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Page 1: Organization of IncRNA at Pax6 Locus

  • Antisense Transcripts

    • Involvement in various regulatory activities in the locus.

  • Intronic Transcript

    • Role in gene expression regulation within introns.

  • Pax6 Proximity

    • Interaction of incRNA with the Pax6 locus indicating a role in development.

  • Bidirectional Transcript

    • Generation of transcripts in both directions along the DNA strand.

  • Promoter-associated Transcript

    • Transcripts that are closely linked to the promoter region, implicating their role in initiating transcription.

  • 3' UTR Associated Transcript

    • Transcripts that interact with the 3' untranslated region, influencing post-transcriptional regulation.

Page 2: General Functions of ncRNA

  • Transcriptional Interference

    • Inhibition of transcription machinery by overlapping ncRNAs.

  • Induce Chromatin Remodeling

    • Sense ncRNAs hybridize with antisense RNAs influencing histone modifications:

    • Modulation of Splicing Patterns

    • Alteration of normal splicing pathways leading to different protein isoforms.

  • Generate Endo-siRNAs

    • Creation of small interfering RNAs from long noncoding RNAs.

  • Structural Role

    • Various structural functions within cellular mechanisms and organization.

  • Alter Protein Activity/Localization

    • ncRNAs can influence the localization and functional activity of proteins.

Page 3: IncRNA Inhibition of RNA Polymerases

  • Inhibition of Pol II

    • IncRNAs can interfere with the transcription activity of Polymerase II, affecting gene expression levels.

  • Inhibition Context

    • Various elements (e.g., heat shock, SINE elements) can be regulated by IncRNA actions.

Page 4: Control of Transcription Initiation by IncRNA

  • TFIID Interaction

    • IncRNA can modulate the binding of TFIID at promoters, crucial for transcription initiation.

  • Triplex Formation

    • Triplex structures formed by IncRNA may inhibit transcription machinery.

  • Targeted Gene Effects

    • Potential influences on housekeeping genes and specific active promoters.

Page 5: Recruitment of Enhancers by IncRNA

  • Enhancer Interactions

    • Analogous to enhancer RNAs, IncRNAs can recruit enhancers to target genes (e.g., DLX2, Dlx6).

  • Evf2 Role

    • Influence on the transcriptional activity via ultraconserved regulatory elements.

Page 6: IncRNA and Chromatin Structure Remodeling

  • Recruitment of Modifying Enzymes

    • IncRNA interacting with chromatin-modifying complexes such as PRC2 and G9a:

    • Histone Modifications

      • K27me3, K9me2, K4me2 alterations impacting gene expression.

    • Cis and Trans Effects

      • Distinction between cis-acting and trans-acting ncRNA functionalities.

Page 7: Structural Components of Chromatin

  • Protein Interactions

    • Summary of histone modifications and their links with IncRNA activities, including specific histone variants and modifications:

    • Enzymatic Changes

      • Potential impacts of modifications on chromatin structure and accessibility for transcription factors.

Page 8: Splicing Alteration via Antisense Transcript

  • Retention of IRES

    • IncRNA influence on splicing through retention of Internal Ribosome Entry Site (IRES), changing the resultant proteins:

    • Zeb2 Influence

      • Specific role of antisense ncRNA in altering mRNA splicing and protein translation.

Page 9: Processing of IncRNA into Smaller ncRNA

  • Formation of Smaller ncRNA

    • Transition of IncRNA to functional smaller ncRNA via processes like splicing:

    • Cleavage Pathways

      • Involvement of enzymes like Dicer and RNase P for processing and maturation.

    • Nuclear Speckles and Export

      • Localization in nuclear speckles and export mechanisms to cytoplasm.

Page 10: Structural Component of Paraspeckles

  • Paraspeckle Formation

    • IncRNAs as fundamental structural units of paraspeckles, locations of regulatory activity in the nucleus:

    • EYFP-PSPC1 Merger

      • Visualization studies demonstrating diving organization.

Page 11: Mechanisms of miRNA Gene Silencing

  • miRNA Processing

    • Pathways from primary miRNA to active forms:

    • Export and Maturation

      • Stages involving Dicer and RISC assembly leading to gene silencing activities.

    • Functional Outcomes

      • Various repression mechanisms leading to inhibition of target mRNAs.

Page 12: Mechanisms of miRNA-mediated Gene Regulation

  • Mechanisms of Gene Silencing

    • Methods through which miRNA can lead to mRNA degradation or impede translation:

    • Inhibitory Actions

      • Slowed translation or premature termination impacts gene function.

Page 13: miRNA Processing Versus siRNA Pathways

  • Dicer Activities

    • Comparison of processing pathways for miRNAs and siRNAs illustrating similarities and differences:

    • Nuclear and Cytoplasmic Roles

      • Elements of gene regulation and their differences in pathways involving various cellular machinery.

Page 14: Piwi RNA Amplification Model

  • Transposon Transcript Interaction

    • The role of Piwi proteins in RNA amplification related to transposable elements:

    • Cleavage and Processing

      • The sequence of interactions leading to functional piRNA activation.