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Article: A Rare Case of Recurrent and Life-Threatening Breus' Mole.

Tripathi, Vartika / Agrawal, Smriti / Shukla, Manu / Pandey, Amita

Journal of obstetrics and gynaecology of India

2021 Volume 71, Issue 2, Page(s) 210–212

Language	English
Publishing date	2021-01-28
Publishing country	India
Document type	Journal Article
ZDB-ID	410688-x
ISSN	0971-9202 ; 0022-3190
ISSN	0971-9202 ; 0022-3190
DOI	10.1007/s13224-020-01417-2
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Article ; Online: DISCRN: A Distributed Storytelling Framework for Intelligence Analysis.

Shukla, Manu / Dos Santos, Raimundo / Chen, Feng / Lu, Chang-Tien

Big data

2017 Volume 5, Issue 3, Page(s) 225–245

Abstract: Storytelling connects entities (people, organizations) using their observed relationships to establish meaningful storylines. This can be extended to spatiotemporal storytelling that incorporates locations, time, and graph computations to enhance ... ...

Abstract	Storytelling connects entities (people, organizations) using their observed relationships to establish meaningful storylines. This can be extended to spatiotemporal storytelling that incorporates locations, time, and graph computations to enhance coherence and meaning. But when performed sequentially these computations become a bottleneck because the massive number of entities make space and time complexity untenable. This article presents DISCRN, or distributed spatiotemporal ConceptSearch-based storytelling, a distributed framework for performing spatiotemporal storytelling. The framework extracts entities from microblogs and event data, and links these entities using a novel ConceptSearch to derive storylines in a distributed fashion utilizing key-value pair paradigm. Performing these operations at scale allows deeper and broader analysis of storylines. The novel parallelization techniques speed up the generation and filtering of storylines on massive datasets. Experiments with microblog posts such as Twitter data and Global Database of Events, Language, and Tone events show the efficiency of the techniques in DISCRN.
MeSH term(s)	Algorithms ; Female ; Humans ; Intelligence ; Male ; Narration
Language	English
Publishing date	2017-09-21
Publishing country	United States
Document type	Journal Article
ISSN	2167-647X
ISSN (online)	2167-647X
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Article ; Online: Epigenetic gene silencing by heterochromatin primes fungal resistance.

Torres-Garcia, Sito / Yaseen, Imtiyaz / Shukla, Manu / Audergon, Pauline N C B / White, Sharon A / Pidoux, Alison L / Allshire, Robin C

Nature

2020 Volume 585, Issue 7825, Page(s) 453–458

Abstract: Heterochromatin that depends on histone H3 lysine 9 methylation (H3K9me) renders embedded genes transcriptionally ... ...

Abstract	Heterochromatin that depends on histone H3 lysine 9 methylation (H3K9me) renders embedded genes transcriptionally silent
MeSH term(s)	Caffeine/pharmacology ; Drug Resistance, Fungal/drug effects ; Drug Resistance, Fungal/genetics ; Gene Silencing/drug effects ; Heterochromatin/drug effects ; Heterochromatin/genetics ; Heterochromatin/metabolism ; Histone Acetyltransferases/metabolism ; Nuclear Proteins/metabolism ; Phenotype ; Schizosaccharomyces/cytology ; Schizosaccharomyces/drug effects ; Schizosaccharomyces/genetics ; Schizosaccharomyces/metabolism ; Schizosaccharomyces pombe Proteins/metabolism
Chemical Substances	Heterochromatin ; Nuclear Proteins ; Schizosaccharomyces pombe Proteins ; epe1 protein, S pombe ; Caffeine (3G6A5W338E) ; Histone Acetyltransferases (EC 2.3.1.48) ; Mst2 protein, S pombe (EC 2.3.1.48)
Language	English
Publishing date	2020-09-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-020-2706-x
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Article ; Online: iNucs: inter-nucleosome interactions.

Oveisi, Mehrdad / Shukla, Manu / Seymen, Nogayhan / Ohno, Masae / Taniguchi, Yuichi / Nahata, Sunil / Loos, Remco / Mufti, Ghulam J / Allshire, Robin C / Dimitrov, Stefan / Karimi, Mohammad M

Bioinformatics (Oxford, England)

2021 Volume 37, Issue 23, Page(s) 4562–4563

Abstract: Motivation: Deciphering nucleosome-nucleosome interactions is an important step toward mesoscale description of chromatin organization but computational tools to perform such analyses are not publicly available.: Results: We developed iNucs, a user- ... ...

Abstract	Motivation: Deciphering nucleosome-nucleosome interactions is an important step toward mesoscale description of chromatin organization but computational tools to perform such analyses are not publicly available. Results: We developed iNucs, a user-friendly and efficient Python-based bioinformatics tool to compute and visualize nucleosome-resolved interactions using standard pairs format input generated from pairtools. Availabilityand implementation: https://github.com/Karimi-Lab/inucs/. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Nucleosomes ; Software
Chemical Substances	Nucleosomes
Language	English
Publishing date	2021-09-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btab698
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Article ; Online: Centromere DNA Destabilizes H3 Nucleosomes to Promote CENP-A Deposition during the Cell Cycle.

Shukla, Manu / Tong, Pin / White, Sharon A / Singh, Puneet P / Reid, Angus M / Catania, Sandra / Pidoux, Alison L / Allshire, Robin C

Current biology : CB

2018 Volume 28, Issue 24, Page(s) 3924–3936.e4

Abstract: Active centromeres are defined by the presence of nucleosomes containing CENP-A, a histone H3 variant, which alone is sufficient to direct kinetochore assembly. Once assembled at a location, CENP-A chromatin and kinetochores are maintained at that ... ...

Abstract	Active centromeres are defined by the presence of nucleosomes containing CENP-A, a histone H3 variant, which alone is sufficient to direct kinetochore assembly. Once assembled at a location, CENP-A chromatin and kinetochores are maintained at that location through a positive feedback loop where kinetochore proteins recruited by CENP-A promote deposition of new CENP-A following replication. Although CENP-A chromatin itself is a heritable entity, it is normally associated with specific sequences. Intrinsic properties of centromeric DNA may favor the assembly of CENP-A rather than H3 nucleosomes. Here we investigate histone dynamics on centromere DNA. We show that during S phase, histone H3 is deposited as a placeholder at fission yeast centromeres and is subsequently evicted in G2, when we detect deposition of the majority of new CENP-A
MeSH term(s)	Centromere/metabolism ; Chromosomal Proteins, Non-Histone/genetics ; Chromosomal Proteins, Non-Histone/metabolism ; DNA, Fungal/metabolism ; Histones/metabolism ; Mitosis ; Nucleosomes/metabolism ; S Phase ; Schizosaccharomyces/genetics ; Schizosaccharomyces/metabolism ; Schizosaccharomyces pombe Proteins/genetics ; Schizosaccharomyces pombe Proteins/metabolism
Chemical Substances	Chromosomal Proteins, Non-Histone ; Cnp1 protein, S pombe ; DNA, Fungal ; Histones ; Nucleosomes ; Schizosaccharomyces pombe Proteins
Language	English
Publishing date	2018-11-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1071731-6
ISSN	1879-0445 ; 0960-9822
ISSN (online)	1879-0445
ISSN	0960-9822
DOI	10.1016/j.cub.2018.10.049
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Article ; Online: Hap2-Ino80-facilitated transcription promotes de novo establishment of CENP-A chromatin.

Singh, Puneet P / Shukla, Manu / White, Sharon A / Lafos, Marcel / Tong, Pin / Auchynnikava, Tatsiana / Spanos, Christos / Rappsilber, Juri / Pidoux, Alison L / Allshire, Robin C

Genes & development

2020 Volume 34, Issue 3-4, Page(s) 226–238

Abstract: Centromeres are maintained epigenetically by the presence of CENP-A, an evolutionarily conserved histone H3 variant, which directs kinetochore assembly and hence centromere function. To identify factors that promote assembly of CENP-A chromatin, we ... ...

Abstract	Centromeres are maintained epigenetically by the presence of CENP-A, an evolutionarily conserved histone H3 variant, which directs kinetochore assembly and hence centromere function. To identify factors that promote assembly of CENP-A chromatin, we affinity-selected solubilized fission yeast CENP-A
MeSH term(s)	Chromatin/genetics ; Chromatin/metabolism ; Chromosomal Proteins, Non-Histone/metabolism ; Chromosomes, Fungal/genetics ; Chromosomes, Fungal/metabolism ; DNA, Fungal/metabolism ; Schizosaccharomyces/genetics ; Schizosaccharomyces/metabolism ; Schizosaccharomyces pombe Proteins/genetics ; Schizosaccharomyces pombe Proteins/metabolism ; Transcription Factors/metabolism ; Transcription, Genetic/physiology
Chemical Substances	Chromatin ; Chromosomal Proteins, Non-Histone ; Cnp1 protein, S pombe ; DNA, Fungal ; Ino80 protein, S pombe ; Schizosaccharomyces pombe Proteins ; Transcription Factors
Language	English
Publishing date	2020-01-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	806684-x
ISSN	1549-5477 ; 0890-9369
ISSN (online)	1549-5477
ISSN	0890-9369
DOI	10.1101/gad.332536.119
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Article ; Online: Generation of Remosomes by the SWI/SNF Chromatin Remodeler Family.

Shukla, Manu Shubhdarshan / Syed, Sajad Hussain / Boopathi, Ramachandran / Simon, Elsa Ben / Nahata, Sunil / Ramos, Lorrie / Dalkara, Defne / Moskalenko, Cendrine / Travers, Andrew / Angelov, Dimitar / Dimitrov, Stefan / Hamiche, Ali / Bednar, Jan

Scientific reports

2019 Volume 9, Issue 1, Page(s) 14212

Abstract: Chromatin remodelers are complexes able to both alter histone-DNA interactions and to mobilize nucleosomes. The mechanism of their action and the conformation of remodeled nucleosomes remain a matter of debates. In this work we compared the type and ... ...

Abstract	Chromatin remodelers are complexes able to both alter histone-DNA interactions and to mobilize nucleosomes. The mechanism of their action and the conformation of remodeled nucleosomes remain a matter of debates. In this work we compared the type and structure of the products of nucleosome remodeling by SWI/SNF and ACF complexes using high-resolution microscopy combined with novel biochemical approaches. We find that SWI/SNF generates a multitude of nucleosome-like metastable particles termed "remosomes". Restriction enzyme accessibility assay, DNase I footprinting and AFM experiments reveal perturbed histone-DNA interactions within these particles. Electron cryo-microscopy shows that remosomes adopt a variety of different structures with variable irregular DNA path, similar to those described upon RSC remodeling. Remosome DNA accessibility to restriction enzymes is also markedly increased. We suggest that the generation of remosomes is a common feature of the SWI/SNF family remodelers. In contrast, the ACF remodeler, belonging to ISWI family, only produces repositioned nucleosomes and no evidence for particles associated with extra DNA, or perturbed DNA paths was found. The remosome generation by the SWI/SNF type of remodelers may represent a novel mechanism involved in processes where nucleosomal DNA accessibility is required, such as DNA repair or transcription regulation.
MeSH term(s)	Adenosine Triphosphate/metabolism ; Adenosine Triphosphate/pharmacology ; Animals ; Cell-Free System ; Chromatin Assembly and Disassembly/genetics ; Chromatin Assembly and Disassembly/physiology ; Chromosomal Proteins, Non-Histone/physiology ; DNA Footprinting ; DNA, Bacterial/metabolism ; Deoxyribonucleases, Type II Site-Specific ; Fungal Proteins/physiology ; Histones/genetics ; Histones/metabolism ; Microscopy, Atomic Force ; Multiprotein Complexes/physiology ; Nucleosomes/physiology ; Nucleosomes/ultrastructure ; Plasmids/chemistry ; RNA-Binding Proteins/physiology ; Recombinant Proteins/metabolism ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae/ultrastructure ; Xenopus laevis/genetics
Chemical Substances	Chromosomal Proteins, Non-Histone ; DNA, Bacterial ; Fungal Proteins ; Histones ; Multiprotein Complexes ; Nucleosomes ; RNA-Binding Proteins ; Recombinant Proteins ; Adenosine Triphosphate (8L70Q75FXE) ; Deoxyribonucleases, Type II Site-Specific (EC 3.1.21.4) ; GGCC-specific type II deoxyribonucleases (EC 3.1.21.4)
Language	English
Publishing date	2019-10-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-019-50572-8
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Article ; Online: Interspecies conservation of organisation and function between nonhomologous regional centromeres.

Tong, Pin / Pidoux, Alison L / Toda, Nicholas R T / Ard, Ryan / Berger, Harald / Shukla, Manu / Torres-Garcia, Jesus / Müller, Carolin A / Nieduszynski, Conrad A / Allshire, Robin C

Nature communications

2019 Volume 10, Issue 1, Page(s) 2343

Abstract: Despite the conserved essential function of centromeres, centromeric DNA itself is not conserved. The histone-H3 variant, CENP-A, is the epigenetic mark that specifies centromere identity. Paradoxically, CENP-A normally assembles on particular sequences ... ...

Abstract	Despite the conserved essential function of centromeres, centromeric DNA itself is not conserved. The histone-H3 variant, CENP-A, is the epigenetic mark that specifies centromere identity. Paradoxically, CENP-A normally assembles on particular sequences at specific genomic locations. To gain insight into the specification of complex centromeres, here we take an evolutionary approach, fully assembling genomes and centromeres of related fission yeasts. Centromere domain organization, but not sequence, is conserved between Schizosaccharomyces pombe, S. octosporus and S. cryophilus with a central CENP-A
MeSH term(s)	Centromere/genetics ; Centromere/metabolism ; Centromere Protein A/genetics ; Centromere Protein A/metabolism ; Chromatin/metabolism ; Chromatin Assembly and Disassembly/genetics ; Chromosomal Proteins, Non-Histone/genetics ; Chromosomal Proteins, Non-Histone/metabolism ; Conserved Sequence ; DNA/metabolism ; Epigenesis, Genetic ; Histones ; Kinetochores ; RNA, Ribosomal, 5S ; RNA, Transfer ; Schizosaccharomyces/genetics ; Schizosaccharomyces pombe Proteins/genetics ; Schizosaccharomyces pombe Proteins/metabolism ; Synteny
Chemical Substances	Centromere Protein A ; Chromatin ; Chromosomal Proteins, Non-Histone ; Cnp1 protein, S pombe ; Histones ; RNA, Ribosomal, 5S ; Schizosaccharomyces pombe Proteins ; DNA (9007-49-2) ; RNA, Transfer (9014-25-9)
Language	English
Publishing date	2019-05-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-019-09824-4
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Article: Functions of the histone chaperone nucleolin in diseases.

Storck, Sébastien / Shukla, Manu / Dimitrov, Stefan / Bouvet, Philippe

Sub-cellular biochemistry

2007 Volume 41, Page(s) 125–144

Abstract: Alteration of nuclear morphology is often used by pathologist as diagnostic marker for malignancies like cancer. In particular, the staining of cells by the silver staining methods (AgNOR) has been proved to be an important tool for predicting the ... ...

Abstract	Alteration of nuclear morphology is often used by pathologist as diagnostic marker for malignancies like cancer. In particular, the staining of cells by the silver staining methods (AgNOR) has been proved to be an important tool for predicting the clinical outcome of some cancer diseases. Two major argyrophilic proteins responsible for the strong staining of cells in interphase are the nucleophosmin (B23) and the nucleolin (C23) nucleolar proteins. Interestingly these two proteins have been described as chromatin associated proteins with histone chaperone activities and also as proteins able to regulate chromatin transcription. Nucleolin seems to be over-expressed in highly proliferative cells and is involved in many aspect of gene expression: chromatin remodeling, DNA recombination and replication, RNA transcription by RNA polymerase I and II, rRNA processing, mRNA stabilisation, cytokinesis and apoptosis. Interestingly, nucleolin is also found on the cell surface in a wide range of cancer cells, a property which is being used as a marker for the diagnosis of cancer and for the development of anti-cancer drugs to inhibit proliferation of cancer cells. In addition to its implication in cancer, nucleolin has been described not only as a marker or as a protein being involved in many diseases like viral infections, autoimmune diseases, Alzheimer's disease pathology but also in drug resistance. In this review we will focus on the chromatin associated functions of nucleolin and discuss the functions of nucleolin or its use as diagnostic marker and as a target for therapy
MeSH term(s)	Animals ; Antineoplastic Agents/pharmacology ; Antineoplastic Agents/therapeutic use ; Biomarkers, Tumor/metabolism ; Cell Proliferation ; Cell Transformation, Neoplastic/genetics ; Cell Transformation, Neoplastic/metabolism ; Chromatin/metabolism ; Chromatin Assembly and Disassembly ; DNA/metabolism ; DNA Repair ; DNA Replication ; Histones/metabolism ; Humans ; Molecular Chaperones/metabolism ; Neoplasms/diagnosis ; Neoplasms/drug therapy ; Neoplasms/genetics ; Neoplasms/metabolism ; Nuclear Proteins/metabolism ; Nucleophosmin ; Phosphoproteins/antagonists & inhibitors ; Phosphoproteins/metabolism ; RNA Polymerase I/metabolism ; RNA Polymerase II/metabolism ; RNA-Binding Proteins/antagonists & inhibitors ; RNA-Binding Proteins/metabolism ; Receptors, Cell Surface/metabolism ; Recombination, Genetic ; Transcription, Genetic ; Tumor Suppressor Proteins/metabolism ; Nucleolin
Chemical Substances	Antineoplastic Agents ; Biomarkers, Tumor ; Chromatin ; Histones ; Molecular Chaperones ; NPM1 protein, human ; Nuclear Proteins ; Phosphoproteins ; RNA-Binding Proteins ; Receptors, Cell Surface ; Tumor Suppressor Proteins ; Nucleophosmin (117896-08-9) ; DNA (9007-49-2) ; RNA Polymerase II (EC 2.7.7.-) ; RNA Polymerase I (EC 2.7.7.6)
Language	English
Publishing date	2007-05-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ISSN	0306-0225 ; 0096-8757
ISSN	0306-0225 ; 0096-8757
DOI	10.1007/1-4020-5466-1_7
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Article ; Online: Structure of an H1-Bound 6-Nucleosome Array Reveals an Untwisted Two-Start Chromatin Fiber Conformation.

Garcia-Saez, Isabel / Menoni, Hervé / Boopathi, Ramachandran / Shukla, Manu S / Soueidan, Lama / Noirclerc-Savoye, Marjolaine / Le Roy, Aline / Skoufias, Dimitrios A / Bednar, Jan / Hamiche, Ali / Angelov, Dimitar / Petosa, Carlo / Dimitrov, Stefan

Molecular cell

2018 Volume 72, Issue 5, Page(s) 902–915.e7

Abstract: Chromatin adopts a diversity of regular and irregular fiber structures in vitro and in vivo. However, how an array of nucleosomes folds into and switches between different fiber conformations is poorly understood. We report the 9.7 Å resolution crystal ... ...

Abstract	Chromatin adopts a diversity of regular and irregular fiber structures in vitro and in vivo. However, how an array of nucleosomes folds into and switches between different fiber conformations is poorly understood. We report the 9.7 Å resolution crystal structure of a 6-nucleosome array bound to linker histone H1 determined under ionic conditions that favor incomplete chromatin condensation. The structure reveals a flat two-start helix with uniform nucleosomal stacking interfaces and a nucleosome packing density that is only half that of a twisted 30-nm fiber. Hydroxyl radical footprinting indicates that H1 binds the array in an on-dyad configuration resembling that observed for mononucleosomes. Biophysical, cryo-EM, and crosslinking data validate the crystal structure and reveal that a minor change in ionic environment shifts the conformational landscape to a more compact, twisted form. These findings provide insights into the structural plasticity of chromatin and suggest a possible assembly pathway for a 30-nm fiber.
MeSH term(s)	Animals ; Binding Sites ; Cloning, Molecular ; Cryoelectron Microscopy ; Crystallography, X-Ray ; DNA/chemistry ; DNA/genetics ; DNA/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Gene Expression ; Genetic Vectors/chemistry ; Genetic Vectors/metabolism ; Histones/chemistry ; Histones/genetics ; Histones/metabolism ; Humans ; Hydroxyl Radical/chemistry ; Models, Molecular ; Nucleosome Assembly Protein 1/chemistry ; Nucleosome Assembly Protein 1/genetics ; Nucleosome Assembly Protein 1/metabolism ; Nucleosomes/chemistry ; Nucleosomes/metabolism ; Nucleosomes/ultrastructure ; Osmolar Concentration ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Protein Multimerization ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Xenopus laevis
Chemical Substances	Histones ; Nucleosome Assembly Protein 1 ; Nucleosomes ; Recombinant Proteins ; Hydroxyl Radical (3352-57-6) ; DNA (9007-49-2)
Language	English
Publishing date	2018-11-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2018.09.027
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