57 posts · 18,247 views
Exploring diverse new biological research
Habib Maroon
57 posts
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- January 22, 2013
- 01:06 PM
- 120 views
Supergenes, Sociality, and Sex Chromosomes
by Habib Maroon in Biobabel
A new paper in Nature shows that the social structure of fire ant colonies is determined by a ‘supergene’ – a single non-recombining cluster of hundreds of genes. The supergene makes up more than 50% of a pair of divergent … Continue reading →... Read more »
Wang, J., Wurm, Y., Nipitwattanaphon, M., Riba-Grognuz, O., Huang, Y., Shoemaker, D., & Keller, L. (2013) A Y-like social chromosome causes alternative colony organization in fire ants. Nature. DOI: 10.1038/nature11832
Bourke, A., & Mank, J. (2013) Genetics: A social rearrangement. Nature. DOI: 10.1038/nature11854
- December 11, 2012
- 07:52 PM
- 133 views
The Transposon/piRNA/Chromatin Nexus
by Habib Maroon in Biobabel
Close observation of chromatin states at piRNA-silenced genomic loci demonstrates the power of transposons to change native gene expression. As reviewed in an earlier post, the Drosophila Piwi/piRNA transposon silencing pathway can be divided into two facets; a complex pathway … Continue reading →... Read more »
Sienski, G., Dönertas, D., & Brennecke, J. (2012) Transcriptional Silencing of Transposons by Piwi and Maelstrom and Its Impact on Chromatin State and Gene Expression. Cell, 151(5), 964-980. DOI: 10.1016/j.cell.2012.10.040
- December 6, 2012
- 02:39 PM
- 129 views
Breaking Neuronal Symmetry by Chromatin Memories
by Habib Maroon in Biobabel
The asymmetric fates of two bilaterally symmetrical neurons are determined by a two-step activation program at a miRNA locus. Very low levels of transcription ‘prime’ the locus many cell generations before the final fate determination is imposed by a bilateral … Continue reading →... Read more »
Cochella, L., & Hobert, O. (2012) Embryonic Priming of a miRNA Locus Predetermines Postmitotic Neuronal Left/Right Asymmetry in C. elegans. Cell, 151(6), 1229-1242. DOI: 10.1016/j.cell.2012.10.049
- November 23, 2012
- 07:52 PM
- 161 views
The Heterodox Dinokaryon
by Habib Maroon in Biobabel
The nuclei of dinoflagellates display a highly derived organisation; chromosomes are permanently condensed and seem to lack histone proteins. A new study in Current Biology links the emergence of these characters to the importation of a novel family of nuclear … Continue reading →... Read more »
Gornik, S., Ford, K., Mulhern, T., Bacic, A., McFadden, G., & Waller, R. (2012) Loss of Nucleosomal DNA Condensation Coincides with Appearance of a Novel Nuclear Protein in Dinoflagellates. Current Biology. DOI: 10.1016/j.cub.2012.10.036
- November 11, 2012
- 10:08 AM
- 154 views
Uploading piRNAs to the Cloud.
by Habib Maroon in Biobabel
A new paper finds a protein linking piRNA transcription with processing in nuage. The Piwi/piRNA system is responsible for protecting the germline from the mutagenic effects of transposon mobilisation. As summarised in an earlier post, in Drosophila large arrays of … Continue reading →... Read more »
Zhang, F., Wang, J., Xu, J., Zhang, Z., Koppetsch, B., Schultz, N., Vreven, T., Meignin, C., Davis, I., Zamore, P.... (2012) UAP56 Couples piRNA Clusters to the Perinuclear Transposon Silencing Machinery. Cell, 151(4), 871-884. DOI: 10.1016/j.cell.2012.09.040
Lin, H. (2012) Capturing the Cloud: UAP56 in Nuage Assembly and Function. Cell, 151(4), 699-701. DOI: 10.1016/j.cell.2012.10.026
- November 3, 2012
- 12:45 PM
- 176 views
A chimeric fusion of RNA and DNA viruses.
by Habib Maroon in Biobabel
The discovery of a new family of viruses leads to speculations on possible modes recombination between RNA and DNA viruses. The virosphere can be divided into three major classes; viruses with DNA genomes, retroviruses that reverse-transcribe their RNA genome into … Continue reading →... Read more »
Diemer, G., & Stedman, K. (2012) A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses. Biology Direct, 7(1), 13. DOI: 10.1186/1745-6150-7-13
- October 25, 2012
- 11:07 AM
- 216 views
Beating a Toxin-Antitoxin System; Evading Suicide
by Habib Maroon in Biobabel
Bacteria have evolved many different systems to evade viral predation. One strategy, abortive infection (Abi), involves altruistic suicide. Mediated by a toxin-antitoxin (TA) system, the suicide of the infected cell protects the clonal bacterial population by preventing the spread of … Continue reading →... Read more »
Blower, T., Evans, T., Przybilski, R., Fineran, P., & Salmond, G. (2012) Viral Evasion of a Bacterial Suicide System by RNA–Based Molecular Mimicry Enables Infectious Altruism. PLoS Genetics, 8(10). DOI: 10.1371/journal.pgen.1003023
- October 23, 2012
- 06:37 PM
- 201 views
Barcoding the Brain
by Habib Maroon in Biobabel
A new DNA-sequencing based idea for mapping the connectome is presented in Plos biology. The defining purpose of neurons is information transmission and processing within a network. Hence, to appreciate neural function we must look at the interactions between neurons; … Continue reading →... Read more »
Zador, A.M., Dubnau, J., Oyibo, H.K., Zhan, H., Cao, G.,Peikon, I.D. (2012) Sequencing the Connectome. Plos Biology, 10(10). info:/10.1371/journal.pbio.1001411
- October 2, 2012
- 03:09 PM
- 182 views
Opening up the RNA-chromatin network
by Habib Maroon in Biobabel
In eukaryotic nuclei, DNA is coiled around histone proteins to form nucleosomes. The pattern by which nucleosomes are compacted into higher-order structures determines the accessibility of chromatin and hence it’s transcriptional activity. Many different factors, including the linker histone H1, … Continue reading →... Read more »
Schubert T, Pusch MC, Diermeier S, Benes V, Kremmer E, Imhof A, & Längst G. (2012) Df31 Protein and snoRNAs Maintain Accessible Higher-Order Structures of Chromatin. Molecular cell. PMID: 23022379
Filion GJ, van Bemmel JG, Braunschweig U, Talhout W, Kind J, Ward LD, Brugman W, de Castro IJ, Kerkhoven RM, Bussemaker HJ.... (2010) Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell, 143(2), 212-24. PMID: 20888037
- September 26, 2012
- 08:42 AM
- 192 views
The CSR-1 siRNA pathway gets more enigmatic
by Habib Maroon in Biobabel
A recent paper forces a reappraisal of the role of CSR-1 its associated 22G-RNAs, and demonstrates a positive regulatory role for this RNAi pathway in C. elegans. As described in a previous post, depletion of the Argonaute protein CSR-1, or … Continue reading →... Read more »
Avgousti DC, Palani S, Sherman Y, & Grishok A. (2012) CSR-1 RNAi pathway positively regulates histone expression in C. elegans. The EMBO journal. PMID: 22863779
Claycomb JM, Batista PJ, Pang KM, Gu W, Vasale JJ, van Wolfswinkel JC, Chaves DA, Shirayama M, Mitani S, Ketting RF.... (2009) The Argonaute CSR-1 and its 22G-RNA cofactors are required for holocentric chromosome segregation. Cell, 139(1), 123-34. PMID: 19804758
- September 24, 2012
- 11:34 AM
- 204 views
Chromosomal Flip-Flop
by Habib Maroon in Biobabel
A study describes how phenotypic switching in Staphylococcus aureus is caused by a reversible large-scale genomic inversion. Clonal bacterial populations often display various phenotypes. This diversity is most obviously identifiable as colony variation. Many different bacterial genera display ‘small colony … Continue reading →... Read more »
Cui L, Neoh HM, Iwamoto A, & Hiramatsu K. (2012) Coordinated phenotype switching with large-scale chromosome flip-flop inversion observed in bacteria. Proceedings of the National Academy of Sciences of the United States of America, 109(25). PMID: 22645353
- September 20, 2012
- 11:29 AM
- 171 views
Expanding the Conjugative Realm
by Habib Maroon in Biobabel
A recent paper demonstrates that a broader range of plasmids can be transferred by conjugation than previously thought. Integrative and conjugative elements (ICEs, aka conjugative transposons) are a variety of bacterial mobile element generally found integrated into the host genome, … Continue reading →... Read more »
Lee CA, Thomas J, & Grossman AD. (2012) The Bacillus subtilis conjugative transposon ICEBs1 mobilizes plasmids lacking dedicated mobilization functions. Journal of bacteriology, 194(12), 3165-72. PMID: 22505685
- September 18, 2012
- 07:12 PM
- 188 views
Epigenetic Licensing of a Sex Determination Gene
by Habib Maroon in Biobabel
A recent series of papers describing interacting small RNA pathways in C. elegans, posited the existence of an anti-silencing pathway responsible for licensing the expression of germline transcripts. Johnson and Spence (Science. 2011) published the first paper suggesting such a … Continue reading →... Read more »
Johnson CL, & Spence AM. (2011) Epigenetic licensing of germline gene expression by maternal RNA in C. elegans. Science (New York, N.Y.), 333(6047), 1311-4. PMID: 21885785
- September 6, 2012
- 06:40 AM
- 238 views
Trans-Extremophile Para-Sex
by Habib Maroon in Biobabel
More than twenty years ago, an extra-ordinary mode of para-sexual genetic exchange was found to occur between cells of the halophilic archaeon Haloferax volcanii, an extremophile isolated from the Dead Sea. This process involves first, cell fusion producing heterodiploid cells. … Continue reading →... Read more »
Naor A, Lapierre P, Mevarech M, Papke RT, & Gophna U. (2012) Low species barriers in halophilic archaea and the formation of recombinant hybrids. Current biology : CB, 22(15), 1444-8. PMID: 22748314
- August 31, 2012
- 01:52 PM
- 229 views
Genomic Rearrangement in Lampreys 2
by Habib Maroon in Biobabel
As discussed in a recent post, during lamprey embryogenesis programmed genomic rearrangements lead to deletion of ~20% of the germline genome in the soma. Smith, Amemiya and co-workers have now published a follow-up study in which they further characterise the … Continue reading →... Read more »
Smith JJ, Baker C, Eichler EE, & Amemiya CT. (2012) Genetic consequences of programmed genome rearrangement. Current biology : CB, 22(16), 1524-9. PMID: 22818913
- August 26, 2012
- 11:33 AM
- 254 views
Upstream ORFs and Regulation of Translation
by Habib Maroon in Biobabel
Protein expression can be rapidly and responsively regulated at the level of translation. Translational regulation commonly involves trans-acting factors such as miRNA complexes or RNA-binding proteins, specifically binding cis-regulatory sequences. A study from last year – Medenbach et al. – … Continue reading →... Read more »
Medenbach J, Seiler M, & Hentze MW. (2011) Translational control via protein-regulated upstream open reading frames. Cell, 145(6), 902-13. PMID: 21663794
- August 19, 2012
- 04:42 PM
- 226 views
Interacting small RNA pathways in worms 5: Global Genome Surveillance
by Habib Maroon in Biobabel
As discussed previously, in C. elegans more than 15,000 21U-RNAs are expressed from two large clusters on chromosome IV. As very few of these piRNAs exhibit perfect sequence complementarity with other endogenous sequences within in the C. elegans genome, it’s … Continue reading →... Read more »
Bagijn MP, Goldstein LD, Sapetschnig A, Weick EM, Bouasker S, Lehrbach NJ, Simard MJ, & Miska EA. (2012) Function, targets, and evolution of Caenorhabditis elegans piRNAs. Science (New York, N.Y.), 337(6094), 574-8. PMID: 22700655
Lee HC, Gu W, Shirayama M, Youngman E, Conte D Jr, & Mello CC. (2012) C. elegans piRNAs Mediate the Genome-wide Surveillance of Germline Transcripts. Cell, 150(1), 78-87. PMID: 22738724
Ashe A, Sapetschnig A, Weick EM, Mitchell J, Bagijn MP, Cording AC, Doebley AL, Goldstein LD, Lehrbach NJ, Le Pen J.... (2012) piRNAs Can Trigger a Multigenerational Epigenetic Memory in the Germline of C. elegans. Cell, 150(1), 88-99. PMID: 22738725
Shirayama M, Seth M, Lee HC, Gu W, Ishidate T, Conte D Jr, & Mello CC. (2012) piRNAs Initiate an Epigenetic Memory of Nonself RNA in the C. elegans Germline. Cell, 150(1), 65-77. PMID: 22738726
- August 2, 2012
- 01:40 PM
- 214 views
Interacting small RNAs in worms 4: 21U-RNAs.
by Habib Maroon in Biobabel
A survey of C. elegans small RNAs from 2006 (Ruby et al) first reported the discovery of a large class of 21nt RNAs with 5’ uridines – 21U-RNAs. The majority of these RNAs mapped to two distinct regions of the … Continue reading →... Read more »
Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, & Bartel DP. (2006) Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell, 127(6), 1193-207. PMID: 17174894
Das PP, Bagijn MP, Goldstein LD, Woolford JR, Lehrbach NJ, Sapetschnig A, Buhecha HR, Gilchrist MJ, Howe KL, Stark R.... (2008) Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline. Molecular cell, 31(1), 79-90. PMID: 18571451
Batista PJ, Ruby JG, Claycomb JM, Chiang R, Fahlgren N, Kasschau KD, Chaves DA, Gu W, Vasale JJ, Duan S.... (2008) PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans. Molecular cell, 31(1), 67-78. PMID: 18571452
Cecere G, Zheng GX, Mansisidor AR, Klymko KE, & Grishok A. (2012) Promoters Recognized by Forkhead Proteins Exist for Individual 21U-RNAs. Molecular cell. PMID: 22819322
- August 2, 2012
- 01:40 PM
- 165 views
Interacting small RNA pathways in worms 4: 21U-RNAs.
by Habib Maroon in Biobabel
A survey of C. elegans small RNAs from 2006 (Ruby et al) first reported the discovery of a large class of 21nt RNAs with 5’ uridines – 21U-RNAs. The majority of these RNAs mapped to two distinct regions of the … Continue reading →... Read more »
Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, & Bartel DP. (2006) Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell, 127(6), 1193-207. PMID: 17174894
Das PP, Bagijn MP, Goldstein LD, Woolford JR, Lehrbach NJ, Sapetschnig A, Buhecha HR, Gilchrist MJ, Howe KL, Stark R.... (2008) Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline. Molecular cell, 31(1), 79-90. PMID: 18571451
Batista PJ, Ruby JG, Claycomb JM, Chiang R, Fahlgren N, Kasschau KD, Chaves DA, Gu W, Vasale JJ, Duan S.... (2008) PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans. Molecular cell, 31(1), 67-78. PMID: 18571452
Cecere G, Zheng GX, Mansisidor AR, Klymko KE, & Grishok A. (2012) Promoters Recognized by Forkhead Proteins Exist for Individual 21U-RNAs. Molecular cell. PMID: 22819322
- July 26, 2012
- 05:51 PM
- 262 views
Interacting small RNA pathways in worms 3: CSR-1 associated 22G-RNAs
by Habib Maroon in Biobabel
During mitosis, duplicated chromosomes are separated and segregated into two daughter cells. This is achieved by the action of spindle microtubules. In metaphase, microtubules radiating from centrosomes at two poles in the cell, attach to the condensed chromosomes at proteinaceous … Continue reading →... Read more »
Claycomb JM, Batista PJ, Pang KM, Gu W, Vasale JJ, van Wolfswinkel JC, Chaves DA, Shirayama M, Mitani S, Ketting RF.... (2009) The Argonaute CSR-1 and its 22G-RNA cofactors are required for holocentric chromosome segregation. Cell, 139(1), 123-34. PMID: 19804758
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