@article {627,
	title = {Developmentally regulated higher-order chromatin interactions orchestrate B cell fate commitment.},
	journal = {Nucleic Acids Res},
	year = {2017},
	month = {2017 Aug 17},
	abstract = {<p>Genome organization in 3D nuclear-space is important for regulation of gene expression. However, the alterations of chromatin architecture that impinge on the B cell-fate choice of multi-potent progenitors are still unclear. By integrating in situ Hi-C analyses with epigenetic landscapes and genome-wide expression profiles, we tracked the changes in genome architecture as the cells transit from a progenitor to a committed state. We identified the genomic loci that undergo developmental switch between A and B compartments during B-cell fate determination. Furthermore, although, topologically associating domains (TADs) are stable, a significant number of TADs display structural alterations that are associated with changes in cis-regulatory interaction landscape. Finally, we demonstrate the potential roles for Ebf1 and its downstream factor, Pax5, in chromatin reorganization and transcription regulation. Collectively, our studies provide a general paradigm of the dynamic relationship between chromatin reorganization and lineage-specific gene expression pattern that dictates cell-fate determination.</p>
},
	issn = {1362-4962},
	doi = {10.1093/nar/gkx722},
	author = {Boya, Ravi and Yadavalli, Anurupa Devi and Nikhat, Sameena and Kurukuti, Sreenivasulu and Palakodeti, Dasaradhi and Pongubala, Jagan M R}
}
@article {493,
	title = {Deep sequencing reveals unique small RNA repertoire that is regulated during head regeneration in Hydra magnipapillata. [Next Generation Genomics facility]},
	journal = {Nucleic Acids Res},
	volume = {41},
	year = {2013},
	month = {2013 Jan 07},
	pages = {599-616},
	abstract = {<p class="rtejustify">Small non-coding RNAs such as miRNAs, piRNAs and endo-siRNAs fine-tune gene expression through post-transcriptional regulation, modulating important processes in development, differentiation, homeostasis and regeneration. Using deep sequencing, we have profiled small non-coding RNAs in Hydra magnipapillata and investigated changes in small RNA expression pattern during head regeneration. Our results reveal a unique repertoire of small RNAs in hydra. We have identified 126 miRNA loci; 123 of these miRNAs are unique to hydra. Less than 50\% are conserved across two different strains of Hydra vulgaris tested in this study, indicating a highly diverse nature of hydra miRNAs in contrast to bilaterian miRNAs. We also identified siRNAs derived from precursors with perfect stem-loop structure and that arise from inverted repeats. piRNAs were the most abundant small RNAs in hydra, mapping to transposable elements, the annotated transcriptome and unique non-coding regions on the genome. piRNAs that map to transposable elements and the annotated transcriptome display a ping-pong signature. Further, we have identified several miRNAs and piRNAs whose expression is regulated during hydra head regeneration. Our study defines different classes of small RNAs in this cnidarian model system, which may play a role in orchestrating gene expression essential for hydra regeneration.</p>
},
	keywords = {Animals, Gene Expression Regulation, Head, High-Throughput Nucleotide Sequencing, Hydra, MicroRNAs, Regeneration, RNA, Small Interfering, RNA, Small Untranslated, Sequence Analysis, RNA, Transcriptome},
	issn = {1362-4962},
	doi = {10.1093/nar/gks1020},
	author = {Krishna, Srikar and Nair, Aparna and Cheedipudi, Sirisha and Poduval, Deepak and Dhawan, Jyotsna and Palakodeti, Dasaradhi and Ghanekar, Yashoda}
}
