Sriharsa Pradhan's research while affiliated with New England Biolabs and other places
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Publications (168)
Nucleosomes are non-uniformly distributed across eukaryotic genomes, with stretches of ‘open’ chromatin strongly associated with transcriptionally active promoters and enhancers. Understanding chromatin accessibility patterns in normal tissue and how they are altered in pathologies can provide critical insights to development and disease. With the...
DNA methylation (DNAme) is an epigenetic mark that includes the modification of cytosine resides (5mC) within CpG islands. In addition to well characterized roles regulating gene expression, imprinting and silencing parasitic DNA elements, the misregulation of DNAme is implicated in multiple diseases. Evidence is emerging that DNAme is not an indep...
Nucleosomes are non-uniformly distributed across eukarytic genomes, with stretches of ‘open’ chromatin strongly associated with transcriptionally active promoters and enhancers. Understanding chromatin accessibility patterns in normal tissue and how they are altered in pathologies can provide critical insights to development and disease. With the a...
While studying myoblast methylomes and transcriptomes, we found that CDH15 had a remarkable preference for expression in both myoblasts and cerebellum. To understand how widespread such a relationship was and its epigenetic and biological correlates, we systematically looked for genes with similar transcription profiles and analyzed their DNA methy...
Very disparate types of cell populations exhibit similar transcription specificity for certain genes. We identified 20 genes that were expressed preferentially in myoblasts and cerebellum (Myob/Cbl genes) and examined their cell/tissue-specific epigenetics using a combined approach of comparing DNA methylation, chromatin accessibility, and RNA expr...
Chromatin remodeling is mediated by ATP-dependent enzymes that play key roles regulating gene expression and genome replication/repair. Aberrant nucleosome organization from dysregulated chromatin remodeling can severely alter chromatin accessibility and disrupt these important processes, thereby driving various cancers. Remarkably, nearly 20% of a...
A novel genome-wide accessible chromatin visualization, quantitation, and sequencing method is described, which allows in situ fluorescence visualization and sequencing of the accessible chromatin in the mammalian cell. The cells are fixed by formaldehyde crosslinking, and processed using a modified nick translation method, where a nicking enzyme n...
Genome-wide accessible chromatin sequencing and identification has enabled deciphering the epigenetic information encoded in chromatin, revealing accessible promoters, enhancers, nucleosome positioning, transcription factor occupancy, and other chromosomal protein binding. The starting biological materials are often fixed using formaldehyde crossli...
Chromatin accessibility has been an immensely powerful metric for identifying and understanding regulatory elements in the genome. Many important regulatory elements, such as enhancers and transcriptional start sites, are characterized by "open" or nucleosome-free regions. Understanding the areas of the genome that are not considered open chromatin...
The relationships between chromosomal compartmentalization, chromatin state and function are poorly understood. Here by profiling long-range contact frequencies in HCT116 colon cancer cells, we distinguish three silent chromatin states, comprising two types of heterochromatin and a state enriched for H3K9me2 and H2A.Z that exhibits neutral three-di...
TBX15, which encodes a differentiation-related transcription factor, displays promoter-adjacent DNA hypermethylation in myoblasts and skeletal muscle (psoas) that is absent from non-expressing cells in other lineages. By whole-genome bisulfite sequencing (WGBS) and enzymatic methyl-seq (EM-seq), these hypermethylated regions were found to border bo...
Compositions and Methods for Detecting Molecular Targets on Chromosomal DNA
Jun 8, 2021 - New England Biolabs, Inc.
Compositions, methods and kits are provided for identifying the presence and location of a target in chromosomal DNA. A nicking endonuclease fused to a binding domain that binds to a constant region of an antibody (NEFP) is provided t...
In mammalian cells, SET8 mediated Histone H4 Lys 20 monomethylation (H4K20me1) has been implicated in regulating mitotic condensation, DNA replication, DNA damage response, and gene expression. Here we show SET8, the only known enzyme for H4K20me1 is post-translationally poly ADP-ribosylated by PARP1 on lysine residues. PARP1 interacts with SET8 in...
TBX15, which encodes a differentiation-related transcription factor, displays promoter-adjacent DNA hypermethylation in myoblasts and skeletal muscle (psoas) that is absent from non-expressing cells in other lineages. By whole-genome bisulfite sequencing (WGBS) and en-zymatic methyl-seq (EM-seq), these hypermethylated regions were found to border b...
Polyglutamylation is a posttranslational modification (PTM) that adds several glutamates on glutamate residues in the form of conjugated peptide chains by a family of enzymes known as polyglutamylases. Polyglutamylation is well documented in microtubules. Polyglutamylated microtubules consist of different α- and β-tubulin subunits with varied numbe...
Background
Accessible chromatin landscape allows binding of transcription factors, and remodeling of promoter and enhancer elements during development. Chromatin accessibility along with integrated multiomics approaches have been used for determining molecular subtypes of cancer in patient samples.
Results
One-pot Universal NicE-seq (One-pot UniNi...
In mammalian cells, SET8 mediated Histone H4 Lys 20 monomethylation (H4K20me1) has been implicated in regulating mitotic condensation, DNA replication, DNA damage response, and gene expression. Here we show SET8, the only known enzyme for H4K20me1 is post-translationally poly ADP-ribosylated by PARP1 on lysine residues. PARP1 interacts with SET8 in...
Two dominant processes organizing chromosomes are loop extrusion and the compartmental segregation of active and inactive chromatin. The molecular players involved in loop extrusion during interphase, cohesin and CTCF, have been extensively studied and experimentally validated. However, neither the molecular determinants nor the functional roles of...
Two dominant processes organizing chromosomes are loop extrusion and the compartmental segregation of active and inactive chromatin. The molecular players involved in loop extrusion during interphase, cohesin and CTCF, have been extensively studied and experimentally validated. However, neither the molecular determinants nor the functional roles of...
Bisulfite sequencing detects 5mC and 5hmC at single-base resolution. However, bisulfite treatment damages DNA, which results in fragmentation, DNA loss, and biased sequencing data. To overcome these problems, enzymatic methyl-seq (EM-seq) was developed. This method detects 5mC and 5hmC using two sets of enzymatic reactions. In the first reaction, T...
Aba-Seq (DNA modification-dependent restriction endonuclease AbaSI coupled with sequencing) provides a cost-effective and non-chemical based method for the high-resolution mapping of genomic 5-hydroxymethylcytosine (5hmC). The high specificity of the AbaSI enzyme allows sensitive detection of 5hmC in the genome. Here, we describe the Aba-Seq techni...
The predominant methodology for DNA methylation analysis relies on the chemical deamination by sodium bisulfite of unmodified cytosine to uracil to permit the differential readout of methylated cytosines. Bisulfite treatment damages the DNA, leading to fragmentation and loss of long-range methylation information. To overcome this limitation of bisu...
Accessible chromatin plays a central role in gene expression and chromatin architecture. Current accessible chromatin approaches depend on limited digestion/cutting and pasting adaptors at the accessible DNA, thus requiring additional materials and time for optimization. Universal NicE-seq (UniNicE-seq) is an improved accessible chromatin profiling...
Chromatin accessibility is a predictor of gene expression, cell division, and cell type specificity. NicE-viewSeq (Nicking Enzyme assisted viewing and Sequencing) allows accessible chromatin visualization and sequencing with overall lower mitochondrial DNA and duplicated sequences interference relative to ATAC-see. Using NicE-viewSeq, we interrogat...
Following fertilization in mammals, the gametes are reprogrammed to create a totipotent zygote, a process that involves de novo establishment of chromatin domains. A major feature occurring during preimplantation development is the dramatic remodelling of constitutive heterochromatin, although the functional relevance of this is unknown. Here, we s...
Tubulin polyglutamylation is a polymeric modification that extends from the carboxyl-terminus of tubulins. Molecular description of amino acids and their branching polyglutamyls is a hallmark of tubulin in microtubules. There are different chemical approaches for detecting these polymeric structures, mostly reported prior to development of nESI pep...
Accessible chromatin plays a central role in gene expression and chromatin architecture. Current accessible chromatin approaches depend on limited digestion/cutting and pasting adaptors at the accessible DNA, thus requiring additional materials and time for optimization. Universal NicE-seq (UniNicE-seq) is an improved accessible chromatin profiling...
Chromatin accessibility is a predictor of gene expression, cell division and cell type specificity. NicE-viewSeq (Nicking Enzyme assisted viewing and Sequencing) allows accessible chromatin visualization and sequencing with overall lower mitochondrial DNA and duplicated sequences interference relative to ATAC-see. Using NicE-viewSeq, we interrogate...
Microtubules are cytoskeletal structures critical for mitosis, cell motility, and protein and organelle transport, and are a validated target for anticancer drugs. However, how tubulins are regulated and recruited to support these distinct cellular processes is incompletely understood. Post-translational modifications of tubulins are proposed to re...
Bisulfite sequencing is widely used to detect 5mC and 5hmC at single base resolution. It is the most accepted method for detecting these cytosine modifications, but it does have significant drawbacks. DNA is frequently damaged resulting in fragmentation, loss of DNA and inherent biases introduced to sequencing data. To overcome this, we developed a...
The predominant methodology for DNA methylation analysis relies on the chemical deamination by sodium bisulfite of unmodified cytosine to uracil to permit the differential readout of methylated cytosines. Bisulfite treatment damages the DNA leading to fragmentation and loss of long-range methylation information. To overcome this limitation of bisul...
In metazoan cell nuclei, heterochromatin constitutes large chromatin domains that are in close contact with the nuclear lamina. These heterochromatin/lamina-associated domains (LADs) domains are difficult to profile and warrants a simpler and direct method. Here we report a new method, Protect-seq, aimed at identifying regions of heterochromatin vi...
Microtubules are critical for mitosis, cell motility, and protein and organelle transport, and are a validated target for anticancer drugs. However, tubulin regulation and recruitment in these cellular processes is less understood. Post-translational modifications of tubulin are proposed to regulate microtubule functions and dynamics. Although many...
DNA methylation is an essential epigenetic mark in mammals. The proper distribution of this mark depends on accurate deposition and maintenance mechanisms, and underpins its functional role. This, in turn, depends on the precise recruitment and activation of de novo and maintenance DNA methyltransferases (DNMTs). In this review, we discuss mechanis...
Insects provide an accessible system to study the contribution of DNA methylation to complex epigenetic phenotypes created to regulate gene expression, chromatin states, imprinting and dosage compensation. The members of genus Drosophila have been used as a model system to study aspects of biology like development, behaviour and genetics. Despite t...
Difference in the levels of 5mC in head tissue and the whole body of adult male and female of Drosophila melanogaster
* and ++ indicate significance of comparisons (α = 0.05, p = 0.0013, Kruskal–Wallis test). All error bars represent SEM.
The neighbour joining tree
The original NJ tree with the scale for the twelve members of genus Drosophila.
Divergence time and DNA methylation of genus Drosophila
The divergence time and levels of 5mC of the twelve members of genus Drosophila.
Ubiquitin-like containing PHD Ring Finger 1 (UHRF1) is a multi-domain protein with a methyl-DNA binding SRA (SET and RING-associated) domain, required for maintenance DNA methylation mediated by DNMT1. Primarily expressed in proliferating cells, UHRF1 is a cell-cycle regulated protein that is required for S phase entry. Furthermore, UHRF1 participa...
DNA (cytosine-5) methyltransferase 1 (DNMT1) is essential for mammalian development and maintenance of DNA methylation following DNA replication in cells. The DNA methylation process generates S-adenosyl-L-homocysteine, a strong inhibitor of DNMT1. Here we report that S-adenosylhomocysteine hydrolase (SAHH/AHCY), the only mammalian enzyme capable o...
DNA methylation can affect tissue-specific gene transcription in ways that are difficult to discern from studies focused on genome-wide analyses of differentially methylated regions (DMRs). To elucidate the variety of associations between differentiation-related DNA hypermethylation and transcription, we used available epigenomic and transcriptomic...
Gametes are highly specialized cells that can give rise to the next generation through their ability to generate a totipotent zygote. In mice, germ cells are first specified in the developing embryo around embryonic day (E) 6.25 as primordial germ cells (PGCs). Following subsequent migration into the developing gonad, PGCs undergo a wave of extensi...
Tissue-specific gene transcription can be affected by DNA methylation in ways that are difficult to discern from studies focused on genome-wide analyses of differentially methylated regions (DMRs). We studied 95 genes in detail using available epigenetic and transcription databases to detect and elucidate less obvious associations between developme...
In mammals, faithful inheritance of genomic methylation patterns ensures proper gene regulation and cell behaviour, impacting normal development and fertility. Following establishment, genomic methylation patterns are transmitted through S-phase by the maintenance methyltransferase Dnmt1. Using a protein interaction screen, we identify Microprocess...
In mammals, faithful inheritance of genomic methylation patterns ensures proper gene regulation and cell behaviour, impacting normal development and fertility. Following establishment, genomic methylation patterns are transmitted through S-phase by the maintenance methyltransferase Dnmt1. Using a protein interaction screen, we identify Microprocess...
Open chromatin profiling integrates information across diverse regulatory elements to reveal the transcriptionally active genome. Tn5 transposase and DNase I sequencing-based methods prefer native or high cell numbers. Here, we describe NicE-seq (nicking enzyme assisted sequencing) for high-resolution open chromatin profiling on both native and for...
Differentially methylated or hydroxymethylated regions (DMRs) in mammalian DNA are often associated with tissue-specific gene expression but the functional relationships are still being unraveled. To elucidate these relationships, we studied 16 human genes containing myogenic DMRs by analyzing profiles of their epigenetics and transcription and qua...
The combination of DNA bisulfite treatment with high-throughput sequencing technologies has enabled investigation of genome-wide DNA methylation at near base pair level resolution, far beyond that of the kilobase-long canonical CpG islands that initially revealed the biological relevance of this covalent DNA modification. The latest high-resolution...
The transcription factor LSF is highly expressed in hepatocellular carcinoma (HCC) and promotes oncogenesis. Factor quinolinone inhibitor 1 (FQI1), inhibits LSF DNA-binding activity and exerts anti-proliferative activity. Here, we show that LSF binds directly to the maintenance DNA (cytosine-5) methyltransferase 1 (DNMT1) and its accessory protein...
Background:
Induced pluripotent mesenchymal stem cells (iPMSCs) are novel candidates for drug screening, regenerative medicine, and cell therapy. However, introduction of transcription factor encoding genes for induced pluripotent stem cell (iPSC) generation which could be used to generate mesenchymal stem cells is accompanied by the risk of inser...
"Microbiome" is used to describe the communities of microorganisms and their genes in a particular environment, including communities in association with a eukaryotic host or part of a host. One challenge in microbiome analysis concerns the presence of host DNA in samples. Removal of host DNA before sequencing results in greater sequence depth of t...
Over half of a century ago methylated cytosine in the genome was discovered. Since then progress has been made on the development of tools to study methylated cytosine. The first of these technologies utilized paper chromatography to measure genomic DNA methylation. Soon afterward researchers discovered that restriction enzymes and antibodies could...
Mammalian DNA (cytosine-5) methyltransferase 1 (DNMT1) is essential for maintenance methylation. Phosphorylation of Ser143
(pSer143) stabilizes DNMT1 during DNA replication. Here, we show 14-3-3 is a reader protein of DNMT1pSer143. In mammalian
cells 14-3-3 colocalizes and binds DNMT1pSer143 post-DNA replication. The level of DNMT1pSer143 increased...
Myogenic regulatory factor (MRF) genes, MYOD1, MYOG, MYF6 and MYF5, are critical for the skeletal muscle lineage. Here, we used various epigenome profiles from human myoblasts (Mb), myotubes (Mt), muscle, and diverse nonmuscle samples to elucidate the involvement of multigene neighborhoods in the regulation of MRF genes. We found more far-distal en...
Methods and compositions are described for detecting hydroxymethylated nucleotides (hmNs) in a polynucleotide preparation with a view to mapping the location of hmNs in a genome, quantifying the occurrence of hmNs at selected loci and correlating the occurrence of hmNs with gene expression and phenotypic traits. Embodiments describe the use of modi...
Mammalian cells contain copious amounts of RNA including both coding and noncoding RNA (ncRNA). Generally the ncRNAs function to regulate gene expression at the transcriptional and post-transcriptional level. Among ncRNA, the long ncRNA and small ncRNA can affect histone modification, DNA methylation targeting and gene silencing. Here we show that...
Mammalian DNA methyltransferases (DNMTs) establish and maintain DNA methylation patterns at specific regions of the nuclear DNA, resulting in modulation of gene expression. Amongst the DNMTs, the maintenance DNA methyltransferase, DNMT1 participates in faithful copying of parental DNA methylation patterns to daughter strands. In the past decade, it...
Recent discoveries have implicated the microbiome of plants and animals as playing a role in health, disease states, and even animal behavior. The majority of microbiome DNA studies to date have employed 16S analysis, but these provide very little information regarding function. In contrast, sequencing of the total DNA of a microbiome sample provid...
Transcriptional gene silencing is mediated by various epigenetic modifications including DNA methylation, histone modifications and recruitment of binding proteins that reads the methyl and other modification marks. The order in which these modifications occur followed by repressor protein recruitment remains contentious. Here, using purified prote...
The mammalian genome is packaged into chromatin that is further compacted into three-dimensional structures consisting of distinct functional domains. The higher order structure of chromatin is in part dictated by enzymatic DNA methylation and histone modifications to establish epigenetic layers controlling gene expression and cellular functions, w...
Notch intercellular signaling is critical for diverse developmental pathways and for homeostasis in various stem cells and progenitor cells. Because Notch gene products need to be precisely regulated spatially and temporally, epigenetics is likely to help control expression of Notch signaling genes. Reduced representation bisulfite sequencing (RRBS...
Inheritance of DNA cytosine methylation pattern during successive cell division is mediated by maintenance DNA (cytosine-5)
methyltransferase 1 (DNMT1). Lysine 142 of DNMT1 is methylated by the SET domain containing lysine methyltransferase 7 (SET7),
leading to its degradation by proteasome. Here we show that PHD finger protein 20-like 1 (PHF20L1)...
Oxidative stress induces genome-wide remodeling of the chromatin structure. In this study, we identify Methyl-CpG Binding Protein 4 (MBD4), a multifunctional enzyme involved in DNA demethylation, base excision repair, and gene expression regulation, as an essential factor in response to oxidative stress. We provide evidence that MBD4 is upregulated...
5-(hydroxymethyl)cytosine (5-hmC) is a newly identified oxidative product of 5-methylcytosine (5-mC) in the mammalian genome, and is believed to be an important epigenetic marker influencing a variety of biological processes. In addition to its relatively low abundance, the fluctuation of 5-hmC levels over time during cell development poses a formi...
DNA samples derived from vertebrate skin, bodily cavities and body fluids contain both host and microbial DNA; the latter
often present as a minor component. Consequently, DNA sequencing of a microbiome sample frequently yields reads
originating from the microbe(s) of interest, but with a vast excess of host genome-derived reads. In this study, we...
DNA methylation was first described almost a century ago; however, the rules governing its establishment and maintenance remain elusive. Here we present data demonstrating that active transcription regulates levels of genomic methylation. We identify a novel RNA arising from the CEBPA gene locus that is critical in regulating the local DNA methylat...
Tight regulation of homeobox genes is essential for vertebrate development. In a study of genome-wide differential methylation, we recently found that homeobox genes, including those in the HOX gene clusters, were highly overrepresented among the genes with hypermethylation in the skeletal muscle lineage. Methylation was analyzed by reduced represe...
A novel scintillation proximity high throughput assay (SPA) to identify inhibitors of DNA methyltransferases was developed and used to screen over 180,000 compounds. The majority of the validated hits shared a quinone core and several were found to generate the reactive oxygen species, H2O2. Inhibition of the production of H2O2 by the addition of c...
GTC's annual drug discovery summit was composed of four parallel tracks: "Orphan Drugs, Research and Commercialization", "Drug Design and Medicinal Chemistry", "Imaging in Drug Discovery and Development" and "Epigenetics in Drug Discovery". The GTC 3rd Epigenetics in Drug Discovery meeting focused on epigenetic mechanisms, biomarkers and diagnostic...
We describe the use of a unique DNA-modification-dependent restriction endonuclease AbaSI coupled with sequencing (Aba-seq) to map high-resolution hydroxymethylome of mouse E14 embryonic stem cells. The specificity of AbaSI enables sensitive detection of 5-hydroxymethylcytosine (5hmC) at low-occupancy regions. Bioinformatic analysis suggests 5hmCs...
5-Hydroxymethylcytosine (5hmC) is an oxidative product of 5-methylcytosine (5mC), catalyzed by the ten eleven translocation (TET) family of enzymes. Although 5hmC was discovered several decades ago, it was only after its recent identification in murine brain and stem cell DNA that it has become a major focus of epigenomic research. Part of the reas...
DNA methylation and histone modification exert epigenetic control over gene expression. CHG methylation by CHROMOMETHYLASE3 (CMT3) depends on histone H3K9 dimethylation (H3K9me2), but the mechanism underlying this relationship is poorly understood. Here, we report multiple lines of evidence that CMT3 interacts with H3K9me2-containing nucleosomes. C...
Hepatocellular carcinoma (HCC) is the fifth most common cancer worldwide. Despite the prevalence of HCC, there is no effective, systemic treatment. The transcription factor LSF is a promising protein target for chemotherapy; it is highly expressed in HCC patient samples and cell lines, and promotes oncogenesis in rodent xenograft models of HCC. Her...
Citations
... Expansion of clones with specific mutations, such as in PPM1D and SRCAP, appears to be associated with various stressors, including https://doi.org/10.1038/s43587-024-00589-0 cytotoxic agents 68,128,129 . Although cancer therapies drive a portion of such instances of CH, the presence of such mutations in the healthy population suggests other as yet unknown 'stress' factors that can promote clone expansion. ...
... Despite the initial characterization of SRCAP for its ability to recruit transcriptional coactivators [11][12][13] , its role in gene regulation has become increasingly viewed through the lens of its H2A.Z deposition activity. This conflates the interpretation of SRCAP and H2A.Z functions in gene regulation 25,87 . ...
... Compared to traditional methods such as DNase-seq [12] and FAIRE-seq [13], ATAC-seq has several advantages. Firstly, ATAC-seq eliminates the need to precisely control the amount of enzyme required for DNase-seq and the need to determine the duration of formaldehyde crosslinking for FAIRE-seq [14]. Second, ATAC-seq requires only a small sample size of 500 to 50,000 cells for library preparation and takes only three hours, as opposed to the two techniques that require two to three days, making it much simpler and faster [15]. ...
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... scatter.size( by='Population', map= (1,8,10), norm=AsinhNorm() ) scatter.color( by='Population', map='magma', norm=LogNorm(), order='reverse' ) A connected scatterplot of the market capitalization over the last five years of top ten S&P500 company according to YCharts. Five linked embedding plots of epigenomic data [4] that are connected to the HiGlass genome browser [5]. ...
... We first identified 20 human genes that are preferentially expressed in myoblasts and cerebellum (Myob/Cbl genes). We then investigated transcription and epigenetics relationships for Myob/Cbl genes using our newly available whole-genome bisulfite sequencing (WGBS) or enzymatic methylseq (EM-seq) myoblast methylomes [17] and a recent WGBS profile for cerebellum neurons from Loyfer et al. [18] as well as chromatin epigenomics databases [19]. Unlike RRBS, which covers only up to 5% of the CpGs [20], WGBS and EM-seq allow the quantitation of methylation at essentially all the CpGs in the genome. ...
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... Interestingly, in the absence of PARP-1, neither PR-SET7 RNA nor protein levels were affected (Figure 3-figure supplements 2 and 3), indicating that PARP-1 is not directly implicated in the regulation of pr-set7. This finding contrasts with recent evidence demonstrating PARP1-induced degradation of PR-SET7/SET8 in human cells (Estève et al., 2022). Subsequently, we integrated PARP-1 and H4K20me1 ChIP-seq data in third-instar larvae and RNA-seq of pr-set7 20 and parp-1 C03256 mutant third-instar larvae. ...
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... Lower methylation patterns in MSCs were also detected for the VGLL4 gene, a co-transcriptional regulator of stem cell survival while fostering the colony formation capacity via interaction with the Rho/Rock pathway (86). In contrast, higher methylation of the T-Box transcription factor 15 in MSCs together with the generally more repressive role of T-box domain transcription factors could resemble a fibroblast-specific phenomenon as lower methylation values of the TBX15 gene might account for increased transcriptionally active TBX15 preventing fibroblasts from a myoblast phenotype (87,88). ...
... Diglutamylation[+258]: Diglutamylation of glutamic acid was detected in PSMs of collagen XI (α2), a protein that regulates collagen fibrillogenesis [32]. Although the polyglutamylation of glutamate residues is a biological PTM well characterized in tubulins [33], it is unclear whether it can occur in collagen. Thus, while a substantial mass shift consistent with the addition of two glutamates was isolated to glutamic acid residues multiple times in multiple PSMs of collagen XI, its interpretation as a preserved biological PTM is tentative. ...
... NicE-seq is a recent approach (Figure 2A,B) that excels at NDR profiling from heavily fixed cells, including FFPE [50,51,79,80]. In contrast to nuclease or Tn5 transposase doublestrand cleavage (as above), Chlorella virus Nt.CviPII (63 kDa) is a nicking endonuclease that cuts only one strand of dsDNA at CCD sites (D = A/G/T), which occur by chance every ~21 bases [49]. ...
... Improvements in Hi-C resolution have recently allowed to shed new light on nucleus 3D organisation and its link to chromatin marks, notably suggesting existence of intermediate sub-compartments within A and B compartments (that we will call here I for "intermediate") [24,28,17,21,3]. Interestingly, these studies point towards a strong enrichment of facultative heterochromatin in the I compartments. ...
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