Ontology highlight
ABSTRACT:
PROVIDER: PRJNA922590 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This study investigated changes in the transcriptome of outdoor grown leafy spurge crown buds as they progress from paradormancy in August and September into endo dormancy in October through to ecodormancy in November and December. Keywords: Dormancy leafy spurge adventitious-buds A series of balanced dyeswap rolling circle hybiridizations were used with each year representing s seperate circle and with direction of the circles reversing on alternate years. Note, the Aug-Sep 04 hybridization failed and is missing from the dataset
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Project description:We present Smart-Seq2 Rolling Circle to Concatemeric Consensus (Smar2C2) for the identification and quantification of transcription start sites. Smar2C2 allows for the identification of upwards of 70 million unique transcription start sites from a single sample with as little as 40 pg of RNA input.
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Project description:Vertebrate sperm genome differs from somatic cells and undergoes dramatic transformation after fertilization. However, the functional implications of the sperm genome structures have not been fully investigated. Here we show, in the sperms of Xenopus tropicalis, tens of genomic regions harbor multi-megabases, super-sized clustered loops (SSCLs) whose anchors are enriched with Helitrons, the only group of rolling-circle transposons. SSCL anchors are inaccessible and absent of active histone modifications, implying that SSCLs are repressive in nature. Moreover, genes associated with SSCL anchors express late during development, suggesting 3D structure in sperm may associate with gene expression control during embryo development. The absence of CTCF and RNAPII at SSCL anchors argues against CTCF-mediated or transcription-related looping for the SSCLs establishment. Furthermore, our molecular simulation excludes looping and supports a phase separation model through which SSCLs may form. Taken together, our work reveals a previously undiscovered, repressive 3D structure in sperm that may mediate intergenerational gene regulation.
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Project description:Vertebrate sperm genome differs from somatic cells and undergoes dramatic transformation after fertilization. However, the functional implications of the sperm genome structures have not been fully investigated. Here we show, in the sperms of Xenopus tropicalis, tens of genomic regions harbor multi-megabases, super-sized clustered loops (SSCLs) whose anchors are enriched with Helitrons, the only group of rolling-circle transposons. SSCL anchors are inaccessible and absent of active histone modifications, implying that SSCLs are repressive in nature. Moreover, genes associated with SSCL anchors express late during development, suggesting 3D structure in sperm may associate with gene expression control during embryo development. The absence of CTCF and RNAPII at SSCL anchors argues against CTCF-mediated or transcription-related looping for the SSCLs establishment. Furthermore, our molecular simulation excludes looping and supports a phase separation model through which SSCLs may form. Taken together, our work reveals a previously undiscovered, repressive 3D structure in sperm that may mediate intergenerational gene regulation.
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Project description:Vertebrate sperm genome differs from somatic cells and undergoes dramatic transformation after fertilization. However, the functional implications of the sperm genome structures have not been fully investigated. Here we show, in the sperms of Xenopus tropicalis, tens of genomic regions harbor multi-megabases, super-sized clustered loops (SSCLs) whose anchors are enriched with Helitrons, the only group of rolling-circle transposons. SSCL anchors are inaccessible and absent of active histone modifications, implying that SSCLs are repressive in nature. Moreover, genes associated with SSCL anchors express late during development, suggesting 3D structure in sperm may associate with gene expression control during embryo development. The absence of CTCF and RNAPII at SSCL anchors argues against CTCF-mediated or transcription-related looping for the SSCLs establishment. Furthermore, our molecular simulation excludes looping and supports a phase separation model through which SSCLs may form. Taken together, our work reveals a previously undiscovered, repressive 3D structure in sperm that may mediate intergenerational gene regulation.
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