Research Topics
Genomes and Genes
| Ranjan SenSummaryAffiliation: National Institutes of Health Country: USA Publications
| Collaborators
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Detail Information
Publications
NF-kappaB and the immunoglobulin kappa gene enhancerRanjan Sen
Lab of Cellular and Molecular Biology, National Institute on Aging, 5600 Nathan Shock Dr, Baltimore, MD 21224, USA
J Exp Med 200:1099-102. 2004..Here, I discuss the implications of the new observation that an NF-kappaB binding site-mutated enhancer in the correct biological context does not appear to affect kappa gene expression...- Memories of lost enhancersRanjan Sen
Laboratory of Cellular and Molecular Biology, National Institute of Aging, Baltimore, Maryland 21224, USA
Genes Dev 24:973-9. 2010..659-669) providing evidence of a transient requirement of an enhancer associated with the CD4 gene, we discuss possible mechanisms by which transcriptional memory can be propagated in the absence of enhancers... 
Control of B lymphocyte apoptosis by the transcription factor NF-kappaBRanjan Sen
Laboratory of Cellular and Molecular Biology, National Institute on Aging, Baltimore, Maryland 21224, USA
Immunity 25:871-83. 2006..In particular, the temporal patterns of NF-kappaB induction, differences between Rel family members, and the intersection between canonical and noncanonical signaling pathways in keeping B cells alive are discussed...- A 220-nucleotide deletion of the intronic enhancer reveals an epigenetic hierarchy in immunoglobulin heavy chain locus activationTirtha Chakraborty
Laboratory of Cellular and Molecular Biology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
J Exp Med 206:1019-27. 2009..These observations define Emu-independent and Emu-dependent phases of locus activation that reveal an unappreciated epigenetic hierarchy in tissue-specific gene expression... 
Activation of 12/23-RSS-dependent RAG cleavage by hSWI/SNF complex in the absence of transcriptionHansen Du
Laboratory of Cellular and Molecular Biology, National Institute on Aging, Baltimore, MD 21224, USA
Mol Cell 31:641-9. 2008..These observations demonstrate a direct role for cis-sequence-regulated local chromatin remodeling in RAG1/2-dependent initiation of V(D)J recombination...- Localized epigenetic changes induced by D(H) recombination restricts recombinase to DJ(H) junctionsRamesh Subrahmanyam
Laboratory of Molecular Biology and Immunology, National Institute on Aging, US National Institutes of Health, Baltimore, Maryland, USA
Nat Immunol 13:1205-12. 2012..We propose that V(H) recombination is precise, because these changes did not extend to germline D(H) segments located 5' of the DJ(H) junction... - Immunoglobulin switch mu sequence causes RNA polymerase II accumulation and reduces dA hypermutationDeepa Rajagopal
Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
J Exp Med 206:1237-44. 2009..We propose that altered DNA structure in the switch region pauses RNA polymerase II and limits access of DNA polymerase eta during hypermutation... - A plant homeodomain in RAG-2 that binds Hypermethylated lysine 4 of histone H3 is necessary for efficient antigen-receptor-gene rearrangementYun Liu
Department of Molecular Biology and Genetics, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
Immunity 27:561-71. 2007..Together, these findings are consistent with the interpretation that recognition of hypermethylated histone H3 K4 promotes efficient V(D)J recombination in vivo... - Two forms of loops generate the chromatin conformation of the immunoglobulin heavy-chain gene locusChangying Guo
Gene Regulation Section, Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD 21224, USA
Cell 147:332-43. 2011..Our observations provide a comprehensive view of the conformation of IgH alleles in pro-B cells and the mechanisms by which it is established... - Single round of antigen receptor signaling programs naive B cells to receive T cell helpBazarragchaa Damdinsuren
Gene Regulation Section, Laboratory of Cellular and Molecular Biology, National Institute on Aging, Baltimore, MD 21224, USA
Immunity 32:355-66. 2010..We propose that transient BCR signals prime B cells to receive T cell help by increasing the probability of B-T encounter and creating a cellular environment that is hyper-responsive to CD40 signaling... - RAGs' eye view of the immunoglobulin heavy chain gene locusRamesh Subrahmanyam
Gene Regulation Section, Laboratory of Cellular and Molecular Biology, National Institute on Aging, National Institutes of Health, 251 Bayview Blvd, Room 06C214, Baltimore, MD 21224, United States
Semin Immunol 22:337-45. 2010..The emerging picture shows that the IgH locus consists of independently regulated domains, each of which requires multiple levels of epigenetic changes to reach the fully activated state... - The requirement for pre-TCR during thymic differentiation enforces a developmental pause that is essential for V-DJβ rearrangementKaren S Hathcock
Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
PLoS ONE 6:e20639. 2011..However, the requirement for pre-TCR signals and the exclusion of alternative stimuli such as CD28 enforce a developmental "pause" in early DN3 cells that is essential for productive TCRβ rearrangement to occur... - A histone-fold complex and FANCM form a conserved DNA-remodeling complex to maintain genome stabilityZhijiang Yan
Laboratory of Genetics, National Institute of Aging, National Institutes of Health, Baltimore, MD 21224, USA
Mol Cell 37:865-78. 2010..Thus, FANCM-MHF is an essential DNA-remodeling complex that protects replication forks from yeast to human... - NF-κB function in B lymphocytesMary Kaileh
Gene Regulation Section, Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
Immunol Rev 246:254-71. 2012..We endeavor throughout to suggest mechanisms and implications of the wide-ranging observations that have been made and conclude by highlighting the need to understand NF-κB-mediated gene expression in more depth... - Regulating antibody diversity: taming a mutagenPatricia J Gearhart
Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, 251 Bayview Boulevard, Baltimore, MD 21224, USA
Mol Cell 31:615-6. 2008..2008) identified a protein that interacts with the activation-induced deaminase protein and affects somatic hypermutation, class switching, and gene conversion in immunoglobulin genes, possibly via the spliceosome transcription complex... - Epigenetic features that regulate IgH locus recombination and expressionRamesh Subrahmanyam
National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
Curr Top Microbiol Immunol 356:39-63. 2012..In this review we discuss the regulatory features of each step of IgH gene assembly and the role of epigenetic mechanisms in achieving regulatory precision... - Genetic and epigenetic regulation of IgH gene assemblyRanjan Sen
Laboratory of Cellular and Molecular Biology, National Institute on Aging/National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD 21224, USA
Curr Opin Immunol 18:237-42. 2006..Orchestration of these regulatory processes is crucial for the generation of a functional B cell repertoire... - Selectivity of the NF-{kappa}B responseRanjan Sen
Laboratory of Cellular and Molecular Biology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21225, USA
Cold Spring Harb Perspect Biol 2:a000257. 2010..Here, we explore the mechanistic framework in which such regulatory aspects of NF-kappaB-dependent gene expression have been analyzed because they are likely to form the basis for physiological responses... - Repeat organization and epigenetic regulation of the DH-Cmu domain of the immunoglobulin heavy-chain gene locusTirtha Chakraborty
Laboratory of Cellular and Molecular Biology, National Institute on Aging, Baltimore, MD 21224, USA
Mol Cell 27:842-50. 2007..We propose that the intervening D(H) genes are actively suppressed by repeat-induced epigenetic silencing, which is reflected in their infrequent representation in DJ(H) junctions compared to the flanking D(H) genes... - Role of NF-kappaB in the anti-inflammatory effects of tocotrienolsMary Kaileh
Laboratory of Cellular and Molecular Biology, National Institute on Aging, Baltimore, MD 21224, USA
J Am Coll Nutr 29:334S-339S. 2010..Because NF-kappaB-dependent gene regulation is important in virtually all mammalian cell types, it is critical to keep in mind some basic features of its functions when considering interventional therapeutics... - Tumor-evoked regulatory B cells promote breast cancer metastasis by converting resting CD4⁺ T cells to T-regulatory cellsPurevdorj B Olkhanud
Immunotherapeutics Unit, Laboratory of Immunology, National Institute on Aging, Baltimore, Maryland 21224, USA
Cancer Res 71:3505-15. 2011..Our findings have important clinical implications, as they suggest that tBregs must be controlled to interrupt the initiation of a key cancer-induced immunosuppressive event that is critical to support cancer metastasis... - Antigen-independent IFN-γ production by human naïve CD4 T cells activated by IL-12 plus IL-18Rachel B Munk
Lymphocyte Cell Biology Unit, Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America
PLoS ONE 6:e18553. 2011..Thus, the present study suggests that naïve CD4(+) T cells may participate in innate immunity or amplify adaptive immune responses through cytokine-induced antigen-independent cytokine production... - Regulation of immunoglobulin heavy-chain gene rearrangementsDipanjan Chowdhury
Laboratory of Cellular and Molecular Biology, National Institute on Aging, Baltimore, MD 21224, USA
Immunol Rev 200:182-96. 2004..VH genes are activated subsequently and, in part, by interleukin-7. These observations lead to a model for feedback inhibition of IgH rearrangements... - Pax5 is required for recombination of transcribed, acetylated, 5' IgH V gene segmentsDavid G T Hesslein
Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06520 8011, USA
Genes Dev 17:37-42. 2003..The finding of transcribed, histone acetylated gene segments that fail to recombine suggests that a Pax5-dependent regulatory mechanism is required in addition to standard constraints of accessibility to control V(H) gene recombination... - NF-kappaB-dependent regulation of the timing of activation-induced cell death of T lymphocytesAkanksha Mittal
Rosensteil Research Center and Department of Biology, Brandeis University, Waltham, MA 02454, USA
J Immunol 176:2183-9. 2006..We propose that the timing of AICD, and thus the length of the effector phase, are regulated by transient expression of a subset of p65/RelA-dependent antiapoptotic genes... - Simple fluorescence assays probing conformational changes of Escherichia coli RNA polymerase during transcription initiationRanjan Sen
Laboratory of Transcription Biology, Center for DNA Fingerprinting and Diagnosis, ECIL Road, Nacharam, Hyderabad 500076, India
Methods Enzymol 370:598-605. 2003 - Combinatorial control of DNase I-hypersensitive site formation and erasure by immunoglobulin heavy chain enhancer-binding proteinsHaruhiko Ishii
Graduate Program in Biophysics and Structural Biology, Brandeis University, Waltham, Massachusetts 02454, USA
J Biol Chem 279:7331-8. 2004..We infer that chromatin constraints for transcription and nuclease sensitivity can differ... - Transient IL-7/IL-7R signaling provides a mechanism for feedback inhibition of immunoglobulin heavy chain gene rearrangementsDipanjan Chowdhury
Department of Biology, Brandeis University, Waltham, MA 02454, USA
Immunity 18:229-41. 2003..Thus, transient signals mediate V(H) gene activation and inactivation during development... - Generality of the branched pathway in transcription initiation by Escherichia coli RNA polymeraseMotoki Susa
Structural Biology Center, National Institute of Genetics and Department of Genetics, The Graduate University for Advanced Studies, 1111 Yata, Mishima, Japan, 411-8540
J Biol Chem 277:15407-12. 2002..These findings suggest a generality of the branched pathway mechanism, which would resolve contradictory observations that have been reported for various promoters... - Naive B lymphocytes undergo homeostatic proliferation in response to B cell deficitMark S Cabatingan
Department of Molecular Genetics and Microbiology, University of Massachusetts Medical School, Worcester, MA 01655, USA
J Immunol 169:6795-805. 2002..Homeostatic B cell proliferation provides an Ag-independent mechanism for the maintenance and expansion of naive B cells selected into the mature B cell pool... - Commitment of activated T cells to secondary responsiveness is enhanced by signals mediated by cAMP-dependent protein kinase A-IMonika Vig
National Institute of Immunology, New Delhi, India
Mol Pharmacol 62:1471-81. 2002..Together, our data suggest that PKA-I-mediated signals triggered by prolonging the half-life of cAMP induced during T-cell priming increase survival of activated T cells and enhance memory T cell commitment... - Pentoxifylline functions as an adjuvant in vivo to enhance T cell immune responses by inhibiting activation-induced deathRadhakrishnan Suresh
National Institute of Immunology, Aruna Asaf Ali Road, New Delhi 110067, India
J Immunol 169:4262-72. 2002.... - Sequence-specific interaction of nascent antiterminator RNA with the zinc-finger motif of Escherichia coli RNA polymeraseRanjan Sen
Section on Microbial Genetics, Laboratory of Molecular Genetics, National Institute of Child Health and Human Development, 6B 3B308, NIH, Bethesda, MD 20892 2785, USA
Mol Microbiol 46:215-22. 2002.... - Using a lac repressor roadblock to analyze the E. coli transcription elongation complexRodney A King
Laboratory of Molecular Genetics, NICHD, NIH, Building 6B, Room 3B-308, Bethesda, Maryland 20892, USA
Methods Enzymol 371:207-18. 2003 - Mechanisms for feedback inhibition of the immunoglobulin heavy chain locusDipanjan Chowdhury
Centre for Blood Research, Boston, MA 02115, USA
Curr Opin Immunol 16:235-40. 2004..Similar transient signals may be responsible for enforcing allelic exclusion in other V(H) gene families. D-proximal V(H) genes, however, appear to be less susceptible to feedback inhibition... - A conserved zinc binding domain in the largest subunit of DNA-dependent RNA polymerase modulates intrinsic transcription termination and antitermination but does not stabilize the elongation complexRodney A King
Laboratory of Molecular Genetics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
J Mol Biol 342:1143-54. 2004..To account for this we suggest that put RNA interacts with an additional site in the elongation complex to mediate antitermination, and that this site is occluded by the wild-type zinc binding domain... - Mechanism of inhibition of Rho-dependent transcription termination by bacteriophage P4 protein PsuBibhusita Pani
Laboratory of Transcription Biology, Centre for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam, Hyderabad-500076, India
J Biol Chem 281:26491-500. 2006..We propose that Psu inhibits Rho-dependent termination by slowing down the translocation of Rho along the RNA because of its slow ATPase activity... - Transcription termination factor rho prefers catalytically active elongation complexes for releasing RNADipak Dutta
Laboratory of Transcription Biology, Centre for DNA Fingerprinting and Diagnostics, Nacharam, Hyderabad, India
J Biol Chem 283:20243-51. 2008.... - Transcription termination defective mutants of Rho: role of different functions of Rho in releasing RNA from the elongation complexJisha Chalissery
Laboratory of Transcription Biology, Centre for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam, Hyderabad 500076, India
J Mol Biol 371:855-72. 2007..The rate of ATP hydrolysis regulates the processivity of translocation along the RNA and is directly correlated with the efficiency of RNA release. NusG improves the speed of RNA release and is not involved in any other step... - Rho-dependent transcription termination: more questions than answersSharmistha Banerjee
Laboratory of Transcription Biology, Center for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam, Hyderabad 500076, India
J Microbiol 44:11-22. 2006..An attempt has also been made to understand the physiology of Rho in the light of its phylogeny... - Inhibition of a transcriptional pause by RNA anchoring to RNA polymeraseNatalia Komissarova
Section on Microbial Genetics, Laboratory of Molecular Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892 2785, USA
Mol Cell 31:683-94. 2008..We propose that RNA anchoring to the elongation complex is a widespread mechanism of pause regulation... - c-Rel-dependent priming of naive T cells by inflammatory cytokinesDaliya Banerjee
Rosenstiel Research Center and Department of Biology, Brandeis University, Waltham, Massachusetts 02454, USA
Immunity 23:445-58. 2005..This mechanism does not operate in effector T cells where cytokine gene expression is c-Rel-independent. We propose that c-Rel plays a crucial role as a target of innate signals in T cells... - Escherichia coli RNA polymerase mutations located near the upstream edge of an RNA:DNA hybrid and the beginning of the RNA-exit channel are defective for transcription antitermination by the N protein from lambdoid phage H-19BAnoop Cheeran
Laboratory of Transcription Biology, Center for DNA Fingerprinting and Diagnostics, Nacharam, Hyderabad-500076, India
J Mol Biol 352:28-43. 2005..We propose that the action of N close to the active center alters the RNAP-nucleic acid interactions around the RNA:DNA hybrid, which impairs proper folding of the terminator hairpin or stabilizes the weak RNA:DNA hybrid, or both... - A move to excludeRanjan Sen
Nat Immunol 6:128-30. 2005 - The site of action of the antiterminator protein N from the lambdoid phage H-19BAnoop Cheeran
Laboratory of Transcription Biology, Centre for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam, Hyderabad 500076, India
J Biol Chem 282:30997-1007. 2007....