CMS A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice(2012) doi: /pnas A non-coding RNA locus mediates environment-conditioned male sterility in rice. (2012) Cell Research 22:791–792. doi: /cr Comparative expression profiling of miRNA during anther development in genetic male sterile and wild type cotton. (2013) BMC Plant Biology 13:66 Differential Proteomic Analysis of Anthers between Cytoplasmic Male Sterile and Maintainer Lines in Capsicum annuum L.(2013) Int. J. Mol. Sci. 14(11), ; doi: /ijms /ijms Transcriptome map of plant mitochondria reveals islands of unexpected transcribed regions (2011) BMC Genomics 12: 279. Heterozygous alleles restore male fertility to cytoplasmic male-sterile radish (Raphanus sativus L.): a case of overdominance(2013) J. Exp. Bot. 64:

Aging Genome 1.DNA damage 2.Epigenetic shifts 3.Telomere shortening Cellular level 1.Mitochondria: ROS, DNA damage, other 2.Misfolded proteins 3.Dysfunctional stem cells Organismal level 1.Autoimmune, other defects in immune system 2.Defective signaling

Journal Clubs Spend ~ 5’ setting the stage: what is the general question? Why is it important? What was previously known? What were the outstanding questions?

Journal Clubs Spend ~ 5’ setting the stage: what is the general question? Why is it important? What was previously known? What were the outstanding questions? Then state the specific question addressed in your paper

Journal Clubs Then state the specific question addressed in your paper Next explain how they studied it General overview of techniques first, then specifics What were they trying to do? how did they do it?

Journal Clubs Then state the specific question addressed in your paper Next explain how they studied it General overview of techniques first, then specifics What were they trying to do? how did they do it? Then describe their results

Journal Clubs Then describe their results General overview first Then specific experiments

Journal Clubs Describe their results General overview first Then specific experiments Specific purpose of each experiment How they tested it Data they collected Controls!! How they analyzed it

Journal Clubs Describe their results General overview first Then specific experiments Specific purpose of each experiment How they tested it Data they collected Controls!! How they analyzed it Conclusions they drew

Journal Clubs Describe their results General overview first Then specific experiments Specific purpose of each experiment How they tested it Data they collected Controls!! How they analyzed it Conclusions they drew Your interpretation Do you agree? How could they improve?

Non-coding RNA Nearly ½ of human genome is transcribed, only 1% is coding 98% of RNA made is non-coding

Non-coding RNA Nearly ½ of human genome is transcribed, only 1% is coding 98% of RNA made is non-coding Fraction increases with organism’s complexity

Non-coding RNA Structural 1.rRNA 2.tRNA 3.snRNA 4.snoRNA 5.cleavage: RNAses P & MRP, U3, snR30, etc Regulatory 1.Small siRNA miRNA 2.Long Activator Enhancer silencing

Other ncRNA? Incredible diversity of functions! Epigenetic Directly regulating transcription Post-transcriptional regulation Some are made by Pol II, others by Pol III

HID1 ncRNA 1.Extracted total RNA from a mix of tissues, separated by size and sequenced nt fraction

HID1 ncRNA 1.Extracted total RNA from a mix of tissues, separated by size and sequenced nt fraction 2.BLAST to find relatives (and discard tRNA, etc)

HID1 ncRNA 1.Extracted total RNA from a mix of tissues, separated by size and sequenced nt fraction 2.BLAST to find relatives (and discard tRNA, etc) 3.T-DNA express to find mutants

HID1 ncRNA 1.Extracted total RNA from a mix of tissues, separated by size and sequenced nt fraction 2.BLAST to find relatives (and discard tRNA, etc) 3.T-DNA express to find mutants 4.ordered seeds for ones they found interesting

HID1 ncRNA ordered seeds for ones they found interesting Grew them under varying light conditions

HID1 ncRNA ordered seeds for ones they found interesting Grew them under varying light conditions Found one specifically defective in sensing continuous red

HID1 ncRNA ordered seeds for ones they found interesting Grew them under varying light conditions Found one specifically defective in sensing continuous red

HID1 ncRNA Found one specifically defective in sensing continuous red Confirmed that the HID1 ncRNA was responsible by adding back wt gene to “rescue phenotype”

HID1 ncRNA Confirmed that the HID1 ncRNA was responsible by adding back wt gene to “rescue phenotype” Checked expression Constitutive Not regulated by light

HID1 ncRNA Checked expression Constitutive Not regulated by light Tested sequence requirements to rule out ORFs

HID1 ncRNA Tested sequence requirements to rule out ORFs Tested structural requirements under cR

HID1 ncRNA Tested sequence requirements to rule out ORFs Tested structural requirements under cR Both SL2 and SL4 are needed for it to function

HID1 ncRNA Tested sequence requirements to rule out ORFs Tested structural requirements under cR Searched for targets by RNA-seq

HID1 ncRNA Searched for targets by RNA-seq HID1 represses PIF3 expression under cR

HID1 ncRNA Does HID1 act alone? Added an S1 aptamer to HID1 RNA to help find it

HID1 ncRNA Does HID1 act alone? Added an S1 aptamer to HID1 RNA to help find it Was part of an ~ 500 kDa complex

HID1 ncRNA Does HID1 act alone? Added an S1 aptamer to HID1 RNA to help find it Was part of an ~ 500 kDa complex ChIP-PCR showed that the complex bound the PIF3 promoter

HID1 ncRNA Does HID1 act alone? Added an S1 aptamer to HID1 RNA to help find it Was part of an ~ 500 kDa complex ChIP-PCR showed that the complex bound the PIF3 promoter Is HID1 conserved in evolution?

HID1 ncRNA Does HID1 act alone? Added an S1 aptamer to HID1 RNA to help find it Was part of an ~ 500 kDa complex ChIP-PCR showed that the complex bound the PIF3 promoter Is HID1 conserved in evolution? Are the orthologs functional?

HID1 ncRNA Does HID1 act alone? Added an S1 aptamer to HID1 RNA to help find it Was part of an ~ 500 kDa complex ChIP-PCR showed that the complex bound the PIF3 promoter Is HID1 conserved in evolution? Are the orthologs functional? What next?

Mitochondria and the immune system Mito play important role in recognizing & fighting viruses Via RLR (retinoic acid-inducible receptors) pathway that detects dsRNA MAVS ( mitochondrial antiviral signaling) protein on MOM is key dsRNA receptors bind MAVS & trigger interferon & cytokine synthesis

Programmed cell death vs necrosisNecrosis: progressive loss of membrane integrity swelling of cytoplasm, release of cell constituents Often follows irreversible injury Passive IndiscriminatePCD Active Orderly process mediated by intracellular death programs May or may not be due to an external factor Nuclear condensation Condensation of PM

Apoptosis Ordered process that breaks cell into easily recycled pieces Caspases digest proteins CAD digests DNA

Apoptosis Two basic steps: commitment and execution Commitment depends on interplay between various signals Bax & Bcl2 have opposite effects 2 main pathways: extrinsic & intrinsic

Apoptosis 2 main pathways: extrinsic & intrinsic Tumor necrosis factor and Fas ligand = extrinsic signals that can trigger apoptosis via death receptor

Apoptosis 2 main pathways: extrinsic & intrinsic Tumor necrosis factor and Fas ligand = extrinsic signals that can trigger apoptosis via death receptor Bind receptors in PM (TNFR or fas)

Tumor necrosis factor and Fas ligand = extrinsic signals that can trigger apoptosis via death receptor Bind receptors in PM (TNFR or fas) Receptors activate FADD & TRADD: Adaptors with death domains that bind receptor’s DDs

Procaspase 8 binds FADD

Receptors activate FADD & TRADD: Adaptors with death domains that bind receptor’s DDs Procaspase 8 binds FADD Procaspase 8 is processed to caspase 8 = initiator caspase

Procaspase 8 binds FADD Procaspase 8 is processed to caspase 8 = initiator caspase Caspase 8 converts procaspase 3 to active form = executioner

Procaspase 8 binds FADD Procaspase 8 is processed to caspase 8 = initiator caspase Caspase 8 converts procaspase 3 to active form = executioner Caspase-3 & CAD execute the cell