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Then you will need a 20-50MΩ HV resistor and a HV (>1200V) transistor (MOS or BJT) and a timing circuit (can be based on a 555 timer).
Connect resistor to the 1000V source. Then connect drain (MOS) or collector(BJT) to this resistor. Source(MOS) or Emitter(BJT) will be connected to 0V.
Output of the 555 timer have to be negated so in OFF stage transistor will be ON ie. will short resistor to 0V...output will be connection resistor-transistor.
If you trigg 555 it will generate an impulse and the transistor will be OFF for the duration of the pulse, so the output voltage will jump to full 1000V.
This above is one of options on how to generate HV pulses, but it is simple.
Working with HV think about safety issue: this is always first!!!
You can improve echo47's ideea by rectifiing the high voltage pulses, and charge an high voltage capacitor.
After Capacitor is charged, you can use an high voltage switching Transistor to apply pulses on the load.
In this way, you can apply any kind of curents to the load at 1000V (the frequency of the pulses depend on the Capacitor charge/discharge time constant.
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