from the consensus sequence and have frequently replaced serine at position 7 by lysine residues (K7). Mass spectrometry analysis revealed modification of K7 residues in heptad-repeats 39, 42, and 47/49 by acetylation and in heptad-repeats 38, 39, 40, 42, and 47/49 by mono-, di-, or trimethylation. Notably, acetylated as well as di- and tri-methylated K7 residues were found exclusively in phosphorylated CTD peptides, while mono-methylated K7 residues occurred also in non-phosphorylated CTD peptides. Methylation of K7 residues was further studied with the monoclonal antibody (mAb) 1F5, which recognizes mono- and di-methylated K7 in CTD. ChIP experiments revealed high levels of K7 methylation at the transcriptional start site of genes. The low levels of K7 methylation in the body of genes results from impairment of epitope recognition in hyper-phosphorylated CTD by mAb 1F5. In agreement with this notion, phosphatase treatment of hyper-phosphorylated CTD or treatment of cells with kinase inhibitor flavopiridol restored the reactivity of mAb 1F5 towards methylated K7 residues in CTD. We conclude that methylation and acetylation of K7 residues further expand the mammalian CTD code and potentially contribute to regulation of gene expression.
2015-12-01 | GSE72698 | GEO
Project description:we performed large-scale co-immunoprecipitation (co-IP) using a DOT1L antibody with nuclear extract from K562 cells, and characterized immunoprecipitated proteins by mass spectrometry.
2021-06-18 | PXD024874 | Pride