Profiling and characterization of constitutive chromatin-enriched RNAs

Shen, Wenlong; Zhang, Yan; Shi, Minglei; Ye, Bingyu; Yin, Meng; Li, Ping; Shi, Shu; Jin, Yifei; Zhang, Zhang; Zhang, Michael Q.; Chen, Yang; Zhao, Zhihu

doi:10.1016/j.isci.2022.105349

Cited by 6 publications

(5 citation statements)

References 43 publications

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“…In addition, the pairwise Pearson's correlation analysis of FAIRE‐seq data sets showed a strong correlation between two biological replicates (Pearson's correlation coefficient in interphase was 0.901 and mitosis was 0.789) (Figure 2C). Further, we compared the data of FAIRE‐seq and ATAC‐seq, 36 and according to the results, they are consistent in the changes of global and individual signal patterns (Figures 2D and S2). These results provide a solid basis for further analysis using these methods.…”

Section: Resultsmentioning

confidence: 58%

FAIRE‐MS reveals mitotic retention of transcriptional regulators on a proteome‐wide scale

Shen²,

et al. 2022

The FASEB Journal

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Mitosis entails global and dramatic alterations, such as higher-order chromatin organization disruption, concomitant with global transcription downregulation. Cells reliably re-establishing gene expression patterns upon mitotic exit and maintaining cellular identities remain poorly understood. Previous studies indicated that certain transcription factors (TFs) remain associated with individual loci during mitosis and serve as mitotic bookmarkers. However, it is unclear which regulatory factors remain bound to the compacted mitotic chromosomes. We developed formaldehydeassisted isolation of regulatory elements-coupled mass spectrometry (FAIRE-MS) that combines FAIRE-based open chromatin-associated protein pull-down and mass spectrometry (MS) to quantify the open chromatin-associated proteome during the interphase and mitosis. We identified 189 interphase and mitosis maintained (IM) regulatory factors using FAIRE-MS and found intrinsically disordered proteins and regions (IDP(R)s) are highly enriched, which plays a crucial role in liquid-liquid phase separation (LLPS) and chromatin organization during the cell cycle. Notably, in these IDP(R)s, we identified mitotic bookmarkers, such as CEBPB, HMGB1, and TFAP2A, and several factors, including MAX, HMGB3, hnRNP A2/B1, FUS, hnRNP D, and TIAL1, which are at least partially bound to the mitotic chromosome.Furthermore, it will be essential to study whether these IDP(R)s through LLPS helps cells transit from mitosis to the G1 phase during the cell cycle.

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Section: Resultsmentioning

confidence: 58%

FAIRE‐MS reveals mitotic retention of transcriptional regulators on a proteome‐wide scale

Shen²,

et al. 2022

The FASEB Journal

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“…The data was analyzed using default parameters as per the Galaxy ATAC-seq analysis guidelines (https://training.galaxyproject.org/trainingmaterial/topics/epigenetics/tutorials/atac-seq/tutorial.html, Hiltemann et al, 2023). The processed bigwig files were then used to plot the signal at published ATAC peaks from interphase and mitosis (Shen et al, 2022) in HeLa. IGV Desktop application was used to visualize data (Robinson et al, 2011).…”

Section: Atac-seq Analysesmentioning

confidence: 99%

Compaction of Active Chromatin Domains and Promoters by H3S10 Phosphorylation during Mitosis Preserves Interphase-Specific Chromatin Structure and Function

Meel,

Mishra,

Mann

et al. 2024

Preprint

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Mitotic chromosomes lose interphase-specific genome organization and transcription but gain histone phosphorylation, specifically H3S10p. This phosphorylation event compacts chromosomes in early mitosis by reducing inter-nucleosomal distance before the loading of condensins. However, it is unclear if H3S10p in mitosis preserves the identity of lost chromatin domains and promoters, both physically and functionally. Here, using the pre-mitotic expression of histone H3S10 and its mutants H3S10A and H3S10D, we show that H3S10p hyper-phosphorylates active promoters and spreads into super-domains A in mitosis, causing compaction of these regions. By spreading into active domains in the absence of genome organization, H3S10p retains their identity physically. Functionally, H3S10p ensures optimal closing of promoters by stabilizing the nucleosomes, thereby protecting them from excess loading of transcription machinery post-mitosis. In the H3S10p phospho-mutants, these chromatin regions fail to condense properly during mitosis. As a result, they exhibit enhanced accessibility and transcription of active genes in the next interphase. We propose that the spreading of mitotic H3S10p into active domains preserves their identity during mitosis and, in subsequent interphase, acts as a rheostat to fine-tune transcription and chromatin domain re-formation.

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“…Recently, Shen et al . sequenced the RNA extracted from mitotic pellets of two human cell lines and mapped the sequenced reads to a large number of annotated genes ( >13,000 per cell) 15 . But despite this high number, no novel genes were noted, perhaps owing to a limited sequencing depth.…”

Section: Background and Summarymentioning

confidence: 99%

“…As an additional means of validation of the mCARs identified here, we compared the mCARs that we identified from the A549 cells with those obtained by Shen et al . 15 from the same cell type. As the latter described their mCARs in terms of genes, rather than transcript isoforms, this comparison was performed at the gene level.…”

Section: Technical Validationmentioning

confidence: 99%

Quantitative catalogue of mammalian mitotic chromosome-associated RNAs

Zhang,

Hu,

et al. 2024

Sci Data

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The faithful transmission of a cell’s identity and functionality to its daughters during mitosis requires the proper assembly of mitotic chromosomes from interphase chromatin in a process that involves significant changes in the genome-bound material, including the RNA. However, our understanding of the RNA that is associated with the mitotic chromosome is presently limited. Here, we present complete and quantitative characterizations of the full-length mitotic chromosome-associated RNAs (mCARs) for 3 human cell lines, a monkey cell line, and a mouse cell line derived from high-depth RNA sequencing (3 replicates, 47 M mapped read pairs for each replicate). Overall, we identify, on average, more than 20,400 mCAR species per cell-type (including isoforms), more than 5,200 of which are enriched on the chromosome. Notably, overall, more than 2,700 of these mCARs were previously unknown, which thus also expands the annotated genome of these species. We anticipate that these datasets will provide an essential resource for future studies to better understand the functioning of mCARs on the mitotic chromosome and in the cell.

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Profiling and characterization of constitutive chromatin-enriched RNAs

Cited by 6 publications

References 43 publications

FAIRE‐MS reveals mitotic retention of transcriptional regulators on a proteome‐wide scale

FAIRE‐MS reveals mitotic retention of transcriptional regulators on a proteome‐wide scale

Compaction of Active Chromatin Domains and Promoters by H3S10 Phosphorylation during Mitosis Preserves Interphase-Specific Chromatin Structure and Function

Quantitative catalogue of mammalian mitotic chromosome-associated RNAs

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