bims-crepig 2023-12-31 papers

bims-crepig

Biomed News

on Chromatin regulation and epigenetics in cell fate and cancer

Issue of 2023–12–31
twelve papers selected by
Connor Rogerson, University of Cambridge

Genetic variation is a key determinant of chromatin accessibility and drives differences in the regulatory landscape of C57BL/6J and 129S1/SvImJ mice.
The Nucleosome Remodelling and Deacetylation complex coordinates the transcriptional response to lineage commitment in pluripotent cells.
Collisions of RNA polymerases behind the replication fork promote alternative RNA splicing in newly replicated chromatin.
Highly cooperative chimeric super-SOX induces naive pluripotency across species.
The Tudor-knot domain of KAT5 regulates nucleosomal substrate acetylation.
One-pot trimodal mapping of unmethylated, hydroxymethylated, and open chromatin sites unveils distinctive 5hmC roles at dynamic chromatin loci.
hRpn13 shapes the proteome and transcriptome through epigenetic factors HDAC8, PADI4, and transcription factor NF-κB p50.
YAP and TAZ couple osteoblast precursor mobilization to angiogenesis and mechanoregulation in murine bone development.
PRC1 directs PRC2-H3K27me3 deposition to shield adult spermatogonial stem cells from differentiation.
A recurrent de novo MAX p.Arg60Gln variant causes a syndromic overgrowth disorder through differential expression of c-Myc target genes.
The chromatin remodeler Ino80 regulates yeast stress tolerance and cell metabolism through modulating nitrogen catabolite repression.
RENGE infers gene regulatory networks using time-series single-cell RNA-seq data with CRISPR perturbations.

Nucleic Acids Res. 2023 Dec 28. pii: gkad1225. [Epub ahead of print]

Genetic variation is a key determinant of chromatin accessibility and drives differences in the regulatory landscape of C57BL/6J and 129S1/SvImJ mice.

Juho Mononen, Mari Taipale, Marjo Malinen, Bharadwaja Velidendla, Einari Niskanen, Anna-Liisa Levonen, Anna-Kaisa Ruotsalainen, Sami Heikkinen.

Most common genetic variants associated with disease are located in non-coding regions of the genome. One mechanism by which they function is through altering transcription factor (TF) binding. In this study, we explore how genetic variation is connected to differences in the regulatory landscape of livers from C57BL/6J and 129S1/SvImJ mice fed either chow or a high-fat diet. To identify sites where regulatory variation affects TF binding and nearby gene expression, we employed an integrative analysis of H3K27ac ChIP-seq (active enhancers), ATAC-seq (chromatin accessibility) and RNA-seq (gene expression). We show that, across all these assays, the genetically driven (i.e. strain-specific) differences in the regulatory landscape are more pronounced than those modified by diet. Most notably, our analysis revealed that differentially accessible regions (DARs, N = 29635, FDR < 0.01 and fold change > 50%) are almost always strain-specific and enriched with genetic variation. Moreover, proximal DARs are highly correlated with differentially expressed genes. We also show that TF binding is affected by genetic variation, which we validate experimentally using ChIP-seq for TCF7L2 and CTCF. This study provides detailed insights into how non-coding genetic variation alters the gene regulatory landscape, and demonstrates how this can be used to study the regulatory variation influencing TF binding.

DOI: https://doi.org/10.1093/nar/gkad1225
Biol Open. 2023 Dec 27. pii: bio.060101. [Epub ahead of print]

The Nucleosome Remodelling and Deacetylation complex coordinates the transcriptional response to lineage commitment in pluripotent cells.

Bertille Montibus, Ramy Ragheb, Evangelia Diamanti, Sara-Jane Dunn, Nicola Reynolds, Brian Hendrich.

  As cells exit the pluripotent state and begin to commit to a specific lineage they must activate genes appropriate for that lineage while silencing genes associated with pluripotency and preventing activation of lineage-inappropriate genes. The Nucleosome Remodelling and Deacetylation (NuRD) complex is essential for pluripotent cells to successfully undergo lineage commitment. NuRD controls nucleosome density at regulatory sequences to facilitate transcriptional responses, and also has been shown to prevent unscheduled transcription (transcriptional noise) in undifferentiated pluripotent cells. How these activities combine to ensure cells engage a gene expression program suitable for successful lineage commitment has not been determined. Here we show that NuRD is not required to silence all genes. Rather it restricts expression of genes primed for activation upon exit from the pluripotent state, but maintains them in a transcriptionally permissive state in self-renewing conditions which facilitates their subsequent activation upon exit from naïve pluripotency. We further show that NuRD coordinates gene expression changes, which acts to maintain a barrier between different stable states. Thus NuRD-mediated chromatin remodelling serves multiple functions, including reducing transcriptional noise, priming genes for activation and coordinating the transcriptional response to facilitate lineage commitment.

Keywords:  Chromatin; Embryonic Stem Cell; Lineage Commitment; MBD3; NuRD; Transcription

DOI:  https://doi.org/10.1242/bio.060101
Mol Cell. 2023 Dec 20. pii: S1097-2765(23)01012-2. [Epub ahead of print]

Collisions of RNA polymerases behind the replication fork promote alternative RNA splicing in newly replicated chromatin.

Federica Bruno, Cristóbal Coronel-Guisado, Cristina González-Aguilera.

  DNA replication produces a global disorganization of chromatin structure that takes hours to be restored. However, how these chromatin rearrangements affect the regulation of gene expression and the maintenance of cell identity is not clear. Here, we use ChOR-seq and ChrRNA-seq experiments to analyze RNA polymerase II (RNAPII) activity and nascent RNA synthesis during the first hours after chromatin replication in human cells. We observe that transcription elongation is rapidly reactivated in nascent chromatin but that RNAPII abundance and distribution are altered, producing heterogeneous changes in RNA synthesis. Moreover, this first wave of transcription results in RNAPII blockages behind the replication fork, leading to changes in alternative splicing. Altogether, our results deepen our understanding of how transcriptional programs are regulated during cell division and uncover molecular mechanisms that explain why chromatin replication is an important source of gene expression variability.

Keywords:  ChOR-seq; RNAPII; cell division; cell identity; chromatin; gene expression; replication; splicing; transcription; transcription-replication conflicts

DOI:  https://doi.org/10.1016/j.molcel.2023.11.036
Cell Stem Cell. 2023 Dec 20. pii: S1934-5909(23)00402-2. [Epub ahead of print]

Highly cooperative chimeric super-SOX induces naive pluripotency across species.

Caitlin M MacCarthy, Guangming Wu, Vikas Malik, Yotam Menuchin-Lasowski, Taras Velychko, Gal Keshet, Rui Fan, Ivan Bedzhov, George M Church, Ralf Jauch, Vlad Cojocaru, Hans R Schöler, Sergiy Velychko.

  Our understanding of pluripotency remains limited: iPSC generation has only been established for a few model species, pluripotent stem cell lines exhibit inconsistent developmental potential, and germline transmission has only been demonstrated for mice and rats. By swapping structural elements between Sox2 and Sox17, we built a chimeric super-SOX factor, Sox2-17, that enhanced iPSC generation in five tested species: mouse, human, cynomolgus monkey, cow, and pig. A swap of alanine to valine at the interface between Sox2 and Oct4 delivered a gain of function by stabilizing Sox2/Oct4 dimerization on DNA, enabling generation of high-quality OSKM iPSCs capable of supporting the development of healthy all-iPSC mice. Sox2/Oct4 dimerization emerged as the core driver of naive pluripotency with its levels diminished upon priming. Transient overexpression of the SK cocktail (Sox+Klf4) restored the dimerization and boosted the developmental potential of pluripotent stem cells across species, providing a universal method for naive reset in mammals.

Keywords:  Oct4; POU linker; Sox17; Sox2; Sox2/Oct4 heterodimer structure; bovine; developmental potential; engineered transcription factor; human; iPSC; mouse; naive pluripotency; non-human primate; porcine; reprogramming; reset; super-SOX; tetraploid complementation

DOI:  https://doi.org/10.1016/j.stem.2023.11.010
J Mol Biol. 2023 Dec 21. pii: S0022-2836(23)00531-4. [Epub ahead of print] 168414

The Tudor-knot domain of KAT5 regulates nucleosomal substrate acetylation.

Fan Xuan, Hongwen Xuan, Mengying Huang, He Wei, Han Xu, Xiaobing Shi, Hong Wen.

  The lysine acetyltransferase KAT5 is a pivotal enzyme responsible for catalyzing histone H4 acetylation in cells. In addition to its indispensable HAT domain, KAT5 also encompasses a conserved Tudor-knot domain at its N-terminus. However, the function of this domain remains elusive, with conflicting findings regarding its role as a histone reader. In our study, we have employed a CRISPR tiling array approach and unveiled the Tudor-knot motif as an essential domain for cell survival. The Tudor-knot domain does not bind to histone tails and is not required for KAT5's chromatin occupancy. However, its absence leads to a global reduction in histone acetylation, accompanied with genome-wide alterations in gene expression that consequently result in diminished cell viability. Mechanistically, we find that the Tudor-knot domain regulates KAT5's HAT activity on nucleosomes by fine-tuning substrate accessibility. In summary, our study uncovers the Tudor-knot motif as an essential domain for cell survival and reveals its critical role in modulating KAT5's catalytic efficiency on nucleosome and KAT5-dependent transcriptional programs critical for cell viability.

Keywords:  H4 acetylation; KAT5; TIP60; Tudor-knot domain; nucleosome

DOI:  https://doi.org/10.1016/j.jmb.2023.168414
Cell Chem Biol. 2023 Dec 20. pii: S2451-9456(23)00433-6. [Epub ahead of print]

One-pot trimodal mapping of unmethylated, hydroxymethylated, and open chromatin sites unveils distinctive 5hmC roles at dynamic chromatin loci.

Kotryna Skardžiūtė, Kotryna Kvederavičiūtė, Inga Pečiulienė, Milda Narmontė, Povilas Gibas, Janina Ličytė, Saulius Klimašauskas, Edita Kriukienė.

  We present a method, named Mx-TOP, for profiling of three epigenetic regulatory layers-chromatin accessibility, general DNA modification, and DNA hydroxymethylation-from a single library. The approach is based on chemo-enzymatic covalent tagging of unmodified CG sites and hydroxymethylated cytosine (5hmC) along with GC sites in chromatin, which are then mapped using tag-selective base-resolution TOP-seq sequencing. Our in-depth validation of the approach revealed its sensitivity and informativity in evaluating chromatin accessibility and DNA modification interactions that drive transcriptional regulation. We employed the technology in a study of chromatin and DNA demethylation dynamics during in vitro neuronal differentiation. The study highlighted the involvement of gene body 5hmC in modulating an extensive decoupling between promoter accessibility and transcription. The importance of 5hmC in chromatin remodeling was further demonstrated by the observed resistance of the developmentally acquired open loci to the global 5hmC erasure in neuronal progenitors.

Keywords:  5hmC; DNA hydroxymethylation; DNA modification; TOP-seq; chromatin accessibility; covalent DNA labeling; methyltransferases; synthetic AdoMet cofactors; uCG

DOI:  https://doi.org/10.1016/j.chembiol.2023.12.003
Mol Cell. 2023 Dec 20. pii: S1097-2765(23)00980-2. [Epub ahead of print]

hRpn13 shapes the proteome and transcriptome through epigenetic factors HDAC8, PADI4, and transcription factor NF-κB p50.

Vasty Osei-Amponsa, Monika Chandravanshi, Xiuxiu Lu, Valentin Magidson, Sudipto Das, Thorkell Andresson, Marzena Dyba, Venkata R Sabbasani, Rolf E Swenson, Caroline Fromont, Biraj Shrestha, Yongmei Zhao, Michelle E Clapp, Raj Chari, Kylie J Walters.

  The anti-cancer target hRpn13 is a proteasome substrate receptor. However, hRpn13-targeting molecules do not impair its interaction with proteasomes or ubiquitin, suggesting other critical cellular activities. We find that hRpn13 depletion causes correlated proteomic and transcriptomic changes, with pronounced effects in myeloma cells for cytoskeletal and immune response proteins and bone-marrow-specific arginine deiminase PADI4. Moreover, a PROTAC against hRpn13 co-depletes PADI4, histone deacetylase HDAC8, and DNA methyltransferase MGMT. PADI4 binds and citrullinates hRpn13 and proteasomes, and proteasomes from PADI4-inhibited myeloma cells exhibit reduced peptidase activity. When off proteasomes, hRpn13 can bind HDAC8, and this interaction inhibits HDAC8 activity. Further linking hRpn13 to transcription, its loss reduces nuclear factor κB (NF-κB) transcription factor p50, which proteasomes generate by cleaving its precursor protein. NF-κB inhibition depletes hRpn13 interactors PADI4 and HDAC8. Altogether, we find that hRpn13 acts dually in protein degradation and expression and that proteasome constituency and, in turn, regulation varies by cell type.

Keywords:  HDAC8; MGMT; MYH10; NF-κB; PADI4; citrulline; cytoskeleton; gene regulation; hRpn13; proteasome

DOI:  https://doi.org/10.1016/j.molcel.2023.11.035
Dev Cell. 2023 Dec 18. pii: S1534-5807(23)00650-0. [Epub ahead of print]

YAP and TAZ couple osteoblast precursor mobilization to angiogenesis and mechanoregulation in murine bone development.

Joseph M Collins, Annemarie Lang, Cristian Parisi, Yasaman Moharrer, Madhura P Nijsure, Jong Hyun Thomas Kim, Saima Ahmed, Gregory L Szeto, Ling Qin, Riccardo Gottardi, Nathaniel A Dyment, Niamh C Nowlan, Joel D Boerckel.

  Fetal bone development occurs through the conversion of avascular cartilage to vascularized bone at the growth plate. This requires coordinated mobilization of osteoblast precursors with blood vessels. In adult bone, vessel-adjacent osteoblast precursors are maintained by mechanical stimuli; however, the mechanisms by which these cells mobilize and respond to mechanical cues during embryonic development are unknown. Here, we show that the mechanoresponsive transcriptional regulators Yes-associated protein (YAP) and transcriptional co-activator with PDZ-binding motif (TAZ) spatially couple osteoblast precursor mobilization to angiogenesis, regulate vascular morphogenesis to control cartilage remodeling, and mediate mechanoregulation of embryonic murine osteogenesis. Mechanistically, YAP and TAZ regulate a subset of osteoblast-lineage cells, identified by single-cell RNA sequencing as vessel-associated osteoblast precursors, which regulate transcriptional programs that direct blood vessel invasion through collagen-integrin interactions and Cxcl12. Functionally, in 3D human cell co-culture, CXCL12 treatment rescues angiogenesis impaired by stromal cell YAP/TAZ depletion. Together, these data establish functions of the vessel-associated osteoblast precursors in bone development.

Keywords:  TAZ; YAP; angiogenesis; bone; development; growth plate; mechanobiology

DOI:  https://doi.org/10.1016/j.devcel.2023.11.029
Nucleic Acids Res. 2023 Dec 24. pii: gkad1203. [Epub ahead of print]

PRC1 directs PRC2-H3K27me3 deposition to shield adult spermatogonial stem cells from differentiation.

Mengwen Hu, Yu-Han Yeh, So Maezawa, Toshinori Nakagawa, Shosei Yoshida, Satoshi H Namekawa.

Spermatogonial stem cells functionality reside in the slow-cycling and heterogeneous undifferentiated spermatogonia cell population. This pool of cells supports lifelong fertility in adult males by balancing self-renewal and differentiation to produce haploid gametes. However, the molecular mechanisms underpinning long-term stemness of undifferentiated spermatogonia during adulthood remain unclear. Here, we discover that an epigenetic regulator, Polycomb repressive complex 1 (PRC1), shields adult undifferentiated spermatogonia from differentiation, maintains slow cycling, and directs commitment to differentiation during steady-state spermatogenesis in adults. We show that PRC2-mediated H3K27me3 is an epigenetic hallmark of adult undifferentiated spermatogonia. Indeed, spermatogonial differentiation is accompanied by a global loss of H3K27me3. Disruption of PRC1 impairs global H3K27me3 deposition, leading to precocious spermatogonial differentiation. Therefore, PRC1 directs PRC2-H3K27me3 deposition to maintain the self-renewing state of undifferentiated spermatogonia. Importantly, in contrast to its role in other tissue stem cells, PRC1 negatively regulates the cell cycle to maintain slow cycling of undifferentiated spermatogonia. Our findings have implications for how epigenetic regulators can be tuned to regulate the stem cell potential, cell cycle and differentiation to ensure lifelong fertility in adult males.

DOI: https://doi.org/10.1093/nar/gkad1203
Am J Hum Genet. 2023 Dec 14. pii: S0002-9297(23)00428-7. [Epub ahead of print]

A recurrent de novo MAX p.Arg60Gln variant causes a syndromic overgrowth disorder through differential expression of c-Myc target genes.

Erica L Harris, Vincent Roy, Martin Montagne, Ailsa M S Rose, Helen Livesey, Margot R F Reijnders, Emma Hobson, Francis H Sansbury, Marjolein H Willemsen, Rolph Pfundt, Daniel Warren, Vernon Long, Ian M Carr, Han G Brunner, Eamonn G Sheridan, Helen V Firth, Pierre Lavigne, James A Poulter.

  Cyclin D2 (CCND2) stabilization underpins a range of macrocephaly-associated disorders through mutation of CCND2 or activating mutations in upstream genes encoding PI3K-AKT pathway components. Here, we describe three individuals with overlapping macrocephaly-associated phenotypes who carry the same recurrent de novo c.179G>A (p.Arg60Gln) variant in Myc-associated factor X (MAX). The mutation, located in the b-HLH-LZ domain, causes increased intracellular CCND2 through increased transcription but it does not cause stabilization of CCND2. We show that the purified b-HLH-LZ domain of MAXArg60Gln (Max∗Arg60Gln) binds its target E-box sequence with a lower apparent affinity. This leads to a more efficient heterodimerization with c-Myc resulting in an increase in transcriptional activity of c-Myc in individuals carrying this mutation. The recent development of Omomyc-CPP, a cell-penetrating b-HLH-LZ-domain c-Myc inhibitor, provides a possible therapeutic option for MAXArg60Gln individuals, and others carrying similar germline mutations resulting in dysregulated transcriptional c-Myc activity.

Keywords:  CCND2; MAX; MYC; b-HLH-LZ; macrocephaly; polydactyly

DOI:  https://doi.org/10.1016/j.ajhg.2023.11.010
Int J Biol Macromol. 2023 Dec 26. pii: S0141-8130(23)05940-8. [Epub ahead of print] 129041

The chromatin remodeler Ino80 regulates yeast stress tolerance and cell metabolism through modulating nitrogen catabolite repression.

Bing Yuan, Wei-Bin Wang, Xue-Qing Wang, Chen-Guang Liu, Tomohisa Hasunuma, Akihiko Kondo, Xin-Qing Zhao.

  Chromatin remodelers are important in maintaining the dynamic chromatin state in eukaryotic cells, which is essential for epigenetic regulation. Among the remodelers, the multi-subunits complex INO80 plays crucial roles in transcriptional regulation. However, current knowledge of chromatin regulation of the core subunit Ino80 on stress adaptation remains mysterious. Here we revealed that overexpressing the chromatin remodeler Ino80 elevated tolerance to multiple stresses in budding yeast Saccharomyces cerevisiae. Analyses of differential chromatin accessibility and global transcription levels revealed an enrichment of genes involved in NCR (nitrogen catabolite repression) under acetic acid stress. We demonstrated that Ino80 overexpression reduced the histone H3 occupancy in the promoter region of the glutamate dehydrogenase gene GDH2 and the allantoinase gene DAL1. Consistently, the decreased occupancy of nucleosome was revealed in the Ino80-inactivation mutant. Further analyses showed that Ino80 was recruited to the specific DNA locus in the promoter region of GDH2. Consistently, Ino80 overexpression facilitated the utilization of non-preferred nitrogen source to enhance ethanol yield under prolonged acetic acid stress. These results demonstrate that Ino80 plays a crucial role in coordinating carbon and nitrogen metabolism during stress adaptation.

Keywords:  Budding yeast S. cerevisiae; Chromatin regulation; Chromatin remodeler Ino80; Nitrogen catabolite repression (NCR); Stress adaptation; Transcription regulation

DOI:  https://doi.org/10.1016/j.ijbiomac.2023.129041
Commun Biol. 2023 Dec 28. 6(1): 1290

RENGE infers gene regulatory networks using time-series single-cell RNA-seq data with CRISPR perturbations.

Masato Ishikawa, Seiichi Sugino, Yoshie Masuda, Yusuke Tarumoto, Yusuke Seto, Nobuko Taniyama, Fumi Wagai, Yuhei Yamauchi, Yasuhiro Kojima, Hisanori Kiryu, Kosuke Yusa, Mototsugu Eiraku, Atsushi Mochizuki.

Single-cell RNA-seq analysis coupled with CRISPR-based perturbation has enabled the inference of gene regulatory networks with causal relationships. However, a snapshot of single-cell CRISPR data may not lead to an accurate inference, since a gene knockout can influence multi-layered downstream over time. Here, we developed RENGE, a computational method that infers gene regulatory networks using a time-series single-cell CRISPR dataset. RENGE models the propagation process of the effects elicited by a gene knockout on its regulatory network. It can distinguish between direct and indirect regulations, which allows for the inference of regulations by genes that are not knocked out. RENGE therefore outperforms current methods in the accuracy of inferring gene regulatory networks. When used on a dataset we derived from human-induced pluripotent stem cells, RENGE yielded a network consistent with multiple databases and literature. Accurate inference of gene regulatory networks by RENGE would enable the identification of key factors for various biological systems.

DOI: https://doi.org/10.1038/s42003-023-05594-4